|
| Status |
Public on Sep 21, 2023 |
| Title |
lean_beta, biological replicate 8 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
FACS-sorted beta cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: beta
Sex: female
status: lean
|
| 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 |
SAMN33209375 |
| SRA |
SRX19312498 |
