Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EGAS00001000088-sc-20120222 - samples

ABSTRACT: Familial Thrombocytosis germline exome sequencing

PROVIDER: EGAD00001000128 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

A founder heterozygous MBD4 mutation prevalent among Israeli Christian Arabs predisposes to somatic mutagenesis

Project description:whole exome sequencing analysis of donors with heterozygous and homozygous germline mutation

2025-02-21 | E-MTAB-14787 | 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

PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age related clonal hematopoiesis and myeloid neoplasia

Project description:Whole exome sequencing of 5 MDS/MPN patients to identify the target of chromosome 22 acquired uniparental disomy (22aUPD). For samples E4051 and E6523, peripheral blood leucocytes (tumour) and cultured T-cells (germline) were prepared for exome sequencing using the Agilent SureSelect kit (Agilent Technologies, Palo Alto, CA, USA) (Human All Exon 50 Mb) and then sequenced on an Illumina HiSeq 2000 (Illumina, Great Abington, UK) at the Wellcome Trust Centre for Human Genetics, Oxford, UK. For samples ULSAM1182, ULSAM1242 and ULSAM1356, peripheral blood leukocyte DNA only were exome sequenced by SciLifeLab (Stockholm, Sweden).

2019-01-22 | E-MTAB-7491 | biostudies-arrayexpress

Exome sequencing in classic Hairy cell leukaemia reveals widespread variation in acquired somatic mutations between individual tumours apart from the signature BRAF V(600)E lesion

Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.

2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress

Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 2

Project description:This dataset contains serum miRNA expression of 94 healthy women, among which 56 harbored germline BRCA1 or BRCA2 mutations. MicroRNA abundance was quantified with sequencing and qPCR, the latter being the subject of separate GEO submission. Data was analyzed with the aim of assessing concordance between two miRNA assays and the possibility of translating miRNA biomarkers from sequencing to qPCR panel. Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

2025-12-16 | GSE299787 | GEO

Targeted MIP sequencing for healthy samples

Project description:We developed Del-Read, an algorithm targeting medium-sized deletions (6-100 BPs) in short-reads, which are challenging for current variant callers relying on alignment. Our focus was on Micro-Homology mediated End Joining deletions (MMEJ-dels), prevalent in myeloid malignancies. MMEJ-dels follow a distinct pattern, occurring between two homologies, allowing us to generate a comprehensive list of MMEJ-dels in the exome. Using Del-Read, we identified numerous novel germline and somatic MMEJ-dels in Beat AML and TCGA-breast datasets. Validation in 500 healthy individuals confirmed their presence.

2023-09-20 | E-MTAB-13306 | 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

Project description:Egyptian familial germline mutations

| PRJNA885763 | ENA

Comparative Analysis of microRNA Expression in Serum and Plasma in Patients Screened for BRCA1 or BRCA2 Mutations - dataset 3 part 1

Project description:This dataset consists of miRNA expression in plasma of 78 women with germline BRCA1/2 mutations and expression in serum of 11 of them. Serum samples of remaining 67 women have been already submitted to GEO in GSE226445 dataset and to SRA as Bioproject PRJNA898621, while counts generated in re-mapping for this project are deposited as GSE299846 data set. MicroRNA abundance was quantified with sequencing in both biological materials. Data was analyzed with the aim of assessing the impact of blood processing steps on quantified miRNA abundance. Generation of this dataset was supported by The Gray Foundation grant “Circulating microRNAs for assessment of risk beyond the BRCA genes and early detection of breast cancer in high-risk families” awarded to Dipanjan Chowdhury and Polish National Research Center grant OPUS “Predictive Potential of Circulating MicroRNA Biomarkers in Patients with High Familial or Genetic Risk of Cancer” (2023/49/B/NZ5/03835) awarded to Wojciech Fendler.

2025-12-16 | GSE300882 | GEO

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

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