|
| Status |
Public on Jun 20, 2018 |
| Title |
RRBS Glioblastoma patient pat_220 Surg.1 FFPE [pat_220_N567_09C] |
| Sample type |
SRA |
| |
|
| Source name |
brain (tumor)
|
| Organism |
Homo sapiens |
| Characteristics |
idh status: wildtype
center: MedUni Vienna
sample group: Glioblastoma patient
surgery number: 1
multisector: No
sample type: FFPE
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from FFPE tissues using the QIAamp DNA FFPE Tissue Kit following manufacturer’s instructions
RRBS was performed using 100 ng of genomic DNA for most samples, while occasionally going down to 2 ng (if not more DNA was available) and up to 200 ng. To assess bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added in a concentration of 0.1%. DNA was digested using the restriction enzymes MspI and Taq1 in combination (as opposed to MspI only in the original protocol) in order to increase genome-wide coverage. Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. The amount of effective library was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion followed by library enrichment by PCR. Enrichment cycles were determined using qPCR and ranged from 12 to 21 (median: 16). Adequate fragment size distributions were confirmed on Bioanalyzer High Sensitivity DNA chips (Agilent).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
pat_220_N567_09C
|
| Data processing |
Adapter sequences were trimmed, and 60 basepair reads were cropped to 50 basepairs using Trimmomatic with the following settings: ILLUMINACLIP:RRBS_adapters.fa:2:40:7 SLIDINGWINDOW:4:15. MAXINFO:20:0.50 CROP:50 MINLEN:18.
Trimmed reads were then aligned to the human genome build hg38 using BSMAP in RRBS mode.
DNA methylation calling was performed with a custom python script (biseqMethCalling.py).
Genome_build: hg38
Supplementary_files_format_and_content: Bed files containing CpG DNA methylation levels
|
| |
|
| Submission date |
Mar 29, 2018 |
| Last update date |
Jun 20, 2018 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE100351 |
The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space |
|
| Relations |
| BioSample |
SAMN08818782 |
