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Sample GSM1044740 Query DataSets for GSM1044740
Status Public on Feb 13, 2014
Title Control_46
Sample type SRA
 
Source name Bone Marrow
Organism Homo sapiens
Characteristics tissue: Bone Marrow
cytogenetic group: BM from healthy donor
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was bisulfite converted using EZ DNA Methylation kit. Libraries were prepared according to Roche 454 instructions for amplicon sequencing. Briefly, bisulfite converted DNA was amplified with specific primers containing the adapters for the Roche 454 sequencer, purified with AMPure beads, quantified with Quant-iT Picogreen dsDNA assay kit and loaded into 16x platforms. Libraries were sequenced on the Roche 454 sequencer following the manifacture's protocols
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model 454 GS FLX Titanium
 
Description BM from healthy donor
Data processing GS Run Processor application provided with 454 Sequencing Software v2.6 was used for basecalling.
Barcoded sequence reads were trimmed for barcode-adaptor sequences and assigned to appriopriate sample.
Methylation status of each CpG site was determined by aligning reads to the germline sequence using character-based user interface version of QUMA program (quantification tool for methylation analysis; http://quma.cdb.riken.jp). The percent identity score was normalized to the reads length. After alignment, sequence reads were filtered according to the following quality control: for the sequencing quality reads with < 90% identity score or > 10 mismatches were removed. For bisulfite conversion control, a lower limit of conversion efficiency was set to 95% and no more than 5 unconverted cytosines in CpH (non-CpG) sites were allowed. The percentage of methylation at each CpG site was calculated based on the number of sequences containing methylated CpGs versus the total number of sequences analysed.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle Track Format (WIG) files: display scores indicating methylation level of covered CpG sites
Supplementary_files_format_and_content: Matrix table containing methylation status for each CpG site (0 - unmethylated; 100 - fully menthylated; NA - not determined). First and second columns indeicate chromosome and genomic position of single CpG site. Subsequent columns contain methylation status for indivifual samples
 
Submission date Nov 27, 2012
Last update date May 15, 2019
Contact name Jacek Dariusz Marzec
E-mail(s) j.marzec@qmul.ac.uk
Organization name Barts Cancer Institute
Department Centre for Haemato-Oncology
Lab Cancer Genomics
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL14603
Series (1)
GSE42543 Loss of imprinting at the CTCF binding sites in the DLK1-DIO3 domain reactivates microRNA expression in acute promyelocytic leukaemia
Relations
SRA SRX206529
BioSample SAMN01819898

Supplementary file Size Download File type/resource
GSM1044740_s_46.meth.WIG.gz 2.2 Kb (ftp)(http) WIG
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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