|
| Status |
Public on May 02, 2013 |
| Title |
BSSeq_Buccal_rep_1_7 |
| Sample type |
SRA |
| |
|
| Source name |
Normal Buccal Cells
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
age: 40
ethnicity: Caucasian
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from Buccal cells was extracted using the Gentra Puregene Buccal cell kit, USA.
50 ng of buccal genomic DNA was sonicated using a Bioruptor (Diagenode) to fragments around 300 bp on average and ligated to methylated pair end adapters (Illumina). Samples were bisulphite converted using EZ DNA methylation kit (ZYMO research) and sequenced using Illumina HiSeq 2000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Buccal rep 1 Sample 7
|
| Data processing |
BS-Seq data was mapped using BIFast with parameters –n 1 and –l 50 to hg19 (https://bitbucket.org/xboxrob/bifast)
Clonal reads were filtered and tDMRs were called using BiFast (dmrcaller)
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated Chromsome/Position of CpG/methylation fraction/Methylated Reads/Total Reads
|
| |
|
| Submission date |
May 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Lowe |
| Organization name |
QMUL
|
| Department |
Blizard Institute
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46572 |
Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies [Bisulfite-Seq] |
|
| Relations |
| BioSample |
SAMN02116216 |
| SRA |
SRX273394 |
