A spatial human thymus cell atlas mapped to a continuous tissue axis
Cite
Yayon, N., Kedlian, V.R., Boehme, L., Suo, C., Wachter, B.T., Beuschel, R.T., Amsalem, O., Polanski, K., Koplev, S., Tuck, E. and Dann, E., 2024. A spatial human thymus cell atlas mapped to a continuous tissue axis. Nature, 635(8039), pp.708-718. https://doi.org/10.1038/s41586-024-07944-6
Abstract
T cells develop from circulating precursor cells, which enter the thymus and migrate through specialized subcompartments that support their maturation and selection1. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the microanatomical underpinnings of this process in pre- and early postnatal stages, we established a quantitative morphological framework for the thymus—the Cortico-Medullary Axis—and used it to perform a spatially resolved analysis. Here, by applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions by the beginning of the the second trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and identify divergence in the timing of medullary entry between CD4 and CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation and OrganAxis construction (TissueTag), which can be applied to any tissue.
Datasets
1. thymus scRNA-seq atlas
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
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Cell type (panfetal 2022)
Cell type level 3
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Cell type level 1
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Assay
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Sex
Tissue
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FCAImmP75792197076 cells
TA92600126764 cells
baut66745 cells
FCAImmP72775566222 cells
T06_TH_TOT_5GEX_1_S96203 cells
T07_TH_TOT_1_S15732 cells
FCAImmP75792315563 cells
FCAImmP78518915539 cells
FCAImmP78518905272 cells
sample85176 cells
T07_TH_TOT_2_S24943 cells
T06_TH_TOT_5GEX_3_S114450 cells
TTA74325 cells
TTA84198 cells
FCAImmP72920344154 cells
FCAImmP72775644027 cells
TA92600133970 cells
FCAImmP72920303829 cells
FCAImmP78518943795 cells
T06_TH_TOT_5GEX_2_S103751 cells
FCAImmP78518953714 cells
T06_TH_TOT_5GEX_4_S123689 cells
F83_TH_EPCAM3580 cells
T03_TH_TOT_5GEX_2_S23561 cells
FCAImmP71793703559 cells
FCAImmP78518963558 cells
FCAImmP75558513504 cells
FCAImmP71793693468 cells
FCAImmP78518933379 cells
FCAImmP78518923030 cells
T07_TH_EPCAM_S33009 cells
T03_TH_TOT_5GEX_1_S12838 cells
FCAImmP71986342775 cells
FCAImmP71986352611 cells
FCAImmP75558522580 cells
FCAImmP75282832491 cells
FCAImmP72775652357 cells
FCAImmP75792182217 cells
FCAImmP75282942119 cells
TA92600162057 cells
FCAImmP75792301963 cells
GSM48389541752 cells
FCAImmP75558611670 cells
FCAImmP75282851640 cells
FCAImmP75282841384 cells
GSM48389521372 cells
FCAImmP75558601323 cells
TA9260014874 cells
GSM4838953726 cells
baut5653 cells
GSM4838951381 cells
FCAImmP7277557290 cells
TA9260015241 cells
baut4219 cells
TA926001713 cells
10x 5' v2202181 cells
10x 3' v2171437 cells
10x 5' v1104583 cells
10x 3' v34450 cells
normal482651 cells
male261304 cells
female161199 cells
Unassigned60148 cells
thymus482651 cells
Cluster 4119572 cells
Cluster 699003 cells
Cluster 285663 cells
Cluster 138977 cells
Cluster 328216 cells
Cluster 825978 cells
Cluster 1021731 cells
Cluster 1220707 cells
Cluster 520176 cells
Cluster 1110133 cells
Cluster 134547 cells
Cluster 73479 cells
Cluster 93452 cells
Cluster 15693 cells
Cluster 14324 cells
2. thymus scRNA-seq atlas - T cell subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh38391462 cells
v98391462 cells
STARsolo 2.7.4a,CellBender391462 cells
P334886 cells
TSC-CT1032836 cells
TSC-CT930269 cells
P129758 cells
TSC-CT1329453 cells
TSC-CT828286 cells
U4826809 cells
TSC-CT1224485 cells
T0617651 cells
F6716428 cells
F4516138 cells
U4015950 cells
T0710983 cells
U0910441 cells
F6410316 cells
F309602 cells
F299515 cells
F418134 cells
T036285 cells
F216069 cells
F385189 cells
F234642 cells
F833110 cells
Z112993 cells
fetal_23w_donor505 cells
postnatal_10m_donor328 cells
6m_thymus_donor301 cells
postnatal_6d_donor80 cells
fetal_19w_donor20 cells
3 months73272 cells
6 months72437 cells
2 months58555 cells
12 weeks (post-conception)32566 cells
14.5 months29758 cells
5 months24485 cells
30 months17651 cells
7 days15950 cells
11 weeks (post-conception)14958 cells
16 weeks (post-conception)14203 cells
17 weeks (post-conception)12625 cells
14 weeks (post-conception)9602 cells
10 months6613 cells
13 weeks (post-conception)5189 cells
2.5 years2993 cells
23 weeks (post-conception)505 cells
6 days80 cells
19 weeks (post-conception)20 cells
True266875 cells
Unassigned124587 cells
fresh391462 cells
surgical resection391462 cells
Unassigned188706 cells
University Hospital Ghent145329 cells
Great Ormond Street Hospital for Children NHS53501 cells
Newcastle Hospitals NHS2993 cells
San Francisco General Hospital525 cells
University of California, San Francisco408 cells
Unassigned265670 cells
CD397124 cells
CD4528668 cells
Unassigned265670 cells
T cell97124 cells
leukocyte28668 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting154096 cells
mechanical dissociation,fluorescence-activated cell sorting64644 cells
enzymatic dissociation,fluorescence-activated cell sorting62755 cells
enzymatic dissociation57054 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting30531 cells
mechanical dissociation,enzymatic dissociation16762 cells
enzymatic dissociation,positive magnetic affinity cell sorting4253 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting1066 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting301 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH188088 cells
Unassigned68110 cells
1.6 mg/ml collagenase IV63580 cells
0.2 mg/ml liberase57016 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH13434 cells
100 μg/ml Liberase TM933 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II301 cells
Unassigned269632 cells
30 minute120596 cells
45-60 minute933 cells
30-45 minute301 cells
Unassigned207026 cells
T cell112982 cells
leukocyte36307 cells
epithelial cell of thymus34846 cells
cortical thymic epithelial cell292 cells
medullary thymic epithelial cell9 cells
Unassigned199307 cells
CD3112982 cells
CD4536307 cells
EpCAM34784 cells
EpCAM,CD2054315 cells
CD1373466 cells
EpCAMlow,CD205+292 cells
EpCAMhigh,CD205-9 cells
9c9a3635-c73c-4cb4-bff5-7c769df23e2017920 cells
0a4171ec-3820-4e99-858f-b74eb70808cd16966 cells
3917a9fb-462f-4f4e-9c1b-b0a6eb1c82f816913 cells
0de02a80-da1b-4fc4-8300-4b4eef3f459816878 cells
908c4e6e-4b3a-430b-9fe1-a97d422db1bb16266 cells
1c030062-faa0-4e47-85c0-6ef009f2a0f214669 cells
247c2c08-063d-417e-add7-ba81f11f259c14354 cells
0590ebeb-11b3-439b-84af-dcd535683a2114174 cells
65e9f5d0-5add-4c09-9cee-316716c2ae7314112 cells
1cac9958-24f7-45aa-9965-472038cb9bbb13391 cells
ac01bcd2-2d03-4a97-8569-ad598a7beb8f13306 cells
f751ebaf-e7c3-4c03-998e-79b3c7fa9f5413187 cells
700d57d4-2466-42f1-9605-88d5e8451c2912140 cells
c25f52a7-8590-4ff4-a9d0-82efe6cbdfdf10948 cells
db5b9b21-f33d-42a7-839e-87ff5faa6d4610648 cells
6a6a25e6-737f-40d3-89e8-3f9f1b0679849230 cells
ea012917-7bd7-46be-817f-42ff310ee5d27572 cells
fe28ef61-6f2a-433a-bbae-355aa9dbe41b6777 cells
eae32bc7-1603-4e34-adee-5a953f4bc45c6724 cells
99ec672f-2d8c-4425-a800-447f3c3256b26080 cells
e130d3d3-63fd-44f2-a545-f5f3d164889c5730 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de5290 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc05257 cells
e23c6097-c75c-4194-9b9b-11eccc636db15230 cells
9b2e913d-ac12-44ca-914a-e8aa21175c295176 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee5026 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c4583 cells
70ac07c6-9ff2-4048-bcfa-332ea9ad8fb04326 cells
72a3a376-2a41-4615-9d6b-7583e1e3e9664315 cells
64eca649-dfd8-47de-8bc8-d05acf1794bc4152 cells
c7760a1e-8622-4500-b914-8bd529b48d964014 cells
80dce0eb-df2b-4bb1-b4bf-7fbb00e89ada4010 cells
cedc71e0-ecb2-43d1-8834-c48b0a0a01de3868 cells
8d62fc28-a5e4-488d-8013-2fec2b16a8783717 cells
810f4e99-5478-4d01-86d9-df0a93dc58383649 cells
1aec6622-be0c-4e25-b82a-833865865e893596 cells
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9aedd5f2-35f6-460b-b2ad-49242d848c433508 cells
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83803089-c547-4329-a671-74352a4949043437 cells
6c959596-7ef9-40ee-9bb0-6044964354d23435 cells
409181fb-ae4d-4bfe-9e20-849ae6420eca3307 cells
fadfcbbf-117f-4a75-bbff-624ea49938583143 cells
bfbf960c-fe5c-4e93-ae1e-ae2a3b2f6b0a3110 cells
05287b63-0a6e-4605-8b25-901469696c2f2794 cells
5999a5e6-b1a9-4bea-a6d0-0a479e8283e22777 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e2762 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f78392551 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b972405 cells
1dcaec0a-2eae-4431-bb5e-ec1c5df9d0fb2381 cells
bd801268-03bc-4bc7-93fe-7fa1646093872194 cells
7af0a1fb-651c-4cac-9571-b8b22896957d2147 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f2091 cells
e1b9c902-597d-4462-9037-eb6386547e2b2047 cells
f307a1fb-28f2-41c4-b5aa-01ecbc8c72342028 cells
0f203abe-b4af-4f73-9ec6-2ca944ebb1761937 cells
42640a48-43a2-4023-9eed-1d6b2149e4c21720 cells
751f08bc-6649-4ab4-826f-f4b20825a9051285 cells
264d56c4-954f-404e-adad-ff691f34dea01267 cells
7175f9ca-dddd-4a4a-a00a-45e7dd4754871143 cells
ad489aeb-d0fc-4515-892a-443e57f438bd808 cells
330a23af-1bdc-434d-9445-83d6a9908212400 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef1380 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba263 cells
5dabbbcc-24af-43d4-b428-6c90f1595099242 cells
dadac003-e5d6-4bed-9fb0-d37b6acf0f03241 cells
23b7f9d6-4fb3-4d8d-a9d4-ecb03078b223222 cells
fe84964e-961b-414c-829e-00b16b0da920208 cells
f837dd0f-0151-4532-bf72-dfcc629d61a2133 cells
d1d0f14a-b49a-410f-8026-f1f8ad84efed106 cells
b4cd9df4-8d0f-40eb-ad5a-cc616195bf0080 cells
4bde7163-d258-46d1-92ce-4a998b6d7e1f51 cells
0259273d-0959-478c-a312-f311e7b8998120 cells
