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Sample GSM1272368 Query DataSets for GSM1272368
Status Public on Oct 20, 2014
Title H1B T0 eluate (new run)
Sample type SRA
 
Source name ES cell, RNA IP against m6A
Organism Homo sapiens
Characteristics cell line: H1B
cell type: embryonic stem (ES) cell
Extracted molecule polyA RNA
Extraction protocol Cells well harvested by direct addition of TRIzol reagent (Ambion Cat.#15596018) to the cell culture plate after removal of the media and extracted using Trizol reagent protocol. Subsequently, the total RNA was DNAse treated using DNAse I (Promega Cat.# M610A) for 20 minutes at 37ºC followed by acid phenol/chloroform extraction, chloroform extraction and overnight NaCl2 precipitation. The precipitated RNA was washed with 70ºC ethanol and re-suspended in ultra pure H2O. RNA concentration and purity were verified by nanodrop followed by BioAnalyzer for quality control. Double polyA+ RNA selection was performed using twice Invitrogen Dynabeads mRNA Purification Kit (Cat. #610.06) protocol. RNA concentration and purity were once again verified by nanodrop followed by BioAnalyzer for quality control.
For the input and post m6A-RNA IP fraction (i.e. m6A positive fraction), 100ng of RNA was used for library construction using TrueSeq Stranded mRNA Sample Preparation Guide, entering the protocol by adding the Fragment, Prime, Finish Mix, skipping the elution step and proceeding directly to synthesis of the First Strand cDNA. From that point on, the exact steps of the Illumina TruSeq Stranded mRNA sample Preparation Guide were followed to the end.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Sample 3
This is additional sequencing run
Data processing 50bp single-end RNA-Seq reads were mapped to hg19 genome using Tophat.
bam files were converted to bedgraphs using genomeCoverageBed, which were in turn converted to bigwigs using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs show number of reads uniquely mapped to the genome
 
Submission date Nov 21, 2013
Last update date May 15, 2019
Contact name Jinkai Wang
Organization name University of California, Los Angeles
Street address 650 Charles E. Young Drive South, CHS 33-228
City Los Angeles
State/province CA
ZIP/Postal code 90095-7278
Country USA
 
Platform ID GPL11154
Series (1)
GSE52600 m6A RNA modification controls cell fate transition in mammalian embryonic stem cells
Relations
BioSample SAMN02418735
SRA SRX381121

Supplementary file Size Download File type/resource
GSM1272368_H1BR_Eluate_T0_mainChr.bw 61.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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