HCA Data Explorer

Cross-tissue immune cell analysis reveals tissue-specific features in humans

Access Granted
Updated April 24, 2023

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. Here, we surveyed the immune compartment of 15 tissues of six deceased adult donors by single-cell RNA sequencing and paired VDJ sequencing. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of 45 finely phenotyped immune cell types and states, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. In summary, our multi-tissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis and antigen receptor sequencing.

C Domínguez CondeWellcome Sanger Institutecc36@sanger.ac.uk
C XuWellcome Sanger Institutecx1@sanger.ac.uk
C Domínguez Conde1
C Xu1
L B Jarvis2
D B Rainbow2
S B Wells3
T Gomes1
S K Howlett2
O Suchanek2
K Polanski1
H W King4
L Mamanova1
N Huang1
P A Szabo3
L Richardson1
L Bolt1
E S Fasouli1
K T Mahbubani5
M Prete1
L Tuck1
N Richoz2
Z K Tuong1
L Campos1
H S Mousa2
E J Needham2
S Pritchard1
T Li1
R Elmentaite1
J Park1
E Rahmani6
D Chen3
D K Menon2
O A Bayraktar1
L K James4
K B Meyer1
N Yosef6
M R Clatworthy1
P A Sims3
D L Farber3
K Saeb-Parsy5
J L Jones2
S A Teichmann1
1Wellcome Sanger Institute
2University of Cambridge
3Columbia University Irving Medical Center
4Blizard Institute
5University of Cambridge and NIHR Cambridge Biomedical Research Centre
6University of California
Enrique Sapena Ventura

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/04e4292c-f62f-4098-ae9b-fd69ae002a90

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://github.com/Teichlab/TissueImmuneCellAtlas2.https://www.tissueimmunecellatlas.org/
INSDC Project Accessions:Array Express Accessions:

Analysis Portals

CZ CELLxGENECZ CELLxGENE
UCSC Cell BrowserUCSC Cell Browser

Project Label

clonalArchitectureHumans

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

10 anatomical entities

Organ Part

11 organ parts

Selected Cell Types

Unspecified

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

6 library construction methods

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

downstream_analysis, scrna_seq_processing, tcr_bcr_processing

File Format

3 file formats

Cell Count Estimate

357.2k

Donor Count

12
fastq.gz820 file(s)h5ad11 file(s)xlsx1 file(s)