23164 results for "ega"

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• Single cell multiomics sequencing and analyses of human colorectal cancer

  Whole genome sequencing data of tumor tissues, adjacent normal tissues, and peripheral blood from CRC patients.

  Dataset EGAD00001004495

• Exome reads

  One sample of human genomic DNA. DNA extracted from whole blood. Reads obtained using an exome enrichment kit (Truseq, Illumina) and sequencing of 100bp paired-end reads on a HiSeq 2500 sequencing system (Illumina).

  Dataset EGAD00001003841

• Homologous recombination deficient breast cancers

  Exome sequencing data from homologous recombination deficient primary breast cancers as assessed by the functional RAD51 based HR test. There are 12 tumour samples, of which 10 also have matching normal.

  Dataset EGAD00001003929

• H3Africa H3AChipDesign TrypanoGEN2

  41 samples from Zambia generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004220

• Infiltrative and drug-resistant slow-cycling cells support metabolic heterogeneity in glioblastoma

  Glioblastoma patient derived Fast/Slow cycling cancer stem cell RNA sequencing. Consists of 3 patient cell lines and 6 files

  Dataset EGAD00001004380

• H3Africa H3AChipDesign TrypanoGEN1

  26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004393

• RNA sequencing of undifferentiated sarcomas

  mRNA sequencing of 50 undifferentiated sarcoma tumour samples and 5 adjacent muscle tissue samples. BAM files are provided, with metadata specifying which samples are tumour/normal.

  Dataset EGAD00001004439

• APCDR AGV Project: Low depth (4x) Illumina HiSeq sequence data for a Zulu population(BAMs)

  Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Zulu from Durban area, South Africa.

  Dataset EGAD00001001007

• Whole exome sequencing for ZNF384-rearranged ALL cases

  Whole exome sequencing for the matched germline and tumor DNA from 10 ALL cases with ZNF384 rearrangements.

  Dataset EGAD00001002152

• WGS and RNA-Seq data from a GBM patient PT-GC1519

  WGS and RNA-Seq data from a GBM patient PT-GC1519

  Dataset EGAD00001004239

• WGS data for medulloblastoma samples (MDT-AP)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003125

• RNASeq on HiSeq platform of 95 pancreatic adenocarcinoma cases

  BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 95 pancreatic adenocarcinoma cases.

  Dataset EGAD00001003298

• RNAseq of LC2AD with AD80 or DMSO

  RNAseq of LC2AD with AD80 or DMSO Plenker et al., Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

  Dataset EGAD00001003316

• GenomeDenmark Phase 2 - HLA validation sequencing data

  Validation of HLA variation of 8 individuals from the GenomeDenmark Phase 2 study. Validation is performed Sanger sequencing of selected amplicons (5-10 amplicons per sample).

  Dataset EGAD00001003454

• Transcriptome - MBD4-deficient AML

  Transcriptome sequencing for WEHI-AML-1 and WEHI-AML-2. RNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit v2 and sequenced on an Illumina HiSeq2500.

  Dataset EGAD00001003569

• Southern African Human Genome Programme dataset

  The SAHGP characterises the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole genome sequencing (WGS).

  Dataset EGAD00001003791

• FFPE_normals_v2_gbm_wtsi_panel (2018-06-06)

  Targeted pulldown of approx 60 ffpe normal samples to use as normal controls . This dataset contains all the data available for this study on 2018-06-06.

  Dataset EGAD00001004152

• WGS and RNA-Seq data from a GBM patient PT-RD1291

  WGS and RNA-Seq data from a GBM patient PT-RD1291

  Dataset EGAD00001004256

• Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826

  Analysis .bam files from HiSeq sequencing of Australian ICGC PDAC study samples, submitted 20130826

  Dataset EGAD00001000660

• DATA FILES FOR SJPhLike-RNASeq

  DATA FILES FOR SJPhLike-RNASeq

  Dataset EGAD00001001016

• Multifocal Breast Project

  Comparison of genomic rearrangements and DNA methylation patterns between different foci of multiple synchronous (multifocal and multicentric) invasive breast cancers.

  Dataset EGAD00001001041

• ICGC PACA-CA Release 18

  Supporting data for ICGC PACA-CA Release 18

  Dataset EGAD00001001095

• G&T-seq: Parallel sequencing of single-cell genomes and transcriptomes

  Development of a method for separation and parallel sequencing of the genomes and transcriptomes of single cells.

  Dataset EGAD00001001332

• Breast RNA Sequencing

  We propose to definitively characterise the somatic genetics of 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.

