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Sample GSM2387233 Query DataSets for GSM2387233
Status Public on Nov 10, 2016
Title NH1
Sample type SRA
 
Source name Heart
Organism Homo sapiens
Characteristics tissue: heart
Extracted molecule total RNA
Extraction protocol Human hypertrophic heart tissue samples were obtained from patients previously diagnosed with HCM, undergoing septal myectomy surgery (n=5). Control samples were obtained from normal heart donor left ventricles (n=4)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Control samples were obtained from normal heart donor left ventricles (n=4)
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
 
Submission date Nov 09, 2016
Last update date Apr 16, 2021
Contact name 李 玉琳
Organization name Beijing Institute of Heart Lung and Blood Vessel Diseases
Street address 2 Anzhen Rd, Chaoyang District,
City Beijing
ZIP/Postal code 100029
Country China
 
Platform ID GPL11154
Series (1)
GSE89714 Differential gene expressions in the heart of hypertrophic cardiomyopathy patients
Relations
BioSample SAMN06007630
SRA SRX2339810

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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