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CITATION.cff
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cff-version: 1.2.0
title: CellTypist
authors:
- family-names: Xu
given-names: Chuan
url: https://github.com/Teichlab/celltypist
message: If you use this software, please cite the article from preferred-citation
preferred-citation:
type: article
title: Cross-tissue immune cell analysis reveals tissue-specific features in humans
doi: 10.1126/science.abl5197
issue: '6594'
journal: Science
month: 5
url: https://dx.doi.org/10.1126/science.abl5197
volume: '376'
year: 2022
abstract: Despite their crucial role in health and disease, our knowledge of immune
cells within human tissues remains limited. We surveyed the immune compartment
of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing
generating a dataset of ~360,000 cells. 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 finely phenotyped
immune cell types, revealing hitherto unappreciated tissue-specific features and
clonal architecture of T and B cells. Our multitissue 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.
authors:
- family-names: Domínguez Conde
given-names: C.
orcid: https://orcid.org/0000-0002-8684-4655
- family-names: Xu
given-names: C.
orcid: https://orcid.org/0000-0002-6265-999X
- family-names: Jarvis
given-names: L. B.
orcid: https://orcid.org/0000-0002-5760-0125
- family-names: Rainbow
given-names: D. B.
orcid: https://orcid.org/0000-0003-4931-3289
- family-names: Wells
given-names: S. B.
orcid: https://orcid.org/0000-0001-5428-0683
- family-names: Gomes
given-names: T.
orcid: https://orcid.org/0000-0003-1333-0191
- family-names: Howlett
given-names: S. K.
orcid: https://orcid.org/0000-0003-0504-4937
- family-names: Suchanek
given-names: O.
- family-names: Polanski
given-names: K.
orcid: https://orcid.org/0000-0002-2586-9576
- family-names: King
given-names: H. W.
orcid: https://orcid.org/0000-0001-5972-8926
- family-names: Mamanova
given-names: L.
orcid: https://orcid.org/0000-0003-1463-8622
- family-names: Huang
given-names: N.
orcid: https://orcid.org/0000-0001-8849-038X
- family-names: Szabo
given-names: P. A.
orcid: https://orcid.org/0000-0003-1603-761X
- family-names: Richardson
given-names: L.
orcid: https://orcid.org/0000-0001-9064-1271
- family-names: Bolt
given-names: L.
orcid: https://orcid.org/0000-0001-7293-0774
- family-names: Fasouli
given-names: E. S.
orcid: https://orcid.org/0000-0003-1621-3396
- family-names: Mahbubani
given-names: K. T.
orcid: https://orcid.org/0000-0002-1327-2334
- family-names: Prete
given-names: M.
orcid: https://orcid.org/0000-0002-5946-821X
- family-names: Tuck
given-names: L.
orcid: https://orcid.org/0000-0002-1837-7549
- family-names: Richoz
given-names: N.
- family-names: Tuong
given-names: Z. K.
orcid: https://orcid.org/0000-0002-6735-6808
- family-names: Campos
given-names: L.
orcid: https://orcid.org/0000-0003-2445-7120
- family-names: Mousa
given-names: H. S.
orcid: https://orcid.org/0000-0002-8327-7114
- family-names: Needham
given-names: E. J.
orcid: https://orcid.org/0000-0001-7042-7462
- family-names: Pritchard
given-names: S.
- family-names: Li
given-names: T.
orcid: https://orcid.org/0000-0002-8240-4476
- family-names: Elmentaite
given-names: R.
orcid: https://orcid.org/0000-0001-7366-5466
- family-names: Park
given-names: J.
orcid: https://orcid.org/0000-0002-1687-2423
- family-names: Rahmani
given-names: E.
- family-names: Chen
given-names: D.
orcid: https://orcid.org/0000-0002-9710-1857
- family-names: Menon
given-names: D. K.
orcid: https://orcid.org/0000-0002-3228-9692
- family-names: Bayraktar
given-names: O. A.
- family-names: James
given-names: L. K.
orcid: https://orcid.org/0000-0002-2252-4636
- family-names: Meyer
given-names: K. B.
orcid: https://orcid.org/0000-0001-5906-1498
- family-names: Yosef
given-names: N.
orcid: https://orcid.org/0000-0001-9004-1225
- family-names: Clatworthy
given-names: M. R.
orcid: https://orcid.org/0000-0002-3340-9828
- family-names: Sims
given-names: P. A.
orcid: https://orcid.org/0000-0002-3921-4837
- family-names: Farber
given-names: D. L.
orcid: https://orcid.org/0000-0001-8236-9183
- family-names: Saeb-Parsy
given-names: K.
orcid: https://orcid.org/0000-0002-0633-3696
- family-names: Jones
given-names: J. L.
orcid: https://orcid.org/0000-0003-4974-1371
- family-names: Teichmann
given-names: S. A.
orcid: https://orcid.org/0000-0002-6294-6366