Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

19e54a3f-4c27-46cc-8104-103d118e8386 - samples

ABSTRACT: The dataset contains a full genomics characterization of 527 Asian breast tumours. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, shallow-whole genome sequencing at 0.1X for copy number analyses, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a HiSEQ4000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturerÃ¢Â€Â™s instructions and also subjected to paired end 75 sequencing on a HiSEQ4000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

PROVIDER: EGAD00001006399 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of canine transmissible venereal tumour biopsies

Project description:To assess expression of mtDNA genes in the canine transmissible venereal tumour (CTVT), biopsy tissue samples from 33 CTVT cases were subjected to total RNA extraction, and stranded RNA sequencing libraries generated with the Ribo-Zero ribosomal RNA removal kit (insert size 100–300 bp) were sequenced using 75-bp paired-end sequencing reads on an Illumina HiSeq4000 instrument. Gene transcript abundance was quantified using the Salmon software (v0.8.2).

2020-04-29 | E-MTAB-9037 | biostudies-arrayexpress

9d174533-4a29-4264-914e-15a9f36b8cd6 - samples

Project description:The dataset contains a genomics characterization of 35 triple-negative Asian breast tumours from the Malaysian Breast Cancer cohort. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a NovaSeq 6000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturerÃ¢Â€Â™s instructions and also subjected to paired end 75 sequencing on a NovaSeq 6000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

| EGAD00001009311 | EGA

Exomes of human leukemic JMML (Juvenile MyeloMonocytic Leukemia) cells and paired fibroblasts (germilne controls) when available

Project description:The study included 15 patients (7 males, 8 females) with JMML. Peripheral blood and/or bone marrow aspirates were collected on EDTA at diagnosis. Non-hematopoietic tissues (fibroblasts) was derived from skin biopsy for each patient. Exome sequencing was performed in several distinct series between 2012 and 2017, which explains the differences in capture kit versions and reference genome version.Targeted enrichment and massive parallel sequencing were performed on paired genomic DNA from leukocytes and fibroblasts. Exome capture was carried out using the SureSelect Human All Exon V4+UTRs or V5 or V5+UTRs or SureSelect Clinical Research (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instruction and protocols by IntegraGen (Evry, France). Paired-end 75 bases sequencing was performed on a HiSeq2000 or HiSeq4000 instrument (Illumina, San Diego, CA, USA). Image analysis and base calling were performed using the Real Time Analysis (RTA) pipeline v. 1.14 (Illumina) with default parameters. The alignment of paired-end reads to the reference human genome (UCSC GRCh37/hg19 or UCSC GRCh38), variant calling and generation of Quality variants scores were carried out using the CASAVA v.1.8 pipeline (Illumina).

2018-03-14 | E-MTAB-6461 | biostudies-arrayexpress

Heterogeneous immune and tumor clonal evolution patterns in liver cancer

Project description:Paired end whole exome sequencing for patient 10, matched normal and tumor

2020-02-01 | E-MTAB-8127 | biostudies-arrayexpress

Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma

Project description:Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%). Methods: mRNA and gDNA were exctracted from fresh frozen tumor tissues and corresponding normal tissue (n=8 pairs) from patients with iCCA who underwent surgical resection. RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end reads. One sample and its paired non-tumoral tissue were eliminated from the subsequent analysis because of bad RNa quality. The same 8 paired tumors were also analyzed by whole-exome seq. Submitter confirms there are no patient privacy concerns with these data. This dataset is part of the TransQST collection.

2015-01-22 | E-GEOD-63420 | biostudies-arrayexpress

Transcriptome of the liver in 15-day-old C3H/HeJ mice

Project description:Male C3H/HeOuJ mice are susceptible to spontaneous liver neoplasms. We collected liver samples from young, tumour-free mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced in an Illumna HiSeq4000 to produce 150bp paired-end reads.

2018-07-29 | E-MTAB-6972 | biostudies-arrayexpress

Project description:whole exome sequencing of differentiated thyroid cancer organoid and paired tissue

| PRJNA1036707 | ENA

Whole-transcriptome of the liver in 15-day-old C3H/HeOuJ and CAST/EiJ mice.

Project description:Male C3H/HeOuJ and CAST/EiJ mice were treated with diethylnitrosamine to induce liver tumours. We collected liver samples from untreated P15 mice for control experiments. Liver tissue samples were snap frozen in liquid nitrogen and total RNA was extracted using the AllPrep 96 DNA/RNA Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumna HiSeq4000 to produce 150bp paired-end reads.

2020-06-18 | E-MTAB-8518 | biostudies-arrayexpress

Exomes of human leukemic JMML (Juvenile MyeloMonocytic Leukemia) xenografts in NSG or NSG-S mice (samples enriched in hCD45)

Project description:The study includes 14 patients with confirmed JMML and known somatic mutations (from exome data of paired tumoral and germline DNA). Bone marrow or peripheral blood mononucleated cells were injected in immundeficient mice to recapitulate the leukemia. Whole exome sequencing was performed in xenograft samples to control the persistance of patients' known mutations and look for new mutations acquired in xenograft sample.

2018-03-15 | E-MTAB-6467 | biostudies-arrayexpress

Characterization of resistance to prexasertib in ovarian cancer cell line OVCAR5

Project description:We developed a CHK1 inhibitor Prexasertib resistant strain of ovarian cancer cell line OVCAR5 in lab. This was used to compare transcriptome profiles to study changes in expression profiles of genes that might be involved with resistance. Total RNA was isolated from three replicate cultures of OVCAR5R (IC50 viability >3 micromolar Prexasertib) and 3 replicate cultures of parental OVCAR5 (IC50 viability=7.5nM) and then subjected to Hiseq4000 illumina RNA-seq analysis, with paired end sequencing. Data file contains CPM-TMM values after zoom normalization.

2020-05-02 | GSE149724 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data