|
| Status |
Public on May 03, 2017 |
| Title |
Methyl-RB-X1 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: retinoblastoma xenograft
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from retinal tissues using the DNeasy Blood & Tissue Kit (QIAGEN #69504) according to the manufacturer's protocol.
Typically, 2 µg of genomic DNA is used to make WGBS libraries.Whole genome bisulfite sequencing was conducted by the Hudson Alpha research institute for Biotechnology using the Cambridge Epigenetix TrumethylSeq kit (BS workflow) per manufacturer's instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Whole genome bisulfite sequencing (WGBS) data were mapped to hg19(GRCh37) by BSMAP2.74 with the following parameters: -z 33 -f 5 -g 3 -r 0 -m 17 -x 600 –u.
raw methylation status was called by Bis-SNP (Version 0.82.2).
Based on bis-SNP results, beta-value of non-abolished and non-established CG have been extracted and converted to bigwig for visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Sep 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE87061 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [WGBS_Hs] |
| GSE87064 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis |
|
| Relations |
| BioSample |
SAMN05787361 |
| SRA |
SRX2174427 |
