|
| Status |
Public on May 06, 2014 |
| Title |
Heart, MI, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart, Sham
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: heart
treatment: infarct
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared according to Illumina long RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
7R
12 week old mice, border zone of sham infarct, 2 weeks after surgery
|
| Data processing |
Base calling was with Illumina GAP Pipeline Software v1.70
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mm9 reference genome using Tophat 2.0.5 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.0.2 with option -G with mm9 reference GTF
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.0.2 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p2
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format
|
| |
|
| Submission date |
Nov 12, 2013 |
| Last update date |
Jan 29, 2021 |
| Contact name |
Frederic Burdet |
| E-mail(s) |
frederic.burdet@sib.swiss
|
| Organization name |
Swiss Institute of Bioinformatics
|
| Street address |
Quartier Sorge - Batiment Amphipole
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE52313 |
Long RNA Seq on Sham vs MI Adult Mouse Heart |
|
| Relations |
| BioSample |
SAMN02401918 |
| SRA |
SRX376821 |
