Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chordoma Sequencing Project RNAseq

ABSTRACT: This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-ERAD-128 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Triple Negative Breast Cancer RNA Sequencing

Project description:We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

2015-04-16 | E-ERAD-113 | biostudies-arrayexpress

Breast Cancer FRT RNA seq

Project description:We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

2013-01-30 | E-ERAD-145 | biostudies-arrayexpress

Genome-wide transcriptome analysis of explant regeneration in be1-3

Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.

2014-02-12 | E-MTAB-4394 | biostudies-arrayexpress

Pseudogene RNAseq

Project description:RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development

2016-05-17 | E-ERAD-223 | biostudies-arrayexpress

Transcriptome Sequencing of Cancer Cell Lines

Project description:In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

2016-05-18 | E-ERAD-64 | biostudies-arrayexpress

Matched Pair Cell Line Tumour RNAseq

Project description:In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

2013-07-11 | E-ERAD-157 | biostudies-arrayexpress

RNAseq of patients with Ewings sarcoma

Project description:Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewings sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings sarcoma tumours.

2016-05-18 | E-ERAD-65 | biostudies-arrayexpress

CGP CORE CELL LINES RNA seq

Project description:Cancer cell lines can provide robust and facile biological models for the generation and testing of hypothesis in the early stages of drug development and caner biology. Although clinical trials remain the ultimate scientific testing ground for anticancer therapies, the use of appropriate model systems to explore the molecular basis of drug activity and to identify predictive biomarkers during their development can have a profound effect on the design, cost and ultimate success of new cancer drug development. In order to capture the high degree of genomic diversity in cancer and to identify rare molecular subtypes, we have assembled a collection of >1000 cancer cell lines. These lines have been characterised using whole exome sequencing, genome wide analysis of copy number, mRNA gene expression profiling and DNA methylation analysis (http://cancer.sanger.ac.uk/cell_lines). To further characterise this panel of cell lines we have now compiled data for RNA sequencing. The current study represent data for ~450 of the cell lines in the panel, data for the remaining lines can be accessed via the CGHUB data browser hosted at UCSC. <br>This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of the EGA data set is EGAD00001001357 under EGA study accession EGAS00001000828.

2017-09-25 | E-MTAB-3983 | biostudies-arrayexpress

Olfactory transcriptomics in a mouse model of Alzheimer s disease

Project description:High-throughput sequencing of RNA from olfactory epithelium of mice modeling Alzheimer's disease with olfactory deficits. We sequenced cDNA libararies from the main olfactory epithelium (MOE) of nine mice from 3 strains (C57BL/6, T43 with P201S mutation, 129S5): 3 groups consists of 9 mice. RNA was extracted using a Qiagen RNAeasy kit and standard methods. All nine RNA samples were multiplexed together and sequenced in three lanes on the Illumina HiSeq platform. 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/ or email dl5@sanger.ac.uk

2012-07-02 | E-ERAD-160 | biostudies-arrayexpress

Transcriptomic study of haemopoietic progenitors in mouse models of AML

Project description:This is a RNA-Seq study from paired mutant-wild type mouse haemopoietic cells (n=4 mutant strains with 6 mice per strain - 3 mutant & 3 wild type). We want to see the transcriptomic effects of these mutation on blood progenitors.

2013-12-16 | E-ERAD-197 | biostudies-arrayexpress

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