Glioma Genomics Committee

Contact Information

Joseph Costello
jcostello@cc.ucsf.edu

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This DAC controls 31 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000714	None		102
EGAD00001000777	Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.		16
EGAD00001001305	Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor		9
EGAD00001001359	Dataset contains Exome-seq and RNA-seq from 2 GBM patients, as well as RNA-seq from the derived cultured cells (GNS).		6
EGAD00001001613	None		10
EGAD00001001614	None		26
EGAD00001001615	None		10
EGAD00001001616	None		2
EGAD00001003763	15 whole exome sequencing datasets from five patients. Data is provided as bam files. Libraries were generated using the SeqCap EZ Exome v3.0 kit and sequenced on an Illumina sequencer		15
EGAD00001003764	Four RNA-sequencing datasets from two patients with initial low-grade glioma and copy number alteration at IDH1 upon recurrence. Data is provided as bam files.		4
EGAD00001003795	This dataset includes Nimblegen SeqCap EZ Exome v3 data for each lesion of three patients with multicentric glioma. For two patients, each lesion was sequenced along with whole blood. For a third patient, 3 pieces from the right lesion and 4 pieces from the left were sequenced along with whole blood. In each case BAM files that have been aligned with BWA mem alignment are available.		15
EGAD00001005221	Dataset contains Exome sequencing data (aligned and base quality score recalibrated BAM files) for 236 tumor samples + matched normal from blood, collected from 21 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.		236
EGAD00001005222	Dataset includes 160 double-stranded RNAseq libraries collected from 16 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.		160
EGAD00001005386	113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.		-
EGAD00001005387	44 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina RNAseq paired-end technology. Dataset contains 44 BAM files aligned to hg19 using Tophat 2.		-
EGAD00001005435	This dataset contains 9 RNA-seq BAM files. RNA was derived from TERT promoter mutant GBM cell lines and sequenced on an Illumina HiSeq4000 sequencer with paired-end reads and an average read length of 50 base pairs. Reads were aligned with TopHat (v2.0.14) using a GENCODE V19 transcriptome-guided alignment.		9
EGAD00001006340	Dataset contains paired-end Whole Exome sequencing data from 2 glioma patients (1 oligodendroglioma and 1 astrocytoma) , derived cultured cells, and derived murine xenografts.		28
EGAD00001008768	Dataset contains paired-end Whole Exome sequencing data from 5 tumor samples and 1 single normal blood sample from a single primary GBM patient.		6
EGAD00001009286	Dataset contains paired-end clinical cancer panel sequencing (UCSF500) data from 2 samples of an initial tumor and one sample of a recurrence from one GBM patient and one sample from a second GBM patient.		4
EGAD00001009496	Dataset contains paired-end Whole Exome sequencing data from 257 glioma samples from 28 patients. 26 normal blood samples are also included.		283
EGAD00001009497	Dataset contains paired-end RNA-seq sequencing data from 221 glioma samples.		221
EGAD00001010289	Dataset contains 50 paired-end Whole Exome sequencing samples from 3 patients. 3 normal blood samples are also included.		50
EGAD00001010290	Dataset contains 46 paired-end RNA-seq samples from 3 patients.		46
EGAD00001010311	Dataset contains 70 paired-end ATAC-seq samples from 8 patients.		70
EGAD00001010312	Dataset contains 21 paired-end Hi-C samples from 9 patients.		21
EGAD00001010313	Dataset contains 11 paired-end snATAC-seq samples from 4 patients.		11
EGAD00001011989	Dataset contains one paired-end Whole Exome sequencing sample. One normal blood sample is also included.		2
EGAD00001011990	Dataset contains one paired-end RNA-seq sample.		1
EGAD00010000827	Illumina Infinium 450K array data		1
EGAD00010000829	Illumina Infinium 450K array data		70
EGAD00010001408	Illumina Infinium 450K array data	Illumina 450K	34