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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 II |
| Organism |
Homo sapiens |
| 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.
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| Overall design |
Single-cell suspensions from eight donor lungs and nine lungs from patients with various forms of pulmonary fibrosis were prepared and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics). This GEO submission contains only processed data (raw counts tables in HDF5 format), raw data (FASTQ files) available from dbGaP/SRA (phs001750.v1.p1).
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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 |
Nov 26, 2018 |
| Last update date |
Mar 21, 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) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA507000 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122960_RAW.tar |
720.5 Mb |
(http)(custom) |
TAR (of H5) |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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