|
| Status |
Public on Apr 28, 2014 |
| Title |
Ischemic rep9 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Left ventricular tissue
disease state: ischemic
|
| Treatment protocol |
Transmural samples were taken from near the apex of the left ventricle and stored at 4°C for a maximum of 6 h from the time of coronary circulation loss. Samples were stored at -80°C until the RNA and protein extractions were performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Heart samples were homogenized with TRIzol® agent in a TissueLysser LT (Qiagen, UK). All RNA extractions were performed using a PureLink™ Kit according to the manufacturer’s instructions (Ambion Life Technologies, CA). RNA was quantified using a NanoDrop1000 spectrophotometer (Thermo Fisher Scientific, UK) and the purity and integrity of RNA samples was measured using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies, Spain). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers ≥ 9.
Total PolyA-RNA samples were used to generate whole transcriptome libraries for sequencing on the SOLiD 5500XL platform, following the manufacturer’s recommendation (Life Technologies, CA). No RNA-spike in controls was used. Amplified cDNA quality was analyzed by the Bioanalyzer 2100 DNA 1000 kit (Agilent Technologies, Spain) and quantified using the Qubit 2.0 Fluorometer (Invitrogen, UK). The whole transcriptome libraries were used for making SOLiD templated beads following the SOLiD Templated Bead Preparation guide. Bead quality was estimated based on WFA (workflow analysis) parameters. The samples were sequenced using the 50625 paired-end protocol, generating 75 nt + 35 nt (Paired-End) + 5 nt (Barcode) sequences. Quality data were measured using software SETS parameters (SOLiD Experimental Tracking System).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
total RNA
|
| Data processing |
Bioscope mapping software version 1.3
Hg19 Homo Sapiens genome. Low quality sequences filter
Htseq-count algorithms for gene counts (Htseq software version 0.5.4p3)
Differential expression using EdgeR method version 3.2.4
Genome_build: Hg19 Homo Sapiens
|
| |
|
| Submission date |
Feb 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Estefanía Tarazón Melguizo |
| Organization name |
Health Research Institute La Fe
|
| Street address |
Avenida Fernando Abril Martorell, 106
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46026 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16288 |
| Series (1) |
| GSE55296 |
RNA-seq analysis of human heart failure |
|
| Relations |
| BioSample |
SAMN02650888 |
| SRA |
SRX475397 |
