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Sample GSM1084238 Query DataSets for GSM1084238
Status Public on Dec 18, 2013
Title A0R_d0_rep1
Sample type SRA
Source name RRBS A459 cell line
Organism Homo sapiens
Characteristics cell line: A549
rounds of in vivo selection: 0
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 Feb 19, 2013
Last update date May 15, 2019
Contact name Christian Rohde
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]
BioSample SAMN01923877
SRA SRX381426

Supplementary file Size Download File type/resource
GSM1084238_A0R_d0_rep1.cpgs.txt.gz 12.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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