|
| Status |
Public on Jun 30, 2016 |
| Title |
siChaer PE |
| Sample type |
SRA |
| |
|
| Source name |
neonatal rat ventricular myocytes_siChaer_phenylephrine
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Heart
cell type: ventricular myocytes
age: 2-day neonatal
|
| Treatment protocol |
After 6-h transfection with Chaer-specific siRNA (siChaer) and negative control siRNA (siNeg), mediums were changed with phenylephrine (50 microM) and collected after 48 h.
|
| Growth protocol |
Neonatal rat ventricular myocytes were isolated from 2-day neonatal rat hearts, plated on 100 mm dishes and cultured with 1% ITS medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with TRIzol reagents.
TruSeq Stranded RNA library prep with 8 base indexing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned to rn5 using tophat2 with parameters -r 200 -a 13 -g 1 --no-mixed --no-discordant.
RPKM was calculated using in-house scripts for Ensembl genes plus H19 from Refseq.
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files contain read counts and RPKM.
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yibin Wang |
| Organization name |
University of California Los Angeles
|
| Street address |
BH-569 CHS, Box 957115
|
| City |
Los Angeles |
| State/province |
Ca |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE82339 |
LncRNA Chaer contributes to the transcriptome reprogramming during phenylephrine-induced hypertrophy in neonatal rat ventricular myocytes |
|
| Relations |
| BioSample |
SAMN05213408 |
| SRA |
SRX1828328 |
