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Series GSE212109 Query DataSets for GSE212109
Status Public on Sep 02, 2022
Title Epigenetic regulation of profibrotic macrophages in systemic sclerosis- associated interstitial lung disease
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Systemic sclerosis-associated interstitial lung disease (SSc-ILD) is the leading cause of death in patients with systemic sclerosis (SSc) with unclear pathogenesis and limited treatment options. Evidence strongly supports an important role for profibrotic, SPP1-expressing macrophages in SSc-ILD. We sought to define the transcriptome and chromatin structural changes of SPP1 SSc-ILD macrophages, so as to better understand their role in promoting fibrosis and to identify transcription factors associated with open chromatin driving their altered phenotype.
Overall design We performed single cell RNA-sequencing on 11 explanted SSc-ILD and healthy control lung samples, as well as single cell ATAC-sequencing on a subset of lung samples to define altered chromatin accessibility of SPP1 macrophages. We predicted transcription factors regulating SPP1 macrophages using SCENIC and determined transcription factor binding sites associated with global alterations in SPP1 chromatin accessibility using Signac/Seurat.
Contributor(s) Papazoglou A, Huang M, Bulik M, Lafyatis A, Tabib T, Morse C, Sembrat J, Rojas M, Valenzi E, Lafyatis R
Citation(s) 35849803, 37706427
Submission date Aug 26, 2022
Last update date May 06, 2024
Contact name Tracy Tabib
Organization name University of Pittsburgh
Department Department of Medicine
Lab Laboratory of Robert Lafyatis
Street address 200 Lothrop Street
City Pittsburgh
State/province PA
ZIP/Postal code 15213
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (17)
GSM6509487 SC277 2019-022-CORE
GSM6509488 SC281 2019-027-LT
GSM6509489 SC284 2019-029-LT
BioProject PRJNA874032

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Supplementary file Size Download File type/resource
GSE212109_RAW.tar 17.7 Gb (http)(custom) TAR (of BAI, BED, CSV, H5, TBI, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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