|
| Status |
Public on Feb 11, 2016 |
| Title |
1156 hiPSC-CMs stimulated |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 1156
tissue: derived cardiomyocytes (CMs) from hiPSC
treatment: with Endothelin stimulation
|
| Treatment protocol |
The hiPSC-CMs were stimulated with endothelin-1 (ET-1) to induce a hypertrophic response following our established CM hypertrophy protocol (Aggarwal et al., 2014. Plos One.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted per manufacturer’s recommendations using total RNA Purification 96-Well Kit (Norgen Biotek Corp.).
Proton RNA-seq libraries were prepared for sequencing using standard ribosomal RNA depletion method for Proton RNA-seq. For library preparation of AmpliSeq whole transcriptome a barcoded cDNA library is first generated with SuperScript® VILO™ cDNA Synthesis kit from 10ng of total RNA. Then cDNA is amplified using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Amplified cDNA Libraries were evaluated for quality and quantified using Agilent Bioanalyzer High sensitivity chip. Libraries were then diluted to 100pM and pooled equally, with eight individual samples per pool.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
CM harvested 18 hours post stimulation
|
| Data processing |
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3) was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and ‘-r 200’ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the “–very-sensitive-local” method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin available for Ion TorrentTM sequencing platforms
Illumina RNA-seq data for UHRR (Agilent Universal Human Reference RNA) and HBRR (Ambion FirstChoice® Human Brain Reference Total RNA):GEO accession number: GSE49712
Proton RNA-seq data for above two reference RNA samples: GEO accession number: GSE46876
Genome_build: UCSC hg19
|
| |
|
| Submission date |
Nov 06, 2015 |
| Last update date |
Feb 26, 2016 |
| Contact name |
Wenli Li |
| E-mail(s) |
wenli@mcw.edu
|
| Phone |
4149552381
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Pediatrics
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE74760 |
Comprehensive Evaluation of AmpliSeq Transcriptome, a Novel Targeted Whole Transcriptome RNA Sequencing Methodology for Global Gene Expression Analysis. |
|
| Relations |
| BioSample |
SAMN04246306 |
