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• Highly recurrent U1 snRNA mutations drive alternative splicing in SHH medulloblastoma

  Highly recurrent U1 snRNA mutations drive alternative splicing in HH medulloblastoma

  Dataset EGAD00001004958

• Burden of DNMs in children born conceived using ART

  The dataset is composed by processed whole genome sequencing data generated from 53 children and their respective parents, forming 49 trios (mother, father and child) and 2 quartets (mother, father and two siblings). A total of 18 children were born after spontaneous conception (n = 18); 17 children were born after in vitro fertilization (IVF) and another 18 children were born after intracytoplasmic sperm injection combined with testicular sperm extraction (ICSI-TESE)

  Dataset EGAD00001008208

• SAFIR02_Cytoscan

  Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_cytoscan)

  Dataset EGAD00010002239

• Single Cell RNA-Seq

  Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq. Nine techniques applied to samples from four PDX models: #105, #177, #233, #264

  Dataset EGAD50000000216

• Induced pluripotent stem cell derived pericytes respond to mediators of proliferation and contractility

  Differentiation of mesoderm pericytes from induced pluripotent stem cell lines.

  Study EGAS50000000176

• Breast Invasive Lobular Carcinoma CDH1 WGS dataset

  We subjected to whole genome sequencing (WGS) one ILC case lacking CDH1 biallelic mutations. Both tumor and normal samples were sequenced.

  Dataset EGAD50000000696

• RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Transcriptomic analysis of K7M2 murine osteosarcoma cells stably modified to overexpress or repress CYR61

  Dataset EGAD50000000747

• Glioblastoma stem cell lines RNA-seq

  RNA-seq data for three Glioblastoma stem cell (GSC) lines exposed to PRMT5 inhibitor and control samples.

  Dataset EGAD00001006095

• ONT Minion reads for a patient with ataxia-pancytopenia syndrome.

  ONT Minion reads to provide 30x coverage for a patient with ataxia-pancytopenia syndrome.

  Dataset EGAD00001005022

• Investigation of relapse prediction in infants with MLL-rearranged Acute Lymphoblastic Leukemia

  In infants with ALL, accurate relapse prediction would enable treatment strategies that take relapse risk into account, with potential benefits for both low- and high-risk patients. Through analysis of bone marrow biopsies taken at initial diagnosis, we show that single-cell RNA sequencing can predict future relapse occurrence.

  Study EGAS00001003986

• Treatment of genetic screening of hypertriglyceridemia type I, III, and V - HTG Amsterdam

  This is a cohort of patients with extreme hypertriglyceridemia. Patients have been screened for loss of function mutations in LPL, GPIHBP1, APOC2, APOA5 and LMF1.

  Study phs000511

• Immuno-nephrology Data Access Committee Amsterdam UMC

  In this experiment we investigated kidney immunology in two autoimmune kidney diseases (ANCA-associated glomerulonephritis and Lupus Nephritis). Single cell transcriptome analysis of CD45+ immune cells from freshly retrieved kidney biopsies of 5 AGN patiënts, 1 disease-control with lupus nephritis (class II), and 1 "healthy" nephrectomy control was performed using 10X Genomics technology.

  Dac EGAC50000000024

• MPNST_Data

  WES from 51 cases initially diagnosed as Malignant Nerve Sheath Tumours (MPNST) and RNA sequencing data from 10 MPNST cases. Find more information in article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Dataset EGAD00001006253

• BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  BLUEPRINT: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cells (WGS)

  Dataset EGAD00001002663

• Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium

  Somatic mutations in epithelial cells from endometriosis and normal uterine endometrium, with a total of 24 samples. Target enrichment was conducted by Agilent SureSelect Human All Exon V5 + IncRNA kit. Sequencing was conducted by Illumina HiSeq 2500 platform. Somatic mutation call was performed by Strelka.

  Dataset EGAD00001004186

• Bulk and single-cell AML RNA-seq post ex vivo culture

  Bulk and single-cell RNA-seq performed on primary AML blasts cultured ex vivo for 3 days in standard or niche-like conditions.

  Study EGAS00001006265

• RNA-seq for identification of neotranscripts

  This dataset contains RNA-seq data (Fastq files of paired-end data) of 18 patient tumors used for identification of neotranscripts in 18 different types of fusion-driven sarcomas and other cancers as described in Vibert et al., Mol Cell 2022 (PMID: 35550257)

  Dataset EGAD00001008832

• Whole Genome Bisulfite sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains Whole Genome Bisulfite sequencing data from seven samples (six tumor samples and on tumor derived cell line). Sequencing was performed Illumina HiSeq 2000 machine resulting in 14 FASTQ files.

  Dataset EGAD00001008805

• scMultiome

  This dataset gather scMultiomic data including RNA-seq and ATAC-seq in MM.1S in control and dex condition at 1h and 4h

  Dataset EGAD00001011140

• Data from Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

  Data from Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models

  Dataset EGAD00001012228

• BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  BLUEPRINT DNA methylation profiles of monocytes, T cells and B cells in type 1 diabetes-discordant monozygotic twins (Bisulfite-Seq data).

  Dataset EGAD00001002682

• HIV exome pilot, exome data part 2 GRCh37_53

  exome sequence data for 25 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000047) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000087

• HV31 - MGI standard short-read sequencing

  MGI standard short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.

  Dataset EGAD00001007044

• R code

  R code to run analyses on anonymized data from IMvigor010 ctDNA publication.

  Dataset EGAD00001007654

• HV31 - MGI CoolMPS short-read sequencing

  MGI CoolMPS short-read sequencing data for individual HV31 generated using DNA from peripheral blood mononuclear cells, to a sequencing depth of ~57×.

  Dataset EGAD00001007048

• HIV exome pilot, exome data part 1 GRCh37_53

  exome sequence data for 49 HIV elite long term non-progressors and rapid progressors. Partial dataset (overlap with EGAD00001000087) of raw BAMs mapped to GRCh37_53.

  Dataset EGAD00001000047

• MDS MSC

  bam files, mapped to hg19 after dedup, recal, recalibration and clipping of overlapping redas

  Dataset EGAD00001006968

• Identification of New Therapeutic Targets for Renal Medullary Carcinoma via Integrated Genomic and Transcriptomic Profiling

  Renal medullary carcinoma (RMC) is a rare, aggressive kidney cancer associated with sickle cell trait, characterized by SMARCB1 loss and resistance to conventional therapies used for other renal cell carcinomas (RCC). We conducted whole exome sequencing (WES) on RMC samples. This study provides a large molecular characterization of RMC, highlighting TROP2 and other cell surface markers as promising therapeutic targets.

  Study EGAS50000001280

• UCSF WCDT WGS/WGBS mCRPC

  This dataset contains 29 paired FASTQ files from whole-genome bisulfite sequencing (WGBS) assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument. It also contains whole-genome sequencing bam files aligned to hg38 using BWA from 36 patients, with tumor and matched tumor-adjacent normal samples. Sequencing was generated using HiSeq X Ten.

  Study EGAS00001006649

• Born in Bradford (BiB)

  Dac EGAC00001003494

• H3K27ac HiChIP Dataset for 19 T-ALL patients and one normal control sample

  19 H3K27ac HICHIP from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference.

  Dataset EGAD50000000023

• Tampere University Celiac Disease Research Data Access Committee

  This DAC will be used to reposit RNAseq data from intestinal biopsies of celiac disease patients on gluten-free diet and post-gluten challenge treated with placebo or TG2 inhibitor

  Dac EGAC50000000233

• Single cell RNA sequencing of samples from core and periphery of human glioblastoma

  Samples taken from various regions of three human glioblastomas were subject to single cell RNA sequencing.

  Dataset EGAD50000002080

• Optimized large-scale longitudinal biorepository of gastroesophageal adenocarcinoma patient-derived organoids: High-fidelity models for personalized treatment to overcome resistance

  Whole exome sequencing of patient tumour samples and matched patient derived organoids.

