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Series GSE139358 Query DataSets for GSE139358
Status Public on Nov 22, 2019
Title Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Two subpopulations of low density granulocytes (LDGs) were defined in terms of different gene expression patterns, transcriptional and epigenetic features as well as functions. This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of lupus.
 
Overall design Transcriptomics and epigenetic assessment of lupus PBMCs, LDGs, autologous normal-density neutrophils (NDN) and healthy control (HC) neutrophils was performed by mRNA sequencing and assay for transposase-accessible chromatin sequencing. NET formation, chemotaxis, phagocytosis, degranulation, induction of endothelial dysfunction and release of oxidized nucleic acids were compared among subsets. This metadata sheet includes 51 RNA-Seq samples of this project.
 
Contributor(s) Mistry P, Nakabo S, O’Neil L, Goel RR, Jiang K, Gupta S, Dell’Orso S, Gutierrez-Cruz G, Sun HW, Kaplan MJ
Citation(s) 31754025
Submission date Oct 24, 2019
Last update date Oct 12, 2022
Contact name Hong-wei Sun
Organization name NIAMS
Department Office of Science & Technology
Lab Biodata Mining & Discovery Section
Street address 9000 Rockville Pile
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (51)
GSM4138684 NDN_ctrl_01 [RNA-seq]
GSM4138685 NDN_ctrl_02 [RNA-seq]
GSM4138686 NDN_ctrl_03 [RNA-seq]
This SubSeries is part of SuperSeries:
GSE139360 Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus
Relations
BioProject PRJNA579374
SRA SRP226877

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
GSE139358_RNA-Seq_gene_rpkm_18_samples.xlsx 4.3 Mb (ftp)(http) XLSX
GSE139358_RNA-Seq_gene_rpkm_33_samples.xlsx 7.0 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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