|
| 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 |
| E-mail(s) |
eric_small@urmc.rochester.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN06018643 |
| SRA |
SRX2350834 |
