Whole Genome, RNA, and ChIP Sequencing of matched brain tumor-normal pairs (ICGC)
Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x
- 27/05/2015
- 7 samples
- DAC: EGAC00001000010
- HMB DUO:0000006 (version: 2021-02-23)health or medical or biomedical researchThis data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry.
- NPUNCU DUO:0000018 (version: 2021-02-23)not for profit, non commercial use onlyThis data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use.
- PS DUO:0000027 (version: 2021-02-23)project specific restrictionThis data use modifier indicates that use is limited to use within an approved project.
- GRU DUO:0000042 (version: 2021-02-23)general research useThis data use permission indicates that use is allowed for general research use for any research purpose.
ICGC Data Access
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF00000242514 | bam | 109.1 GB | ||
| EGAF00000242515 | bam | 49.4 GB | ||
| EGAF00000242516 | bam | 41.2 GB | ||
| EGAF00000242517 | bam | 6.3 GB | ||
| EGAF00000242518 | bam | 73.4 GB | ||
| EGAF00000242525 | bam | 79.9 GB | ||
| EGAF00000242526 | bam | 25.9 GB | ||
| EGAF00000242527 | bam | 27.7 GB | ||
| EGAF00000242528 | bam | 9.9 GB | ||
| EGAF00000242529 | bam | 76.4 GB | ||
| 10 Files (499.1 GB) | ||||