53a4c3d0-d56d-47df-96be-e6c89c20e1485 cells
9a658b0a-0cc6-4a7e-af9c-6cd1a02f8e085 cells
9bb9ebf7-112d-4f60-b27f-98f8246f0d104 cells
5 prime tag285633 cells
3 prime tag105829 cells
Ghent University209973 cells
Wellcome Sanger Institute180255 cells
General Community1234 cells
Unassigned266166 cells
ERX38060776777 cells
ERX38061256080 cells
ERX38061005730 cells
ERX38061205290 cells
ERX38061115257 cells
ERX38060785230 cells
ERX38061195026 cells
ERX38061124583 cells
ERX38061274326 cells
ERX38060964014 cells
ERX38060953868 cells
ERX38061263649 cells
ERX38061283596 cells
ERX38061233588 cells
ERX38061013577 cells
ERX38061163508 cells
ERX38061073466 cells
ERX38061243437 cells
ERX38060983435 cells
ERX38060973307 cells
ERX38061223143 cells
ERX38061093110 cells
ERX38061212794 cells
ERX38061152777 cells
ERX38060822762 cells
ERX38060902551 cells
ERX38060932381 cells
ERX38060912194 cells
ERX38060832147 cells
ERX38060762091 cells
ERX38060942028 cells
ERX38060921937 cells
ERX38060811720 cells
ERX38060991285 cells
ERX38060841267 cells
ERX38061081143 cells
ERX3806080400 cells
ERX3806079380 cells
SRX8089347263 cells
SRX8089346242 cells
SRX9323992241 cells
SRX8089350222 cells
ERX3806085208 cells
SRX8089349106 cells
SRX808934880 cells
SRX932399151 cells
SRX808934520 cells
SRX93239935 cells
SRX93239944 cells
Illumina NovaSeq 6000 (EFO:0008637)172258 cells
Illumina HiSeq 4000 (EFO:0008563)150677 cells
Unassigned54434 cells
Illumina NextSeq 500 (EFO:0009173)10983 cells
Illumina HiSeq 2500 (EFO:0008565)3110 cells
T_DP(Q)120686 cells
T_DP(P)74240 cells
T_αβT(entry)40060 cells
Unassigned36773 cells
T_CD425224 cells
T_DN(Q)21389 cells
T_CD815987 cells
T_DP(Q)-early12545 cells
T_DN(P)8247 cells
T_Treg(agonist)6457 cells
T_CD8αα(I)6216 cells
T_CD8αα(entry)4865 cells
T_CD8αα(II)3677 cells
T_Treg-diff_23278 cells
T_NK2363 cells
T_Treg_recirc2323 cells
T_γδT1977 cells
T_DN(early)1658 cells
T_Treg-diff_11331 cells
T_Treg_mature1160 cells
T_Treg_CD8645 cells
T_Treg-intermediate140 cells
T_ETP116 cells
T_CD8_memory105 cells
Unassigned308975 cells
proliferating82487 cells
none313384 cells
congenital heart disease78078 cells
paed (early)301794 cells
fetal89668 cells
Park2020188706 cells
HTSA_Ghent145329 cells
HTSA_Sanger56193 cells
Bautista2021933 cells
Campinoti2020301 cells
CD3P112982 cells
CD3N96991 cells
TOT73816 cells
45P36307 cells
MACS30664 cells
45N23915 cells
FACS8767 cells
EPCAM4253 cells
CD1373466 cells
CD205+CD49F-241 cells
CD205+CD49F+51 cells
EpCAM+CD49F+5 cells
EpCAM+CD49F-4 cells
Unassigned279048 cells
double-positive, alpha-beta thymocyte54516 cells
double negative thymocyte21857 cells
CD4-positive, alpha-beta T cell9558 cells
CD8-positive, alpha-beta T cell8107 cells
alpha-beta T cell5837 cells
CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell4235 cells
regulatory T cell3865 cells
T cell2202 cells
natural killer cell823 cells
gamma-delta T cell798 cells
CD4-positive, alpha-beta memory T cell242 cells
CD8-positive, alpha-beta memory T cell238 cells
early T lineage precursor96 cells
progenitor cell23 cells
group 3 innate lymphoid cell15 cells
plasma cell1 cells
mast cell1 cells
Unassigned320430 cells
DP(P)_T20192 cells
DP(Q)_T11375 cells
DN(Q)_T10754 cells
DN(P)_T6701 cells
ABT(ENTRY)5149 cells
CD4+T4084 cells
CD8AA3924 cells
CD8+T3177 cells
TREG2927 cells
DN(early)_T981 cells
TYPE_3_INNATE_T367 cells
TYPE_1_INNATE_T357 cells
NK316 cells
HIGH_MITO258 cells
CYCLING_T211 cells
CYCLING_NK89 cells
LMPP_MLP74 cells
LOW_Q_INCONSISTENT31 cells
HSC_MPP21 cells
CMP13 cells
ILC35 cells
MEMP4 cells
CYCLING_MPP4 cells
GMP3 cells
DOUBLET3 cells
DOUBLET_ERY_B2 cells
ILC22 cells
PROMONOCYTE1 cells
EARLY_MK1 cells
MAST_CELL1 cells
LOW_QUALITY_MID_ERY_(HIGH_RIBO)1 cells
MATURE_B1 cells
PRE_PRO_B1 cells
CYCLING_ILC1 cells
CYCLING_DC1 cells
T_DP(Q)133231 cells
T_DP(P)74240 cells
T_αβT(entry)40060 cells
Unassigned36773 cells
T_CD425224 cells
T_DN(Q)21389 cells
T_CD816092 cells
T_CD8αα14758 cells
T_Treg(agonist)11206 cells
T_DN(P)8247 cells
T_NK2363 cells
T_Treg_recirc2323 cells
T_γδT1977 cells
T_DN(early)1774 cells
T_Treg_mature1160 cells
T_Treg_CD8645 cells
T_DP(Q)133231 cells
T_DP(P)74240 cells
T_αβT(entry)40060 cells
Unassigned36773 cells
T_CD425224 cells
T_DN(Q)21389 cells
T_CD816092 cells
T_CD8αα14758 cells
T_Treg(agonist)11206 cells
T_DN(P)8247 cells
T_Treg4128 cells
T_NK2363 cells
T_γδT1977 cells
T_DN(early)1774 cells
T_DP207471 cells
T_αβT(entry)40060 cells
Unassigned36773 cells
T_DN29636 cells
T_CD425224 cells
T_innate16735 cells
T_CD816092 cells
T_Treg15334 cells
T_NK2363 cells
T_DN(early)1774 cells
T_DP207471 cells
T_SP115808 cells
Unassigned36773 cells
T_DN31410 cells
T_DP(Q)120686 cells
T_DP(P)74240 cells
T_αβT(entry)40060 cells
T_CD425224 cells
T_DN(Q)21389 cells
T_CD815987 cells
T_DP(Q)-early12545 cells
T_DP(Q)-HSPH18794 cells
T_DN(P)8247 cells
T_DP(Q)-CD996927 cells
T_Treg(agonist)6457 cells
T_CD8αα(I)6216 cells
T_DP(Q)-late_vdj5692 cells
T_CD8αα(entry)4865 cells
T_SP-HSP4114 cells
T_DN(Q)-stress_13862 cells
T_CD8αα(II)3677 cells
T_Treg-diff_23278 cells
T_NK2363 cells
T_Treg_recirc2323 cells
T_DN(Q)-intermediate2155 cells
T_γδT1977 cells
T_DN(early)1658 cells
T_SP8or41332 cells
T_Treg-diff_11331 cells
T_Treg_mature1160 cells
T_DN(Q)-stress_21108 cells
T_SP_fetal_ambigouous1063 cells
T_innate_type_3950 cells
T_Treg_CD8645 cells
T_innate_type_1347 cells
T_CD8-Prolif323 cells
T_Treg-intermediate140 cells
T_ETP116 cells
T_cycling106 cells
T_CD8_memory105 cells
TTA1317920 cells
TTA1416966 cells
sample916913 cells
sample416878 cells
sample616266 cells
U48-THY-0-SC-EPCP-2_5GEX14669 cells
sample1214354 cells
sample214174 cells
sample114112 cells
sample313391 cells
sample1113306 cells
sample513187 cells
U48-THY-0-SC-EPCP-1_5GEX12140 cells
TTA1010948 cells
TTA910648 cells
U48-THY-0-SC-1_5GEX9230 cells
sample107572 cells
FCAImmP75792196777 cells
TA92600126724 cells
T06_TH_TOT_5GEX_1_S96080 cells
FCAImmP72775565730 cells
FCAImmP78518915290 cells
T07_TH_TOT_1_S15257 cells
FCAImmP75792315230 cells
sample85176 cells
FCAImmP78518905026 cells
T07_TH_TOT_2_S24583 cells
T06_TH_TOT_5GEX_3_S114326 cells
U40-THY-0-SC-F-24315 cells
TTA74152 cells
FCAImmP72920344014 cells
TTA84010 cells
FCAImmP72775643868 cells
TA92600133717 cells
T06_TH_TOT_5GEX_2_S103649 cells
T06_TH_TOT_5GEX_4_S123596 cells
FCAImmP78518943588 cells
FCAImmP72920303577 cells
T03_TH_TOT_5GEX_2_S23508 cells
FCAImmP78518963466 cells
FCAImmP78518953437 cells
FCAImmP75558513435 cells
FCAImmP71793693307 cells
FCAImmP78518933143 cells
F83_TH_EPCAM3110 cells
FCAImmP78518922794 cells
T03_TH_TOT_5GEX_1_S12777 cells
FCAImmP71793702762 cells
FCAImmP71986342551 cells
U40-THY-0-SC-F-12405 cells
FCAImmP75282832381 cells
FCAImmP75792182194 cells
FCAImmP75558522147 cells
FCAImmP71986352091 cells
TA92600162047 cells
FCAImmP75282942028 cells
FCAImmP75792301937 cells
FCAImmP72775651720 cells
FCAImmP75558601285 cells
FCAImmP75558611267 cells
T07_TH_EPCAM_S31143 cells
TA9260014808 cells
FCAImmP7528285400 cells
FCAImmP7528284380 cells
baut3263 cells
baut2242 cells
GSM4838952241 cells
baut6222 cells
FCAImmP7277557208 cells
TA9260015133 cells
baut5106 cells
baut480 cells
GSM483895151 cells
baut120 cells
TA92600175 cells
GSM48389535 cells
GSM48389544 cells
10x 5' v2188088 cells
10x 3' v2105448 cells
10x 5' v197545 cells
10x 3' v3381 cells
normal391462 cells
male248463 cells
female142066 cells
Unassigned933 cells
thymus391462 cells
Cluster 886200 cells
Cluster 175787 cells
Cluster 570608 cells
Cluster 462893 cells
Cluster 231120 cells
Cluster 630507 cells
Cluster 320358 cells
Cluster 713989 cells
3. thymus scRNA-seq atlas - vascular cell subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh3826313 cells
v9826313 cells
STARsolo 2.7.4a,CellBender26313 cells
fetal_23w_donor17713 cells
fetal_19w_donor4898 cells
postnatal_10m_donor2749 cells
U40531 cells
F67127 cells
T0744 cells
U4844 cells
6m_thymus_donor40 cells
F6436 cells
F3836 cells
F2318 cells
F3016 cells
F2115 cells
Z1112 cells
postnatal_6d_donor10 cells
F8310 cells
U098 cells
F416 cells
23 weeks (post-conception)17713 cells
19 weeks (post-conception)4898 cells
10 months2749 cells
7 days531 cells
12 weeks (post-conception)127 cells
6 months92 cells
11 weeks (post-conception)54 cells
3 months44 cells
13 weeks (post-conception)36 cells
16 weeks (post-conception)21 cells
14 weeks (post-conception)16 cells
2.5 years12 cells
6 days10 cells
17 weeks (post-conception)10 cells
Unassigned22919 cells
True3394 cells
fresh26313 cells
surgical resection26313 cells
San Francisco General Hospital22611 cells
University of California, San Francisco2759 cells
Great Ormond Street Hospital for Children NHS623 cells
Unassigned308 cells
Newcastle Hospitals NHS12 cells
CD4526022 cells
Unassigned285 cells
CD36 cells
leukocyte26022 cells
Unassigned285 cells
T cell6 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting25376 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting531 cells
enzymatic dissociation153 cells
enzymatic dissociation,fluorescence-activated cell sorting139 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting52 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting40 cells
enzymatic dissociation,positive magnetic affinity cell sorting16 cells
mechanical dissociation,enzymatic dissociation6 cells
100 μg/ml Liberase TM25370 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH575 cells
0.2 mg/ml liberase134 cells
1.6 mg/ml collagenase IV126 cells
Unassigned48 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II40 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH20 cells
45-60 minute25370 cells
Unassigned643 cells
30 minute260 cells
30-45 minute40 cells
Unassigned26211 cells
epithelial cell of thymus52 cells
medullary thymic epithelial cell34 cells
leukocyte10 cells
cortical thymic epithelial cell6 cells
Unassigned26147 cells
EpCAM68 cells
CD13748 cells
EpCAMhigh,CD205-34 cells
CD4510 cells
EpCAMlow,CD205+6 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba9072 cells
