|
| Status |
Public on Jul 02, 2010 |
| Title |
Pancreatic islets-pregnant-rp1 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic islets
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
organ: pancreatic islets
pregnancy: adult prengnat female
|
| Growth protocol |
C57BL/6J mice were housed on a 12-h light/dark cycle in climate-controlled, pathogen-free barrier facilities. Mating was confirmed by the presence of a vaginal plug the next morning, designated day 0 of gestation (G0).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from pooled islets from 4 non-pregnant or pregnant (G13−G15) mice was converted into a library of template molecules using mRNA-Seq Sample Prep Kit (Illumina) according to manufacturer’s protocol. Poly(A)+ mRNA purified using poly-dT oligo-attached Dynal magnetic beads (Invitrogen) was fragmented in RNA fragmentation buffer (Ambion) at 94 ˚C for 5 minutes. First strand cDNA synthesis from the RNA fragments using Superscript III (Invitrogen) and random hexamers was followed by second strand synthesis using DNA Polymerase I and RNaseH, addition of a 3’deoxyadenosine, and ligation of adaptors. Double stranded cDNAs of 200 ± 25 bp were purified by electrophoresis through a 2% low melting-point agarose gel, extracted using the QIAquick Gel Extraction Kit (Qiagen) and further purified using a QiaQuick PCR purification kit (Qiagen). Libraries were expanded with the Illumina Cluster generation protocol and sequenced at the UCSF Genomics Core Facility using the 36 cycle sequencing kit v3 (Illumina). Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
12 weeks old pregnant (G13~15)
|
| Data processing |
31-bp reads were mapped to the Refseq collection of mouse transcripts generated from mouse genome build MM9 using Seqmap34. Mapped reads were quantified using the reads per kilobase exon model metric. Sequencing was performed with 3 independent libraries from 3 separate islet preparations per group. The quantified transcription levels were expressed as reads per kilobase of exon model per million mapped reads (RPKM).
|
| |
|
| Submission date |
May 17, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Hail Kim |
| Organization name |
University of California San Francisco
|
| Department |
Diabetes Center
|
| Lab |
Michale German's Lab
|
| Street address |
513 Parnassus avenue HSW1090
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE21860 |
RNA-seq of pancreatic islets isolated from normal female and pregnant female mice |
|
| Relations |
| SRA |
SRX021621 |
| BioSample |
SAMN00014499 |
