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Sample GSM2872625 Query DataSets for GSM2872625
Status Public on Dec 01, 2018
Title 932S
Sample type SRA
 
Source name IDH1WT tumor line (RAS glioma)
Organism Mus musculus
Characteristics tissue: cell line derived from tumor
idh genotype: IDH wildtype
mouse genotype: N::TVA; Cdkn2alox/lox
cell type: Cell line derived from brain tumor
background strain: C57Bl/6, 129, and FVB/n
Growth protocol DMEM, 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Qiagen DNeasy DNA extraction kit.
Genomic DNA was processed with the Agilent SureSelect XT Mouse Methyl-Seq Enrichment System capture kit following manufacturer’s recommendations.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Description IDH1WT tumor line (RAS glioma)
14323X6_932S
Data processing Paired reads were aligned to the genome with Novocraft Novoalign v3.7.1 with options -b 2 -t 360 -h 120 -r random.
Reads were de-duplicated with Picard MarkDuplicates v2.9.0.
Alignments were processed with USeq (v9.0.8) NovoalignBisulfiteParser. Point data was filtered for CpG contexts using USeq ParsePointDataContexts. Base fraction CpG methylation tracks were generated with USeq BisStat with a minimum read coverage of 10.
Genome_build: mm10
Supplementary_files_format_and_content: tar bundle of bar.zip point data representing Converted and NonConverted CpG observations from NovoalignBisulfiteParser.
Supplementary_files_format_and_content: bigWig file representation of the fraction methylation at CpG sites
Supplementary_files_format_and_content: bed file of the covered regions with a mean depth of 10 bp across samples used in differential methylation analysis
 
Submission date Dec 01, 2017
Last update date May 15, 2019
Contact name Sheri Holmen
E-mail(s) sheri.holmen@hci.utah.edu
Phone 801-213-4237
Organization name University of Utah
Department Surgery
Street address 2000 Circle of Hope Dr.
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Platform ID GPL17021
Series (2)
GSE107614 Mutant IDH1 promotes glioma formation in vivo [Bisulfite-seq]
GSE107616 Mutant IDH1 promotes glioma formation in vivo
Relations
BioSample SAMN08120329
SRA SRX3437638

Supplementary file Size Download File type/resource
GSM2872625_14323X6_932S.tar.gz 34.4 Mb (ftp)(http) TAR
GSM2872625_14323X6_932S_BaseFraction_MeCpG.bw 14.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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