|
| Status |
Public on Dec 01, 2021 |
| Title |
Control biological replicate 2 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Isolated cardiac myocytes
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Control
|
| Treatment protocol |
RNA was isolated from mouse cardiomyocytes 3 days and 3 weeks after transverse aortic constriction (TAC) and CTCF depletion.
|
| Growth protocol |
-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from left ventricular isolated adult cardiomyocytes was isolated using the RNeasy Mini Kit (Qiagen).
Ribosomal RNA was removed using an Illumina Ribo-Zero rRNA Removal Kit and the RNA-seq libraries prepared by the Technology Center for Genomics & Bioinformatics Core (UCLA) following Illunmina standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end 150bp reads were demultiplexed into sample-specific *_R1.fastq and *_R2.fastq files using custom scripts and then pseudoaligned to the mm10 genome using the ultra-fast pseudoalignment tool, Salmon.
Briefly, we ran salmon index to generate a mm10 (mouse) transcriptome index using the appropriate “known cDNA” FASTA file from Ensembl release 81.
Corresponding read pairs were pseudoaligned to the appropriate transcriptome using salmon quant with mm10-specific index, *_R1.fastq and *_R2.fastq files as inputs.
Salmon transcript quantifications (*.sf files) for all samples were loaded into a single R object using the tximport package, and then differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Tom Vondriska |
| E-mail(s) |
vondriska.web@gmail.com
|
| Organization name |
UCLA
|
| Street address |
650 Charles E Young Dr, BH553
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE154519 |
Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq] |
| GSE154521 |
Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation |
|
| Relations |
| BioSample |
SAMN15602821 |
| SRA |
SRX8793170 |
