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| Status |
Public on Dec 15, 2018 |
| Title |
Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pulmonary fibrosis is a heterogeneous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplification, these data provide a molecular atlas of disease pathobiology. We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to non-overlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. Analysis of a cryobiopsy specimen from a patient with early disease supports the clinical application of single-cell RNA-Seq to develop personalized approaches to therapy. This dataset contains single-cell RNA-seq data generated from the lungs of the two naive mice, human data for this study has been submitted to dbGap/SRA.
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| Overall design |
Single-cell suspension from two 4 mo old C57Bl/6 male mice was prepared and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).
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| Web link |
https://www.atsjournals.org/doi/abs/10.1164/rccm.201712-2410OC
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| Contributor(s) |
Reyfman PA, Walter JM, Joshi N, McQuattie AC, Anekalla K, Budinger GS, Misharin AV |
| Citation(s) |
30554520 |
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Paul A Reyfman, James M Walter, Nikita Joshi, Kishore R Anekalla, Alexandra C McQuattie-Pimentel, Stephen Chiu, Ramiro Fernandez, Mahzad Akbarpour, Ching-I Chen, Ziyou Ren, Rohan Verma, Hiam Abdala-Valencia, Kiwon Nam, Monica Chi, SeungHye Han, Francisco J Gonzalez-Gonzalez, Saul Soberanes, Satoshi Watanabe, Kinola J.N. Williams, Annette S Flozak, Trevor T Nicholson, Vince K Morgan, Deborah R Winter, Monique Hinchcliff, Cara L Hrusch, Robert D Guzy, Catherine A Bonham, Anne I Sperling, Remzi Bag, Robert B Hamanaka, Gökhan M Mutlu, Anjana V Yeldandi, Stacy A Marshall, Ali Shilatifard, Luis A.N. Amaral, Harris Perlman, Jacob I. Sznajder, A. Christine Argento, Colin T Gillespie, Jane Dematte, Manu Jain, Benjamin D Singer, Karen M Ridge, Anna P Lam, Ankit Bharat, Sangeeta M. Bhorade, Cara J. Gottardi, G.R. Scott Budinger, and Alexander V Misharin. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. Am J Respir Crit Care Med. 2018. doi:10.1164/rccm.201712-2410OC
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| Submission date |
Oct 22, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Alexander V Misharin |
| E-mail(s) |
a-misharin@northwestern.edu
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| Phone |
3125031958
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| Organization name |
Northwestern University
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| Department |
Pulmonary and Critical Care
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| Lab |
Misharin lab
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| Street address |
240 E Huron
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA497875 |
| SRA |
SRP166330 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121611_RAW.tar |
115.8 Mb |
(http)(custom) |
TAR (of H5, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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