Genomics

Dataset Information

0

WGSeq_RNAseq_ChIPseq_Cancer_ICGC_DATA_SET_xmas_MB_2013_07_10 - samples

ABSTRACT: 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: 20x MB59 macroH2A1: 11x H3K36me3: 11x

PROVIDER: EGAD00001000664 | EGA |

REPOSITORIES: EGA

Json Xml
altmetric image

Publications

Hypermutation of the inactive X chromosome is a frequent event in cancer.

Jäger Natalie N   Schlesner Matthias M   Jones David T W DT   Raffel Simon S   Mallm Jan-Philipp JP   Junge Kristin M KM   Weichenhan Dieter D   Bauer Tobias T   Ishaque Naveed N   Kool Marcel M   Northcott Paul A PA   Korshunov Andrey A   Drews Ruben M RM   Koster Jan J   Versteeg Rogier R   Richter Julia J   Hummel Michael M   Mack Stephen C SC   Taylor Michael D MD   Witt Hendrik H   Swartman Benedict B   Schulte-Bockholt Dietrich D   Sultan Marc M   Yaspo Marie-Laure ML   Lehrach Hans H   Hutter Barbara B   Brors Benedikt B   Wolf Stephan S   Plass Christoph C   Siebert Reiner R   Trumpp Andreas A   Rippe Karsten K   Lehmann Irina I   Lichter Peter P   Pfister Stefan M SM   Eils Roland R  

Cell 20131017 3

Mutation is a fundamental process in tumorigenesis. However, the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. Here, we performed a cross-cancer comparison of 402 whole genomes comprising a diverse set of childhood and adult tumors, including both solid and hematopoietic malignancies. Surprisingly, we found that the inactive X chromosome of many female cancer genomes accumulates on av  ...[more]

Similar Datasets

Genomics,Multiomics 2013-11-19-17-24-36-breez-MB-2013-10-18-Targeted_DNAseq_Medulloblastoma_ICGC - samples
| EGAD00001000699 | EGA
Genomics,Multiomics 2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_genome_DNAseq_Medulloblastoma_ICGC - samples
| EGAD00001000697 | EGA
Transcriptomics RNA-seq analysis for resistance to PI3K inhibition in Glioblastoma (GBM)
2018-12-14 | GSE123821 | GEO
Genomics,Multiomics 2013-11-19-17-24-36-breez-MB-2013-10-18-Whole_exome_DNAseq_Medulloblastoma - samples
| EGAD00001000698 | EGA
Genomics WGSeq_PreMalignant_DATA_SET_xmas_MB_2013_07_10 - samples
| EGAD00001000665 | EGA
Transcriptomics Transcriptome sequencing of human hepatocellular carcinoma
2013-04-02 | E-GEOD-33294 | biostudies-arrayexpress
Genomics Low coverage whole genome sequencing of subsequent passages of soft tissue sarcoma patient-derived xenografts
2019-04-30 | E-MTAB-7826 | biostudies-arrayexpress
Transcriptomics Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes
2021-10-21 | GSE186112 | GEO
Transcriptomics Transcriptome sequencing of human hepatocellular carcinoma
2013-04-02 | GSE33294 | GEO
Transcriptomics Human benign adrenocortical tumors miRNome
2020-08-12 | E-MTAB-6553 | biostudies-arrayexpress