22980 results for "ega"

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• Sequencing data for rare tumors and sarcomas

  This dataset contains DNA and RNA sequencing information for AML, Gliomas, brain tumors (medulloblastoma and ependymoma), DIPG, rhabdoid tumors and soft tissue sarcomas. In total 39 samples are present (14 matched normal, 25 tumor samples). Not all samples have matched normals and not all samples have RNA sequencing data..

  Dataset EGAD00001008974

• Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4

  Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.

  Dataset EGAD00001000850

• Mitochondrial DNA sequencing of human iPSC, parental cells, and iPSC derived cardiomyocytes

  Dataset contains whole mitochondrial DNA sequencing data in fastq format (Illumina MiSeq paired-end) of 62 samples, in total. Those samples include sequencing data of the endothelial cell populations of 10 different donors and of 26 early-passage iPSC clones derived thereof. Moreover, the dataset contains the data of 7 of those iPSC clones sequenced additionally in passage 30 and 50, each. Lastly, 4 iPSC clones were sequenced during directed cardiomyocyte differentiation, each at day 0, 5, and 15 of differentiation.

  Dataset EGAD00001008021

• Amplicon-based sequencing of drug resistant organoids

  A BRAF V600E colorectal organoid which is sensitive to MAP kinase inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a combination of Trametinib, Dabrafenib and Cetuximab. Single cell derived organoids were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors from a screen in 2 2D BRAF V600E colorectal cell lines. Pools of resistant clones were also sequenced.

  Dataset EGAD00001003248

• CPC-GENE primary prostate benign and tumour tissue Hi-C sequencing reads

  This dataset contains the raw sequencing data, in FASTQ format, for Hi-C assays from 17 primary prostate tissue samples. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine, and contains 5 benign tissue samples and 12 primary tumour samples from the Canadian Prostate Cancer Genome Network (CPC-GENE) project. Tumour samples have IDs starting with the "CPCG" prefix, and benign tissue samples have IDs starting with the "BP" suffix.

  Dataset EGAD00001008024

• Patient-derived gene and protein expression signatures of NGLY1 deficiency

  Single-end bulk RNA sequencing results of cell lines derived from patients described with NGLY1 deficiency as well as parent and CRISPR edited controls. The cell lines represent 4 different cell types: fibroblasts, lymphoblastoid cells, induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs.).

  Dataset EGAD00001008094

• ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K4me1) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001232

• BLUEPRINT release August 2015, RNA-Seq for regulatory T cell, on genome GRCh38

  RNA-Seq data for 1 regulatory T cell sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001546

• BLUEPRINT release January 2015, RNA-Seq for CD8-positive, alpha-beta T cell

  RNA-Seq data for 2 CD8-positive, alpha-beta T cell sample(s). 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001137

• DNA methylation (RRBS) data for the validation the glioblastoma progression study (GBMatch).

  Genome-wide profiling of DNA methylation levels by RRBS in 150 glioblastoma tumor samples. Patients were selected to represent the general population of glioblastoma patients based on Austrian Brain Tumor Registry. These DNA methylation profiles were created for the validation of the glioblastoma progression study (GBMatch) and consist of 106 profiles from FFPE samples and 44 profiles from fresh-frozen samples. For the 44 fresh-frozen samples also WGS data (43 genomes) and RNA-seq data (37 transcriptomes) have been produced for validation purposes.

  Dataset EGAD00001004074

• A95618A

  Whole genome sequencing for single cells for library A95618A 876 samples; filetype=bam

  Dataset EGAD00001008220

• Gene expression in CSF and whole blood of adults with proven bacterial meningitis in Malawi

  Dataset of BAM files from patients with proven bacterial meningitis in Malawi. Samples consist of BAM files from PolyA RNA seq runs from patients classifed as admission whole blood or CSF on admission (pre-antibiotics) in the Emergency Department. Subsequent BAM files are identical runs from whole blood from the same patients, taken at either day 10 or day 40 post admission to hospital. All patients have disease, they are divided into survivors and non-survivors at the day 40 time point.

  Dataset EGAD00001004488

• BLUEPRINT release January 2015, ChIP-Seq for CD14-positive, CD16-negative classical monocyte

  ChIP-Seq data for 10 CD14-positive, CD16-negative classical monocyte sample(s). 73 run(s), 69 experiment(s), 69 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001179

• WCDT Hi-C assays performed mCRPC biopsies

  Paired FASTQ files from a Hi-C assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument.

  Dataset EGAD00001009408

• RNAseq from PDAC samples

  BAM files from RNA-seq of PDAC samples used in the COMPASS hENT1 study

  Dataset EGAD00001009409

• microRNA-seq of human serum from a longitudinal study of 66 women with no history of cancer

  This dataset includes microRNA sequencing data from 198 human serum samples, representing a subset of 66 women with no history of cancer who participated in the UKCTOCS study and with serum samples collected at three timepoints over a period of up to 5 years. Small RNA libraries prepared from the serum samples were sequenced with 50-bp single end reads on an Illumina HiSeq 2000 instrument. Data is provided as FASTQ files.

  Dataset EGAD00001004348

• Mutational Signatures of relapse in rectal cancer FFPE samples in the CR07 clinical trial

  The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse.

  Dataset EGAD00001000875

• ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (H3K9me3) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001234

• December 2016 data update (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  December 2016 data update (bam/fastq for WGBS on samples CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001003122

• June 2016 data update for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  June 2016 data update (bam/fastq for CEMT0062, CEMT0068, CEMT0072, CEMT0086, CEMT0087 ChIP-Seq and RNA-Seq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001002239

• BLUEPRINT release August 2016, ChIP-Seq for endothelial cell of umbilical vein (proliferating), on genome GRCh38

  ChIP-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002424

• BLUEPRINT release January 2015, ChIP-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  ChIP-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001182

• Validation of SNVs found by Exome-seq in S2-SF1, -SF5 and -SF9 hiPSCs

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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/

  Dataset EGAD00001000631

• Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4

  Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.

  Dataset EGAD00001000794

• Analysis of tumor periphery and center-specific mutations in renal cell carcinoma

  Renal cell carcinoma (RCC) is a genomically heterogeneous tumor. In the present project, the question whether intratumoral heterogeneity follows a zonal pattern indicating spatial niches was addressed. Whole exome sequencing of 16 paired samples from tumor periphery and center revealed a number of region-specific functional SNVs and Indels. Therefore, RCCs are not composed of evenly admixed tumor cells but show topological differences in their clonal composition.

  Dataset EGAD00001002067