HCA Data Explorer

A cell atlas of human thymic development defines T cell repertoire formation

Updated March 1, 2022

We performed single-cell RNA-sequencing to create a cell census of the human thymus during development, early childhood and adult life. We sampled 15 embryonic and fetal thymi spanning thymic developmental stages between 7 post-conception weeks (PCW) to 17 PCW, and 9 postnatal thymi from paediatric and adult samples. We compared the cellular composition and T cell differentiation within human and mouse thymus using newly generated and repository mouse datasets. Finally, we investigated the bias in the recombination and selection of human versus mouse TCR repertoires.

Jong-Eun ParkWellcome Sanger Institutejp24@sanger.ac.uk
T TaghonGhent Universitytom.taghon@ugent.be
M HaniffaInstitute of Cellular Medicine, Newcastle Universitym.a.haniffa@newcastle.ac.uk
S A TeichmannWellcome Sanger Institutest9@sanger.ac.uk
Jong-Eun Park (Experimental Scientist)1
Rachel A Botting (Experimental Scientist)2
C Domínguez Conde (Experimental Scientist)1
D M Popescu (Experimental Scientist)2
M Lavaert (Experimental Scientist)3
D J Kunz (Experimental Scientist)1
I Goh (Experimental Scientist)2
E Stephenson (Experimental Scientist)2
R Ragazzini (Experimental Scientist)4
E Tuck (Experimental Scientist)1
A Wilbrey-Clark (Experimental Scientist)1
K Roberts (Computational Scientist)1
V R Kedlian1
J R Ferdinand5
X He5
S Webb (Computational Scientist)2
D Maunder2
N Vandamme6
K T Mahbubani (Biomaterial Provider)7
K Polanski (Computational Scientist)1
L Mamanova (Experiment Performer)1
L Bolt1
D Crossland2
F de Rita8
A Fuller2
A Filby2
G Reynolds2
D Dixon2
K Saeb-Parsy (Clinician)5
S Lisgo (Biomaterial Provider)9
D Henderson (Experimental Scientist)2
R Vento-Tormo (Co-Investigator)1
O A Bayraktar (Co-Investigator)1
R A Barker (Co-Investigator)5
K B Meyer (Co-Investigator)1
Y Saeys (Co-Investigator)6
P Bonfanti (Co-Investigator)4
S Behjati (Principal Investigator)5
M R Clatworthy (Principal Investigator)5
T Taghon (Principal Investigator)3
M Haniffa (Principal Investigator)10
S A Teichmann (Principal Investigator)1
1Wellcome Sanger Institute
2Newcastle University
3Ghent University
4Francis Crick Institute
5University of Cambridge
6VIB Center for Inflammation Research
7Cambridge Biorepository for Translational Medicine
8Newcastle Hospitals NHS Foundation Trust
9Institute of Genetic Medicine
10Institute of Cellular Medicine, Newcastle University
M F Shadbolt

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/c1810dbc-16d2-45c3-b45e-3e675f88d87b

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://developmentcellatlas.ncl.ac.uk/datasets/HCA_thymus/2.https://doi.org/10.5281/zenodo.3572421
INSDC Project Accessions:
ERP119282
Array Express Accessions:
E-MTAB-8581
INSDC Study Accessions:
PRJEB36131

Downloaded and exported data is governed by the HCA Data Release Policy and licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information please see our Data Use Agreement.

Analysis Portals

CZ CELLxGENECZ CELLxGENE
UCSC Cell BrowserUCSC Cell Browser

Project Label

HumanThymicDevelopment

Species

2 species

Sample Type

specimens

Anatomical Entity

2 anatomical entities

Organ Part

Unspecified

Selected Cell Types

4 cell types

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

16 development stages

Library Construction Method

4 library construction methods

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

optimus_post_processing_v1.0.0, optimus_v4.2.3

File Format

5 file formats

Cell Count Estimate

250.0k

Donor Count

24
bam28 file(s)fastq.gz206 file(s)h5ad1 file(s)loom30 file(s)zip2 file(s)