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Sample GSM2392507 Query DataSets for GSM2392507
Status Public on Mar 14, 2018
Title clt_20130813_1_CF_5d_MI
Sample type SRA
Source name heart
Organism Mus musculus
Characteristics tissue: Cardiac fibroblast
age: post natal week 10-14
genotype: wild type
strain: C57BL/6
gender: male
condition: 5 day MI
Extracted molecule total RNA
Extraction protocol polyA + mRNA was extracted from heart cells using Qiagen RNEasyPlus kit.
Stranded RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description 5 day MI
Data processing Illumina bcltofastq v1.8.4 software used data formatting and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using SHRiMP v2.2.3 with the following parameters: -qv-offset 33 --all-contigs
The FASTX toolkit (fastq_quality_trimmer) was applied to remove bases with quality scores below Q=13 from the end of each read
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Differential expression analysis was performed using cufflinks v2.0.2; cufdiff2 with the following parameters: --FDR 0.05 -u -b $GENOME
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Submission date Nov 15, 2016
Last update date May 15, 2019
Contact name Eric Small
Organization name University of Rochester
Street address 601 Elmwood Avenue, Box CVRI
City Rochester
State/province NY
ZIP/Postal code 14642
Country USA
Platform ID GPL17021
Series (1)
GSE89885 Transcriptional profiling reveals gene programs that are differentially regulated in cardiac fibroblasts during exercise and disease
BioSample SAMN06018643
SRA SRX2350834

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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