|
| Status |
Public on Jan 01, 2015 |
| Title |
P00333 Idiopathic Dilated CMP Left Ventricle |
| Sample type |
SRA |
| |
|
| Source name |
heart left ventricle, idiopathic dilated CMP
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: heart left ventricle
heart failure: yes
disease status: idiopathic dilated CMP
gender: female
age: 59
ethnicity: White/Caucasian
|
| Treatment protocol |
Explanted myocardium snap frozen in liquid nitrogen.
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Illumina TruSeq® RNA Sample Preparation v2 with the final product size selected between 350 and 650 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
P00333
PolyA mRNA
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The RNA-seq data were aligned to the hg19 reference genome using Tophat with default options.
Transcripts were assembled using Cufflinks. For differentially expressed genes, we carried out functional annotation analysis using DAVID; we further examined whether they were more likely to overlap with GWAS findings, the analysis was based on all GWAS signals summarized in the NHGRI GWAS catalogue.
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM_TRACKING file: Expression values as FPKMs were calculated using Cufflinks and RefSeq gene annotations. Columns are Official gene symbol, hg19 gene locus, FPKM expression value.
Supplementary_files_format_and_content: cuffdiff .txt file: Differential expression results from the cuffdiff program. Columns are Gene Symbol, gene locus, FPKM of group 1, FPKM of group 2 and an adjusted P value.
|
| |
|
| Submission date |
May 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Patrick Morley |
| E-mail(s) |
mmorley@pennmedicine.upenn.edu
|
| Phone |
215-898-2026
|
| Organization name |
Perelman School of Medicine at the University of Pennsylvania
|
| Department |
Penn Cardiovascular Institute
|
| Street address |
3400 Civic Center Blvd, Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE57344 |
RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure [RNA-seq] |
| GSE57345 |
RNA-Seq Identifies Novel Myocardial Gene Expression Signatures of Heart Failure |
|
| Relations |
| BioSample |
SAMN02746606 |
| SRA |
SRX533785 |
