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• Copy-choice recombination during mitochondrial L-strand synthesis causes DNA deletions

  The dataset comprises of seven samples described below 1. Muscle samples from three patients with late-onset PEO caused by compound heterozygous POLG variants M0305 POLG W748S/R1096C M1105 POLG A467T/T251I+P587L M1804 POLG A467T/X1240G+35aa 2. Muscle sample from a patient with adPEO with heterozygous TWNK variants M0230 TWNK p.Arg357Pro 3. Blood control samples from two patients with late-onset PEO caused by compound heterozygous POLG variants DNA2012-1630_S1 POLG W748S/R1096C DNA2018-0168_S2 POLG A467T/T251I+P587L 4. Muscle samples from healthy control individuals DNA2018-0172_S4 Healthy control 2 DNA2018-0173_S5 Healthy control 1

  Dataset EGAD00001004271

• Transposome Bisulfite Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Dataset EGAD00001001028

• Cancer Cell Line Exome Sequencing

  Genomic characterisation of a large series of cancer cell lines.

  Dataset EGAD00001001039

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006797

• mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

  PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

  Dataset EGAD00001006796

• Cell-free DNA and bone marrow samples from myelodysplastic syndromes

  We have assessed the molecular profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA.

  Dataset EGAD00001008567

• Blood plasma and FFPE derived total RNA seq dataset from DLBCL and PMBCL patients

  Blood plasma samples (n=168) and matched diagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples (n=69) of DLBCL patients, PMBCL patients and healthy controls were collected between 2016-2021. Plasma samples were collected at diagnosis, at interim evaluation, after treatment, and in case of refractory or relapsed disease. RNA was extracted from 200 µl plasma using the miRNeasy serum/plasma kit and from FFPE tissue using the miRNeasy FFPE kit. RNA was subsequently sequenced on a NovaSeq 6000 instrument using the SMARTer Stranded Total RNA-seq pico v3 library preparation kit.

  Dataset EGAD00001011679

• Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes

  RNA-seq files and other data associated with an investigation of the relationship between microbes, genes and immune cells present in the sputum of humans with asthma.

  Study phs002224

• Single-cell genotype-to-phenotype mapping via co-capture of DNA mutations and mRNA transcripts

  We developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure.

  Dac EGAC50000000833

• RNAseq of 7 MPNSTs

  RNAseq of 7 MPNSTs for Magallon-Lorenz 2026. Contains 5 samples sequenced with DNBseq at BGI (four 2x100bp and one 2x150bp) and 2 samples sequenced with Illumina stranded mRNA-seq technology. BGI samples have been prefiltered with SOAPnuke. Two fastq files provided per sample with no additional filtering or QC.

  Dataset EGAD50000002493

• 909 bulk mRNA sequencing samples from the UPTIDER program

  Raw sequencing data for 909 bulk mRNA samples that correspond to 749 metastases, 64 primary tumours and 96 normal tissue. These samples were sequenced using NovaSeq6000. Library was prepared with Lexogen QuantSeq 3' FWD. Raw single-end fastq samples have been deposited as gzipped files.

  Dataset EGAD50000001910

• Dataset for Multiple Myeloma WGS data, part 2

  This dataset contains 518 case and control WGS sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X using TruSeq Nano DNA Kits. The sequencing was always paired.

  Dataset EGAD50000000681

• Dataset for Multiple Myeloma WGS samples

  This dataset contains 221 case and control WGS sequencing samples of patients with multiple myeloma. Sequencing was performed on Illumina NovaSeq 6000 and HiSeq X using TruSeq Nano DNA Kits. The sequencing was always paired.

  Dataset EGAD50000000682

• Altered Blood and Keratinocyte microRNA/transfer RNA Fragment Profiles Related to Fibromyalgia Syndrome and its Severity

  We show dysregulated microRNA and tRNA fragment profiles related to FMS pathopyhsiology and opening new perspectives for FMS diagnostics and symptom monitoring. This dataset includes all sequencing raw files from whole blood (tempus tube) and keratinocyte sequencing.

  Dataset EGAD50000000900

• Sample metadata

  Sample metadata for this experiment. Includes treatment and donor derivation information.

  Dataset EGAD50000000827

• ctDNA diva aggregate data

  ctDNA biomarker and relevant clinical data for divarasib phase I GO42144 study, including tumor type, KRAS G12C mutation detectability in plasma at baseline, baseline SLD, sites of metastasis, lines of therapy, best response, confirmed best response, PFS, ctDNA tumor fraction and KRAS G12C VAF at baseline/C1D15/C3D1.

  Dataset EGAD50000000454

• CHIC_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in glucose, lactate or with DCA. Samples were collected 7 hours after the treatments and processed for bulk CHIC-seq.

  Dataset EGAD50000000090

• Dataset for acute myeloid leukemia samples

  This dataset contains RNA, ATAC and WGS sequencing data of 9 acute myeloid leukemia samples. Sequencing was performed on Illumina HiSeq 2000, HiSeq 4000, NovaSeq 6000 and HiSeq X Ten. The sequencing was always paired.

  Dataset EGAD50000000175

• WES dataset used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 72 paired fastq files of raw Whole exome sequencing data from 14 patients with Extramedullary myeloma, 8 paired samples from the same patients at the time of Newly diagnosed myeloma, and the corresponding normal samples

  Dataset EGAD50000000052

• Iso-seq or Long-read RNAseq Dataset for 7 T-ALL patient samples

  7 Isoform sequencing or Long-read RNAseq mapped bam files. Reads were aligned to HG38 reference using Minimap2.

  Dataset EGAD50000000022

• ATAC Dataset for 19 T-ALL patient samples and 1 normal control sample

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

  Dataset EGAD50000000024

• Sequencing data for oesophageal and related samples - BOs release 2 (RNA)

  Dataset EGAD00001003840

• EGAD00000000047

  Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples

  Dataset EGAD00000000047

• Dataset of whole genome bisulfite data of 4 different monocyte samples

  Regions of common inter-individual DNA methylation differences in human monocytes – potential function and genetic basis WGBS Data of Samples: 43_Hm03_BlMo_Ct, 43_Hm02_BlMo_Ct, 43_Hm05_BlMo_Ct, 43_Hm01_BlMo_Ct For details about sequencing or sample metadata check http://deep.dkfz.de/

  Dataset EGAD00001003259