22941 results for "ega"

in 43.03 milliseconds.

• ScRNA-seq of kidney organoids expressing different APOL1 variants and treated with IFN-γ

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 3 samples of hiPSC-derived kidney organoid cells cultured in vitro in presence of IFN-γ. Samples were obtained from kidney organoids with APOL1 G1G1 variant, APOL1 G2G2 variant and an isogenic control.

  Dataset EGAD50000001743

• Targeted sequencing data on sequential liquid biopsy samples from CSPC patients

  Sequencing data from newly diagnosed high emtastatic burder prostate cancer patients receiving an AR pathway inhibitor (ARPI) or docetaxel. Targeted sequencing data of prostate cancer relevant genes using the PCF-SELECT capture panel. cfDNA from PreADT, baseline, on-treatment (Cycle1 to 6) taken on ARPI or Docetaxel were sequenced as well as patient-matched WBC DNA

  Dataset EGAD50000001960

• Dataset of 5 RNAseq from 3 non-muscle-invasive bladder cancer patients

  RNAseq (FASTQ files) of 5 tumor from 3 non-muscle-invasive bladder cancer patients. For patient UC2, RNA from 3 different synchronous tumors was extracted. Relating to the other datasets from the project : no RNA was available from patient UC4. NB : patients aliases are the following : ROXY : UC1, OMAD : UC2, MAKI : UC3, HAPE : UC4

  Dataset EGAD50000002009

• RNA sequencing of intestinal metaplasia

  We perform bulk RNA-seq of 10 and single cell RNAseq of 2 intestinal metaplasia samples. We also perform stereoseq spatial transcriptomic analysis of 4 gastric cancer samples. The dataset contain cram files from 10 bulk RNAseq samples, and raw fastq files from 2 single cell RNAseq and 4 stereo-seq samples.

  Dataset EGAD50000002010

• Extended longitudinal single-cell RNA-seq data from ovarian cancer across multiple treatment phases

  The dataset contains single-cell RNA-seq data of 73 tumor samples high-grade serous carcinoma (HGSC) patients sequenced with Novaseq. The samples were collected at primary, interval, and relapse treatment phases from multiple tissue sites. The files provided are fastq files.

  Dataset EGAD50000001855

• SIA Subtyping TSO500 (Targetted Sequencing)

  Associated with Molecular classification of small intestinal adenocarcinomas. TSO500 Targetted sequencing panel generated 292 .fastq files from 145 samples (primary and recurrent small intestine adenocarcinomas as well as normal samples) from 133 patients. TruSight Oncology 500 (TSO500; Illumina, San Diego, USA) high-throughput assays were run on genomic DNA samples through next-generation sequencing (NGS) on Illumina’s NovaSeq6000 at GenomeScan.

  Dataset EGAD50000001761

• Whole-genome sequencing data of metastatic salivary gland cancer

  This dataset contains whole-genome sequencing data of three patients with metastatic salivary gland cancer who underwent autopsy to harvest tumor biopsies from spatially separated metastatic sites and biopsies from healthy skin as a control. Two patients had the subtype adenoid cystic carcinoma (patients 1 and 4) and one patient had the subtype myoepithelial carcinoma.

  Dataset EGAD50000002056

• BestAgeingMiRNA

  Processed miRNA expression profiles and clinical phenotype data from patients with cardiovascular diseases (dilated cardiomyopathy, acute coronary syndrome, ischemic cardiomyopathy, and coronary artery disease) and healthy controls. MicroRNA expression was assessed using Agilent human miRNA microarrays with RMA normalization and log2 transformation. Dataset includes expression values for all detected case/control miRNAs from miRBase v21, along with clinical metadata including disease status, age, sex, and study center.

  Dataset EGAD00010002788

• Cancer Research UK Manchester Institute/ Cancer Research UK National Biomarker Centre Data Access Committee

  Cancer Research UK Manchester Institute/Cancer Research UK National Biomarker Centre Data Access Committee is created to • Review and approve data access requests. • Ensure data security and compliance with institutional and legal obligations. • Maintain accurate records of access decisions For questions or further information, please contact: Chair of the Data Access Committee: Caroline Wilkinson Email: dac@cruk.manchester.ac.uk

  Dac EGAC50000000795

• Baseline epigenetic clock measures in the Northern Ireland Cohort for the Longitudinal Study of Ageing (NICOLA)

  Epigenetic clock measures for a subset of 1,870 participants within the NICOLA cohort. The following epigenetic clocks were generated: (±PC)PhenoAge, (±PC)GrimAge, (±PC)Horvath1, (±PC)Hannum, PCDNAmTL and DunedinPACE. +PC represents the use of the principal component adjusted version of the clock.

