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• MethylScan data of plasma samples

  10ng from each cfDNA sample was used as the input material. For gDNA samples, 1.5-2ug each was first sonicated by Covaris R230 system (Woburn, MA). Next, size-selection with 0.8x-1.5x two-step Ampure XP beads was performed to enrich the 150-200bp fragments. 200ng of the size-selected gDNA was used as input material. The pre-capture library construction was performed with NEB UltraII DNA library prep kit for Illumina (Ipswich, MA) and the adapter was the methylated EM-seq adapter. Before the first PCR amplification, the gDNA samples were subjected to bisulfite conversion by QIAGEN Epitect kit, and cfDNA samples were subjected to enzymatic conversion by NEBNext enzymatic methyl-seq kit if the hybrid capture panel designed for converted DNA was used downstream. Twist panel hybrid capture was performed with their standard protocol (Twist Bioscience, South San Francisco, CA). The concentration of the post-capture library after the second PCR amplification was measured by Qubit 1xdsDNA HS kit (ThermoFisher, Waltham, MA). Their quality was examined by TBE-UREA PAGE and Bioanalyzer before sequencing. Libraries were then sequenced with 150bp paired-end reads on Illumina machines by Genewiz, Inc. (South Plainfield, NJ, USA). This dataset contains MethylScan data of the plasma samples from 248 noncancer individuals and 27 cancer patients (17 liver and 10 GI-tract cancers).

  Dataset EGAD00001015815

• TB-DAR Whole Genome Sequencing Study

  116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, based on a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania. WGS was performed at the Health2030 Genome Center in Geneva on the Illumina NovaSeq 6000 instrument (Illumina Inc, San Diego CA, USA), starting from1μg of whole blood genomic DNA and using Illumina TruSeq DNA PCR-Free reagents for library preparation and the 150nt paired-end sequencing configuration. Average coverage was above 30X for 75 samples, between 10X and 30Xfor 40 samples, and approximately 8X for a single sample. Sequencing reads were aligned to the GRCh38 (GCA_000001405.15) reference genome using bwa (Version 0.7.17).

  Dataset EGAD00001008400

• EGAD00010000768

  Replication data for HipSci normal samples using both HumanCoreExome-12_v1 and HumanOmni2.5-8 BeadChips

  Dataset EGAD00010000768

• Dataset for Parkinson's disease target re-sequencing project

  The dataset regards the sequencing of coding and putative regulatory sequences of 38 genes associated to either sporadic or Mendelian form of Parkinson's disease

  Dataset EGAD00001001029

• FASTQ NGS dataset for EGAS00001001632:New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

  Dataset EGAD00001001927

• iPSC variation file (VCF) for EBiSC

  EBiSC Whole Genome Sequencing processed VCF including VEP consequences

  Dataset EGAD00001003934

• Yemen_Somali.Omni5

  The individuals were assayed for genome-wide SNP genotypes using the Illumina Human Omni5 Bead Chip (Illumina), which surveys 4,284,426 single nucleotide markers regularly spaced across the genome

  Dataset EGAD00010001651

• Colorectal cancer methylation profiling

  4 AC samples, each with adenoma, carcinoma and normal colon tissue (12 samples in total) were analysed on the Infinium MethylationEPIC BeadChip for copy number alteration analyses.

  Dataset EGAD00010001691

• Sequencing data for oesophageal and related samples - OACs release 6 (RNA)

  Dataset EGAD00001005375

• PromethION (and Illumina) WGS and MinION transcriptome for a patient with diffuse large B-cell lymphoma.

  Dataset EGAD00001006204

• P50_P681_P763_PTC209_DMSO_24h_48h_72h_Illumina HT12v4_Gene_Expression.xlsx

  Expression dataset for DAC+PTC209 treated CD34 sorted primary CML bone marrow samples

  Dataset EGAD00010002210

• Benchmark Dataset DIA Clinical Proteomics LymphNodes E.coli

  Real patient variability Benchmark Dataset for Optimization of DIA data analysis workflows

  Dataset EGAD00010002223

• Sequencing data for oesophageal and related samples - OACs release 3 (RNA)

  Dataset EGAD00001003900

• banfora_20150706_X

  Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - X chromosome.

  Dataset EGAD00010002579

• banfora_20150706_autosomes

  Genotype data (in binary PLINK format) and imputed data (with merged 1000Gp3 and AGVP reference panel in GEMMA BIMBAM dosage format) for 355 individuals from the VAC050 trial performed in Banfora, Burkina Faso - autosomes.

  Dataset EGAD00010002581

• Batch1_Genotypes_Raw

  Genotypes generated for Puno cohort Batch 1. Case (PRE) and control (PUN) families were recruited in hospital, and additional unrelated controls were recruited in university (UNA). Raw genotypes no QC.

  Dataset EGAD00010002126

• 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

• Adaptive nanopore sequencing of chrX from peripheral samples

  Analysis of skewed X inactivation for X-linked disorders

  Dataset EGAD50000000638

• Patient TSO500 VCF files

  Tumours from MMRd EC patients treated with 2 cycles neoadjuvant ICI. TruSight Oncology 500 (TSO 500) panel for all 10 tumour samples from patients included in the trial.

  Dataset EGAD50000000694

• UniKilinikum Wuerzburg MSNZ AGRasche/AG Riedel EMD DAC

  This is a Data access committee for the Data presented in the paper tilted "Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma"

  Dac EGAC50000000173

• Profiling of human fecal microbiota for succinate consumption

  Enrichments of human stool samples in culture medium containing succinate as the main carbon source and the corresponding stool samples.

  Dataset EGAD50000000740

• Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types

  Raw bam file for bulk RNA-seq of checkpoint-blockade treated lung cancer cohorts

  Dataset EGAD50000000469

• 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

  Study EGAS50000000526

• Sequencing data for filanesib-treated hepatoblastoma samples

  This dataset contains RNA sequencing data of two hepatoblastoma PDX cell models. Cells were either treated with KSP inhibitor filanesib or with DMSO (controls).

  Dataset EGAD50000001314

• GCAT| SNParray coreSpain V3 TopMed

  4988 samples issued from GCAT cohort, genotyped with MEGAex-Infinium Array, with data for Cr1-23. Plink files with QC and imputed using TOPMed r2.

  Dataset EGAD00010002749

• RNA sequencing of mCRPC patient biopsies

  RNA sequencing of mCRPC patient biopsies obtained for the profiling of the prevalence of immune transcripts. Manuscript can be found at PMID: 35491356

  Dataset EGAD50000001811

• GCAT| SNParray GSA TopMed

  2746 samples issued from GCAT cohort, genotyped with GSA Array, with data for Cr1-23. Plink files with QC and imputed using TOPMed.

  Dataset EGAD00010002758

• Transcriptome analysis of Hepatitis B for drug discovery and clinical applications

  We analyzed blood transcriptome of HBV positive untreated patients (men) using the CAGE technology.

  Study JGAS000053

• ERDERA WES reanalysis - DPF1 Batch 1

  Processed data for 100 WES from the Data Processing Freeze 1

  Dataset EGAD50000002187

• 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

• single-cell ATAC-seq

  Single-cell ATAC-seq data for 5 CLL samples (2 controls, 3 tumor) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005965

• RNA seq data (56 cases) for study EGAS00001001394

  Part of RNA sequencing data of Malignant Lymphoma Study (ICGC)

  Dataset EGAD00001001672

• Primary Neuroblastoma Circle-seq Data

  Circle-seq data for 21 primary neuroblastoma samples supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).

  Dataset EGAD00001006580

• WGS data for medulloblastoma samples (SJMB)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003126

• Single-cell RNA sequencing for metastatic gastric adenocarcinoma

  Single-cell RNA sequencing was performed on a total of 20 PC specimens.

  Dataset EGAD00001006172

• G3BP2-KIT drives leukemia amenable to kinase inhibition in Ph-like ALL

  G3BP2-KIT drives leukemia amenable to kinase inhibition in Ph-like ALL: RNAseq for human sample

  Dataset EGAD00001007564

• Dataset for the "Study on the proliferation history of colorectal adenomas"

  Targeted genome sequences of the human X chromosome in 4 colorectal adenomas and 4 matched normal tissues from male patients

  Dataset EGAD00001000882

• APCDR AGV Project: Low depth (4x) sequence data from an Ugandan population (BAMs)

  Low depth (4x) Illumina HiSeq raw sequence data for 100 unrelated Baganda from rural Uganda.

  Dataset EGAD00001001008

• High grade serous ovarian carcinoma sample

  Multi-region whole genome sequencing of an high grade serous ovarian carcinoma sample for characterization of genomic intra-tumoural heterogeneity.

  Dataset EGAD00001000978

• RNA sequencing for gastric cancer ascites

  Whole transcriptome sequencing (RNA-seq) was performed on 39 PC specimens. Among them, 21 specimens also had WES data.

  Dataset EGAD00001004365

• Angiopredict Whole genome Shallow Sequencing

  Shallow sequencing of metastatic colorectal cancer samples for the Angiopredict and Nobev cohorts described in: van Dijk et al., JCO, in revision

  Dataset EGAD00001003990

• SEARCH FOR BACTERIA IN NEURAL TISSUE FROM AMYOTROPHIC LATERAL SCLEROSIS

  The study aims to find bacteria in neural tissue from patients with amyotrophic lateral sclerosis

  Study EGAS00001003295

• 10x Single Cell Gene Expression Library TENX069

  10x Single Cell Gene Expression library TENX069 for Triple negative breast cancer patient-derived xenograft SA609X4XB03083

  Dataset EGAD00001011211

• Beta values of methylation data of the CUP/reference/validation cohort (H021)

  Beta values of methylation data of the CUP/reference/validation cohort (H021) used for the validation cohort described in the publication

  Dataset EGAD00001008669

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0148_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0148_001 for Triple negative breast cancer patient-derived xenograft SA535X4XB02498

  Dataset EGAD00001011221

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0189_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0189_001 for Triple negative breast cancer patient-derived xenograft SA535X7XB03448

  Dataset EGAD00001011226

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0173_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0173_002 for Triple negative breast cancer patient-derived xenograft SA535X9XB03617

  Dataset EGAD00001011232

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0173_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0173_001 for Triple negative breast cancer patient-derived xenograft SA535X9XB03616

  Dataset EGAD00001011233

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0195_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0195_001 for Triple negative breast cancer patient-derived xenograft SA535X8XB03664

  Dataset EGAD00001011234

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0208_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0208_002 for Triple negative breast cancer patient-derived xenograft SA535X9XB03776

  Dataset EGAD00001011237