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Series GSE134174 Query DataSets for GSE134174
Status Public on Apr 06, 2020
Title Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cigarette smoke first interacts with the lung through the cellularly diverse airway epithelium and goes on to drive development of most chronic lung diseases. Here, through single cell RNA-sequencing analysis of the tracheal epithelium from smokers and nonsmokers, we generate a comprehensive atlas of epithelial cell types and states, connect these into lineages, and define cell-specific responses to smoking. Our analysis infers multi-state lineages that develop into surface mucus secretory and ciliated cells and then contrasts these to the unique specification of submucosal gland (SMG) cells. Accompanying knockout studies reveal that tuft-like cells are the likely progenitor of both pulmonary neuroendocrine cells and CFTR-rich ionocytes. Our smoking analysis finds that all cell types, including protected stem and SMG populations, are affected by smoking through both pan-epithelial smoking response networks and hundreds of cell-specific response genes, redefining the penetrance and cellular specificity of smoking effects on the human airway epithelium.
Overall design For the in vivo dataset, we sequenced a total of 68,370 (36,248 after QC) epithelial cells from across 15 human tracheal donors (6 heavy smokers, 6 never-smokers, 2 light smokers, and 1 pediatric subject). For the in vitro dataset we sequenced a total of 8,722 (5,976 after QC) epithelial cells sampled from 20 time points along the differentiation process taken by air-liquid interface (ALI) cultures seeded from primary basal cells of 3 human tracheal donors (from ALI seed day to day 32 post-airlift)
Contributor(s) Goldfarbmuren KC, Jackson ND, Sajuthi SP, Dyjack N, Li KS, Rios CL, Plender EG, Montgomery MT, Everman JL, Bratcher PE, Vladar EK, Seibold MA
Citation(s) 32427931
Submission date Jul 11, 2019
Last update date Jun 01, 2020
Contact name Nathan Jackson
Organization name National Jewish Health
Department Center for Genes, Environment, and Health
Street address 1400 Jackson St.
City Denver
State/province CO
ZIP/Postal code 80206
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (28)
GSM4213824 T84_invivo
GSM4213825 T85_invivo
GSM4213826 T89_invivo
BioProject PRJNA554141
SRA SRP214324

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

Supplementary file Size Download File type/resource
GSE134174_Processed_invitro_metadata.txt.gz 47.9 Kb (ftp)(http) TXT
GSE134174_Processed_invitro_norm.txt.gz 95.4 Mb (ftp)(http) TXT
GSE134174_Processed_invitro_raw.txt.gz 14.3 Mb (ftp)(http) TXT
GSE134174_Processed_invivo_integrated.txt.gz 779.8 Mb (ftp)(http) TXT
GSE134174_Processed_invivo_metadata.txt.gz 244.1 Kb (ftp)(http) TXT
GSE134174_Processed_invivo_norm.txt.gz 174.9 Mb (ftp)(http) TXT
GSE134174_Processed_invivo_raw.txt.gz 139.0 Mb (ftp)(http) TXT
GSE134174_Processed_invivo_seurat.Rdata.gz 2.8 Gb (ftp)(http) RDATA
GSE134174_T84_invitro_metadata.txt.gz 18.6 Kb (ftp)(http) TXT
GSE134174_T85_invitro_metadata.txt.gz 20.6 Kb (ftp)(http) TXT
GSE134174_T89_invitro_metadata.txt.gz 20.5 Kb (ftp)(http) TXT
GSE134174_invitro_expression_matrix.txt.tar.gz 16.4 Mb (ftp)(http) TAR
GSE134174_invivo_expression_matrix.txt.tar.gz 227.1 Mb (ftp)(http) TAR
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Raw data are available in SRA
Processed data are available on Series record

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