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Sample GSM1251242 Query DataSets for GSM1251242
Status Public on Dec 18, 2013
Title H2R_d0
Sample type SRA
 
Source name RRBS HTB56 intermediate metastatic cell line
Organism Homo sapiens
Characteristics cell line: HTB56
rounds of in vivo selection: 2
5-azacytidine status: untreated
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 Illumina TruSeq adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 280 bps insert size were purified from a SYBR gold (Invitrogen) pre-stained agarose gel (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). The libraries were sequenced on an Illumina HiScanSQ instrument with version 3 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 Reduced Representation
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
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 Oct 25, 2013
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)
GSE44390 DNA Methyltransferase inhibition reverses epigenetically embedded phenotypes in lung cancer preferentially affecting Polycomb target genes
GSE52140 Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [RRBS-Seq experiments]
Relations
BioSample SAMN02384444
SRA SRX381442

Supplementary file Size Download File type/resource
GSM1251242_H2R_d0.cpgs.txt.gz 13.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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