5dabbbcc-24af-43d4-b428-6c90f15950998641 cells
0259273d-0959-478c-a312-f311e7b899814898 cells
23b7f9d6-4fb3-4d8d-a9d4-ecb03078b2232646 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b97531 cells
d1d0f14a-b49a-410f-8026-f1f8ad84efed103 cells
6bf7479c-b3ec-4167-b6d7-a50eaf70669e48 cells
53a4c3d0-d56d-47df-96be-e6c89c20e14834 cells
83803089-c547-4329-a671-74352a49490425 cells
700d57d4-2466-42f1-9605-88d5e8451c2924 cells
330a23af-1bdc-434d-9445-83d6a990821222 cells
fadfcbbf-117f-4a75-bbff-624ea499385821 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc020 cells
1c030062-faa0-4e47-85c0-6ef009f2a0f220 cells
7ba3652f-d73f-4974-a9b0-6a0af87bd3f219 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee18 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c18 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de18 cells
42640a48-43a2-4023-9eed-1d6b2149e4c216 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e15 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef114 cells
05287b63-0a6e-4605-8b25-901469696c2f14 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f783910 cells
bfbf960c-fe5c-4e93-ae1e-ae2a3b2f6b0a10 cells
b4cd9df4-8d0f-40eb-ad5a-cc616195bf0010 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f8 cells
8d62fc28-a5e4-488d-8013-2fec2b16a8788 cells
f837dd0f-0151-4532-bf72-dfcc629d61a26 cells
ad489aeb-d0fc-4515-892a-443e57f438bd6 cells
7175f9ca-dddd-4a4a-a00a-45e7dd4754876 cells
4bde7163-d258-46d1-92ce-4a998b6d7e1f6 cells
264d56c4-954f-404e-adad-ff691f34dea06 cells
3 prime tag25495 cells
5 prime tag818 cells
General Community25410 cells
Wellcome Sanger Institute903 cells
SRX80893479072 cells
SRX80893468641 cells
SRX80893454898 cells
SRX80893502646 cells
Unassigned595 cells
SRX8089349103 cells
ERX380610748 cells
SRX932399334 cells
ERX380612425 cells
ERX380608022 cells
ERX380612221 cells
ERX380611120 cells
ERX380612319 cells
ERX380611218 cells
ERX380611918 cells
ERX380612018 cells
ERX380608116 cells
ERX380608215 cells
ERX380607914 cells
ERX380612114 cells
SRX808934810 cells
ERX380609010 cells
ERX380610910 cells
ERX38060768 cells
SRX93239916 cells
ERX38061086 cells
ERX38060846 cells
Unassigned25993 cells
Illumina HiSeq 4000 (EFO:0008563)254 cells
Illumina NextSeq 500 (EFO:0009173)44 cells
Illumina NovaSeq 6000 (EFO:0008637)12 cells
Illumina HiSeq 2500 (EFO:0008565)10 cells
EC-Cap12649 cells
EC-Art5425 cells
EC-Ven5058 cells
EC-Cap-Prolif1617 cells
EC-Ven-ELN645 cells
EC-Lymphatic524 cells
EC-Art-ELN395 cells
Unassigned24696 cells
proliferating1617 cells
none26293 cells
congenital heart disease20 cells
fetal22875 cells
paed (early)3438 cells
Bautista202125370 cells
HTSA_Sanger595 cells
Park2020308 cells
Campinoti202040 cells
45N25451 cells
FACS531 cells
TOT159 cells
MACS58 cells
CD13748 cells
EpCAM+CD49F+34 cells
EPCAM16 cells
45P10 cells
CD205+CD49F+6 cells
Unassigned26091 cells
endothelial cell194 cells
lymphocyte26 cells
megakaryocyte1 cells
CD4-positive, alpha-beta T cell1 cells
Unassigned26090 cells
ENDOTHELIUM_I149 cells
ENDOTHELIUM_II60 cells
ENDOTHELIUM_III6 cells
ENDOTHELIUM_IV4 cells
LOW_QUALITY3 cells
EARLY_MK1 cells
EC-Cap14266 cells
EC-Art5820 cells
EC-Ven5703 cells
EC-Lymphatic524 cells
EC-Cap14266 cells
EC-Art5820 cells
EC-Ven5703 cells
EC-Lymphatic524 cells
EC26313 cells
Stroma26313 cells
EC-Cap12649 cells
EC-Art5425 cells
EC-Ven5058 cells
EC-Cap-Prolif1617 cells
EC-Ven-ELN645 cells
EC-Lymphatic524 cells
EC-Art-ELN395 cells
baut39072 cells
baut28641 cells
baut14898 cells
baut62646 cells
U40-THY-0-SC-F-1531 cells
baut5103 cells
FCAImmP785189648 cells
GSM483895334 cells
FCAImmP785189525 cells
U48-THY-0-SC-EPCP-1_5GEX24 cells
FCAImmP752828522 cells
FCAImmP785189321 cells
U48-THY-0-SC-EPCP-2_5GEX20 cells
T07_TH_TOT_1_S120 cells
FCAImmP785189419 cells
FCAImmP785189118 cells
T07_TH_TOT_2_S218 cells
FCAImmP785189018 cells
FCAImmP727756516 cells
FCAImmP717937015 cells
FCAImmP785189214 cells
FCAImmP752828414 cells
baut410 cells
FCAImmP719863410 cells
F83_TH_EPCAM10 cells
TA92600138 cells
FCAImmP71986358 cells
TA92600146 cells
TA92600156 cells
GSM48389516 cells
T07_TH_EPCAM_S36 cells
FCAImmP75558616 cells
10x 3' v225445 cells
10x 5' v2575 cells
10x 5' v1243 cells
10x 3' v350 cells
normal26313 cells
Unassigned25370 cells
female734 cells
male209 cells
thymus26313 cells
Cluster 26395 cells
Cluster 36214 cells
Cluster 15532 cells
Cluster 74060 cells
Cluster 41437 cells
Cluster 61427 cells
Cluster 5720 cells
Cluster 8528 cells
4. thymus scRNA-seq atlas - thymic epithelial cell subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh3825726 cells
v9825726 cells
STARsolo 2.7.4a,CellBender25726 cells
fetal_19w_donor6710 cells
U406283 cells
6m_thymus_donor3672 cells
fetal_23w_donor2650 cells
U482247 cells
T072021 cells
postnatal_10m_donor1246 cells
F83434 cells
U09230 cells
postnatal_6d_donor100 cells
F2143 cells
F3824 cells
F3021 cells
F6415 cells
F4510 cells
Z118 cells
F676 cells
F236 cells
19 weeks (post-conception)6710 cells
7 days6283 cells
6 months6149 cells
23 weeks (post-conception)2650 cells
3 months2021 cells
10 months1246 cells
17 weeks (post-conception)434 cells
6 days100 cells
16 weeks (post-conception)43 cells
13 weeks (post-conception)24 cells
14 weeks (post-conception)21 cells
11 weeks (post-conception)21 cells
12 weeks (post-conception)16 cells
2.5 years8 cells
True13786 cells
Unassigned11940 cells
fresh25726 cells
surgical resection25726 cells
Great Ormond Street Hospital for Children NHS12432 cells
San Francisco General Hospital9360 cells
Unassigned2580 cells
University of California, San Francisco1346 cells
Newcastle Hospitals NHS8 cells
CD4517748 cells
Unassigned7978 cells
leukocyte17748 cells
Unassigned7978 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting10706 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting6269 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting3672 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting2485 cells
enzymatic dissociation,positive magnetic affinity cell sorting2245 cells
enzymatic dissociation231 cells
enzymatic dissociation,fluorescence-activated cell sorting104 cells
mechanical dissociation,enzymatic dissociation14 cells
100 μg/ml Liberase TM10706 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH8530 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II3672 cells
1.6 mg/ml collagenase IV2356 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH238 cells
0.2 mg/ml liberase224 cells
45-60 minute10706 cells
Unassigned8768 cells
30-45 minute3672 cells
30 minute2580 cells
Unassigned16566 cells
epithelial cell of thymus5488 cells
medullary thymic epithelial cell2348 cells
cortical thymic epithelial cell1324 cells
Unassigned14321 cells
EpCAM4730 cells
EpCAM,CD2053003 cells
EpCAMhigh,CD205-2348 cells
EpCAMlow,CD205+1324 cells
0259273d-0959-478c-a312-f311e7b899816710 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b973266 cells
72a3a376-2a41-4615-9d6b-7583e1e3e9663003 cells
7175f9ca-dddd-4a4a-a00a-45e7dd4754871811 cells
9bb9ebf7-112d-4f60-b27f-98f8246f0d101728 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba1357 cells
5dabbbcc-24af-43d4-b428-6c90f15950991293 cells
1c030062-faa0-4e47-85c0-6ef009f2a0f21137 cells
700d57d4-2466-42f1-9605-88d5e8451c291110 cells
dadac003-e5d6-4bed-9fb0-d37b6acf0f031048 cells
23b7f9d6-4fb3-4d8d-a9d4-ecb03078b2231030 cells
53a4c3d0-d56d-47df-96be-e6c89c20e148620 cells
bfbf960c-fe5c-4e93-ae1e-ae2a3b2f6b0a434 cells
4bde7163-d258-46d1-92ce-4a998b6d7e1f276 cells
8d62fc28-a5e4-488d-8013-2fec2b16a878230 cells
d1d0f14a-b49a-410f-8026-f1f8ad84efed216 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc0120 cells
b4cd9df4-8d0f-40eb-ad5a-cc616195bf00100 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c90 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e43 cells
42640a48-43a2-4023-9eed-1d6b2149e4c221 cells
6a6a25e6-737f-40d3-89e8-3f9f1b06798414 cells
330a23af-1bdc-434d-9445-83d6a990821213 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef111 cells
e23c6097-c75c-4194-9b9b-11eccc636db110 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee8 cells
9a658b0a-0cc6-4a7e-af9c-6cd1a02f8e088 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de7 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f6 cells
83803089-c547-4329-a671-74352a4949046 cells
3 prime tag14472 cells
5 prime tag11254 cells
General Community14378 cells
Wellcome Sanger Institute11348 cells
Unassigned8768 cells
SRX80893456710 cells
ERX38061081811 cells
SRX93239941728 cells
SRX80893471357 cells
SRX80893461293 cells
SRX93239921048 cells
SRX80893501030 cells
SRX9323993620 cells
ERX3806109434 cells
SRX9323991276 cells
SRX8089349216 cells
ERX3806111120 cells
SRX8089348100 cells
ERX380611290 cells
ERX380608243 cells
ERX380608121 cells
ERX380608013 cells
ERX380607911 cells
ERX380607810 cells
ERX38061198 cells
ERX38061207 cells
ERX38061246 cells
ERX38060766 cells
Unassigned23138 cells
Illumina NextSeq 500 (EFO:0009173)2021 cells
Illumina HiSeq 2500 (EFO:0008565)434 cells
Illumina HiSeq 4000 (EFO:0008563)125 cells
Illumina NovaSeq 6000 (EFO:0008637)8 cells
mcTEC5821 cells
cTECI5356 cells
mTECI3913 cells
cTECIII2151 cells
cTECII1941 cells
TEC-neuro1628 cells
TEC-myo1053 cells
mTECIII998 cells
mTECII897 cells
mTECI-trans754 cells
TEC-cilliated623 cells
mcTEC-Prolif525 cells
Unassigned66 cells
Unassigned25201 cells
proliferating525 cells
none25488 cells
congenital heart disease238 cells
paed (early)15807 cells
fetal9919 cells
Bautista202110706 cells
HTSA_Sanger8768 cells
Campinoti20203672 cells
Park20202580 cells
45N10810 cells
FACS6269 cells
MACS2485 cells
EPCAM2245 cells
EpCAM+CD49F-1728 cells
CD205+CD49F-1048 cells
EpCAM+CD49F+620 cells
CD205+CD49F+276 cells
TOT245 cells
Unassigned23579 cells
medullary thymic epithelial cell1864 cells
cortical thymic epithelial cell166 cells
epithelial cell of thymus98 cells
dendritic cell15 cells
fibroblast2 cells
double negative thymocyte1 cells
CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell1 cells
