23272 results for "ega"

in 54.12 milliseconds.

• Whole exome sequencing data of 57 matched esophageal tumor-normal pairs

  The dataset includes whole exome sequencing (WES) data on 57 matched esophageal tumor-normal pair. The Agilent Sure-Select Human All Exon V4 plus UTRs reagent was used to capture the target exons and UTRs and Illumina HiSeq 2000 instrument was used to sequence the target region with approximately 72-fold coverage.

  Dataset EGAD00001004542

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB52_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: BvB52_F

  Dataset EGAD00001001764

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW20_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: MW20_C

  Dataset EGAD00001001796

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW22_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: MW22_C

  Dataset EGAD00001001799

• Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

  Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

  Dataset EGAD00001010250

• scRNA-seq of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-10551

  Dataset EGAD00001009386

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW50_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: MW50_M

  Dataset EGAD00001001837

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW51_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: MW51_C

  Dataset EGAD00001001838

• DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files

  DDD DATAFREEZE 2014-11-04: 4293 trios - VCF files

  Dataset EGAD00001001848

• ICR1000 UK exome series

  Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. 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 EGAD00001001021

• Transcriptome and Exome from longitudinal samples of human glioblastoma (newly added after 2015)

  We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases).

  Dataset EGAD00001002143

• CASCADE germline whole genome sequencing data

  High-coverage whole genome sequencing data (median coverage: 23.5X, range: 14.14X-32.62X)) from white blood cells of the patients from isolated buffy coat of the blood drawn postmortem from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009493

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute promyelocytic leukemia

  Bisulfite-Seq data for 3 Acute promyelocytic leukemia sample(s). 24 run(s), 3 experiment(s), 3 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_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001167

• RNA-seq data from hypothalamic tissue from individuals with Prader-Willi syndrome and age-matched controls.

  RNA-seq data (bam files) from the hypothalamus of 4 individuals with Prader-Willi syndrome and 4 age-matched control individuals. Detailed information about the study design, case-control matching and RNA-seq data processing is provided in the accompanying publication [Bochukova et al (2018) Cell Reports].

  Dataset EGAD00001004034

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB4_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: BvB4_C

  Dataset EGAD00001001754

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW52_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: MW52_F

  Dataset EGAD00001001842

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB15_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: BvB15_F

  Dataset EGAD00001001698

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_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: BvB21_M

  Dataset EGAD00001001705

• Transcriptome/Exome for glioblastoma intra-tumoral heterogeneity

  Total of 49 tumor specimens from 20 patients were subjected for whole-exome and/or whole-transcriptome sequencing including matched normal/blood. Tumor samples are acquired based on 4 categories; 1) locally adjacent tumors, 2) multifocal/multicentric tumors, 3) 5-ALA (+/-) tumors and 4) Longitudinal tumors.

  Dataset EGAD00001002248

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_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: BvB1_M

  Dataset EGAD00001001702

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_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: BvB21_C

  Dataset EGAD00001001703

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_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: BvB21_F

  Dataset EGAD00001001704

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_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: BvB1_C

  Dataset EGAD00001001700

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_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: BvB27_C

  Dataset EGAD00001001718

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB24_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: BvB24_M

  Dataset EGAD00001001714

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB41_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: BvB41_F

  Dataset EGAD00001001743

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB51_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: BvB51_M

  Dataset EGAD00001001762

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB55_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: BvB55_M

  Dataset EGAD00001001768

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB8_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: BvB8_M

  Dataset EGAD00001001783

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW49_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: MW49_F

  Dataset EGAD00001001830

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW51_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: MW51_M

  Dataset EGAD00001001840

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB38_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: BvB38_C

  Dataset EGAD00001001736

• SPATC1L variants associated with age-related and hereditary hearing loss.

  The dataset contains three BAM files that include SPATC1L variants identified in Italian patients affected by hearing loss (both hereditary and age-related hearing loss). Data have been produced by whole exome sequencing and targeted re-sequencing, using Ion Proton and Ion Torrent PGM platforms respectively.

  Dataset EGAD00001004147

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB24_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: BvB24_C

  Dataset EGAD00001001712

• WES of probands in KLB project

  These are the vcf files of exome sequencing of the two probands who were found to harbor mutations in KLB. Sample: EGAN00001564799 is the proband 1; Sample: EGAN00001564800 is the proband 11 in the KLB paper. Exome capture was performed using the SureSelect All Exon capture (Agilent Technologies, Santa Clara, CA USA) and sequenced on the HiSeq2500 (Illumina, San Diego CA USA).

  Dataset EGAD00001003463

• Tam-seq of tumor samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of DNA extracted from 300 samples of 142 patients (158 methanol-fixed relapse biopsies and 142 FFPE archival diagnostic tissues). Samples were sequenced on Illumina HiSeq 2500 and were aligned to human genome assembly GRCh37 (hg19)to produce 600 bam files (2 technical replicates per sample).

