|
| Status |
Public on Dec 19, 2013 |
| Title |
ICM pooled |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: heart
diagnosis: ischemic cardiomyopathy (ICM)
|
| Treatment protocol |
Left ventricular (LV) myocardial samples, remote from infarcted areas, were snap frozen in liquid nitrogen within 2 hours of explantation and stored at -80 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol (Invitrogen) and further purified on RNeasy columns (Qiagen) with on column DNase digestion. Ribosomal RNA was depleted using the RiboMinus kit (Invitrogen). 1 µg rRNA-depleted RNA was used for the construction of sequencing libraries
Illumina RNA-seq libraries were prepared from rRNA-depleted samples using the standard Illumina protocol. SOLiD RNA-seq libraries were prepared from a pool of all of 15 ICM samples and a pool of all of 15 Ctrl samples using the standard SOLiD strand-specific library protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
Illumina Casava1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat (v1.2.0) with parameters -r 120 -p 5
Differential expression was analyzed using edgeR
To identify novel transcripts, we used cufflinks to reconstruct all transcripts, and compared them to reference gene annotations.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in each sample.
|
| |
|
| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
LIGUO WANG |
| E-mail(s) |
wang.liguo@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Division of Computational Biology
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE48166 |
RNA-seq identifies novel transcript elements and transcript processing in the normal and failing hearts |
|
| Relations |
| BioSample |
SAMN02209925 |
| SRA |
SRX312155 |
