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| 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.
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| 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
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| |
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| 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
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| Organization name |
NORTHWESTERN UNIVERSITY
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| Department |
Medicine
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| Lab |
Joseph Bass
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| Street address |
303 E. Superior St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60613 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA773959 |
| SRA |
SRP342865 |
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