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Sample GSM1953579 Query DataSets for GSM1953579
Status Public on Feb 11, 2016
Title HBRR
Sample type SRA
Source name HBRR-AmpliSeq
Organism Homo sapiens
Characteristics reference: Ambion FirstChoice® Human Brain Reference Total RNA
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
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
Genome_build: UCSC hg19
Submission date Nov 24, 2015
Last update date May 15, 2019
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 SAMN04292697
SRA SRX1447439

Supplementary file Size Download File type/resource
GSM1953579_AmpliSeq_HBRR_raw_read_counts.txt.gz 168.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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