|
| Status |
Public on Oct 10, 2013 |
| Title |
SmoA1 [RRBS] |
| Sample type |
SRA |
| |
|
| Source name |
medulloblastoma
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: medulloblastoma
genotype: SmoA1 -/+
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from all sources was isolated using the DNeasy Blood and Tissue Kit (Qiagen).
EpiQuest libraries were prepared from 500 ng genomic DNA. The DNA was digested with 60 units of TaqI and 30 units of MspI (NEB) sequentially. Size-selected TaqI-MspI fragments (40–120bp and 120–350bp) were filled-in and 30-terminal-A extended, extracted with Zymo Research DNA Clean and Concentrator(tm) kit. Ligation to pre-annealed adaptors containing 50-methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor-ligated fragments were bisulphite treated using the EZ DNA Methylation-Direct(tm) Kit (Zymo Research). Preparative-scale PCR was performed and DNA Clean and Concentrator-purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 or 210–460bp in size were excised. Library material was recovered from the gel (Zymoclean(tm) Gel DNA Recovery Kit) and sequenced on an Illumina GAIIx genome analyzer.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RRBS
|
| Data processing |
Basecalls were performed using on-instrument real time analysis (RTA) as part of the Sequence Control Software (on Illumina IIGAx) or HiSeq Control Software(on Illumina HiSeq2000).
Alignment and Methylation calls: reads were mapped to human (hg18) and mouse (mm9) genomes using BSMAP (version 2.74), with the option -q 20 A AGATCGGAAGAGC to trim adaptor sequences and low quality base calls. The methylation calls were performed using python script methratio.py in the BSMAP package. CpG statistics: the number of cytosines covered, and the average coverage on covered cytosines for each sample were reported by BSMAP. The average CpG methylation ratios were computed from estimated methylation ratios, weighted by the corresponding coverage.
Genome_build: mm9
Supplementary_files_format_and_content: A file (.ratio) was generated for each sample as standard out from BSMAP (version 2.74).
|
| |
|
| Submission date |
Mar 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Scott J. Diede |
| E-mail(s) |
scott.diede@merck.com
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Street address |
1100 Fairview Avenue North, Mailstop c3-168
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE45341 |
Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer [RRBS] |
| GSE45342 |
Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer |
|
| Relations |
| SRA |
SRX252570 |
| BioSample |
SAMN01984868 |