  Dataset EGAD00001004173

• RNAseq profiling of pediatric osteosarcoma

  Primary pediatric osteosarcoma samples were collected and profiled using RNAseq. When possible, germline and tumor samples were collected. For some patients, multiple tumor tissues were collected and sequenced. Some of the samples were used to derive PDTX models, which were also profiled with RNAseq. Paired end sequencing was performed on Illumina HiSeq instruments and FASTQ files reported.

  Dataset EGAD00001004538

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW50_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: MW50_F

  Dataset EGAD00001001836

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB43_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: BvB43_C

  Dataset EGAD00001001748

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_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: BvB25_M

  Dataset EGAD00001001717

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB50_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: BvB50_F

  Dataset EGAD00001001758

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB30_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: BvB30_M

  Dataset EGAD00001001726

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB8_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: BvB8_C

  Dataset EGAD00001001781

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW51_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: MW51_F

  Dataset EGAD00001001839

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW52_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: MW52_C

  Dataset EGAD00001001841

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW2_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: MW2_M

  Dataset EGAD00001001813

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW32_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: MW32_C

  Dataset EGAD00001001814

• 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

• Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort.

  Ovarian Carcinosarcoma DNA and RNA sequencing of patient samples in the UK cohort (n=18).

  Dataset EGAD00001011068

• Whole exome sequencing files for St. Jude Clinical Pilot

  This dataset contains whole exome 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 EGAD00001004287

• Whole Genome Sequencing of hiPS cells

  Human induced pluripotent stem (hiPS) cells hold great promise for regenerative medicine. Safety issues of use of hiPS cells however remain to be addressed. One of such issues is mutations derived from somatic donor cells and introduced during genome manipulation. We sequence whole genomes of hiPS cells and analyzed mutations. Our study brings hiPS cell technology one step closer to application to regenerative medicine.

  Dataset EGAD00001000362

• RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue.

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Dataset EGAD00001015534

• Learning from the thymic human cell atlas for T cell engineering: Paediatric RNA (2025-10-02)

  T cells are central to adaptive immunity and thus crucial for understanding and treating human disease. While extensively studied in model organisms, translating this knowledge to humans can sometimes be limited by their rapid cross-species evolution and diverse . This dataset contains all the data available for this study on 2026-03-10.

  Dataset EGAD00001015720

• A next-generation dual guide CRISPR system for genetic interaction library screening

  Raw sgRNA sequencing data from a pilot CRISPR screening library to test the dual guide vector system (8,914 guide pairs), and from a large scale genetic interaction screen (~100,136 guide pairs) in HT-29 cells. This data refers to Burgold et al. Nature Communications 2025.

  Dataset EGAD00001015754

• CBD-RAW-SC-ADT: 10X Single-Cell Features Barcode (CITE-seq)

  Raw Illumina sequencing data and CellRanger BAM output files. For further information regarding this dataset, please contact Stephen Sansom at contact@combat.ox.ac.uk.

  Dataset EGAD00001007962

• Human cross-tissue ILC1

  scRNASeq analysis of human Lin neg lymphocytes from control liver, cirrhotic liver, tonsil, duodenum, and colon tissues.

  Dataset EGAD00001009861

• OMKar: optical map based automated karyotyping of genomes to identify constitutional disorders

  This dataset contains optical genome mapping (OGM) data from 56 samples, processed for structural variation and copy number analysis. The data includes .xmap, .cmap, and .smap files representing high-resolution genome maps and structural variant calls. These samples were used to identify complex rearrangements and reconstruct genome karyotypes.

  Dataset EGAD00001015674

• RNA data for medulloblastoma samples (ICGC)

  RNA sequencing data for 170 medulloblastoma tumor samples

  Dataset EGAD00001003279

• AT2 COPD Methylomics

  We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung AT2 cells isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease

  Study EGAS00001007386

• DNA Dataset

  The DNA dataset includes 5 samples sequenced using the Oncomine Comprehensive Assay (OCA) panel. Libraries were prepared following the manufacturer’s protocol and sequenced on the Ion Torrent S5 System. The dataset contains FASTQ files and includes information on single nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs). (non so se hanno sequenziato su ION Torrent)

  Dataset EGAD50000002501

• Genomic Profiling of Advanced Pancreatic Cancer to inform therapy - WGS mapped reads

  Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer - Early Results from the COMPASS Trial - WGS mapped reads

  Dataset EGAD00001003585

• Isotype-resolved sequencing of B cell receptor in measles virus infection (2017-09-13)

  Isotype-resolved sequencing of B cell receptor in measles virus infection 1) 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 please see http://www.sanger.ac.uk/datasharing/ This dataset contains all the data available for this study on 2017-09-13.

