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| Status |
Public on Jun 30, 2022 |
| Title |
HCM-4 |
| Sample type |
SRA |
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| Source name |
heart left ventricle
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| Organism |
Homo sapiens |
| Characteristics |
tissue: heart left ventricle
status: hypertrophic cardiomyopathy
Sex: female
age: 62
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| Extracted molecule |
total RNA |
| Extraction protocol |
Myocardial samples from HCM and AS patients undergoing surgical myoectomy or aortic valve replacement, respectively, were obtained from interventricular septum in the part under the right aortic coronary leaflet. After extraction tissue samples were immediately cut into fragments up to ≤ 0.5 cm in any single dimension, submerged in 5 volumes of RNAlater solution (Thermo Fisher Scientific, USA), and stored at -20ºC for further processing.
Disruption of tissue samples was performed using the TissueLyser LT bead mill (Qiagen, USA). Total RNA was extracted from disrupted samples using RNeasy Mini Kit (Qiagen, USA)
RNA libraries were constructed from 1 μg RNA using MGIEasy RNA Library Prep Set following manufacturer instructions. Global transcriptome profiling was performed by high throughput RNA sequencing (RNA-seq) on MGISEQ-200 platform
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G50 |
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| Description |
primary hypertrophied left ventricle sample
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| Data processing |
Quality control of raw sequencing reads was assessed with FASTQC. Low quality nucleotides were trimmed from the raw fastq files using Trimmomatic (Version 0.39).
Samples were mapped on Genome primary assembly GRCh38 with the Gencode annotation using STAR (Version 2.7.6a)
Reads per gene were counted using GeneCounts option of STAR software.
DESeq2 Bioconductor package (Version 1.32.0) was used for normalization, principal component analysis, and differential gene expression analysis
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw gene counts for every gene and every sample
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| Submission date |
Jun 27, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Maxim Kozin |
| E-mail(s) |
kozinmax1992@gmail.com
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| Organization name |
Pirogov Russian National Research Medical University
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| Street address |
Ostrovitanova 1
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| City |
Moscow |
| ZIP/Postal code |
117997 |
| Country |
Russia |
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| Platform ID |
GPL28337 |
| Series (1) |
| GSE206978 |
Hypertrophic cardiomyopathy: data of transcriptome profiling and epigenome-wide DNA methylation analysis |
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| Relations |
| BioSample |
SAMN29363663 |
| SRA |
SRX15902741 |
| 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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