|
| Status |
Public on Aug 10, 2020 |
| Title |
CTR |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal rat ventricle myocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain background: Sprague-Dawley
age: Neonatal Day 1-2
treatment: Untreated
cell type source: Primarily isolated from heart
cell type: Neonatal rat ventricle myocytes (NRVMs)
|
| Treatment protocol |
NRVMs were infected with CryABR120G adenovirus and either siUbe2v1 or AdUbe2v1. Five days later, cells were collected. Each group was in triplicate.
|
| Growth protocol |
Neonatal rat ventricular myocytes were primarily isolated and cultured in DMEM+10%FBS. After AdCryABR120G infection, cells were cultured in DMEM+2%FBS for 5 days prior to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and pooled from NRVMs per group using RNAzol reagent (Molecular Research Center; RN190) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
run2375_lane12_read*_indexD712-D508=ctr
|
| Data processing |
Fastq files were trimmed to remove adapter and low quality sequences using Cutadapt
Trimmed reads were mapped to the reference Rattus norvegicus (Rn6) using TopHat
Quantification was done using Cufflinks
Genome_build: Rat Rn6
Supplementary_files_format_and_content: Tab-delimited text files for FPKM
|
| |
|
| Submission date |
Feb 07, 2020 |
| Last update date |
Aug 10, 2020 |
| Contact name |
Katherine E Yutzey |
| E-mail(s) |
katherine.yutzey@cchmc.org
|
| Phone |
513-636-8340
|
| Organization name |
Cinicnnati Children's Hospital Medical Center
|
| Department |
Divison of Molecular Cardiovascular Biology
|
| Street address |
240 Albert Sabin Way
|
| City |
Cinicnnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE144974 |
RNAseq of NRVMs infected with AdCryABR120G by the manipulation of Ube2v1 expression |
|
| Relations |
| BioSample |
SAMN14069410 |
| SRA |
SRX7695527 |
