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| Status |
Public on Dec 22, 2017 |
| Title |
GK_1st_4w |
| Sample type |
SRA |
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| Source name |
Pancreatic Islet cells
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: GK
age: week 4
tissue: Pancreatic Islet cells
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Briefly, total RNA was extracted from islets using TRIzol reagent (Invitrogen , cat. no. 15596018). Poly(A+) RNAs were enriched with biotinylated oligo(dT) and converted to cDNA with Superscript III (Invitrogen, cat. no. 18080-051). A ddNTP was added to the 3’-end of the cDNA by a terminal transferase. After second-strand cDNA synthesis, 23 cycles of PCR were performed to amplify the cDNA. PCR products with lengths of 200-400 nt were subjected to deep sequencing on a HiSeq 2500 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Fastq files were aligned with Bowtie (v1.1.1) to merged transcript sequences from the UCSC RefGene database. The parameter for the mapping program Bowtie was “-l25 -n2 –M3 -e 200 --best --strata --phred33-quals --trim5 4”.
The unmapped tags in the first round were then mapped to the rat genome (rn6)
For each gene, only tags uniquely mapped and localized in exons or exon-exon junctions were counted
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw counts of genes for each sample
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| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Wen Zhong |
| E-mail(s) |
zhongwenhust@gmail.com
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| Organization name |
Institute of Biophysics, Chinese Academy of Sciences
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| Street address |
Datun Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE81811 |
Temporal Transcriptomic and Proteomic Landscapes of Deteriorating Pancreatic Islets in Type 2 Diabetic Rats |
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| Relations |
| BioSample |
SAMN05170977 |
| SRA |
SRX1796109 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2175905_GK_1st_4w.BigWig |
22.4 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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