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Sample GSM1333763 Query DataSets for GSM1333763
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

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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