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Series GSE171923 Query DataSets for GSE171923
Status Public on Feb 07, 2022
Title Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle
Organism Rattus norvegicus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which together with RNA-seq was used to investigate regulatory elements underlying tissue-specific gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs mapped to differentially expressed genes that were enriched in distinct biological processes in each tissue. Motif enrichment analysis on tissue-specific DARs predicted binding sites for transcription factors (TFs), several of which were up-regulated in the corresponding tissue. Positive relationship between DARs and target gene expression further supported a functional role for these TF binding motifs. Our study identifies cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.
 
Overall design ATAC-seq was performed on 9 abdominal white adipose tissue (WAT) and 9 gastrocnemius muscle (skeletal muscle) tissue samples obtained from Fischer 344 rats. Tissue samples were either collected from individual animals, or represented pulverized aliquots of tissues pooled from 15 males.
 
Contributor(s) Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser K, Sealfon SC
Citation(s) 34547403
Submission date Apr 12, 2021
Last update date Nov 28, 2022
Contact name Venugopalan Nair
E-mail(s) venugopalan.nair@mssm.edu
Phone 212-241-5809
Organization name Icahn School of Medicine at Mount Sinai
Department Neurology
Street address 1468 Madison Avenue
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platforms (1)
GPL25947 Illumina NovaSeq 6000 (Rattus norvegicus)
Samples (10)
GSM5237457 Adipose Tissue_Rat1
GSM5237458 Adipose Tissue_Rat2
GSM5237459 Adipose Tissue_Rat3
Relations
BioProject PRJNA721402
SRA SRP314498

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Supplementary file Size Download File type/resource
GSE171923_RAW.tar 48.2 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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