Unassigned25614 cells
KERATINOCYTE91 cells
NEURON10 cells
MUSCLE_SATELLITE5 cells
ENTEROENDOCRINE_I5 cells
LOW_QUALITY1 cells
mcTEC6346 cells
cTECI5356 cells
mTECI3913 cells
cTECIII2151 cells
cTECII1941 cells
TEC-neuro1628 cells
TEC-myo1053 cells
mTECIII998 cells
mTECII897 cells
mTECI-trans754 cells
TEC-cilliated623 cells
Unassigned66 cells
cTEC9448 cells
mTEC6562 cells
mcTEC6346 cells
mTEC-mimetic3304 cells
Unassigned66 cells
TEC22356 cells
TEC-mimetic3304 cells
Unassigned66 cells
Epithelial25660 cells
Unassigned66 cells
mcTEC5821 cells
cTECI5356 cells
mTECI3913 cells
cTECIII2151 cells
cTECII1941 cells
TEC-neuro1628 cells
TEC-myo1053 cells
mTECIII998 cells
mTECII897 cells
mTECI-trans754 cells
TEC-cilliated623 cells
mcTEC-Prolif525 cells
TEC-tuft66 cells
baut16710 cells
U40-THY-0-SC-F-13266 cells
U40-THY-0-SC-F-23003 cells
T07_TH_EPCAM_S31811 cells
GSM48389541728 cells
baut31357 cells
baut21293 cells
U48-THY-0-SC-EPCP-2_5GEX1137 cells
U48-THY-0-SC-EPCP-1_5GEX1110 cells
GSM48389521048 cells
baut61030 cells
GSM4838953620 cells
F83_TH_EPCAM434 cells
GSM4838951276 cells
TA9260013230 cells
baut5216 cells
T07_TH_TOT_1_S1120 cells
baut4100 cells
T07_TH_TOT_2_S290 cells
FCAImmP717937043 cells
FCAImmP727756521 cells
U48-THY-0-SC-1_5GEX14 cells
FCAImmP752828513 cells
FCAImmP752828411 cells
FCAImmP757923110 cells
TA92600178 cells
FCAImmP78518908 cells
FCAImmP78518917 cells
FCAImmP78518956 cells
FCAImmP71986356 cells
10x 3' v210700 cells
10x 5' v28530 cells
10x 3' v33772 cells
10x 5' v12724 cells
normal25726 cells
Unassigned10706 cells
female10643 cells
male4377 cells
thymus25726 cells
Cluster 49274 cells
Cluster 66113 cells
Cluster 54437 cells
Cluster 22631 cells
Cluster 31827 cells
Cluster 11076 cells
Cluster 7368 cells
5. thymus scRNA-seq atlas - fibroblast subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh3820779 cells
v9820779 cells
STARsolo 2.7.4a,CellBender20779 cells
fetal_19w_donor9133 cells
fetal_23w_donor2539 cells
F381869 cells
postnatal_10m_donor1823 cells
U401645 cells
F41717 cells
F21589 cells
F23539 cells
F67503 cells
F45421 cells
F30372 cells
F64262 cells
6m_thymus_donor178 cells
F29106 cells
T0740 cells
postnatal_6d_donor27 cells
U488 cells
Z118 cells
19 weeks (post-conception)9133 cells
23 weeks (post-conception)2539 cells
13 weeks (post-conception)1869 cells
10 months1823 cells
7 days1645 cells
16 weeks (post-conception)1306 cells
12 weeks (post-conception)924 cells
11 weeks (post-conception)801 cells
14 weeks (post-conception)372 cells
6 months186 cells
17 weeks (post-conception)106 cells
3 months40 cells
6 days27 cells
2.5 years8 cells
Unassigned17090 cells
True3689 cells
fresh20779 cells
surgical resection20779 cells
San Francisco General Hospital11672 cells
Unassigned5418 cells
University of California, San Francisco1850 cells
Great Ormond Street Hospital for Children NHS1831 cells
Newcastle Hospitals NHS8 cells
CD4519788 cells
Unassigned983 cells
CD38 cells
leukocyte19788 cells
Unassigned983 cells
T cell8 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting13530 cells
enzymatic dissociation,fluorescence-activated cell sorting4630 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting1631 cells
enzymatic dissociation788 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting178 cells
mechanical dissociation,enzymatic dissociation14 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting8 cells
100 μg/ml Liberase TM13522 cells
1.6 mg/ml collagenase IV3615 cells
0.2 mg/ml liberase1786 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH1653 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II178 cells
Unassigned17 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH8 cells
45-60 minute13522 cells
30 minute5401 cells
Unassigned1678 cells
30-45 minute178 cells
Unassigned20437 cells
leukocyte147 cells
cortical thymic epithelial cell101 cells
medullary thymic epithelial cell77 cells
epithelial cell of thymus17 cells
Unassigned20420 cells
CD45147 cells
EpCAMlow,CD205+101 cells
EpCAMhigh,CD205-77 cells
CD13717 cells
EpCAM,CD2059 cells
EpCAM8 cells
0259273d-0959-478c-a312-f311e7b899819133 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b971622 cells
23b7f9d6-4fb3-4d8d-a9d4-ecb03078b2231609 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba1274 cells
5dabbbcc-24af-43d4-b428-6c90f15950991265 cells
330a23af-1bdc-434d-9445-83d6a99082121023 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef1846 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e589 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f449 cells
42640a48-43a2-4023-9eed-1d6b2149e4c2366 cells
7af0a1fb-651c-4cac-9571-b8b22896957d366 cells
264d56c4-954f-404e-adad-ff691f34dea0351 cells
e23c6097-c75c-4194-9b9b-11eccc636db1240 cells
d1d0f14a-b49a-410f-8026-f1f8ad84efed214 cells
fe28ef61-6f2a-433a-bbae-355aa9dbe41b181 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de141 cells
83803089-c547-4329-a671-74352a494904139 cells
05287b63-0a6e-4605-8b25-901469696c2f133 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee121 cells
fadfcbbf-117f-4a75-bbff-624ea4993858114 cells
7ba3652f-d73f-4974-a9b0-6a0af87bd3f2100 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f783990 cells
53a4c3d0-d56d-47df-96be-e6c89c20e14857 cells
fe84964e-961b-414c-829e-00b16b0da92055 cells
dadac003-e5d6-4bed-9fb0-d37b6acf0f0354 cells
4bde7163-d258-46d1-92ce-4a998b6d7e1f47 cells
e130d3d3-63fd-44f2-a545-f5f3d164889c29 cells
b4cd9df4-8d0f-40eb-ad5a-cc616195bf0027 cells
bcc0a8e3-ae57-418f-897a-f08f7d41cddf22 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c21 cells
9bb9ebf7-112d-4f60-b27f-98f8246f0d1020 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc019 cells
6bf7479c-b3ec-4167-b6d7-a50eaf70669e17 cells
6a6a25e6-737f-40d3-89e8-3f9f1b06798414 cells
72a3a376-2a41-4615-9d6b-7583e1e3e9669 cells
f837dd0f-0151-4532-bf72-dfcc629d61a28 cells
700d57d4-2466-42f1-9605-88d5e8451c298 cells
c7760a1e-8622-4500-b914-8bd529b48d966 cells
3 prime tag17694 cells
5 prime tag3085 cells
General Community13700 cells
Wellcome Sanger Institute7079 cells
SRX80893459133 cells
Unassigned1661 cells
SRX80893501609 cells
SRX80893471274 cells
SRX80893461265 cells
ERX38060801023 cells
ERX3806079846 cells
ERX3806082589 cells
ERX3806076449 cells
ERX3806083366 cells
ERX3806081366 cells
ERX3806084351 cells
ERX3806078240 cells
SRX8089349214 cells
ERX3806077181 cells
ERX3806120141 cells
ERX3806124139 cells
ERX3806121133 cells
ERX3806119121 cells
ERX3806122114 cells
ERX3806123100 cells
ERX380609090 cells
SRX932399357 cells
ERX380608555 cells
SRX932399254 cells
SRX932399147 cells
ERX380610029 cells
SRX808934827 cells
ERX380610122 cells
ERX380611221 cells
SRX932399420 cells
ERX380611119 cells
ERX380610717 cells
ERX38060966 cells
Unassigned15353 cells
Illumina HiSeq 4000 (EFO:0008563)5378 cells
Illumina NextSeq 500 (EFO:0009173)40 cells
Illumina NovaSeq 6000 (EFO:0008637)8 cells
PeriloFb10011 cells
InterloFb4893 cells
medFb1552 cells
PeriloFb-Prolif1387 cells
InterloFb-COL9A31121 cells
medFb-RGS5846 cells
medFB-MHCIIh633 cells
Unassigned336 cells
Unassigned19392 cells
proliferating1387 cells
none20771 cells
congenital heart disease8 cells
fetal17050 cells
paed (early)3729 cells
Bautista202113522 cells
Park20205418 cells
HTSA_Sanger1661 cells
Campinoti2020178 cells
45N17988 cells
FACS1631 cells
TOT802 cells
45P147 cells
EpCAM+CD49F+57 cells
CD205+CD49F-54 cells
CD205+CD49F+47 cells
EpCAM+CD49F-20 cells
CD13717 cells
MACS16 cells
Unassigned15486 cells
fibroblast5258 cells
vascular associated smooth muscle cell26 cells
lymphocyte3 cells
medullary thymic epithelial cell2 cells
endothelial cell2 cells
epithelial cell of thymus1 cells
dendritic cell1 cells
Unassigned15583 cells
FIBROBLAST_XI3234 cells
FIBROBLAST_XII468 cells
CYCLING_FIBROBLAST_I452 cells
FIBROBLAST_I437 cells
MYOFIBROBLAST432 cells
FIBROBLAST_VII48 cells
FIBROBLAST_XIV41 cells
MESENCHYMAL_LYMPHOID_TISSUE_ORGANISER37 cells
FIBROBLAST_VI23 cells
FIBROBLAST_XIII11 cells
FIBROBLAST_X6 cells
LOW_QUALITY4 cells
VSMC_PERICYTE2 cells
GLIAL1 cells
PeriloFb11398 cells
InterloFb6014 cells
medFb2398 cells
medFB-MHCIIh633 cells
Unassigned336 cells
PeriloFb11398 cells
InterloFb6014 cells
medFb3031 cells
Unassigned336 cells
Fb20443 cells
Unassigned336 cells
Stroma20443 cells
Unassigned336 cells
PeriloFb10011 cells
InterloFb4893 cells
medFb1552 cells
PeriloFb-Prolif1387 cells
InterloFb-COL9A31121 cells
medFb-RGS5846 cells
medFB-MHCIIh633 cells
fetFB-NKX2-5138 cells
fetFB-RSPO2115 cells
fetFB-CCL2183 cells
baut19133 cells
U40-THY-0-SC-F-11622 cells
baut61609 cells
baut31274 cells
baut21265 cells
FCAImmP75282851023 cells
FCAImmP7528284846 cells
FCAImmP7179370589 cells
FCAImmP7198635449 cells
FCAImmP7277565366 cells
FCAImmP7555852366 cells
FCAImmP7555861351 cells
FCAImmP7579231240 cells
baut5214 cells
FCAImmP7579219181 cells
FCAImmP7851891141 cells
FCAImmP7851895139 cells
FCAImmP7851892133 cells
FCAImmP7851890121 cells
FCAImmP7851893114 cells
FCAImmP7851894100 cells
FCAImmP719863490 cells
GSM483895357 cells
FCAImmP727755755 cells
GSM483895254 cells
GSM483895147 cells
FCAImmP727755629 cells
baut427 cells
FCAImmP729203022 cells
T07_TH_TOT_2_S221 cells
GSM483895420 cells
T07_TH_TOT_1_S119 cells
FCAImmP785189617 cells
U48-THY-0-SC-1_5GEX14 cells
U40-THY-0-SC-F-29 cells
U48-THY-0-SC-EPCP-1_5GEX8 cells
TA92600158 cells
FCAImmP72920346 cells
10x 3' v217489 cells
10x 5' v21653 cells
10x 5' v11432 cells
10x 3' v3205 cells
normal20779 cells
Unassigned13522 cells
male3679 cells
female3578 cells
thymus20779 cells
Cluster 85921 cells
Cluster 73712 cells
Cluster 43294 cells
Cluster 22588 cells
Cluster 61715 cells
Cluster 51384 cells
Cluster 11309 cells
Cluster 3856 cells
6. thymus scRNA-seq atlas - smooth muscle cell subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh3810019 cells
v9810019 cells
STARsolo 2.7.4a,CellBender10019 cells
fetal_23w_donor5184 cells
fetal_19w_donor2192 cells
postnatal_10m_donor1251 cells
