NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7032536 Query DataSets for GSM7032536
Status Public on Sep 21, 2023
Title obob_alpha, biological replicate 3 (RNA-seq)
Sample type SRA
 
Source name FACS-sorted alpha cells
Organism Mus musculus
Characteristics cell type: alpha
Sex: male
status: obob
Growth protocol Pancreatic islets were isolated by injection of collagenase up the common bile duct after clamping of the Ampulla of Vater. Isolates were purified by density gradient centrifugation and dissociated by gentle trituration in 0.25% Trypsin -EDTA. mIns1-H2b-mCherry positive beta cells were collected and processed immediately for ATAC-Seq library preparation.
Extracted molecule total RNA
Extraction protocol Cells were collected in Trizol post FACS purification and isolated by a chloroform extraction, assisted by phase lock tubes. RNA was precipitated by isopropanol and cleaned up over an RNEasy microcolumn per the Qiagen's taking great care to avoid carry over of ethanol following the column washes. Elution volume was 30 microliter.
Indexed sequencing libraries were constructed using the TruSeq RNA sample prep Kit v2 per Illumina instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description bulk RNA expression
Data processing FastQC
Trimmomatic
STAR Aligner
edgeR
Assembly: mm10
Supplementary files format and content: Raw Expression Counts
 
Submission date Feb 08, 2023
Last update date Sep 21, 2023
Contact name Mark O. Huising
E-mail(s) mhuising@ucdavis.edu
Organization name University of California, Davis
Department Neurobiology, Physiology and Behavior
Lab Huising lab
Street address One Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
 
Platform ID GPL13112
Series (2)
GSE224797 Genome wide assessment of gene expression in alpha and beta cells from lean and obese mice
GSE224798 Genome wide assessment alpha and beta cells from lean and obese mice
Relations
BioSample SAMN33209382
SRA SRX19312491

Supplementary file Size Download File type/resource
GSM7032536_4709_YFP_Pos_S8_L001.featureCounts.txt.gz 2.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap