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| Status |
Public on Sep 06, 2014 |
| Title |
3-month-old male rat, biological replicate 1_mRNA |
| Sample type |
SRA |
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| Source name |
islets of control 3-month male rat
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: islets
age (weeks): 12
Sex: M
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol (Invitrogen) following the manufacturer's instructions, but allowing 30 min room temperature isopropanol precipitation to enhance miRNA extraction.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
base-calling quality score = phred33
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| Data processing |
Illumina Casava1.8 software was used for basecalling; all reads are 50 nt with phred33 quality scores
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the rn5 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC rn5 genes.gtf.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene
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| Submission date |
Sep 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot J Matkovich |
| E-mail(s) |
sjmatkovich@lilly.com
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| Organization name |
Eli Lilly and Company
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| Street address |
Lilly Corporate Center
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46285 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (2) |
| GSE61179 |
Islet-specific microRNA changes driven by nutrient shift trigger postnatal beta-cell maturation - intact islet mRNAs |
| GSE61182 |
MicroRNA and mRNA expression analyses of postnatal and adult rat pancreatic islets |
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| Relations |
| BioSample |
SAMN03022327 |
| SRA |
SRX693520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1498954_rat_adult-1_mRNA_HTSeq-count.txt.gz |
63.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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