U40852 cells
F38232 cells
F3061 cells
F2152 cells
F4148 cells
T0732 cells
F4528 cells
F2323 cells
F6717 cells
F6412 cells
F8310 cells
6m_thymus_donor10 cells
U488 cells
F297 cells
23 weeks (post-conception)5184 cells
19 weeks (post-conception)2192 cells
10 months1251 cells
7 days852 cells
13 weeks (post-conception)232 cells
16 weeks (post-conception)100 cells
14 weeks (post-conception)61 cells
12 weeks (post-conception)45 cells
11 weeks (post-conception)35 cells
3 months32 cells
6 months18 cells
17 weeks (post-conception)17 cells
Unassigned7898 cells
True2121 cells
fresh10019 cells
surgical resection10019 cells
San Francisco General Hospital7376 cells
University of California, San Francisco1251 cells
Great Ormond Street Hospital for Children NHS870 cells
Unassigned522 cells
CD459940 cells
Unassigned79 cells
leukocyte9940 cells
Unassigned79 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting8627 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting852 cells
enzymatic dissociation,fluorescence-activated cell sorting451 cells
enzymatic dissociation55 cells
enzymatic dissociation,positive magnetic affinity cell sorting16 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting10 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting8 cells
100 μg/ml Liberase TM8627 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH860 cells
1.6 mg/ml collagenase IV410 cells
0.2 mg/ml liberase112 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II10 cells
45-60 minute8627 cells
Unassigned860 cells
30 minute522 cells
30-45 minute10 cells
Unassigned10001 cells
medullary thymic epithelial cell10 cells
epithelial cell of thymus8 cells
Unassigned9985 cells
EpCAM24 cells
EpCAMhigh,CD205-10 cells
5dabbbcc-24af-43d4-b428-6c90f15950992607 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba2577 cells
0259273d-0959-478c-a312-f311e7b899812192 cells
23b7f9d6-4fb3-4d8d-a9d4-ecb03078b2231238 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b97852 cells
330a23af-1bdc-434d-9445-83d6a9908212142 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef190 cells
42640a48-43a2-4023-9eed-1d6b2149e4c261 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e52 cells
7af0a1fb-651c-4cac-9571-b8b22896957d28 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f23 cells
264d56c4-954f-404e-adad-ff691f34dea020 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c16 cells
fe28ef61-6f2a-433a-bbae-355aa9dbe41b15 cells
e23c6097-c75c-4194-9b9b-11eccc636db113 cells
d1d0f14a-b49a-410f-8026-f1f8ad84efed13 cells
bfbf960c-fe5c-4e93-ae1e-ae2a3b2f6b0a10 cells
53a4c3d0-d56d-47df-96be-e6c89c20e14810 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc010 cells
fadfcbbf-117f-4a75-bbff-624ea49938589 cells
83803089-c547-4329-a671-74352a4949048 cells
700d57d4-2466-42f1-9605-88d5e8451c298 cells
fe84964e-961b-414c-829e-00b16b0da9207 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee6 cells
7175f9ca-dddd-4a4a-a00a-45e7dd4754876 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de6 cells
3 prime tag9055 cells
5 prime tag964 cells
General Community8637 cells
Wellcome Sanger Institute1382 cells
SRX80893462607 cells
SRX80893472577 cells
SRX80893452192 cells
SRX80893501238 cells
Unassigned860 cells
ERX3806080142 cells
ERX380607990 cells
ERX380608161 cells
ERX380608252 cells
ERX380608328 cells
ERX380607623 cells
ERX380608420 cells
ERX380611216 cells
ERX380607715 cells
SRX808934913 cells
ERX380607813 cells
SRX932399310 cells
ERX380610910 cells
ERX380611110 cells
ERX38061229 cells
ERX38061248 cells
ERX38060857 cells
ERX38061206 cells
ERX38061086 cells
ERX38061196 cells
Unassigned9497 cells
Illumina HiSeq 4000 (EFO:0008563)480 cells
Illumina NextSeq 500 (EFO:0009173)32 cells
Illumina HiSeq 2500 (EFO:0008565)10 cells
SMC4686 cells
Pericyte3602 cells
Pericyte_CCL19678 cells
Pericyte_COL1A1594 cells
ProlifPericyte459 cells
Unassigned9560 cells
proliferating459 cells
none10019 cells
fetal7866 cells
paed (early)2153 cells
Bautista20218627 cells
HTSA_Sanger860 cells
Park2020522 cells
Campinoti202010 cells
45N9078 cells
FACS852 cells
TOT55 cells
EPCAM16 cells
EpCAM+CD49F+10 cells
MACS8 cells
Unassigned9517 cells
vascular associated smooth muscle cell492 cells
fibroblast10 cells
Unassigned9560 cells
VSMC_PERICYTE440 cells
MYOFIBROBLAST7 cells
MESENCHYMAL_LYMPHOID_TISSUE_ORGANISER6 cells
FIBROBLAST_XI3 cells
FIBROBLAST_XIV2 cells
DOUBLET_IMMUNE_FIBROBLAST1 cells
Pericyte5333 cells
SMC4686 cells
Pericyte5333 cells
SMC4686 cells
Vascular10019 cells
Stroma10019 cells
SMC4686 cells
Pericyte3602 cells
Pericyte_CCL19678 cells
Pericyte_COL1A1594 cells
ProlifPericyte459 cells
baut22607 cells
baut32577 cells
baut12192 cells
baut61238 cells
U40-THY-0-SC-F-1852 cells
FCAImmP7528285142 cells
FCAImmP752828490 cells
FCAImmP727756561 cells
FCAImmP717937052 cells
FCAImmP755585228 cells
FCAImmP719863523 cells
FCAImmP755586120 cells
T07_TH_TOT_2_S216 cells
FCAImmP757921915 cells
FCAImmP757923113 cells
baut513 cells
F83_TH_EPCAM10 cells
T07_TH_TOT_1_S110 cells
GSM483895310 cells
FCAImmP78518939 cells
U48-THY-0-SC-EPCP-1_5GEX8 cells
FCAImmP78518958 cells
FCAImmP72775577 cells
T07_TH_EPCAM_S36 cells
FCAImmP78518906 cells
FCAImmP78518916 cells
10x 3' v29045 cells
10x 5' v2860 cells
10x 5' v1104 cells
10x 3' v310 cells
normal10019 cells
Unassigned8627 cells
female972 cells
male420 cells
thymus10019 cells
Cluster 42780 cells
Cluster 52182 cells
Cluster 62172 cells
Cluster 31129 cells
Cluster 2914 cells
Cluster 1842 cells
7. thymus scRNA-seq atlas - B cell subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh383460 cells
v983460 cells
STARsolo 2.7.4a,CellBender3460 cells
T07348 cells
T06310 cells
P1310 cells
F29292 cells
TSC-CT10261 cells
TSC-CT9252 cells
TSC-CT12251 cells
U48241 cells
U40197 cells
F45126 cells
F30119 cells
P3110 cells
Z1199 cells
TSC-CT1390 cells
F6778 cells
F2169 cells
TSC-CT868 cells
F3866 cells
T0361 cells
F4151 cells
U0933 cells
F6417 cells
F2311 cells
3 months699 cells
6 months384 cells
2 months320 cells
30 months310 cells
14.5 months310 cells
17 weeks (post-conception)292 cells
5 months251 cells
12 weeks (post-conception)204 cells
7 days197 cells
16 weeks (post-conception)120 cells
14 weeks (post-conception)119 cells
2.5 years99 cells
13 weeks (post-conception)66 cells
10 months61 cells
11 weeks (post-conception)28 cells
True1912 cells
Unassigned1548 cells
fresh3460 cells
surgical resection3460 cells
Unassigned1968 cells
University Hospital Ghent922 cells
Great Ormond Street Hospital for Children NHS471 cells
Newcastle Hospitals NHS99 cells
Unassigned1848 cells
CD31344 cells
CD45268 cells
Unassigned1848 cells
T cell1344 cells
leukocyte268 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting985 cells
enzymatic dissociation790 cells
enzymatic dissociation,fluorescence-activated cell sorting739 cells
mechanical dissociation,fluorescence-activated cell sorting420 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting250 cells
mechanical dissociation,enzymatic dissociation209 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting48 cells
enzymatic dissociation,positive magnetic affinity cell sorting19 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH1360 cells
1.6 mg/ml collagenase IV802 cells
0.2 mg/ml liberase741 cells
Unassigned425 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH132 cells
Unassigned1917 cells
30 minute1543 cells
Unassigned2635 cells
leukocyte497 cells
epithelial cell of thymus282 cells
T cell46 cells
Unassigned2611 cells
CD45497 cells
EpCAM269 cells
CD346 cells
EpCAM,CD20532 cells
CD1375 cells
ac01bcd2-2d03-4a97-8569-ad598a7beb8f261 cells
3917a9fb-462f-4f4e-9c1b-b0a6eb1c82f8251 cells
1cac9958-24f7-45aa-9965-472038cb9bbb238 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc0195 cells
e130d3d3-63fd-44f2-a545-f5f3d164889c178 cells
80dce0eb-df2b-4bb1-b4bf-7fbb00e89ada154 cells
6a6a25e6-737f-40d3-89e8-3f9f1b067984144 cells
64eca649-dfd8-47de-8bc8-d05acf1794bc139 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c134 cells
700d57d4-2466-42f1-9605-88d5e8451c29125 cells
1c030062-faa0-4e47-85c0-6ef009f2a0f2116 cells
9c9a3635-c73c-4cb4-bff5-7c769df23e20101 cells
70ac07c6-9ff2-4048-bcfa-332ea9ad8fb096 cells
bcc0a8e3-ae57-418f-897a-f08f7d41cddf95 cells
f751ebaf-e7c3-4c03-998e-79b3c7fa9f5484 cells
99ec672f-2d8c-4425-a800-447f3c3256b283 cells
fe28ef61-6f2a-433a-bbae-355aa9dbe41b73 cells
810f4e99-5478-4d01-86d9-df0a93dc583870 cells
65e9f5d0-5add-4c09-9cee-316716c2ae7368 cells
1aec6622-be0c-4e25-b82a-833865865e8961 cells
f837dd0f-0151-4532-bf72-dfcc629d61a248 cells
409181fb-ae4d-4bfe-9e20-849ae6420eca47 cells
cedc71e0-ecb2-43d1-8834-c48b0a0a01de44 cells
ad489aeb-d0fc-4515-892a-443e57f438bd41 cells
42640a48-43a2-4023-9eed-1d6b2149e4c240 cells
c7760a1e-8622-4500-b914-8bd529b48d9635 cells
e23c6097-c75c-4194-9b9b-11eccc636db133 cells
72a3a376-2a41-4615-9d6b-7583e1e3e96632 cells
5999a5e6-b1a9-4bea-a6d0-0a479e8283e231 cells
9aedd5f2-35f6-460b-b2ad-49242d848c4330 cells
1dcaec0a-2eae-4431-bb5e-ec1c5df9d0fb29 cells
eae32bc7-1603-4e34-adee-5a953f4bc45c24 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e22 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b9721 cells
83803089-c547-4329-a671-74352a49490421 cells
7ba3652f-d73f-4974-a9b0-6a0af87bd3f220 cells
6c959596-7ef9-40ee-9bb0-6044964354d220 cells
fe84964e-961b-414c-829e-00b16b0da92019 cells
7175f9ca-dddd-4a4a-a00a-45e7dd47548719 cells
fadfcbbf-117f-4a75-bbff-624ea499385818 cells
7af0a1fb-651c-4cac-9571-b8b22896957d15 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef114 cells
05287b63-0a6e-4605-8b25-901469696c2f14 cells
0de02a80-da1b-4fc4-8300-4b4eef3f459814 cells
bd801268-03bc-4bc7-93fe-7fa16460938714 cells
330a23af-1bdc-434d-9445-83d6a990821213 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f783911 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee10 cells
f307a1fb-28f2-41c4-b5aa-01ecbc8c723410 cells
e1b9c902-597d-4462-9037-eb6386547e2b10 cells
0a4171ec-3820-4e99-858f-b74eb70808cd9 cells