  Dataset EGAD00001003749

• Cancer Genomics of the Kidney

  The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC.

  Dataset EGAD00001004018

• Whole exome profiling of spatial biopsies of high grade serous epithelial ovarian cancer patients

  This data set is comprised of data from seven distinct high grade serous epithelial ovarian cancer (HGS-EOC) partients, from whom multiple biopsies were taken at the time of surgery, from the ovary and from different locations in the peritoneal cavity. This data set contains 28 samples, sequenced with a whole exome sequencing approach.

  Dataset EGAD00001004154

• Primary breast cancers and paired brain metastases

  Targeted next-generation-sequencing of 494 cancer-associated genes was done in a series of 14 frozen pairs of matched primary breast cancers and brain metastases (28 samples). DNA libraries of all coding exons were prepared using the Haloplex Target Enrichment System. Sequencing was done using the 2*150bp paired-end technology on the Illumina NextSeq500 platform.

  Dataset EGAD00001004309

• Low-coverage whole-genome sequencing of cancer and healthy plasma circulating DNA

  Plasma samples from patients with melanoma (stage II/III/IV) and breast cancer (stage IV) as well as healthy individuals were subjected to low-coverage whole-genome sequencing (less than 10x average depth). This dataset contains raw fastq files from 39 breast cancer, 127 melanoma and 42 healthy control plasma samples.

  Dataset EGAD00001011817

• NIHR BioResource Rare Diseases WGS project - Pulmonary Arterial Hypertension (PAH) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Pulmonary Arterial Hypertension (PAH) Rare Disease domain

  Dataset EGAD00001004525

• ENGAGE - Amendment "500 genes exon sequencing"

  The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes

  Dataset EGAD00001000403

• Transcriptome sequencing of cancer cell lines

  This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000

  Dataset EGAD00001000725

• RRBS data of 48 individuals of the Dutch Hunger Winter Families Study

  The dataset entails 48 RRBS libraries of 24 siblings. 24 individuals are conceived during the Dutch Famine, a severe 6 month famine at the end of World War 2. A same sex sibling was added as a control, allowing partial matching for (early) familial environment and genetics.

  Dataset EGAD00001000733

• BLUEPRINT release January 2015, DNase-Hypersensitivity for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  DNase-Hypersensitivity data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 1 run(s), 1 experiment(s), 1 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_dnaseseq_analysis_20140811

  Dataset EGAD00001001161

• BLUEPRINT release January 2015, Bisulfite-Seq for Acute myeloid leukemia

  Bisulfite-Seq data for 1 Acute myeloid leukemia sample(s). 18 run(s), 1 experiment(s), 1 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_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001162

• MethylCap-seq based DNA methylation profiles of 65 glioblastoma and 5 non-tumoral tissues

  Data represent genome-wide DNA methylation profiles obtained by MethylCap-seq (Diagenode’s MethylCap-kit based purification followed by Illumina GAIIx sequencing), for 70 brain tissue samples, including 65 glioblastoma samples and 5 non-tumoral tissues (obtained from epilepsy surgery).

  Dataset EGAD00001001399

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - 100_all_samples

  All samples from the "100" project

  Dataset EGAD00001001457

• Whole exome sequencing for HELIC

  The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.

  Dataset EGAD00001001638

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB22_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: BvB22_C

  Dataset EGAD00001001706

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_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: BvB27_F

  Dataset EGAD00001001719

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB33_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: BvB33_M

  Dataset EGAD00001001732

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB42_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: BvB42_C

  Dataset EGAD00001001745

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB4_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: BvB4_M

  Dataset EGAD00001001756

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW50_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: MW50_C

  Dataset EGAD00001001835

• H3Africa CAfGEN Exome

  Whole Exome Sequencing data from a retrospective paediatric HIV-disease progression cohort defined on the World Health Organization's criteria for paediatric HIV progression. Data comprises of BAM and VCF files for 314 participants from 2 countries: Botswana and Uganda. DNA and RNA samples are linked in bio-repository.

  Dataset EGAD00001006224

• WGS data of paediatric ETV6::RUNX1 B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and CRAM files from second relapse and matched remission (control) samples of one ETV6::RUNX1 ALL patient (ALLK-104). Sequencing libraries were made using Novogene NGS DNA Library Prep Set (Cat No. PT004). Both second relapse (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002286

• Congenital anosmia 2

  Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). Here we obtained genomic DNA from families with multiple individuals with anosmia, suggesting they are congenital. These include those inherited in a manner consistent with dominant and recessive alleles. We have sequenced the exomes of both affected and unaffected family members on the Illumina platform.