  Dataset EGAD00001001340

• BASIS RNA Sequencing

  We propose to definitively characterise the somatic genetics of 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.

  Dataset EGAD00001001341

• BASIS WGBS

  Whole-genome bisulfite sequencing (WGBS) on 30 breast cancer cases from the BASIS project.

  Dataset EGAD00001001388

• Single Cell Targeted Sequence Capture

  This study is to ascertain whether it is feasible to extract single cell from a tumour, perform amplification, generate a library and sequence a targeted pulldown.

  Dataset EGAD00001001450

• EBV-AID project

  Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements.

  Dataset EGAD00001001458

• RNA sequencing data of child-mother pairs, maternal smoking.

  RNA sequencing data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years.

  Dataset EGAD00001002011

• Spatial and Temporal Homogeneity of Driver Mutations in Diffuse Intrinsic Pointine Glioma

  70 Whole exome sequencing from 9 patients with DIPG for project Spatial and Temporal Homogeneity of Driver Mutations in Diffuse Intrinsic Pointine Glioma

  Dataset EGAD00001002111

• HELIUS cohort gut microbiome batch2

  The gut microbiota composition is unique to every individual but is shaped by common factors including diet, lifestyle, medication use, early-life determinants, living environment or genetics. Most of these factors may be influenced by ethnicity. This study explored variations in fecal microbiota composition in 6048 individuals with different ethnic backgrounds living in the same geographical area (Amsterdam, the Netherlands). The HELIUS data are owned by the Amsterdam University Medical Centers, location AMC in Amsterdam, The Netherlands. To allow sharing of microbiome data collected in HELIUS with (inter)national researchers, 16s rRNA sequence analysis has been stored at the European genome-phenome archive (EGA; accession code EGAD00001004106). This requires that access needs to be granted, also because the HELIUS data are stored with relevant phenotypical variables. Access is granted to all researchers affiliated with an internationally recognized research institution who request to use the HELIUS data within the EGA context, after having signed the data transfer agreement. Any researcher can request the data by submitting a proposal to the HELIUS Executive Board as outlined at http://www.heliusstudy.nl/en/researchers/collaboration, by email: heliuscoordinator at amsterdamumc dot nl. The HELIUS Executive Board will check proposals if they do not conflict with ethical approvals and informed consent forms of the HELIUS study.

  Dataset EGAD00001009732

• HELIUS cohort gut microbiome

  The gut microbiota composition is unique to every individual but is shaped by common factors including diet, lifestyle, medication use, early-life determinants, living environment or genetics. Most of these factors may be influenced by ethnicity. This study explored variations in fecal microbiota composition in 6048 individuals with different ethnic backgrounds living in the same geographical area (Amsterdam, the Netherlands). The HELIUS data are owned by the Amsterdam University Medical Centers, location AMC in Amsterdam, The Netherlands. To allow sharing of microbiome data collected in HELIUS with (inter)national researchers, 16s rRNA sequence analysis has been stored at the European genome-phenome archive (EGA; accession code EGAD00001004106). This requires that access needs to be granted, also because the HELIUS data are stored with relevant phenotypical variables. Access is granted to all researchers affiliated with an internationally recognized research institution who request to use the HELIUS data within the EGA context, after having signed the data transfer agreement. Any researcher can request the data by submitting a proposal to the HELIUS Executive Board as outlined at http://www.heliusstudy.nl/en/researchers/collaboration, by email: heliuscoordinator at amsterdamumc dot nl. The HELIUS Executive Board will check proposals if they do not conflict with ethical approvals and informed consent forms of the HELIUS study.

