Search Results - EGA European Genome-Phenome Archive

Cell type-specific transcriptomics of esophageal adenocarcinoma

3' mRNA-Seq obtained from distinct isolated cell types (epithelia cells,immune cells, fibroblasts) of endoscopically obtained esophageal adenocarcinoma tissue as well as normal esophageal mucosa. Libraries for RNA-sequencing were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina according to the low input protocol. Libraries were sequenced on a HiSeq 4000 (Illumina) by 1x 50 bases.

Dataset EGAD00001005508

UCSF Pediatric Bithalamic Glioma Genome Project

Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

Dataset EGAD00001005499

20191008_EGA_MELA_Acral_WGS+RNASeq

Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 87 cases of melanoma Acral subtype. 63 cases also have RNASeq sequencing from the tumour sample.

Dataset EGAD00001005500

20191008_EGA_MELA_Immunology

Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma

Dataset EGAD00001005501

ICGC_Pedbrain_WGBS_Pilocytic_Astrocytoma

18 WGBS lanes for 9 samples of pilocytic astrocytoma.

Dataset EGAD00001005504

Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

Dataset EGAD00001005519

A Protein Neddylation Inhibitor MLN4924 Suppresses Patient-Derived Glioblastoma Cells via Inhibition of ERK and AKT Signaling

To identify what factors cause a different reactivity to MLN4924, 15 cells were categorized into high, intermediate, and low MLN4924 resistance groups based on the half-maximal inhibitory concentration (IC50) of MLN4924. PDC1, PCD2, PDC3, PDC4, and PDC5 showed high MLN4924 sensitivity, whereas PDC12, PDC13, PDC14, and PDC15 showed low MLN4924 sensitivity. Whole-transcriptome sequencing of these 9 patient-derived glioblastoma stem cells was performed.

Dataset EGAD00001005709

Uncovering tumor intrinsic and extrinsic factors that regulate hepatocellular carcinoma growth using patient derived xenograft assays

Exome Sequencing and RNA Sequencing Data for PDX Samples

Dataset EGAD00001005734

20191204_EGA_MELA_Rizos

79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy.

Dataset EGAD00001005738

Single-cell expression of Hodgkin lymphoma

Single-cell gene expression was profiled for 22 Hodgkin lymphoma tumors and 5 reactive lymph nodes (2 replicates were performed for RLN-1). Library preparation was performed with the 10x Chromium platform (3' version 2 assay). Sequencing was performed on an Illumina NextSeq. The BAM files were generated from the raw sequencing data using Cell Ranger (v2.1.0) mkfastq and count commands.

Dataset EGAD00001005739

KRAS Mutations in Multiple Myeloma

Fastq files for 80 Multiple Myeloma Patients and 12 cell-lines

Dataset EGAD00001005743

Whole genome sequencing generated from metastatic gliosarcoma patient samples

This dataset contains whole genome sequencing data aligned to the b37 reference genome for 4 spatially and temporally distinct tumors from one patient with a matched normal blood sample.

Dataset EGAD00001005745

Somatic mutation and clonal evolution in the human pancreas - WGS (2019-12-17)

In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma. This dataset contains all the data available for this study on 2019-12-17.

Dataset EGAD00001005751

Phased melanoma whole genomes

We have sequenced whole genomes of 10 melanoma samples (1 cell line; A375 and 9 patient derived short term cultures). Libraries were prepared with 10X linked reads technology in order to obtain phase information and subsequently sequenced on Illumina NovaSeq6000.

Dataset EGAD00001005773

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