  Dataset EGAD50000002063

• Early-onset Colorectal Cancer Study TOGETHER Data Access Committee

  The Early-onset Colorectal Cancer Study TOGETHER Data Access Committee (DAC) is responsible for reviewing requests to access sequencing and clinical data from the study. Access to the data is restricted to researchers with approved ethical clearance and scientifically valid research projects. Each request will be evaluated by the DAC to ensure compliance with participants’ informed consent and all applicable data protection regulations.

  Dac EGAC50000000752

• human placenta snRNA-seq (n=12)

  This dataset include the snRNA-seq raw sequencing files from the placentas of 4 normal weight control and 8 obese individuals. The files are paired-end fastq files. The snRNA-seq libraries were generated with Chromium Single Cell 3’ kit v3.1 (10X Genomics) and sequenced on Illumina NovaSeq 6000 at Novogene, UK.

  Dataset EGAD50000001222

• BCL11B Enhancer Hijacking by t(14;16)(q32;q24) Translocation Defines a Novel High-Risk Subtype of T-ALL

  We performed integrated analysis of pediatric and adult T-ALL and mixed phenotype acute leukemias (MPALs) by whole-genome and whole-transcriptome sequencing.

  Study EGAS50000001254

• Dataset for desmoplastic small round cell tumor - RNA

  This dataset contains 32 RNA sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq RNA and TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000912

• Data Access Committee for Genomics of bone marrow failure (BMF) and myelodysplastic syndromes (MDS)

  The Data Access Committee for the genomics of bone marrow failure and myelodysplastic syndrome project is responsible for reviewing applications for access to controlled human genomic and phenotypic datasets generated as part of this project. The DAC ensures that data sharing with qualified researchers is conducted in accordance with participant consent, institutional ethical approvals, and all applicable data protection regulations. 

  Dac EGAC50000000754

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578

• Effects of GATA4-inhibiting compound 3i-2012 on HB-243 hepatoblastoma cells

  In order to study the effects of GATA4 inhibition, HB-243 hepatoblastoma cells were treated with GATA4-inhibiting compound 3i-2012 for 24 hours. Total RNA was extracted and sequenced.

  Study EGAS50000000999

• Aging and viral evolution impair immunity against dominant pan-coronavirus-reactive T cell epitope

  In this project we have analysed gene expression and Tcell repertoires of CD40L+41bb+ and CD40L-41bb- Tcells from young and old donors after stimulation with the iCope peptide.

  Study EGAS50000001150

• Bulk 3' mRNA-Sequencing of human ASC-derived kidney tubuloids

  Bulk 3' mRNA-Seq raw files (FASTQ) from human kidney tubuloids derived from 4 separate donors in collagen-based dome culture and suspension culture. Samples were collected for sequencing on day 7 of passage 3, 4, and 5. Total = 24 samples.

  Dataset EGAD50000002335

• Indigenous American Genomic Diversity Project (IAGDP).

  Here we present the Indigenous American Genomic Diversity Project (IAGDP), comprising 128 newly generated high-coverage (NGS; ~44X) whole genomes from Indigenous individuals across eight Latin American countries, representing 45 populations and 28 language families. This dataset expands Indigenous representation in genomics, with emphasis on geographically and linguistically diverse populations, particularly from the South American lowlands.

  Dataset EGAD50000002396

• DAC Wachten Laboratory and Toma Laboratory, University of Bonn/University Hospital Bonn

  DAC for collaborative projects of the Wachten Laboratory (Institute of Innate Immunity, University of Bonn, University Hospital Bonn) and the Toma Laboratory (Institute of Pathology, University Hospital Bonn). Contact: Prof. Dr. Dagmar Wachten dwachten@uni-bonn.de Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Germany Prof. Dr. Marieta I. Toma Marieta.Toma@ukbonn.de Institute of Pathology, University Hospital Bonn, Germany

  Dac EGAC50000000916

• Von Hippel-Lindau syndrome multi-region exome sequencing project from two patients undertaken at Cancer Research UK's London Research Institute

  Multi-region whole exome sequencing of tumours from patients with Von Hippel-Lindau syndrome reveals convergence of mutayional events upon the PI3L-AKT-mTOR signalling pathway.

  Study EGAS00001000907

• Whole_Exome_sequencing_in_a_large_IBD_pedigree

  We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.

