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Sample GSM2718434 Query DataSets for GSM2718434
Status Public on Jul 27, 2017
Title shRNA_SCR_RRBSseq
Sample type SRA
Source name T-cell acute lymphoblastic leukemia_shRNA_SCR
Organism Mus musculus
Characteristics cell type: T-cell
strain: FVB/N
genotype: EuSR[gamma]-tTA;tet-o-MYC
treatment: shRNA_SCR
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the Macherey-Nagel NucleoSpin Tissue Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 3000
Data processing Sequencing was carried out on an Illumina HiSeq 3000.
Quality control of sequencing reads was performed using FastQC.
Adapter removal was performed using Trim Galore! v0.4.1.
Reads were then aligned to the reference genome using bismark v0.16.1, followed by methylation calling using the corresponding bismark functionality.
The comparative RRBS analysis was carried out using methylKit, based on reference genome mm9.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph represent the CpG methyaltion status
Submission date Jul 26, 2017
Last update date May 15, 2019
Contact name Jan van Riggelen
Organization name Augusta University
Street address 1410 Laney Walker Blvd.
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
Platform ID GPL21493
Series (1)
GSE101907 DNMT3B overexpression contributes to aberrant DNA methylation and MYC-driven tumor maintenance in T-ALL and Burkitt’s lymphoma
BioSample SAMN07416905
SRA SRX3038579

Supplementary file Size Download File type/resource
GSM2718434_6780_shRNA_SCR.bedGraph.gz 38.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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