  Dataset EGAD00001002228

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

  RNA-Seq data for 4 macrophage - T=6days B-glucan 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 EGAD00001002522

• NIHR-BioResource Rare Diseases SPEED IRD August 2016

  Whole exome sequencing BAM files and whole genome sequencing CRAM files for 722 individuals from the NIHR-BioResource Rare Diseases Consortium (SPEED project) with inherited retinal disease.

  Dataset EGAD00001002656

• ETMR ATACSeq

  ATACSeq library amplification was performed on 5 ETMR tumour samples using the NEBnext High Fidelity 2xPCR Master Mix (New England Biolabs, Cat#M0541S) according to the manufacturer’s protocol. ATAC-seq libraries were sequenced using single-end 50 bp reads on the Illumina HiSeq 2000 platform. ATAC-seq peaks analysed was conducted as published previously(Torchia et al. 2016).

  Dataset EGAD00001004805

• Illumina TSO500 DNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Illumina TSO500 DNA Dataset for Manuscript titled: Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing

  Dataset EGAD00001015396

• Whole genome sequencing

  The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC) is not well understood. We performed whole genome sequencing on primary and metastatic sites from highly clinically annotated HGSC samples. Samples were obtained pre-treatment based on a laparoscopic triage algorithm from patients who underwent R0 tumor debulking, or received neoadjuvant chemotherapy (NACT) with excellent or poor response.

  Dataset EGAD00001005240

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• Epigenomics and Single-cell Sequencing Define Cellular Heterogeneity in Langerhans Cell Histiocytosis

  Epigenomic and transcriptomic analysis of Langerhans cell histiocytosis (LCH) biopsies. Single-cell RNA-seq (10x Genomics) of seven LCH biopsies. ATAC-seq data from four sorted cell populations (in duplicate) from one LCH biopsy.

  Dataset EGAD00001005280

• The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer

  The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer includes 538 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001005339

• Natural Killer Cell Plasticity During IL-15-driven Homeostatic Proliferation

  Here we performed single-cell RNA sequencing to address repertoire stability and subset plasticity during IL-15 driven homeostatic proliferation. Sorted NK cell subsets representing discrete stages of NK cell differentiation are compared with the corresponding subsets after proliferation and further sorted into two subsets depending on the rate of proliferation.

  Dataset EGAD00001005420

• Sequencing data for personalized therapy design and endotype identification

  Whole exome sequencing of 15 DNA samples, and whole genome sequencing of 2 matched DNA samples. Whole exome sequencing is of RMS samples (both alveolar and embryonal) and from cell lines as well as patient samples. Patient samples are of pediatric RMS patients.

  Dataset EGAD00001005458

• Validation data for the SV analysis package: GRIDSS, PURPLE, LINX

  Validation data containing sequencing data of 13 samples. An hybrid capture approach was used to validate findings of both Manta and GRIDSS for the samples in the validation set. The dataset also contains the reference sequences used.

  Dataset EGAD00001005525

• Colon Cancer Organoid Cultures and Tumors RNASeq Data

  Four micrograms of total RNA was used for cDNA library construction using the KAPA Stranded mRNA-Seq Kit (KR0960-v3.15), following manufacturer's protocol. The adaptor-ligated libraries were enriched by 6 cycles of polymerase chain reaction (PCR). Libraries were sequenced using the Novaseq 6000 with paired end 151bp reads.

  Dataset EGAD00001005753

• Long read sequencing of 5 Intellectual Disability (ID) trios with PacBio Sequel. Dataset of samples: T2P, T2F and T2M

  5 trios were whole genome sequenced with PacBio Sequel to a depth of 15X (Trios 1-4) or 40X (Trio 5). For each trio the child was affected with severe ID, and the parents were unaffected. Dataset consists of Trio 2 samples: T2P, T2F and T2M

  Dataset EGAD00001006050

• Whole genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

  The dataset comprises of an aggregate level VCF (version 4.1), containing the somatic point and indel mutations found across the glioblastoma cohort (SweGBM-1, n=38 samples). The VCF file is in accordance with the HTS format specifications (https://samtools.github.io/hts-specs/).

  Dataset EGAD00001006084

• Human tumour ChIP-seq.

  We profiled 16 patient tumour samples by ChIP-seq. H3K27ac and Input are provided for 16 samples and H3K27me3 is provided for 14 samples. Among the 16 samples, 9 are G34WT and 7 are G34R/V. The raw fastq or bam files are provided.

  Dataset EGAD00001006100

• smMIP-seq of 18 FFPE prostate samples (normal and tumour pairs) to identify mutations

  smMIP-Seq was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 18). Library prep was done by capture of targeted sequences with single molecule (unique molecular index) tagged molecular inversion probes (MIP) and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

  Dataset EGAD00001006109