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Series GSE186469 Query DataSets for GSE186469
Status Public on Nov 03, 2021
Title High-throughput screen reveals purinergic receptor as a therapeutic target in circadian β-cell failure
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary We report a screen of 2,640 pharmacologically-active compounds in clock-deficient pancreatic β cells and reveal a mechanism by which ivermectin induces insulin secretion and regulates transcription in wild type and P2ry1 receptor knockout BetaTC6 β-cell lines by mRNA-seq.
 
Overall design Examination of mRNA expression changes in wild type and P2ry1 receptor knockout BetaTC6 β-cell lines treated with 20 mM glucose in the presence or absence of ivermectin.

The records have been updated with third-party re-analysis data as described below, on Jan 11, 2022:
Sequencing data from the study under SRA accession ERP017126 (Bioproject: PRJEB15401; ENA-SUBMISSION: ERA705448) (PMID: 27667667) was downloaded and converted to fastq files using the commands 'prefetch' followed by 'fastq-dump' via sra-toolkit (v2.10.5). Each individual cell/file was aligned and transcript abundance quantified using RSEM (v1.3.3) with Hg38 (GRCh38.p12) as a reference. Raw single-cell expression count values were imported into Rstudio and count files were aggregated into count matrices for each condition (ctrl.data.txt, t2d.data.txt) for analysis using Seurat. Following low-quality cell removal using the author-provided metadata (https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.sdrf.txt), normalized expression values were used in uniform manifold approximation and projection (UMAP) dimensional reduction analyses to cluster distinct cell types (As outlined in E-MTAB-5061_analysis.R).

E-MTAB-5061.sdrf.txt: Direct downloaded file from original authors including metadata on single-cell RNA-sequencing data. Available through https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5061/E-MTAB-5061.sdrf.txt
ctrl.data.txt: Single-cell RNA count matrix for cells from non-type 2 diabetic donors
t2d.data.txt: Single-cell RNA count matrix for cells from type 2 diabetic donors
E-MTAB-5061_analysis.R: Custom script for Seurat analysis of single-cell RNA count data from the study E-MTAB-5061
 
Contributor(s) Weidemann BJ
Citation(s) 35188462
Submission date Oct 23, 2021
Last update date Mar 03, 2022
Contact name Benjamin J Weidemann
E-mail(s) benjamin.weidemann@northwestern.edu
Phone 3127920532
Organization name NORTHWESTERN UNIVERSITY
Department Medicine
Lab Joseph Bass
Street address 303 E. Superior St.
City Chicago
State/province IL
ZIP/Postal code 60613
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (16)
GSM5652642 20-WT-Con-RNA-1
GSM5652643 21-WT-Con-RNA-2
GSM5652644 22-WT-Con-RNA-3
Relations
BioProject PRJNA773959
SRA SRP342865

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
GSE186469_DESeq2_normalized_counts_table.txt.gz 1.2 Mb (ftp)(http) TXT
GSE186469_DESeq2_raw_counts_table.txt.gz 356.4 Kb (ftp)(http) TXT
GSE186469_E-MTAB-5061.sdrf.txt.gz 121.9 Kb (ftp)(http) TXT
GSE186469_E-MTAB-5061_analysis.R.gz 1.1 Kb (ftp)(http) R
GSE186469_RAW.tar 6.5 Mb (http)(custom) TAR (of RESULTS)
GSE186469_ctrl.data.txt.gz 11.4 Mb (ftp)(http) TXT
GSE186469_t2d.data.txt.gz 11.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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