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| Status |
Public on May 10, 2016 |
| Title |
WT 6h Refed |
| Sample type |
SRA |
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| Source name |
Pancreatic islets
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
protocol: Fasted for 48 hours, and refed for 6 hours
genotype: WT
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| Extracted molecule |
total RNA |
| Extraction protocol |
Isolated primary islets from 3 WT and 3 KR mutant mice after 24 hr-fasted or 24 hr-fasted followed by 6 hr-refeeding were combined per genotype and total RNA isolation was performed using RNeasy Mini Kit (QIAGEN).
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
Tophat v2.0.4 to map the reads to a mm9 with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements
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| Submission date |
Feb 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Youngjung Rachel Kim |
| E-mail(s) |
rachelyjk@gmail.com
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| Organization name |
Columbia University
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| Department |
Medicine
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| Lab |
c/o Dr. Domenico Accili, MD
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| Street address |
1150 St. Nicholas Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE77652 |
FoxO1 Deacetylation Decreases Fatty Acid Oxidation in beta-cells and Sustains Insulin Secretion in Diabetes |
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| Relations |
| BioSample |
SAMN04479238 |
| SRA |
SRX1564693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2055669_JD0019_genes.csv.gz |
852.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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