  Study EGAS00001000240

• 20_Matched_Pair_Breast_Cancer_Genomes

  We propose to definitively characterise the somatic genetics of 20 breast cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic data.

  Study EGAS00001000170

• Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Study EGAS00001000472

• Mutant clone mapping in normal oesophagus (2019-04-03)

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004888

• 666PG Whole genome alignment

  Aligned whole genome sequences in this dataset are from CPCG-GENE Normal/Tumor pairs used in the 666PG study. Raw sequences data was aligned against the human reference (GRCh37 + decoy) using bwa-mem and GATK for indel-realignment and recalibration

  Dataset EGAD00001004957

• H3Africa H3AChipDesign Phenotype

  Basic phenotypic data (country, ethnicity and sex) for 348 samples of the H3Africa Chip Design Study. Divided into 8 datasets of 41 samples from Zambia, 24 samples from Cameroon, 50 samples from Mali, 26 samples from Cameroon, 49 samples from Nigeria, 48 samples from Botswana, 50 samples from Benin, 60 samples from Burkina Faso and Ghana.

  Dataset EGAD00001005310

• Transcriptome sequence data from a metastatic breast cancer patient

  Transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003690

• Transcriptome sequencing of Gingivo-buccal Cancer - ICGC India Project YR03

  This dataset pertains to transcriptome sequencing of paired RNA samples.RNA was isolated from the tumor and adjacent normal tissues of 12 patients (24 samples). We have performed rRNA removal followed by total RNA sequencing in Illumina HiSeq platform.We have uploaded TopHat2 aligned BAM files.

  Dataset EGAD00001003981

• WES of oral-mucosa-derived organoids

  Tumor and matching normal tissues were collected from 8 patients and organoids were derived from each tissue. Whole exome libraries were prepared for tumor tissue, normal tissue, tumor organoids and normal organoids, and paired-end sequencing was performed using Illumina Novaseq 6000 system. Only tumor and matching normal tissues were sequenced for the patients without available organoids.

  Dataset EGAD00001005063

• RNA sequencing and whole-genome mate-pair sequencing of osteosarcoma

  This data set includes 72 mate pair sequenced osteosarcomas (36 as part of a discovery cohort and 36 as part of a validation cohort). It also includes RNA-sequencing data on 67 osteosarcomas (mostly overlapping with the above mate pair sequenced cases) and 13 osteoblastomas used as controls for gene expression levels.

  Dataset EGAD00001005307

• Exome sequencing of 277 rainforest hunter-gatherers and neighbouring farmers from Central Africa

  Exome sequencing of 277 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. After QC filters, exomes of 266 unrelated individuals were obtained at high coverage (Lopez et al., Curr Biol 2019).

  Dataset EGAD00001005138

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

  Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003051

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

  Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002537

• Genome and transcriptome sequence data from an oligodendroglioma patient

  Genome and transcriptome sequence data from an oligodendroglioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002539

• Genome and transcriptome sequence data from a melanoma patient

  Genome and transcriptome sequence data from a melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002546

• aCGH CNV detection by CNsolidate for 6,827 DDD probands

  aCGH CNV detection by CNsolidate for 6,827 DDD probands

  Dataset EGAD00001005728

• WGS from PDAC samples

  Bam files from WGS of PDAC samples described in: Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution

  Dataset EGAD00001006152

• Genome and transcriptome sequence data from a porocarcinoma patient

  Genome and transcriptome sequence data from a porocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002596

• Genome and transcriptome sequence data from an osteosarcoma patient

  Genome and transcriptome sequence data from an osteosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005870

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

  Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005849

• IBD Whole Genome Sequencing (2019-08-14)

  Whole genome sequences at 15X depth of patients with Inflammatory Bowel Disease. 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/ . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005254

• High coverage Whole exome DNA sequencing on pre-treatment tumor samples (n=3) matched with post-treatment metastasized lymph nodes isolated with laser microdissection (n=3)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes High coverage Whole exome DNA sequencing on pre-treatment bladder tumor samples (n=3) matched with post-treatment metastasised adjacent lymph nodes isolated with laser microdissection (n=3) for 3 unique patients

  Dataset EGAD00001006852

• Genome and transcriptome sequence data from a chordoma patient

  Genome and transcriptome sequence data from a chordoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003040

• Genome and transcriptome sequence data from a leiomyosarcoma patient

  Genome and transcriptome sequence data from a leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002891

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB15_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_M

  Dataset EGAD00001001699

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_C

  Dataset EGAD00001001715

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB28_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB28_M

  Dataset EGAD00001001723

• RNA-sequencing

  RNA-sequencing for a cohort of B-ALL samples : 5 Down Syndrome (DS), 16 Hyperdiploid (HeH), 6 iAMP21, 9 other. RNA-sequencing for B-cell progenitors from 3 healthy. It also contains RNA-sequencing datasets of Patient-Derived Xenografts (X) developed from the B-ALL samples : 4 Down Syndrome (DS), 4 Hyperdiploid (HeH), 1 iAMP21, 3 other.

