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Sample GSM1031223 Query DataSets for GSM1031223
Status Public on Nov 08, 2012
Title RRBS remission bone marrow APL_16
Sample type SRA
 
Source name Density centrifuged bone marrow
Organism Homo sapiens
Characteristics disease state: Remission bone marrow
Sex: m
age: 66
sample pairs: APL_19
Extracted molecule genomic DNA
Extraction protocol 0.3 – 1 µg of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with 5mC-methylated Illumina paired end sequencing adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 220 bps insert size were gel-purified (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). Each library was sequenced on a separate lane using an Illumina HiScanSQ instrument with version 2.5 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiScanSQ
 
Data processing Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
Off-Line Basecaller (OLB) was used for bcl to qseq conversion
Illumina paired-end adapter sequences were removed using Cutadapt version 0.9.3
Reads were mapped using Bismark version 0.5
Methylation calls from Bismark were extracted with a modified methylation_extractor script which removed 3’-MspI-sites
The extracted methylation data was further analyzed in R/Bioconductor with the BiSeq package
Genome_build: hg19 for human samples and mm9 for mouse samples
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using R/Bioconductor with help of the BiSeq package. Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.
 
Submission date Nov 05, 2012
Last update date May 15, 2019
Contact name Christian Rohde
E-mail(s) christian.rohde@uni-heidelberg.de
Organization name Heidelberg University
Lab Molecular Hematology and Oncology
Street address Im Neuenheimer Feld 410
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL15456
Series (2)
GSE42044 DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding (sequencing)
GSE42119 DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding
Relations
SRA SRX203040
BioSample SAMN01801787

Supplementary file Size Download File type/resource
GSM1031223_APL_16.cpgs.txt.gz 15.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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