|
| Status |
Public on Aug 09, 2018 |
| Title |
Sham 4 (mRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Left ventricle myocardium
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Left ventricle myocardium
surgery: Sham
drug treatment: None
sample id: Ear tag #606
|
| Treatment protocol |
Mice subjected to sham or TAC (cardiac pressure-overload) surgeries were treated with either a PDE5A or PDE9A inhibitor for 4 weeks, with treatment initiated 1 week after surgery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Left ventricle myocardium was collected and flash-frozen in liquid nitrogen. Total RNA was extracted using Qiazol and Qiagen's miRNeasy kit according to manufacturer protocol, and samples were run on an Agilent Bioanalyzer to evaluate RIN score prior to library construction
Sequencing libraries were constructed using the Illumina TruSeq Stranded Total RNA sample preparation kit (with barcodes) and 500 ng of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
606_sham 4
|
| Data processing |
Illumina CASAVA 1.8.4 was used for BCL to FASTQ file conversion and for base-calling using default parameters
RNA-seq reads were trimmed and mapped to the Ensembl mouse reference genome (mm10) using HISAT2 version 2.0.5
Transcript counts were quantified using RSEM v1.3.0 with default parameters
Bioconductor's DESeq2 1.18.1 was used for differential expression analysis of RNA count data
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain transcripts-per-million (TPM) normalized counts of mRNAs
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Aug 09, 2018 |
| Contact name |
Kristen Kokkonen-Simon |
| Organization name |
Johns Hopkins University
|
| Department |
Medicine
|
| Lab |
David Kass
|
| Street address |
720 Rutland Ave, Ross 858
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE112055 |
Evaluation of PDE5A and PDE9A Inhibition Impacts on Cardiac mRNA Expression in a Mouse Pressure-Overload-Induced Heart Failure Model |
| GSE112056 |
Marked Disparity of MicroRNA Modulation by cGMP-selective PDE5 versus PDE9 Inhibitors in Heart Disease |
|
| Relations |
| BioSample |
SAMN08741754 |
| SRA |
SRX3822984 |
