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Sample GSM2831544 Query DataSets for GSM2831544
Status Public on Jul 08, 2018
Title G34R_RNASeq
Sample type SRA
 
Source name ES Cells
Organism Mus musculus
Characteristics cell type: Targeted H3.3 G34R ES cells
passages: < 20
strain: 129S1/SvImJ
Growth protocol Mouse ESCs were cultured in Dulbecco's modified Eagle's medium supplemented with 15% heat-inactivated foetal calf serum, 10e3 units/ml leukemia inhibitory factor and 0.1 mM β-mercaptoethanol. 
Extracted molecule total RNA
Extraction protocol RNA was extracted from 5 million cells with TRI Reagent (Sigma, 93289) according to manufacturer’s instructions.
Sample quality was assessed using a Bioanalyzer and quantified by Qubit. All samples were processed starting with 500 ng of total RNA according to the Illumina Stranded Total RNA protocol (15031048 Rev C, Sept 2012) except that 12 cycles of amplification was used to minimise amplification artefacts. Libraries were quantitated by Qubit and qPCR, and an equimolar pool were made based upon qPCR results. Following denaturation, 200 pM of the library pool was clustered in one lane of a HiSeq 3000 (Illumina Protocol 15006165 v02 Jan 2016) and 50 bp SR sequencing was carried out (Illumina Protocol 15066493 Rev A, February 2015).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Stranded 50 bp single-end RNA-seq reads were aligned to mouse (mm9) with STAR (v.2.4.2a) using default parameters.
Primary alignments were imported into Seqmonk as single-ended RNA-seq. The RNA-Seq quantitation pipeline was used to estimate RPKM read counts with the following parameters: mRNA as transcript feature, strand-specific, merge transcript isoforms, apply transcript length correction and exclude probes with no counts. A total of 26127 mRNA probes were quantitated.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Wig/BedGraph-to-bigWig (v1.1.0) in Galaxy with default parameters. Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments.
Supplementary_files_format_and_content: Tab delimited text files contain RPKM values of UCSC annotated genes.
 
Submission date Oct 26, 2017
Last update date May 15, 2019
Contact name Hsiao Phin Joanna Voon
E-mail(s) Joanna.Voon@monash.edu
Organization name Monash University
Department Biochemistry and Molecular Biology
Lab Epigenetics and Chromatin
Street address Monash University, Wellington Road
City Clayton
State/province Victoria
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL21493
Series (2)
GSE106204 RNA-seq in WT and H3.3 G34R mouse ES cells
GSE106205 The H3.3 G34R glioma-associated mutation alters H3K9me3 and H3K36me3 chromatin modifications
Relations
BioSample SAMN07837511
SRA SRX3329720

Supplementary file Size Download File type/resource
GSM2831544_G34R_GeneList_RNASeq_RPKM.txt.gz 404.8 Kb (ftp)(http) TXT
GSM2831544_G34R_RNASeq.bw 65.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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