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Sample GSM1931830 Query DataSets for GSM1931830
Status Public on Feb 11, 2016
Title 1104 hiPSC-CMs unstimulated
Sample type SRA
Source name hiPSC cardiomyocytes
Organism Homo sapiens
Characteristics individual: 1104
tissue: derived cardiomyocytes (CMs) from hiPSC
treatment: without 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
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.
BioSample SAMN04246307

Supplementary file Size Download File type/resource
GSM1931830_AmplSeq_hiPSC_CM_1104_icmm_unstim_raw_read_counts.txt.gz 84.3 Kb (ftp)(http) TXT
GSM1931830_Proton_1104_unstim_icmm_gene_raw_read_counts.txt.gz 98.2 Kb (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file

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