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Sample GSM1429638 Query DataSets for GSM1429638
Status Public on Dec 01, 2015
Title X9006
Sample type SRA
 
Source name Neutrophil
Organism Homo sapiens
Characteristics cell type: Neutrophil isolated from peripheral blood
Extracted molecule genomic DNA
Extraction protocol Neutrophils were extracted from peripehral blood of healthy individuals with Ficoll-Paque method.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina HiSeq 2000
 
Data processing DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)
Supplementary_files_format_and_content: *fastq_bismark.sam_methpcNF2t10.txt files provide a fragment-based DNA methylomes in .txt format (contains chromosome, start, end, length of the fragment, number of CpG site in the fragment, count of methylated and methylated CPGs and percentage methylation of the fragment). We selected the fragments having 10 or more reads at 2 CpG sites in each sample to provide fragment-based methylomes for these individuals (F2 t10 switch in the diffmeth program of DMAP tool, Reference: Stockwell, P. A., Chatterjee, A., Rodger, E. J. & Morison, I. M. DMAP: differential methylation analysis package for RRBS and WGBS data. Bioinformatics 30, 1814-1822, doi:10.1093/bioinformatics/btu126 (2014)."
 
Submission date Jul 07, 2014
Last update date May 15, 2019
Contact name Aniruddha Chatterjee
E-mail(s) aniruddha.chatterjee@otago.ac.nz
Phone +64-210701558
Organization name University of Otago
Department Pathology
Lab Epigenetics and Disease
Street address 270 Great king Street
City Dunedin
State/province Otago
ZIP/Postal code 9054
Country New Zealand
 
Platform ID GPL11154
Series (1)
GSE59163 Genome-wide DNA methylation map reveals widespread epigenetic variation in healthy individuals (RRBS)
Relations
BioSample SAMN02904580
SRA SRX647424

Supplementary file Size Download File type/resource
GSM1429638_X9006_ad3tr65.fastq_bismark.sam_methpcNF2t10.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record
Processed data provided as supplementary file

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