Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EGAS00001000089-sc-20120216 - samples

ABSTRACT: Myelodysplastic Syndrome Exome Sequencing

PROVIDER: EGAD00001000117 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts.

Papaemmanuil E E Cazzola M M Boultwood J J Malcovati L L Vyas P P Bowen D D Pellagatti A A Wainscoat J S JS Hellstrom-Lindberg E E Gambacorti-Passerini C C Godfrey A L AL Rapado I I Cvejic A A Rance R R McGee C C Ellis P P Mudie L J LJ Stephens P J PJ McLaren S S Massie C E CE Tarpey P S PS Varela I I Nik-Zainal S S Davies H R HR Shlien A A Jones D D Raine K K Hinton J J Butler A P AP Teague J W JW Baxter E J EJ Score J J Galli A A Della Porta M G MG Travaglino E E Groves M M Tauro S S Munshi N C NC Anderson K C KC El-Naggar A A Fischer A A Mustonen V V Warren A J AJ Cross N C P NC Green A R AR Futreal P A PA Stratton M R MR Campbell P J PJ

The New England journal of medicine 20110926 15

<h4>Background</h4>Myelodysplastic syndromes are a diverse and common group of chronic hematologic cancers. The identification of new genetic lesions could facilitate new diagnostic and therapeutic strategies.<h4>Methods</h4>We used massively parallel sequencing technology to identify somatically acquired point mutations across all protein-coding exons in the genome in 9 patients with low-grade myelodysplasia. Targeted resequencing of the gene encoding RNA splicing factor 3B, subunit 1 (SF3B1), ...[more]

PMID: 21995386

Similar Datasets

Affymetrix SNP array data for myelodysplastic syndromes (MDS) samples

Project description:The progressive mechanism of myelodysplastic syndrome (MDS) remains unknown. We report that ROBO1 and ROBO2 are identified as novel progression-related somatic mutations using whole-exome and targeted sequencing in six of 16 (37.5%) paired MDS patients undergoing disease progression. To investigated the effect of ROBO1 or ROBO2 on ROBO1/2 CN number and LOH, we employed a Cytosan 750K chip to analyze the copy-number variations (CNVs) and loss of heterogeneity (LOH) in MDS patients with ROBO1&2 mutations.

2015-09-15 | GSE73005 | GEO

Affymetrix SNP array data for myelodysplastic syndromes (MDS) samples

2015-09-15 | E-GEOD-73005 | biostudies-arrayexpress

Whole exome sequencing of human MDS/AML OCI-M2 and patient-derived bone marrow cell lines treated with 5-azacytidine

Project description:The whole exome sequencing experiment is part of the study: “Analysis of 5-azacytidine resistance models reveals a set of targetable pathways”. In the study we generated myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) OCI-M2 cell lines as well as patient-derived bone marrow cell lines that are resistant to hypomethylating therapy by 5-azacytidine (AZA). By integrated analysis of expression and mutation data obtained from these samples we have identified multiple signaling pathways whose modulation by specific small molecule inhibitors significantly block proliferation of AZA-resistant cell lines without increasing their sensitivity to AZA. The understanding of the molecular mechanisms which characterize the AZA-R phenotype can be used for broadening therapeutic options at progressing states during AZA therapy.

2022-05-02 | E-MTAB-11172 | biostudies-arrayexpress

Whole exome sequencing of Cervical Squamous samples

Project description:The raw data consist of whole exome sequencing data of cervical squamous samples

2022-02-11 | E-MTAB-11407 | biostudies-arrayexpress

EGAS00001000163-sc-20120216 - samples

Project description:Osteosarcoma Exome Sequencing

| EGAD00001000118 | EGA

EGAS00001000188-sc-20120216 - samples

Project description:Chordoma Exome Sequencing

| EGAD00001000119 | EGA

b5b87427-9848-4ac7-85ac-3cc649258dc1 - samples

Project description:This dataset consists of 6 BAM files. These are whole exome sequencing data of pediatric patients with myelodysplastic syndrome.

| EGAD00001005272 | EGA

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

Nascent transcript sequencing visualizes mouse preimplantation embryonic genome activation

Project description:Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development.

2026-01-01 | GSE297541 | GEO

Candidate driver genes in SÑzary syndrome

Project description:Illumina human Omni5Exome arrays were used to investigate CNVs in SÑzary syndrome tumours as part of a larger study involving whole exome sequencing of the same samples and targeted resequencing of a further cohort. 16 Samples underwent SNP array including 10 tumour/gDNA matched samples that also underwent whole exome sequencing, public databases were used as further control data for calling CNVs.

2016-07-22 | E-GEOD-80650 | 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