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Sample GSM1314017 Query DataSets for GSM1314017
Status Public on Jan 25, 2014
Title Twin pair T Case MeDIP-seq
Sample type SRA
 
Source name Human blood
Organism Homo sapiens
Characteristics diagnosis: Major Depressive Disorder (MDD)
gender: Male
tissue: blood
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from whole blood using a salt extraction method
MeDIP-Sequencing was performed by BGI at its Shenzhan laboratory. Extracted DNA was fragmented using a Covaris sonication system and sequencing libraries were prepared from 5µg fragmented gDNA. End repair, <A> base addition and adaptor ligation steps were performed using Illumina's Single-End DNA Sample Prep kit. Adaptor-ligated DNA was immunoprecipitated by anti-5mC using a commercial antibody (Diagenode). MeDIP DNA was purified with ZYMO DNA Clean & Concentrator-5 columns, and amplified using adaptor-mediated PCR. DNA fragments between 220 and 320 bp in size were gel-excised.
 
Library strategy MeDIP-Seq
Library source genomic
Library selection 5-methylcytidine antibody
Instrument model Illumina HiSeq 2000
 
Data processing From the raw fastq files, Illumina quality scores were converted into Sanger Phred quality scores using MAQ
Alignment to hg19 was performed using the Burrows-Wheeler algorithm
MEDIPS package was used to calculate RPM (reads per millions scores) by defining bin sizes of 500bp with an overlap of 250bp across the genome
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated file containing RPM (reads per million) scores for each 500bp window and each sample; only windows with at least one aligned read are included.
 
Submission date Jan 24, 2014
Last update date May 15, 2019
Contact name Lutz Krause
E-mail(s) Lutz.Krause@qimr.edu.au
Organization name QIMR Berghofer Medical Research Institute
Department Genetics and Computational Biology
Lab Bioinformatics
Street address 300 Herston Rd
City Herston
State/province QLD
ZIP/Postal code 4006
Country Australia
 
Platform ID GPL11154
Series (1)
GSE54370 Hypermethylation in the ZBTB20 gene is associated with major depressive disorder
Relations
BioSample SAMN02595671
SRA SRX448212

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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