c25f52a7-8590-4ff4-a9d0-82efe6cbdfdf9 cells
8d62fc28-a5e4-488d-8013-2fec2b16a8789 cells
751f08bc-6649-4ab4-826f-f4b20825a9058 cells
db5b9b21-f33d-42a7-839e-87ff5faa6d468 cells
264d56c4-954f-404e-adad-ff691f34dea08 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de7 cells
908c4e6e-4b3a-430b-9fe1-a97d422db1bb6 cells
0f203abe-b4af-4f73-9ec6-2ca944ebb1766 cells
6bf7479c-b3ec-4167-b6d7-a50eaf70669e5 cells
5 prime tag2501 cells
3 prime tag959 cells
Wellcome Sanger Institute2118 cells
Ghent University1342 cells
Unassigned1912 cells
ERX3806111195 cells
ERX3806100178 cells
ERX3806112134 cells
ERX380612796 cells
ERX380610195 cells
ERX380612583 cells
ERX380607773 cells
ERX380612670 cells
ERX380612861 cells
ERX380609747 cells
ERX380609544 cells
ERX380608140 cells
ERX380609635 cells
ERX380607833 cells
ERX380611531 cells
ERX380611630 cells
ERX380609329 cells
ERX380608222 cells
ERX380612421 cells
ERX380612320 cells
ERX380609820 cells
ERX380610819 cells
ERX380608519 cells
ERX380612218 cells
ERX380608315 cells
ERX380612114 cells
ERX380609114 cells
ERX380607914 cells
ERX380608013 cells
ERX380609011 cells
ERX380609410 cells
ERX380611910 cells
ERX38060998 cells
ERX38060848 cells
ERX38061207 cells
ERX38060926 cells
ERX38061075 cells
Illumina NovaSeq 6000 (EFO:0008637)1392 cells
Illumina HiSeq 4000 (EFO:0008563)1249 cells
Unassigned471 cells
Illumina NextSeq 500 (EFO:0009173)348 cells
B-memory1659 cells
B-naive1192 cells
small_pre_B180 cells
B-Prolif120 cells
B-plasma115 cells
pro_B95 cells
late_pro_B87 cells
large_pre_B12 cells
Unassigned3340 cells
proliferating120 cells
none2908 cells
congenital heart disease552 cells
paed (early)2631 cells
fetal829 cells
Park20201968 cells
HTSA_Ghent922 cells
HTSA_Sanger570 cells
CD3N1296 cells
TOT999 cells
45P497 cells
MACS298 cells
45N237 cells
FACS63 cells
CD3P46 cells
EPCAM19 cells
CD1375 cells
Unassigned1898 cells
naive B cell1214 cells
precursor B cell231 cells
memory B cell52 cells
plasma cell43 cells
dendritic cell15 cells
T cell2 cells
erythrocyte1 cells
double negative thymocyte1 cells
double-positive, alpha-beta thymocyte1 cells
early T lineage precursor1 cells
CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell1 cells
Unassigned2787 cells
B1286 cells
MATURE_B108 cells
PRO_B57 cells
CYCLING_B53 cells
LATE_PRO_B48 cells
SMALL_PRE_B47 cells
LARGE_PRE_B30 cells
IMMATURE_B18 cells
PRE_PRO_B10 cells
PLASMA_B7 cells
DOUBLET4 cells
MIGRATORY_DC2 cells
HIGH_MITO2 cells
LATE_MK1 cells
B_mature2971 cells
B_dev374 cells
B-plasma115 cells
B_mature2971 cells
B_dev374 cells
B-plasma115 cells
B3460 cells
B3460 cells
B-memory1659 cells
B-naive1192 cells
small_pre_B180 cells
B-Prolif120 cells
B-plasma115 cells
pro_B95 cells
late_pro_B87 cells
large_pre_B12 cells
sample11261 cells
sample9251 cells
sample3238 cells
T07_TH_TOT_1_S1195 cells
FCAImmP7277556178 cells
TTA8154 cells
U48-THY-0-SC-1_5GEX144 cells
TTA7139 cells
T07_TH_TOT_2_S2134 cells
U48-THY-0-SC-EPCP-1_5GEX125 cells
U48-THY-0-SC-EPCP-2_5GEX116 cells
TTA13101 cells
T06_TH_TOT_5GEX_3_S1196 cells
FCAImmP729203095 cells
sample584 cells
T06_TH_TOT_5GEX_1_S983 cells
FCAImmP757921973 cells
T06_TH_TOT_5GEX_2_S1070 cells
sample168 cells
T06_TH_TOT_5GEX_4_S1261 cells
TA926001548 cells
FCAImmP717936947 cells
FCAImmP727756444 cells
TA926001441 cells
FCAImmP727756540 cells
FCAImmP729203435 cells
FCAImmP757923133 cells
U40-THY-0-SC-F-232 cells
T03_TH_TOT_5GEX_1_S131 cells
T03_TH_TOT_5GEX_2_S230 cells
FCAImmP752828329 cells
TA926001224 cells
FCAImmP717937022 cells
U40-THY-0-SC-F-121 cells
FCAImmP785189521 cells
FCAImmP785189420 cells
FCAImmP755585120 cells
FCAImmP727755719 cells
T07_TH_EPCAM_S319 cells
FCAImmP785189318 cells
FCAImmP755585215 cells
FCAImmP785189214 cells
FCAImmP757921814 cells
sample414 cells
FCAImmP752828414 cells
FCAImmP752828513 cells
FCAImmP719863411 cells
FCAImmP752829410 cells
FCAImmP785189010 cells
TA926001610 cells
TTA149 cells
TA92600139 cells
TTA109 cells
FCAImmP75558618 cells
TTA98 cells
FCAImmP75558608 cells
FCAImmP78518917 cells
sample66 cells
FCAImmP75792306 cells
FCAImmP78518965 cells
10x 5' v21360 cells
10x 5' v11141 cells
10x 3' v2959 cells
normal3460 cells
male2204 cells
female1256 cells
thymus3460 cells
Cluster 51244 cells
Cluster 3712 cells
Cluster 1527 cells
Cluster 4455 cells
Cluster 2338 cells
Cluster 7116 cells
Cluster 668 cells
8. thymus scRNA-seq atlas - myeloid p1 subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh382923 cells
v982923 cells
STARsolo 2.7.4a,CellBender2923 cells
U40507 cells
F29383 cells
F67267 cells
U48223 cells
F30220 cells
T07190 cells
P3164 cells
T06131 cells
F38129 cells
F21128 cells
F64116 cells
F2388 cells
F4174 cells
Z1160 cells
T0352 cells
P151 cells
TSC-CT1245 cells
U0922 cells
F4519 cells
TSC-CT819 cells
TSC-CT1011 cells
TSC-CT99 cells
F839 cells
6m_thymus_donor6 cells
7 days507 cells
6 months415 cells
17 weeks (post-conception)392 cells
12 weeks (post-conception)286 cells
14 weeks (post-conception)220 cells
11 weeks (post-conception)204 cells
16 weeks (post-conception)202 cells
3 months201 cells
30 months131 cells
13 weeks (post-conception)129 cells
2.5 years60 cells
10 months52 cells
14.5 months51 cells
5 months45 cells
2 months28 cells
Unassigned1806 cells
True1117 cells
fresh2923 cells
surgical resection2923 cells
Unassigned2021 cells
Great Ormond Street Hospital for Children NHS758 cells
University Hospital Ghent84 cells
Newcastle Hospitals NHS60 cells
Unassigned2433 cells
CD3342 cells
CD45148 cells
Unassigned2433 cells
T cell342 cells
leukocyte148 cells
enzymatic dissociation,fluorescence-activated cell sorting1058 cells
enzymatic dissociation722 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting428 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting229 cells
mechanical dissociation,fluorescence-activated cell sorting215 cells
mechanical dissociation,enzymatic dissociation196 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting43 cells
enzymatic dissociation,positive magnetic affinity cell sorting26 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting6 cells
0.2 mg/ml liberase996 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH814 cells
1.6 mg/ml collagenase IV793 cells
Unassigned232 cells
3.2 mg/ml collagenase IV, 50 ug/ml liberase TH82 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II6 cells
30 minute1789 cells
Unassigned1128 cells
30-45 minute6 cells
Unassigned1445 cells
leukocyte964 cells
epithelial cell of thymus508 cells
cortical thymic epithelial cell6 cells
Unassigned1402 cells
CD45964 cells
EpCAM,CD205279 cells
EpCAM255 cells
CD13717 cells
EpCAMlow,CD205+6 cells
72a3a376-2a41-4615-9d6b-7583e1e3e966279 cells
e130d3d3-63fd-44f2-a545-f5f3d164889c260 cells
9c9a3635-c73c-4cb4-bff5-7c769df23e20164 cells
6a6a25e6-737f-40d3-89e8-3f9f1b067984163 cells
bcc0a8e3-ae57-418f-897a-f08f7d41cddf123 cells
1c030062-faa0-4e47-85c0-6ef009f2a0f2114 cells
700d57d4-2466-42f1-9605-88d5e8451c29109 cells
409181fb-ae4d-4bfe-9e20-849ae6420eca104 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc0100 cells
cedc71e0-ecb2-43d1-8834-c48b0a0a01de93 cells
c7760a1e-8622-4500-b914-8bd529b48d9692 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f783977 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c73 cells
83803089-c547-4329-a671-74352a49490472 cells
1dcaec0a-2eae-4431-bb5e-ec1c5df9d0fb67 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b9765 cells
05287b63-0a6e-4605-8b25-901469696c2f63 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee62 cells
f307a1fb-28f2-41c4-b5aa-01ecbc8c723462 cells
fadfcbbf-117f-4a75-bbff-624ea499385860 cells
7ba3652f-d73f-4974-a9b0-6a0af87bd3f255 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de54 cells
3917a9fb-462f-4f4e-9c1b-b0a6eb1c82f845 cells
f837dd0f-0151-4532-bf72-dfcc629d61a243 cells
6c959596-7ef9-40ee-9bb0-6044964354d241 cells
99ec672f-2d8c-4425-a800-447f3c3256b240 cells
42640a48-43a2-4023-9eed-1d6b2149e4c235 cells
1aec6622-be0c-4e25-b82a-833865865e8932 cells
810f4e99-5478-4d01-86d9-df0a93dc583831 cells
5999a5e6-b1a9-4bea-a6d0-0a479e8283e229 cells
70ac07c6-9ff2-4048-bcfa-332ea9ad8fb028 cells
64eca649-dfd8-47de-8bc8-d05acf1794bc26 cells
751f08bc-6649-4ab4-826f-f4b20825a90526 cells
80dce0eb-df2b-4bb1-b4bf-7fbb00e89ada25 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e24 cells
9aedd5f2-35f6-460b-b2ad-49242d848c4323 cells
65e9f5d0-5add-4c09-9cee-316716c2ae7319 cells
6bf7479c-b3ec-4167-b6d7-a50eaf70669e17 cells
7175f9ca-dddd-4a4a-a00a-45e7dd47548717 cells
ad489aeb-d0fc-4515-892a-443e57f438bd17 cells
eae32bc7-1603-4e34-adee-5a953f4bc45c16 cells
0f203abe-b4af-4f73-9ec6-2ca944ebb17611 cells
ac01bcd2-2d03-4a97-8569-ad598a7beb8f11 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f11 cells
1cac9958-24f7-45aa-9965-472038cb9bbb9 cells
bfbf960c-fe5c-4e93-ae1e-ae2a3b2f6b0a9 cells
bd801268-03bc-4bc7-93fe-7fa1646093878 cells
264d56c4-954f-404e-adad-ff691f34dea07 cells
dadac003-e5d6-4bed-9fb0-d37b6acf0f036 cells
8d62fc28-a5e4-488d-8013-2fec2b16a8786 cells
5 prime tag1982 cells
3 prime tag941 cells
Wellcome Sanger Institute2618 cells
Ghent University299 cells
General Community6 cells
Unassigned1111 cells
ERX3806100260 cells
ERX3806101123 cells
ERX3806097104 cells
ERX3806111100 cells
ERX380609593 cells
ERX380609692 cells
ERX380609077 cells
ERX380611273 cells
ERX380612472 cells
ERX380609367 cells
ERX380612163 cells
ERX380609462 cells
ERX380611962 cells
ERX380612260 cells
ERX380612355 cells
ERX380612054 cells
ERX380609841 cells
ERX380612540 cells
ERX380608135 cells
ERX380612832 cells
ERX380612631 cells
ERX380611529 cells
ERX380612728 cells
ERX380609926 cells
ERX380608224 cells
ERX380611623 cells
ERX380610717 cells
ERX380610817 cells
ERX380607611 cells
ERX380609211 cells
ERX38061099 cells
ERX38060918 cells
ERX38060847 cells
SRX93239926 cells
Illumina HiSeq 4000 (EFO:0008563)1639 cells
Unassigned758 cells
Illumina NovaSeq 6000 (EFO:0008637)327 cells
Illumina NextSeq 500 (EFO:0009173)190 cells
Illumina HiSeq 2500 (EFO:0008565)9 cells
