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Sample GSM1310451 Query DataSets for GSM1310451
Status Public on Jan 21, 2014
Title MeDIP-seq data_30144
Sample type SRA
 
Source name monozygotic twin pair_MDD case
Organism Homo sapiens
Characteristics twin pair: 19
subject status: major depressive disorder
tissue: whole blood sample
Extracted molecule genomic DNA
Extraction protocol Whole blood samples were collected from the twins and stored at -80°C in EDTA tubes. DNA was extracted from 2 x 6ml EDTA blood using the Nucleon Genomic DNA Extraction Kit BACC3 and stored at -20°C in TE Buffer.
BGI protocol
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina Genome Analyzer
 
Description 30144
Data processing Basecalls performed using CASAVA version 1.4
MeDIP-seq reads were aligned to the hg19 genome assembly using bwa
Genome_build: hg19
bed files were generated from bam files using the bedtools package
Supplementary_files_format_and_content: RPKM files were generated from bed files using the MEDIPS R package
 
Submission date Jan 20, 2014
Last update date May 15, 2019
Contact name Matthew N Davies
Organization name King's College London
Department Twin Research
Lab Twin Research
Street address St Thomas' Hospital Campus
City London
State/province Greater London
ZIP/Postal code SE1 7EH
Country United Kingdom
 
Platform ID GPL9052
Series (1)
GSE54222 Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Relations
BioSample SAMN02592827
SRA SRX443162

Supplementary file Size Download File type/resource
GSM1310451_SingleMeth_30144_chrTOTAL.rpkm.gz 79.0 Mb (ftp)(http) RPKM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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