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Sample GSM1282302 Query DataSets for GSM1282302
Status Public on Jan 27, 2014
Title mES_shLuc_ctrl
Sample type SRA
Source name shLuc ES cells
Organism Mus musculus
Characteristics cell line: R1 ES cell
antibody: NULL
Growth protocol ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For ChIP experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 ┬ÁM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For differentiation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.
Extracted molecule polyA RNA
Extraction protocol RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description RNA-Seq
Data processing Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
Sequence reads were obtained and mapped to the mouse (mm8) genomes with Bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries).
Genome_build: mm8
Supplementary_files_format_and_content: The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Submission date Dec 06, 2013
Last update date May 15, 2019
Contact name Benjamin L Kidder
Organization name Wayne State University
Department Oncology
Lab Laboratory of Epigenomics
Street address 4100 John R St
City Detroit
State/province MI
ZIP/Postal code 48201
Country USA
Platform ID GPL13112
Series (2)
GSE53090 KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [RNA-Seq]
GSE53093 KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Reanalyzed by GSE80797
BioSample SAMN02438001
SRA SRX388451

Supplementary file Size Download File type/resource
GSM1282302_GA2426-shLuc-EB-72h-mouse-Ben-r515l1.bed.gz 692.6 Mb (ftp)(http) BED
GSM1282302_GA2426-shLuc-EB-72h-mouse-Ben-r515l1_RPBM.bedgraph.gz 33.7 Mb (ftp)(http) BEDGRAPH
GSM1282302_GA2426-shLuc-EB-72h-mouse-Ben-r515l1_expr.rpkm.gz 485.9 Kb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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