|
Status |
Public on Jan 25, 2014 |
Title |
Twin pair N Control MeDIP-seq |
Sample type |
SRA |
|
|
Source name |
Human blood
|
Organism |
Homo sapiens |
Characteristics |
diagnosis: Healthy (Control) 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 |
SAMN02595660 |
SRA |
SRX448200 |