  Dataset EGAD00001004106

• Team

  The Team Mallory Freeberg Roderic Guigó Arcadi Navarro Helen Parkinson Jordi Rambla Ana T. Alonso Silvia Bahena Àlex Bedmar Kenneth Buckley Aldar Cabrelles Ángel Carreño Marcos Casado Giulia Cellerino Amy Curwin Teresa D'Altri Abeer Fadda Teresa Garcia Sara Gregorio Max Fischer Bela Juhasz Oriol Lopez-Doriga Mireia Marin Óscar Martínez Andrea Mero Akiris Moctezuma Aurora Moreno Liina Nagirnaja Francesc de Puig Santiago Rensonnet Gabriele Rinck Aravind Sankar Andres Silva Coline Thomas Sabela de la Torre Gemma Vicente The EGA Team at the CRG co-manages the European Genome and phenome Archive together with the EGA Team at the European Bioinformatics Institute. In addition to maintaining and distributing data, we enrich the contents of the EGA contributing with our knowledge about genomics and the relationship between genomes and phenomes. Previous Team Members Alexander Vikhorev Jeff Almeida-King Mario Alberich Sergi Aguilo Pablo Arce Minjie Ding Alfred Gil Leslie Glass Jag Kandasamy Vasudev Kumanduri llkka Lapalainen Audald Lloret i Villas Sira Martinez Anand Mohan Dietmar Orth Justin Paschall Saif Ur Rehman Gary Saunders Thomas Smith Ashutosh Shimpi Marc Sitges Dhvani Solanki Giselle Kerry Nino Spataro Dylan Spalding Matthieu Vizuete-Forster Cristina Yenyxe Gonzalez Garcia Paul Flicek Anna Foix Emilio Garcia Rios Jorge Izquierdo Roberto Ariosa Marta Ferri Peradalta Daniel Barrowdale Babita Singh Umuthan Uyan Aleix Canalda Dona Shaju Mauricio Moldes Carles Garcia Frédéric Haziza Alegria Aclan Lauren Fromont Alvis Brazma Marta Huertas Arnau Soler Gemma Milla Claudia Vasallo Aina Jené Csaba Halmagyi Raül Garcia Thomas Keane Mei Gascón

  Documentation about/team

• A genome-wide meta analysis on stroke and ischemic stroke within four populations

  In this analysis a genome-wide meta-analysis was performed on all stroke and ischemic stroke.

  Study EGAS00000000060

• UHN Genomics Data Access Committee

  Dac EGAC00001000912

• EGAD00000000008

  WTCCC1 project Type 1 Diabetes (T1D) samples

  Dataset EGAD00000000008

• EGAD00010000444

  Agilent ncRNA 60k txt files

  Dataset EGAD00010000444

• Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood

  Pilot study Pilocytic Astrocytoma ICGC PedBrain, whole genome sequencing of 5 tumors and matched blood

  Dataset EGAD00001000271

• RNA sequencing

  We propose to definitively characterise the somatic genetics of 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.

  Dataset EGAD00001000285

• Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

  Dataset EGAD00001000308

• release_2: ICGC PedBrain: whole genome mate-pair sequencing

  release_2: ICGC PedBrain: whole genome mate-pair sequencing

  Dataset EGAD00001000327

• MPN mutation order followup

  To evaluate the presence of mutations in frequently mutated genes in MPN by performing targeted resequencing of a selected gene panel comprising of 111 genes across 40 samples with MPN.

  Dataset EGAD00001000848

• GATCI_Oncoscan_Data

  This dataset contains files generated from Affymetrix Oncoscan Arrays. For each sample there are two paired cel files containing the raw data from AT and GT channels. Raw data has been transfromed to OSCHP signal files also within this dataset.

  Dataset EGAD00010001579

• arcOGEN_HumanCoreExome-24v1-0_subset_1

  Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-24v1-0 with broader consent.

  Dataset EGAD00010000922

• arcOGEN_HumanCoreExome-12v1-1_subset_1

  Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-1 with broader consent.

  Dataset EGAD00010000926

• arcOGEN_HumanCoreExome-12v1-0_subset_1

  Subset 1 of osteoarthritis cases from the arcOGEN Consortium (http://www.arcogen.org.uk/) genotyped on HumanCoreExome-12v1-0 with broader consent.

  Dataset EGAD00010000925

• APCDR AGV Ethiopia (Amhara, Oromo, Somali)

  APCDR AGV Project: Array data from 107 Ethiopians (Amhara, Oromo, Somali; subset of Ethiopian Genome Project Genotyping). Raw data, intensity files and post-QC Plink files.

  Dataset EGAD00010001047

• Indonesian Methylation dataset

  Illumina Infinium MethylationEPIC BeadChip kit (Illumina, Inc., San Diego, CA). Standard Illumina procedures using Illumina iScan scanner.

  Dataset EGAD00010001711

• Oncoscan SNP arrays for study "Molecular and functional profiling of plasmablastic lymphoma"

  1 cell line and 82 Oncoscan SNP tumor initial samples, zipped Affymetrix CEL file types, Oncoscan CNV FFPE Assay Kit, Thermo Fisher Scientific GeneChipTM Scanner 3000 7G

  Dataset EGAD00010001978

• med-pchic-dac

  The data are accessible under the terms of the following Data Access Agreement that needs to be filled in, signed (by yourself and your institution’s official contact) and returned by email to med-pchic-dac@lists.cam.ac.uk

  Dac EGAC00001000523