|
| Status |
Public on Oct 03, 2014 |
| Title |
ET1-CM, experiment1 |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-CM from experiment1 after ET-1 stimulation
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived cardiomyocytes
|
| Treatment protocol |
After two days of recovery, the cells were cultured in William’s E medium supplemented with Cocktail B (1:25) from the Hepatocyte Maintenance Supplement Pack (Life Technologies). After an additional 11 days of recovery, cells were stimulated for 18 h with ET-1 (Sigma Aldrich) at 10-8M as recommended by the manufacturer. Experiments were performed in triplicate for both unstimulated controls (control-CM) and ET-1 stimulated cells (ET1-CM).
|
| Growth protocol |
iCell-CMs were obtained from one single batch of cells. iCell Cardiomyocytes were plated at 2.0 × 104 cells/well in a 96-well plate precoated with 0.1% gelatin solution.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
18 h post ET-1 stimulation, cells were harvested with Total RNA Purification 96-Well Kit (Norgen Biotek Corp.). Total RNA was extracted per manufacturer’s recommendations, resuspended in nuclease-free water, and quantified by UV spectrophotometry (NanoDrop™ 2000, Thermo Scientific).
MicroRNA libraries from rRNA depleted total RNA (Ribo-Zero rRNA removal Kit, Epicentre) were prepared using Ion Torrent Total RNA Seq small RNA kit as per manufacturer’s recommendations (Life Technologies).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
miRNA sequencing based expression data from ET-1 stimulated hiPSC-CMs from experiment 1
|
| Data processing |
Ion Torrent's Torrent Suite version 3.6 was used for basecalling
Raw sequencing reads were aligned using the SHRiMP2 aligner and were aligned against the human reference genome (hg19) for novel miRNA prediction and then against a custom reference sequence file containing miRBase v.20 known human miRNA hairpins, tRNA, rRNA, adapter sequences and predicted novel miRNA sequences.
SHRiMP aligner's gmapper-ls was used with the following parameters: -s 00111111001111111100,00111111110011111100,00111111111100111100,00111111111111001100,00111111111111110000,11111111111 -o 1 -H -E -a -1 -q -30 -g -30 --qv-offset 33 --strata -N 6
miRNA quanitification was done using HTSeq v0.5.3p3 using the default union parameter.
Differential miRNA expression was analyzed using the DESeq (v.1.12.1) R/Bioconductor package
Genome_build: hg19, miRBase v.20 human miRNA hairpins
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts for known mature human miRNAs.
|
| |
|
| Submission date |
Aug 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Broeckel |
| Organization name |
Medical College of Wisconsin
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL17301 |
| Series (2) |
| GSE60292 |
RNA Expression Profiling of Human iPSC-Derived Cardiomyocytes in a Cardiac Hypertrophy Model [miRNA expression] |
| GSE60293 |
RNA Expression Profiling of Human iPSC-Derived Cardiomyocytes in a Cardiac Hypertrophy Model |
|
| Relations |
| BioSample |
SAMN02980999 |
| SRA |
SRX674307 |