DC1571 cells
pDC396 cells
aDC3350 cells
DC1-Prolif347 cells
DC2264 cells
Macrophage-APOC2215 cells
Macrophage-SPIC1174 cells
Macrophage-LYVE1162 cells
aDC2159 cells
aDC1137 cells
DC2-Prolif122 cells
pDC-Prolif26 cells
Unassigned1782 cells
activated646 cells
proliferating495 cells
none2626 cells
congenital heart disease297 cells
paed (early)1490 cells
fetal1433 cells
Park20202021 cells
HTSA_Sanger812 cells
HTSA_Ghent84 cells
Campinoti20206 cells
45P964 cells
TOT918 cells
FACS344 cells
CD3N299 cells
MACS272 cells
45N77 cells
EPCAM26 cells
CD13717 cells
CD205+CD49F-6 cells
dendritic cell1311 cells
Unassigned1110 cells
plasmacytoid dendritic cell264 cells
macrophage225 cells
monocyte9 cells
early T lineage precursor2 cells
progenitor cell1 cells
double negative thymocyte1 cells
Unassigned1633 cells
DC1515 cells
MACROPHAGE_LYVE1_HIGH213 cells
MIGRATORY_DC158 cells
DC2134 cells
PDC94 cells
MACROPHAGE_MHCII_HIGH41 cells
CYCLING_DC35 cells
LOW_QUALITY_MACROPHAGE28 cells
MACROPHAGE_PROLIFERATING20 cells
CYCLING_PDC10 cells
MONOCYTE_II_CCR210 cells
MACROPHAGE_IRON_RECYCLING8 cells
LANGERHANS_CELLS6 cells
MONOCYTE_III_IL1B5 cells
DOUBLET_LYMPHOID_MACROPHAGE4 cells
MOP3 cells
LMPP_MLP2 cells
MONOCYTE_I_CXCR42 cells
PROMONOCYTE1 cells
HSC_MPP1 cells
DC1918 cells
pDC422 cells
DC2386 cells
aDC3350 cells
Macrophage-APOC2215 cells
Macrophage-SPIC1174 cells
Macrophage-LYVE1162 cells
aDC2159 cells
aDC1137 cells
DC1304 cells
aDC646 cells
Macrophage551 cells
pDC422 cells
DC2372 cells
Macrophage551 cells
Myeloid2923 cells
DC1571 cells
pDC396 cells
aDC3350 cells
DC1-Prolif347 cells
DC2264 cells
Macrophage-APOC2215 cells
Macrophage-SPIC1174 cells
Macrophage-LYVE1162 cells
aDC2159 cells
aDC1137 cells
DC2-Prolif122 cells
pDC-Prolif26 cells
U40-THY-0-SC-F-2279 cells
FCAImmP7277556260 cells
TTA13164 cells
U48-THY-0-SC-1_5GEX163 cells
FCAImmP7292030123 cells
U48-THY-0-SC-EPCP-2_5GEX114 cells
U48-THY-0-SC-EPCP-1_5GEX109 cells
FCAImmP7179369104 cells
T07_TH_TOT_1_S1100 cells
FCAImmP727756493 cells
FCAImmP729203492 cells
FCAImmP719863477 cells
T07_TH_TOT_2_S273 cells
FCAImmP785189572 cells
FCAImmP752828367 cells
U40-THY-0-SC-F-165 cells
FCAImmP785189263 cells
FCAImmP752829462 cells
FCAImmP785189062 cells
FCAImmP785189360 cells
FCAImmP785189455 cells
FCAImmP785189154 cells
sample945 cells
TA926001543 cells
FCAImmP755585141 cells
T06_TH_TOT_5GEX_1_S940 cells
FCAImmP727756535 cells
T06_TH_TOT_5GEX_4_S1232 cells
T06_TH_TOT_5GEX_2_S1031 cells
T03_TH_TOT_5GEX_1_S129 cells
T06_TH_TOT_5GEX_3_S1128 cells
TTA726 cells
FCAImmP755586026 cells
TTA825 cells
FCAImmP717937024 cells
T03_TH_TOT_5GEX_2_S223 cells
sample119 cells
FCAImmP785189617 cells
T07_TH_EPCAM_S317 cells
TA926001417 cells
TA926001216 cells
sample1111 cells
FCAImmP719863511 cells
FCAImmP757923011 cells
sample39 cells
F83_TH_EPCAM9 cells
FCAImmP75792188 cells
FCAImmP75558617 cells
TA92600136 cells
GSM48389526 cells
10x 5' v11168 cells
10x 3' v2935 cells
10x 5' v2814 cells
10x 3' v36 cells
normal2923 cells
female1463 cells
male1460 cells
thymus2923 cells
Cluster 3666 cells
Cluster 6633 cells
Cluster 5532 cells
Cluster 4421 cells
Cluster 1407 cells
Cluster 2264 cells
9. thymus scRNA-seq atlas - myeloid p2 subset
ExploreReference genome
Gene annotation version
Alignment software
Subject ID
Age
Donor living at sample collection
Sample preservation method
Sample collection method
Tissue source
Suspension depletion factors
Suspension depleted cell types
Suspension derivation process
Suspension dissociation reagent
Suspension dissociation time
Suspension enriched cell types
Suspension enrichment factors
Library ID
Sequenced fragment
Institute
Library ID repository
Sequencing platform
Cell type
Cell state
Reported disease
Age group
Study
Enrichment
Cell type (park 2020)
Cell type (panfetal 2022)
Cell type level 3
Cell type level 2
Cell type level 1
Cell type level 0
Cell type level 4
Sample ID
Assay
Disease
Sex
Tissue
Leiden clustering
GRCh38843 cells
v98843 cells
STARsolo 2.7.4a,CellBender843 cells
fetal_23w_donor240 cells
U40176 cells
F3062 cells
F3857 cells
F2341 cells
fetal_19w_donor38 cells
F2138 cells
F4538 cells
F6430 cells
F2930 cells
6m_thymus_donor20 cells
P116 cells
F4116 cells
T0714 cells
P311 cells
F6710 cells
U486 cells
23 weeks (post-conception)240 cells
7 days176 cells
11 weeks (post-conception)71 cells
14 weeks (post-conception)62 cells
13 weeks (post-conception)57 cells
16 weeks (post-conception)54 cells
12 weeks (post-conception)48 cells
19 weeks (post-conception)38 cells
6 months37 cells
17 weeks (post-conception)30 cells
14.5 months16 cells
3 months14 cells
Unassigned614 cells
True229 cells
fresh843 cells
surgical resection843 cells
Unassigned363 cells
San Francisco General Hospital278 cells
Great Ormond Street Hospital for Children NHS202 cells
CD45612 cells
Unassigned204 cells
CD327 cells
leukocyte612 cells
Unassigned204 cells
T cell27 cells
enzymatic dissociation,fluorescence-activated cell sorting282 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting278 cells
mechanical dissociation,enzymatic dissociation,fluorescence-activated cell sorting153 cells
enzymatic dissociation54 cells
mechanical dissociation,fluorescence-activated cell sorting27 cells
mechanical dissociation,enzymatic dissociation23 cells
mechanical dissociation,enzymatic dissociation,negative magnetic affinity cell sorting,fluorescence-activated cell sorting20 cells
mechanical dissociation,enzymatic dissociation,positive magnetic affinity cell sorting6 cells
100 μg/ml Liberase TM278 cells
1.6 mg/ml collagenase IV205 cells
3.2 mg/ml Collagenase Type IV + 50 ug/ml liberase TH182 cells
0.2 mg/ml liberase131 cells
Unassigned27 cells
0.4 mg/mL Collagenase D, 0.6 mg/mL Dispase II20 cells
30 minute336 cells
45-60 minute278 cells
Unassigned209 cells
30-45 minute20 cells
Unassigned696 cells
leukocyte111 cells
cortical thymic epithelial cell20 cells
epithelial cell of thymus16 cells
Unassigned696 cells
CD45111 cells
EpCAMlow,CD205+20 cells
EpCAM,CD20510 cells
EpCAM6 cells
18e5ee2c-2580-4efe-bb1d-caf28b349b97143 cells
5dabbbcc-24af-43d4-b428-6c90f1595099135 cells
a3433b42-05ce-4be8-b95b-82cf18d8f6ba105 cells
42640a48-43a2-4023-9eed-1d6b2149e4c248 cells
0259273d-0959-478c-a312-f311e7b8998138 cells
b1c20e6b-aa09-419a-b807-a0be91b0659e29 cells
1fcf4f51-48bb-4c90-9841-9d5ece7f783928 cells
6a6a25e6-737f-40d3-89e8-3f9f1b06798423 cells
dadac003-e5d6-4bed-9fb0-d37b6acf0f0320 cells
e23c6097-c75c-4194-9b9b-11eccc636db120 cells
e130d3d3-63fd-44f2-a545-f5f3d164889c20 cells
330a23af-1bdc-434d-9445-83d6a990821219 cells
fe28ef61-6f2a-433a-bbae-355aa9dbe41b18 cells
bfdfa90d-5c1a-4ed0-b073-e2278d7c71ee17 cells
fd59bea8-e8d3-4b94-8b46-b4c72ebe8ef114 cells
6a72699b-8b9b-4162-9af6-3e061e4c13de13 cells
8c78bfc7-4e5c-45ca-b813-3498d5f0c23f13 cells
f307a1fb-28f2-41c4-b5aa-01ecbc8c723413 cells
1dcaec0a-2eae-4431-bb5e-ec1c5df9d0fb11 cells
9c9a3635-c73c-4cb4-bff5-7c769df23e2011 cells
72a3a376-2a41-4615-9d6b-7583e1e3e96610 cells
7af0a1fb-651c-4cac-9571-b8b22896957d10 cells
bcc0a8e3-ae57-418f-897a-f08f7d41cddf10 cells
fadfcbbf-117f-4a75-bbff-624ea499385810 cells
409181fb-ae4d-4bfe-9e20-849ae6420eca9 cells
cd03bedd-d3b4-4445-bed8-51f743a16cc08 cells
64eca649-dfd8-47de-8bc8-d05acf1794bc8 cells
80dce0eb-df2b-4bb1-b4bf-7fbb00e89ada8 cells
cedc71e0-ecb2-43d1-8834-c48b0a0a01de7 cells
c7760a1e-8622-4500-b914-8bd529b48d967 cells
8d72ca04-1d8c-4594-aeaf-ae0ff5b3813c6 cells
6c959596-7ef9-40ee-9bb0-6044964354d26 cells
700d57d4-2466-42f1-9605-88d5e8451c296 cells
3 prime tag557 cells
5 prime tag286 cells
Wellcome Sanger Institute518 cells
General Community298 cells
Ghent University27 cells
Unassigned209 cells
SRX8089346135 cells
SRX8089347105 cells
ERX380608148 cells
SRX808934538 cells
ERX380608229 cells
ERX380609028 cells
SRX932399220 cells
ERX380610020 cells
ERX380607820 cells
ERX380608019 cells
ERX380607718 cells
ERX380611917 cells
ERX380607914 cells
ERX380609413 cells
ERX380612013 cells
ERX380607613 cells
ERX380609311 cells
ERX380612210 cells
ERX380610110 cells
ERX380608310 cells
ERX38060979 cells
ERX38061118 cells
ERX38060957 cells
ERX38060967 cells
ERX38061126 cells
ERX38060986 cells
Unassigned480 cells
Illumina HiSeq 4000 (EFO:0008563)349 cells
Illumina NextSeq 500 (EFO:0009173)14 cells
RBC319 cells
Monocyte_IL1B93 cells
GMP89 cells
Myelocyte78 cells
Neutrophil76 cells
CMP74 cells
Promonocyte71 cells
Monocyte_CCR243 cells
Unassigned843 cells
none816 cells
congenital heart disease27 cells
fetal600 cells
paed (early)243 cells
Park2020363 cells
Bautista2021278 cells
HTSA_Sanger182 cells
Campinoti202020 cells
45N449 cells
FACS153 cells
45P111 cells
TOT77 cells
CD3N27 cells
CD205+CD49F-20 cells
MACS6 cells
Unassigned557 cells
monocyte110 cells
erythrocyte90 cells
progenitor cell68 cells
dendritic cell15 cells
early T lineage precursor3 cells
Unassigned591 cells
MID_ERY80 cells
MONOCYTE_II_CCR240 cells
PROMONOCYTE31 cells
MONOCYTE_III_IL1B29 cells
GMP24 cells
CMP17 cells
MONOCYTE_I_CXCR414 cells
MOP9 cells
LOW_QUALITY_MID_ERY_(HIGH_RIBO)4 cells
PROMYELOCYTE1 cells
HSC_MPP1 cells
DC21 cells
DOUBLET_LYMPHOID_MACROPHAGE1 cells
RBC319 cells
Mono207 cells
Myeloid_progenitor163 cells
Neut154 cells
RBC319 cells
Mono207 cells
Myeloid_progenitor163 cells
Neut154 cells
RBC319 cells
Mono207 cells
Myeloid_progenitor163 cells
Neut154 cells
Myeloid524 cells
RBC319 cells
RBC319 cells
Monocyte_IL1B93 cells
GMP89 cells
Myelocyte78 cells
Neutrophil76 cells
CMP74 cells
Promonocyte71 cells
Monocyte_CCR243 cells
U40-THY-0-SC-F-1143 cells
baut2135 cells
baut3105 cells
FCAImmP727756548 cells
baut138 cells
FCAImmP717937029 cells
FCAImmP719863428 cells
U48-THY-0-SC-1_5GEX23 cells
FCAImmP757923120 cells
GSM483895220 cells
FCAImmP727755620 cells
FCAImmP752828519 cells
FCAImmP757921918 cells
FCAImmP785189017 cells
FCAImmP752828414 cells
FCAImmP752829413 cells
FCAImmP719863513 cells
FCAImmP785189113 cells
FCAImmP752828311 cells
TTA1311 cells
FCAImmP755585210 cells
FCAImmP729203010 cells
