GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE122960 Query DataSets for GSE122960
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
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.
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).
Web link
Contributor(s) Reyfman PA, Walter JM, Joshi N, McQuattie AC, Anekalla K, Budinger GS, Misharin AV
Citation(s) 30554520
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
Submission date Nov 26, 2018
Last update date Mar 21, 2019
Contact name Alexander V Misharin
Phone 3125031958
Organization name Northwestern University
Department Pulmonary and Critical Care
Lab Misharin lab
Street address 240 E Huron
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (17)
GSM3489182 Donor_01
GSM3489183 IPF_01
GSM3489184 IPF_02
BioProject PRJNA507000

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap