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• 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

• 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

• RNA-seq data from 224 advanced prostate tumors generated by the West Coast Dream Team

  224 pairs of FASTQ files from metastatic Castration-Resistant Prostate Cancer (mCRPC) sequenced on HiSeq 4000 instruments. Patients were enrolled in the West Coast Dream Team study. Biopsies include various tissue sites including bone, soft tissue, and lymph node.

  Dataset EGAD00001008487

• 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

• 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

• Haplotype-specific assembly of shattered chromosomes in oesophageal adenocarciomas

  Genomic and epigenomic sequencing of 5 oesphageal adenocarciomas with evidence of chromothripsis. Genomic sequencing includes: Pacbio circular consensus sequencing, Pacbio continuous long read sequencing, 10X linked read and Illumia HiSeq X Ten sequencing. Epigenomic sequencing includes: Hi-C chromosome capture, ATAC-seq, ChIP seq (for H3K27ac, H3K4me3, H3K27me3 and CTCF) and long read RNA sequencing. All data types have the bam files which have not undergone haplotype resolution (demarcated as unresolved) and some data types also have haplotype resolved reads (demarcated as resolved).

  Dataset EGAD00001010871

• Melanoma PEACE Dataset

  Dataset for the initial melanoma PEACE paper in Cancer Discovery, March 2023.

  Dataset EGAD00001010877

• 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

• 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

• 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

• 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