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| Status |
Public on Feb 13, 2014 |
| Title |
APL_1 |
| Sample type |
SRA |
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| Source name |
Bone Marrow
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cytogenetic group: t(15;17) diagnosis
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| 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
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
454 GS FLX Titanium |
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| Description |
AML with t(15;17)
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| 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
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| Submission date |
Nov 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacek Dariusz Marzec |
| E-mail(s) |
j.marzec@qmul.ac.uk
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| Organization name |
Barts Cancer Institute
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| Department |
Centre for Haemato-Oncology
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| Lab |
Cancer Genomics
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| Street address |
Charterhouse Square
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| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
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| 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 |
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| Relations |
| SRA |
SRX206491 |
| BioSample |
SAMN01819860 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1044702_s_1.meth.WIG.gz |
2.4 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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