  Dataset EGAD50000002315

• Sequence of breast cancer bone metastases PDX from 2 targeted panels

  Targeted sequencing analyses was made on samples of PDX engrafted with breast cancer bone metastases, 2 PDX acquired resistance to palbociclib.

  Dataset EGAD00001006070

• TFL unique case study

  Whole exome sequencing of a normal sample, primary tumor sample, and relapse tumor sample of a transformed non-Hodgkins follicular lymphoma patient with extraordinary response to treatment.

  Dataset EGAD00001002707

• Paediatric glioma cell line WGS

  Whole genome sequencing of 5 paediatric glioma cells lines - KNS42, SF188, UW479, RES186 and RES259. Illumina paired end sequencing is provided as 5 BAM files aligned to hg19 with bwa.

  Dataset EGAD00001004123

• ATAC-seq of cohesin-mutated and -wildtype adult AMLs

  ATAC-seq (Illumina TDE1 Transposase) to profile accessible chromatin regions of cohesin-mutated (STAG2 or RAD21 mutations) and -wildtype adult AMLs.

  Dataset EGAD00001011267

• Genomic WES plasma control samples

  This datasets consists os genomic WES of paired-end raw data (FASTQ R1, R2 and UMI sequence) obtained from plasma and HapMap control samples. Specifically, it consists in two Hapmap samples (NA12877, NA12878) and 2 plasma standarts (HD780 and HD816) with VAF mutations at 0.0%, 0.1%, 1.0%, and 5.0%, in total 21 plasma samples.

  Dataset EGAD50000000805

• S_CORT_Stratification_in_COloRecTal_cancer_

  Colorectal cancer samples will be submitted for Illumina sequencing using a custom capture of 116 genes implicated in colorectal tumourigenesis. Driver mutations will be detected and ultimately correlated with phenotypic data.

  Study EGAS00001001521

• CTCF ChIP-sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains CTCF ChIP-sequencing data from seven samples (six tumor samples and one tumor derived cell line). Following library amplification, DNA fragments were sequenced using Illumina HiSeq 2000 paired-end sequencing resulting in 14 FASTQ files.

  Dataset EGAD00001008806

• Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WGS

  Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WGS

  Dataset EGAD00001010042

• small RNA next generation sequencing in head and neck cancer

  small RNA next generation sequencing in head and neck cancer

  Dataset EGAD00001008402

• GWG in T1DM - DAC

  Dac EGAC00001001580

• TCRseq in cancers DAC

  Dac EGAC00001002235

• ID1 in glioblastoma

  Study EGAS00001003711

• CHIP and LOY in AD

  Dac EGAC00001003606

• Gene Expression Analysis in Clonal Evolution of Fanconi Anemia

  We examined hematopoietic progenitor cells derived from iPSCs from patients with Fanconi anemia, including bone marrow failure cells (FANCA-/- HPCs), 'healthy', complemented cells (FANCA-/- cells with a wild-type FANCA cDNA), MDS-like cells (FANCA-/- HPCs with introduced mutations in RUNX1 and other MDS-associated genes), and Fanconi AML-like cells ('FAL'; MDS-like cells expressing FLT3-ITD).

  Study phs003024

• Exome Sequencing in an Ancestrally Diverse Autism Cohort

  Autism spectrum disorder (ASD) is a collection of neurodevelopmental disorders manifested by impaired social communication, repetitive behaviors, and restricted interests. We performed whole exome sequencing (WES) on a total of 754 individuals from 195 families, including 222 probands with ASD, from diverse ancestral backgrounds. We identified potentially pathogenic variants in known and novel ASD or neurodevelopmental disease genes.

  Study phs003603

• Methylation sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA"

  Methylation sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA." This dataset was created by running samples through Northstar Response, where bisulfite converted samples are amplified in a multiplex PCR targeting more than 500 genomic regions. Samples in this dataset include contrived samples made from 84 different tumors DNA, each mixed with their matched buffy coat DNA at varying ratios, as well as cfDNA and buffy coat DNA samples collected from 67 cancer patients undergoing treatment. All samples were sequenced on Illumina NextSeq 2000 with single end 100 cycle sequencing; files are in fastq.gz format.

  Dataset EGAD50000001015