Search Results - EGA European Genome-Phenome Archive

Un-mapped RNA-Seq data

Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.

Dataset EGAD00001001940

Vcf RNA-Seq data

Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.

Dataset EGAD00001001941

Genomic Analysis of Focal Nodular Hyperplasia with Associated Hepatocellular Carcinoma Unveils its Malignant Potential

Whole exome sequencing of FNH and two HCC compartments from a single patient, along with matched germline.

Dataset EGAD00001007702

mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

mRNA capture sequencing data (FASTQ files) of 28 FFPE sarcoma tumors

Dataset EGAD00001007696

Genomic analysis for intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinomas (iCCs) are characterized by their rarity, difficulty in diagnosis, and overall poor prognosis. We performed comprehensive genomic characterization of treatment-naive iCC. This study reports a large-scale genomic analysis of iCC. The findings could assist in patient stratification with iCCs and in developing rational therapeutic strategies.

Dataset EGAD00001008557

Glioblastoma stem cell lines RNA-seq (Guilhamon et al.)

RNA was extracted from GSCs using the Qiagen RNeasy Plus kit. RNA sample quality was measured by Qubit (Life Technologies) for concentration and by Agilent Bioanalyzer for RNA integrity. All samples had RIN above 9. Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina). Two hundred nanograms from each sample were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads, then fragmented post-purification. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” base was added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries. Final cDNA libraries were verified by the Agilent Bioanalyzer for size and concentration quantified by qPCR. All libraries were pooled to a final concentration of 1.8nM, clustered and sequenced on the Illumina NextSeq500 as a pair-end 75 cycle sequencing run using v2 reagents to achieve a minimum of ~40 million reads per sample.

Dataset EGAD00001006813

Acquired RAD51C promoter methylation loss causes PARP inhibitor resistance in high grade serous ovarian carcinoma

Analysis of RAD51C promoter methylation using targeted bisulfite sequencing (amplicon sequencing) in ovarian cancer pre-clinical models and patient samples.

Dataset EGAD00001007799

Neuroblastoma WGS samples used for detection of seismic amplification

Paired-end WGS data of 27 neuroblastoma patient samples (10 obtained at diagnosis, 6 at relapse and 11 matched blood samples as controls) used for detection of complex "seismic" amplification. Mean coverage is 24-55x per sample. The remaining patient samples of the dataset can be found under accession number EGAS00001001308.

Dataset EGAD00001007807

Genome and transcriptome sequence data from a recurrent glioma patient

Genome and transcriptome sequence data from a recurrent glioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001002043

Single Cell Genome Sequence for DLP+ library A95634A

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1091A passage 1 on DLP+ library A95634A

Dataset EGAD00001009323

SOX11+ and SOX11- mantle cell lymphoma cell lines RNAseq data

Fastq transcriptomic sequencing files from Z138 SOX11+ and JVM2 SOX11- mantle cell lymphoma (MCL) cell lines upon SOX11 knock out (KO) and ectopic overexpression, respectively. Dataset includes 3 samples of Z138-SOX11KO, 3 of Z138 control, 3 of JVM2 control and 3 of JVM2-SOX11 MCL cell lines.

Dataset EGAD00001009421

Mantle cell lymphoma primary cases RNAseq data

Dataset includes fastq transcriptomic sequencing files from 8 conventional (SOX11+) and 4 non-nodal (SOX11-) mantle cell lymphoma (MCL) primary cases. RNA-sequencing has performed from peripheral blood and lymph node diagnostic samples.

Dataset EGAD00001009422

Genome and transcriptome sequence data from a uveal melanoma patient

Genome and transcriptome sequence data from a uveal melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001010956

Melanoma microRNA profiling

This dataset includes microRNA profiling of 61 early-passage metastatic melanoma cell lines. The data are provided as single-end small RNA seq fastq files.

Dataset EGAD00001006269

Comprehensive RNA repository of tissue and plasma from patients with esophageal cancer or precursor lesions

A comprehensive RNA repository (both coding and non-coding) from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were collected. This dataset includes both mRNA and small RNA sequencing data (fastq.gz files) of all tissue and plasma samples. In total,102 RNA-seq libraries from 51 samples (17 plasma and 34 tissue samples) were sequenced (plasma mRNA libraries were sequenced twice).

Dataset EGAD00001006857

Deep targeted DNA sequencing dataset for the study "Molecular characteristics in Burkitt lymphoma over age groups"

We performed deep targeted DNA sequencing with a panel of 134 selected cancer-related genes previously identified to be recurrently mutated in BL/B-AL. A Nextera rapid capture custom kit was designed using the Illumina DesignStudio. For every gene, all regions in which previous mutations had been described were covered. For 40 of these genes, the entire coding sequence was covered. Targeted deep sequencing was performed on a MiSeq-Sequencer using MiSeq Reagent Kit v2 (300 cycle) with 24 samples per run. There are 396 samples in this targetedDNAseq-dataset with 298 tumors (288 patients and 10 cell lines) and 98 normals. There are 132 female, 262 male, and 2 unknown gender samples in this dataset.

Dataset EGAD00001007708

RNA-seq analysis of transcriptome variation with human ESC subclones

Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

Dataset EGAD00001004266

Cohort of NGS lymphoma samples used as control

Control cohort of lymphoma samples sequenced with a hybrid capture panel designed to be able to detect translocations and mutations in lymphoma samples. used in the paper "Robust detection of translocations in lymphoma FFPE samples using Targeted Locus Capture-based sequencing"

Dataset EGAD00001007711

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