  Dataset EGAD00001005426

• RNA-seq dataset of lung adenocarcinomas

  This dataset includes the RNA-seq data from a study entitled "Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma". PolyA tails were captured by Oligo-dT beads, and sequencing run was made in HiSeq 2500 machines. Paired-end FASTQ files are provided in our dataset.

  Dataset EGAD00001004794

• Genome and transcriptome sequence data from a melanoma patient

  Genome and transcriptome sequence data from a melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005878

• Genome and transcriptome sequence data from a chondrosarcoma patient

  Genome and transcriptome sequence data from a chondrosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005848

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

  Genome and transcriptome sequence data from a cholangiocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005838

• Transcriptomic signatures of CD4+ T cells from visceral leishmaniasis (VL) patients

  Bulk RNA-sequencing was performed on CD4+ T cells isolated from the blood of visceral leishmaniasis patients (n = 12) and endemic controls (EC; n = 12). CD4+ T cells were obtained by magnetic-activated cell sorting (MACS). Alterations in the transcripts of T helper (Th) cells during infection were identified.

  Dataset EGAD00001005807

• Genome and transcriptome sequence data from a chordoma patient

  Genome and transcriptome sequence data from a chordoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005871

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB4_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB4_F

  Dataset EGAD00001001755

• Single Cell DNA amplicon sequencing of 12 B-ALL patients (at diagnosis and during treatment)

  This dataset contains single cell DNA amplicon sequencing of 12 B-ALL patients. For all patients a diagnosis sample was processed, while 4 patients were also followed up during treatment, summing up to a total of 23 samples. Mutations were called in the predefined set of amplicons.

  Dataset EGAD00001006955

• Genome and transcriptome sequence data from a meningioma patient

  Genome and transcriptome sequence data from a meningioma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004920

• ICR Exome Optimization series

  Exome sequencing of 142 samples with corresponding Sanger sequencing results for 416 variants and 288 negative sites. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001462

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB23_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_M

  Dataset EGAD00001001711

• Transcriptional programming in whole blood reveals changes in pro-inflammatory phenotype explained by changed food and changed life style.

  We here focused on whole blood from paxgene tubes from healthy Tanzanians and the impact of urbanization and diet on innate immune responses. We performed RNA-sequencing of whole blood from paxgene tubes from healthy Tanzanians and investigate that transcriptional changes depend of diet and location.

  Dataset EGAD00001006051

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB50_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB50_M

  Dataset EGAD00001001759

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB51_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_C

  Dataset EGAD00001001760

• Genome and transcriptome sequence data from a breast cancer patient

  Genome and transcriptome sequence data from a patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002019

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW14_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_F

  Dataset EGAD00001001788

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_F

  Dataset EGAD00001001701

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_M

  Dataset EGAD00001001720

• Circulating tumor DNA in urine and plasma of glioma patients - sequencing data

  Dataset consisting of sequence data from 36 glioma patients. Data includes; -Whole exome sequencing of tumour tissue and matched germline -Shallow whole genome sequencing of urine cell-free DNA -Targeted capture sequencing of plasma and CSF cell-free DNA Additional sequencing data are provided from non-glioma and healthy controls

  Dataset EGAD00001006156

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW4_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW4_F

  Dataset EGAD00001001833

• BLUEPRINT release August 2016, RNA-Seq for macrophage - T=6days untreated, on genome GRCh38

  RNA-Seq data for 4 macrophage - T=6days untreated sample(s). 4 run(s), 4 experiment(s), 4 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002457

• Myeloid cancer sequencing data

  SmMIP libraries using DNA from patients diagnosed with myeloid malignancies were generated in replicates and were sequenced on the NovaSeq SP platform (Illumina)

  Dataset EGAD00001007791

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB58_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_F

  Dataset EGAD00001001773

• Genome and transcriptome sequence data from a leiomyosarcoma patient

  Genome and transcriptome sequence data from a leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002570

