|
| Status |
Public on Jan 23, 2019 |
| Title |
24023_benign_prostate_TABseq |
| Sample type |
SRA |
| |
|
| Source name |
prostate biopsy DNA from a single donor
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 24023
tissue: adjacent benign normal prostate
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Five 2 mm core biopsies were taken from 1) each of the dominant nodule in areas of >90% cancer cell density, and 2) adjacent benign prostate tissue.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen, USA)
β-Glucosetransferase (GT)-mediated 5hmC protection and TET1-mediated 5mC oxidation were performed using the 5hmC TAB-seq Kit (WiseGene, USA, cat no K001). Bisulphite treatment of TET1-oxidised DNA followed by the library preparation was performed using the TrueMethyl Whole-Genome kit from Cambridge Epigenetix according to the manufacturer’s instructions. Paired-end 150bp sequencing was performed for each library on the Illumina HiSeqX platform using the HiSeq X™ Ten Reagent Kit v2.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: TAB-seq
Sequencing reads from TAB-seq data were aligned to the human genome using version 1.0 of an internally developed pipeline, publicly available for download from https://github.com/luuloi/WGBSX10.
Adaptor sequences and poor-quality bases were removed using cutadapt (https://github.com/marcelm/cutadapt) in paired-end mode with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bw
|
| |
|
| Submission date |
Oct 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ksenia Skvortsova |
| E-mail(s) |
k.skvortsova@garvan.org.au
|
| Phone |
478135210
|
| Organization name |
Garvan Institute
|
| Department |
Genomics and Epigenetics
|
| Lab |
Developmental Epigenomics
|
| Street address |
384 Victoria St, Darlinghurst
|
| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE104780 |
DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [TAB-Seq] |
| GSE104791 |
DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 mono-methylation patterns. |
|
| Relations |
| BioSample |
SAMN07768245 |
| SRA |
SRX3267826 |
