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Status |
Public on Nov 10, 2016 |
Title |
NH1 |
Sample type |
SRA |
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Source name |
Heart
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Organism |
Homo sapiens |
Characteristics |
tissue: heart
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
Control samples were obtained from normal heart donor left ventricles (n=4)
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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 …
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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
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Street address |
2 Anzhen Rd, Chaoyang District,
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City |
Beijing |
ZIP/Postal code |
100029 |
Country |
China |
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Platform ID |
GPL11154 |
Series (1) |
GSE89714 |
Differential gene expressions in the heart of hypertrophic cardiomyopathy patients |
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Relations |
BioSample |
SAMN06007630 |
SRA |
SRX2339810 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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