FCAImmP785189310 cells
U40-THY-0-SC-F-210 cells
FCAImmP71793699 cells
TTA88 cells
TTA78 cells
T07_TH_TOT_1_S18 cells
FCAImmP72775647 cells
FCAImmP72920347 cells
T07_TH_TOT_2_S26 cells
U48-THY-0-SC-EPCP-1_5GEX6 cells
FCAImmP75558516 cells
10x 3' v2537 cells
10x 5' v2182 cells
10x 5' v1104 cells
10x 3' v320 cells
normal843 cells
female290 cells
Unassigned278 cells
male275 cells
thymus843 cells
Cluster 4199 cells
Cluster 3178 cells
Cluster 1150 cells
Cluster 2112 cells
Cluster 675 cells
Cluster 572 cells
Cluster 757 cells
10. merged thymus visium pediatric samples
ExploreMapped reference annotation
Subject ID
Donor living at sample collection
Sample preservation method
Sample derivation process
Sample source
Tissue section thickness
Library ID
Sequencing platform
Reported disease
Lobules
Tissue annotation level 1
Tissue annotation level 0
Cortico-Medullary axis (Manual v2)
Cell type
Assay
Disease
Sex
Tissue
Age
Sample ID
Leiden clustering
GENCODE 3225593 cells
Z65883 cells
U095748 cells
U115255 cells
Z44813 cells
Z23119 cells
Z1775 cells
True25593 cells
OCT embedding25593 cells
resection25593 cells
Newcastle Hospitals NHS14590 cells
Great Ormond Street Hospital for Children NHS11003 cells
7 μm14590 cells
10 μm11003 cells
0bb687b4-ba18-4fad-aa81-ac39251c3d2d2729 cells
96d33753-a87f-40b3-84fe-34e71f4c48cc2161 cells
7549b9ec-e3a7-416c-8510-6aedea8747b72118 cells
b36b0dbc-9b83-4387-ac74-55f401b21b231964 cells
ae095422-4e5f-43a7-9383-12fce02170a51926 cells
fd9b0fe4-40f0-48ae-8a0a-41a0f5a66e121868 cells
085f08cd-0f6a-498a-a855-2dd7ca737aae1802 cells
c752fbaa-c771-4f19-876e-49efc7d7ecbe1801 cells
bbd1de50-4300-4871-90bc-745afd2029b91618 cells
e6160c68-f76c-433e-9dea-fe448aef00171476 cells
3ddd17f9-ff73-4668-9bc3-8e0edf4e3b521394 cells
05228bdf-e61f-4d99-ab55-9a2f8259b8011317 cells
8297db7f-7111-4bf0-a7bf-6227ce66d2fb1090 cells
f8d5b094-d411-491a-8acf-4f36e691d8d6864 cells
17c9d944-5f55-46e3-9b57-5ec0c735d6f9775 cells
db704906-20f5-4b31-a1f8-cd522a710b23690 cells
Illumina NovaSeq 600014590 cells
Unassigned11003 cells
congenital heart disease25593 cells
lobule_53452 cells
lobule_83132 cells
lobule_62552 cells
lobule_22400 cells
lobule_72279 cells
lobule_12075 cells
lobule_31829 cells
lobule_91778 cells
lobule_41686 cells
lobule_101272 cells
lobule_11959 cells
lobule_12546 cells
lobule_17440 cells
lobule_14309 cells
Unassigned185 cells
lobule_16184 cells
lobule_18149 cells
lobule_13133 cells
lobule_15115 cells
lobule_2076 cells
lobule_1942 cells
Unassigned25102 cells
perivascular space (PVS)246 cells
medullary Hassall’s corpuscles (HCs)225 cells
fat17 cells
vessels3 cells
Cortex16019 cells
Medulla6770 cells
Edge2804 cells
Cortical level 14848 cells
Cortical level 24273 cells
Capsular2808 cells
Cortical level 32612 cells
Sub-Capsular2252 cells
Medullar level 32089 cells
Cortical CMJ1950 cells
Medullar CMJ1946 cells
Medullar level 11544 cells
Medullar level 21271 cells
T cell24446 cells
epithelial cell972 cells
B cell115 cells
macrophage27 cells
endothelial cell9 cells
fibroblast8 cells
dendritic cell8 cells
myelocyte5 cells
smooth muscle cell3 cells
Visium Spatial Gene Expression25593 cells
normal25593 cells
female14455 cells
male11138 cells
thymus25593 cells
2 years5883 cells
6 months5748 cells
5 months5255 cells
3 months4813 cells
14 months3119 cells
19 months775 cells
TA115564932729 cells
WSSS_THYst95180302161 cells
TA115564952118 cells
TA115564961964 cells
WSSS_THYst91420891926 cells
WSSS_THYst91420881868 cells
TA115564921802 cells
TA114861631801 cells
WSSS_THYst95180331618 cells
WSSS_THYst95180321476 cells
TA114861621394 cells
TA114861641317 cells
WSSS_THYst91420861090 cells
WSSS_THYst9142087864 cells
TA11486161775 cells
TA11556494690 cells
Cluster 75351 cells
Cluster 15256 cells
Cluster 44833 cells
Cluster 54818 cells
Cluster 22720 cells
Cluster 31900 cells
Cluster 6715 cells
11. merged thymus visium fetal samples
ExploreMapped reference annotation
Subject ID
Donor living at sample collection
Sample preservation method
Sample derivation process
Sample source
Tissue section thickness
Library ID
Sequencing platform
Lobules
Tissue annotation level 1
Tissue annotation level 0
Cortico-Medullary Axis (Manual v2)
Cell type
Assay
Disease
Sex
Tissue
Age
Sample ID
Leiden clustering
GENCODE 3212918 cells
F1333120 cells
F1212913 cells
F1301892 cells
F1351511 cells
F1141453 cells
F1361415 cells
F113614 cells
na12918 cells
OCT embedding12918 cells
dissection12918 cells
Human Developmental Biology Resource12918 cells
15 μm12918 cells
938a699b-76f7-4073-8c97-ab5c443f59cd1673 cells
fedf2442-4ea8-4962-b4fc-c796107cddc41555 cells
9ef43e70-22bf-4f55-8b70-e3898f4e03751511 cells
aae9e06c-2dc9-4666-a519-af65c5ee47fa1447 cells
c1cabba6-259f-4461-8def-836bd45874431415 cells
c7cc62af-1784-4c75-8206-f48eabd426b11358 cells
2effe55b-0d4f-4a65-a349-c906bbbad4c81149 cells
952d3607-4c6e-4725-8c84-906b677b7dcd750 cells
255e83ec-ba59-4e33-8487-9d4020be1de2743 cells
d7bcaf82-1bb1-4471-9992-2ca9da1255e8703 cells
831b36ad-bcff-499a-ba7e-d820a69ece41308 cells
fab39132-f679-4271-8035-47c3d11b6cd8306 cells
Illumina NovaSeq 600012918 cells
lobule_5503 cells
lobule_10466 cells
unassigned463 cells
lobule_7438 cells
lobule_3433 cells
lobule_25424 cells
lobule_4390 cells
lobule_23365 cells
lobule_11356 cells
lobule_18350 cells
lobule_15336 cells
lobule_26334 cells
lobule_6332 cells
lobule_16328 cells
lobule_22310 cells
lobule_24304 cells
lobule_19295 cells
lobule_8294 cells
lobule_21281 cells
lobule_9280 cells
lobule_46265 cells
lobule_34260 cells
lobule_28257 cells
lobule_17252 cells
lobule_12241 cells
lobule_27234 cells
lobule_1228 cells
lobule_30226 cells
lobule_29225 cells
lobule_14214 cells
lobule_2206 cells
lobule_13201 cells
lobule_20201 cells
lobule_31198 cells
lobule_32192 cells
lobule_39155 cells
lobule_44153 cells
lobule_38151 cells
lobule_40149 cells
lobule_48143 cells
lobule_37131 cells
lobule_35129 cells
lobule_42114 cells
lobule_50107 cells
lobule_33106 cells
lobule_4199 cells
lobule_4998 cells
lobule_4594 cells
lobule_4793 cells
lobule_3690 cells
lobule_4385 cells
lobule_5171 cells
lobule_5365 cells
lobule_5254 cells
lobule_5737 cells
lobule_5637 cells
lobule_5429 cells
lobule_5822 cells
lobule_5521 cells
lobule_593 cells
unassigned12798 cells
PVS117 cells
HS3 cells
Cortex7400 cells
Medulla3190 cells
Edge2210 cells
lymph118 cells
Cortical level 12270 cells
Capsular2214 cells
Cortical level 21833 cells
Cortical level 31184 cells
Medullar CMJ1165 cells
Sub-Capsular1151 cells
Medullar level 1997 cells
Cortical CMJ940 cells
Medullar level 2667 cells
Medullar level 3379 cells
unassigned118 cells
T cell11056 cells
epithelial cell1367 cells
fibroblast394 cells
endothelial cell37 cells
pericyte28 cells
macrophage18 cells
dendritic cell6 cells
B cell5 cells
smooth muscle cell4 cells
erythrocyte2 cells
granulocyte monocyte progenitor cell1 cells
Visium Spatial Gene Expression12918 cells
normal12918 cells
unknown12918 cells
thymus12918 cells
17 weeks (post-conception)4424 cells
18 weeks (post-conception)3120 cells
13 weeks (post-conception)2506 cells
16 weeks (post-conception)1453 cells
19 weeks (post-conception)1415 cells
WSSS_F_IMMsp117658681673 cells
WSSS_F_IMMsp98387161555 cells
WSSS_F_IMMsp117658701511 cells
WSSS_F_IMMsp117658671447 cells
WSSS_F_IMMsp108641831415 cells
WSSS_F_IMMsp98387111358 cells
WSSS_F_IMMsp116046861149 cells
WSSS_F_IMMsp11604687750 cells
WSSS_F_IMMsp11604685743 cells
WSSS_F_IMMsp11604688703 cells
WSSS_F_IMMsp11604690308 cells
WSSS_F_IMMsp11604689306 cells
Cluster 13692 cells
Cluster 72662 cells
Cluster 31787 cells
Cluster 61510 cells
Cluster 51394 cells
Cluster 2683 cells
Cluster 9621 cells
Cluster 8461 cells
Cluster 4108 cells
12. Multimodal profiling of human postnatal thymocytes using CITE-seq
ExploreSample ID
GEO accession
Age
Enrichment
Subject ID
Sex
Cell cycle
Cell type
Tissue
Sample collection method
Sample preservation method
Assay
Disease
Leiden clustering
TT-CITE-915902 cells
TT-CITE-614278 cells
TT-CITE-413809 cells
TT-CITE-113272 cells
TT-CITE-1113149 cells
TT-CITE-1212928 cells
TT-CITE-312880 cells
TT-CITE-512537 cells
TT-CITE-212151 cells
TT-CITE-105798 cells
TT-CITE-83840 cells
GSM837424215902 cells
GSM837424014278 cells
GSM837423813809 cells
GSM837423513272 cells
GSM837424413149 cells
GSM837424512928 cells
GSM837423712880 cells
GSM837423912537 cells
GSM837423612151 cells
GSM83742435798 cells
GSM83742413840 cells
3 months56732 cells
2 months52112 cells
5 months21700 cells
CD3N67740 cells
CD3P62804 cells
TSC-CT1029917 cells
TSC-CT1326815 cells
TSC-CT926689 cells
TSC-CT825423 cells
TSC-CT1221700 cells
Male83421 cells
Female47123 cells
G1101846 cells
S16205 cells
G2M12493 cells
DP(Q)_rearr48603 cells
DP(P)23706 cells
DP_4hi8lo10738 cells
committed_CD4pos6002 cells
SP_CD4_semimature4581 cells
DP_pos_sel4575 cells
DP(Q)4221 cells
SP_CD4_immature4096 cells
SP_CD8_semimature3863 cells
committed_CD4neg2933 cells
DP_early_CD312517 cells
SP_Treg_mature2229 cells
SP_Treg_immature1869 cells
SP_CD8_immature1478 cells
committed_CD4neg(P)1171 cells
B906 cells
CD8aaI_mature817 cells
SP_CD4_mature771 cells
CD8aaI_immature746 cells
CD8aaII_immature633 cells
committed_CD4pos(P)557 cells
CD8aaII_mature530 cells
SP_Treg_CD8504 cells
SP_CD8_mature376 cells
SP_Treg_PD1310 cells
gdT_semimature301 cells
gdT_mature202 cells
gdT_immature195 cells
NK_tr_itg_hi189 cells
SP_CD8_memory175 cells
uncommitted165 cells
SP_Treg_recirc132 cells
NK_circ_56hi16lo98 cells
DC90 cells
NKT_dev87 cells
gdT_Vd275 cells
NK_tr_itg_lo70 cells
NK_circ_56lo16hi33 cells
thymus130544 cells
cardiac surgery130544 cells
frozen in FBS containing 10% DMSO130544 cells
10x chromium 5' v2, CITE-seq and TCR-seq130544 cells
normal130544 cells
Cluster 241360 cells
Cluster 324755 cells
Cluster 119886 cells
Cluster 613363 cells
Cluster 513113 cells
Cluster 412358 cells
Cluster 74716 cells
Cluster 8993 cells
Alias names
GSE271304, EGAD00001015384, PRJEB77091, E-MTAB-8581, S-BIAD1257