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_F

  Dataset EGAD00001001716

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB42_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB42_F

  Dataset EGAD00001001746

• RNASeq on HiSeq platform of 56 samples from 46 melanoma cases

  BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70

  Dataset EGAD00001003353

• Genome and transcriptome sequence data from a melanoma patient

  Genome and transcriptome sequence data from a melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005890

• Genome and transcriptome sequence data from an adenocarcinoma patient

  Genome and transcriptome sequence data from an adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005905

• Genome and transcriptome sequence data from an osteosarcoma patient

  Genome and transcriptome sequence data from an osteosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005913

• A73047D

  Whole genome sequencing for single cells for library A73047D 2091 cells; filetype=bam

  Dataset EGAD00001007102

• He et al. RNA-seq data

  This dataset are the bam files of RNA-seq data from the paper by He et al.

  Dataset EGAD00001007135

• BC WGS Dataset

  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 EGAD00001001338

• Shallow whole genome sequencing on stage 1 epithelial ovarian cancer

  BAM files (aligned against the hg38 genome) from a shallow whole-genome sequencing experiment (median depth 0.5X) on 218 samples from Stage 1 epithelial ovarian cancer biopises. Samples labeled "bis" or "tris" with the same ID are relapses; "left" or "right" samples indicate, in the case of bilateral tumor, from which ovary the sample was taken.

  Dataset EGAD00001006881

• DESIGN II HNSCC RNA-Seq

  RNA-Seq data of 28 HPV-negative HNSCC specimens from patients treated at the Netherlands Cancer Institute (Amsterdam), VU Medical Centre (Amsterdam) or MAASTRO Clinic (Maastricht) in The Netherlands. HNSCC biopsy samples were obtained prior to treatment (chemo-radiotherapy) for the prospective study within the DESIGN project and used for polyA mRNA sequencing.

  Dataset EGAD00001005722

• Whole genome sequencing files for St. Jude Clinical Pilot

  This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"

  Dataset EGAD00001004290

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB44_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB44_C

  Dataset EGAD00001001751

• Collection of Genotypic and Ethnographic Information from Individuals of South African Ethnic Groups

  Whole genome sequencing data of 84 Nama individuals with KhoeSan ancestry from southern Africa in phased VCF format. Variants were called/phased as part of the African Genome Resource. The data has been aligned to GRCh37.

  Dataset EGAD00001006198

• BLUEPRINT release August 2014, DNase-Hypersensitivity for CD14-positive, CD16-negative classical monocyte

  DNase-Hypersensitivity data for 5 CD14-positive, CD16-negative classical monocyte sample(s). 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_dnaseseq_analysis_20140811

  Dataset EGAD00001000905

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB58_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_M

  Dataset EGAD00001001774

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB40_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB40_C

  Dataset EGAD00001001739

• WholeGenomeSeq-EGAS00001001306

  Whole Genome sequencing. 2 μg of genomic DNA from each sample was used for the construction of two short-insert paired-end sequencing libraries. Both types of libraries were sequenced in paired-end mode on Illumina GAIIx (2 × 151 bp) using Sequencing kit v4 or Illumina HiSeq2000 (2x101 bp) using TruSeq SBS Kit v3.

  Dataset EGAD00001001466

• McGill EMC Community projects Release 7 for cell line "SaOS-2"

  Complete reference epigenome (as defined by IHEC) of a SaOS-2 cell line with osteosarcoma.

  Dataset EGAD00001007678

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

  Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 241 tumour samples

  Dataset EGAD00001005388

• NIHR BioResource Rare Diseases WGS project - Neuropathic Pain Disorders (NPD) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Neuropathic Pain Disorders (NPD) Rare Disease domain

  Dataset EGAD00001004516

• BLUEPRINT release August 2015, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 1 alternatively activated macrophage 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_dnaseseq_analysis_20150820

  Dataset EGAD00001001545

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB10_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_M

  Dataset EGAD00001001696

• Single-cell TCR sequencing of DQ2.2-glut-L1-specific T cells

  In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.

  Dataset EGAD00001005047

• BLUEPRINT release August 2016, DNase-Hypersensitivity for alternatively activated macrophage, on genome GRCh38

  DNase-Hypersensitivity data for 2 alternatively activated macrophage sample(s). 2 run(s), 2 experiment(s), 2 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_dnaseseq_analysis_20160816

  Dataset EGAD00001002481

• Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

  Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

  Dataset EGAD00001005519