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Sample GSM1365547 Query DataSets for GSM1365547
Status Public on Feb 23, 2015
Sample type SRA
Source name B-cell acute lymphoblastic leukemia with ETV6/RUNX1 translocation
Organism Homo sapiens
Characteristics tissue: bone marrow / peripheral blood
subjects: children with B-ALL (California Childhood Cancer Study)
age: 1
gender: M
cytogenetics: ETV6/RUNX1
Extracted molecule genomic DNA
Extraction protocol AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions
We sheared the DNA by sonication to 50–500 bp with a Covaris E220, followed by selecting 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience).
Genomic DNA libraries were constructed using the TruSeq Sample Preparation kit (Illumina).
Two rounds of sodium bisulfite-conversion of DNA using the EpiTexy Bisulfite kit (Qiagen) was performed to get a conversion efficiency of >99%.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Description WGBS data of B-cell acute lymphoblastic leukemia cells
Data processing From the human genome (GRCh37) and NCBI viral genome (v35), two reference sequences including reference C2T (all Cs were replaced by T) and reference G2A (all Gs were replaced by A) were generated, and to these, each paired-end read was aligned using the GEM software.
Up to four mismatches were allowed, and read pairs with unique compatible mappings (to the same chromosome and in the expected orientation) were selected.
After mapping, most likely genotype and methylation % in each C were estimated, using the software developed at the Centro Nacional de Análisis Genómico, which takes into account the observed bases, base quality scores and the strand origin of each read pair.
The confidence in the genotype call was estimated by the Phred-scaled likelihood. CpG sites were selected where both bases were called as homozygous CC followed by GG with a Phred score of ≥20.
Sites with >500× coverage depth were excluded to avoid highly repetitive regions
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: tab-delimited text file include methylation % estimation for each CpG
Submission date Apr 08, 2014
Last update date May 15, 2019
Contact name Seung-Tae Lee
Phone +82-10-9933-5465
Organization name UCSF
Street address 1450 3rd Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platform ID GPL11154
Series (2)
GSE56601 WGBS data of pediatric B-cell acute leukemias
GSE56602 Two-Track Epigenetic Remodeling and Backtracking to Embryonic Stem Cell Bivalency in B-cell Acute Lymphoblastic Leukemias
BioSample SAMN02721469
SRA SRX513206

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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