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• Dataset of methylation data from whole blood DNA

  This dataset includes raw data (.idat) for the Illumina Human450k beadchip and methylation levels (.txt files). Methylation level were treated for normalization and background substraction. We removed probes with at least one of the following characteristics: (1) weak signal (p > 0.01) (2128 CpG sites), (2) SNP-enriched sites (4100 sites), (3) out of a CpG context (not on a CG) (3149 sites), or (4) located on sex chromosomes (11,129 sites). A total of 465,071 CpG sites were analyzed initially. Signal was then normalized, first by scaling to the internal controls using the methylumi R package, then by applying the method of subset-quantile within array normalization (SWAN) implemented in the minfi R package.

  Dataset EGAD00010001593

• Raw scRNA-seq data from B-lineage cells in the blood of celiac disease patients

  Raw scRNA-seq data from 355 IgA+ peripheral blood B-lineage cells of two untreated celiac disease patients. The data was generated with the Smart-seq2 protocol and sequenced on a NextSeq500 instrument (Illumina) with 75 bp paired-end reads in high-output mode. The dataset contains R1 and R2 reads for each single cell (fastq.gz files) for cells passing quality control based on number of detected genes, reads, mitochondrial genes, reads mapping to the reference transcriptome and a productively rearranged immunoglobulin heavy chain IgA isotype reconstructed by the computational tool BraCeR. Metadata for the cells is provided in a csv file.

  Dataset EGAD50000000340

• Oncogenic FOXL2C134W has gain-of-function chromatin remodeling activity that reprograms glucocorticoid receptor occupancy to promote ovarian granulosa cell tumor growth

  This dataset contains bam files from the whole exome sequencing performed on granulosa cell tumors and 7 sequencing experiments performed on human-derived KGN granulosa cell tumor cells and isogenic cell lines. The latter include transcription factor ChIP-seq for Foxl2 as well as transcription factor ChIP-seq for Foxl2 and GR under dexamethasone treatment and untreated conditions, two ATAC-seq data sets, two RNA-seq data sets, and Histone marks ChIP-seq.

  Dataset EGAD50000000880

• Paired-end RNA-Seq Dataset of 72 Brain Organoid Samples: Sequencing and Gene Expression Analysis

  72 fastq sequencing files of 72 brain-organoid paired-end sequenced samples (R1/R2). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (New England Biolabs, USA). mRNAs were first enriched with Oligo(dT) beads. The samples were sequenced using a 2x150 Pair-End configuration (ver. 1.5) on an Illumina NovaSeq 6000 The raw sequence reads were aligned to the human reference genome GRCh38 using the STAR aligner (Dobin et al., 2013). Gene expression levels were quantified using the FeatureCounts tool (Liao et al., 2014) (file: "All_Counts_final.xlsx") For more information, see "Study Description"

  Dataset EGAD50000000935

• Targeted panel somatic variant sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA"

  Targeted panel somatic variant sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA." This dataset was created by running 60 cfDNA samples from patients with metastatic cancer to the lung through a research-use, tumor-naive, targeted-panel assay for measuring somatic mutations across a panel of 80 genes. All samples were sequenced on Illumina NextSeq 2000 with 150x2 paired end sequencing; files are in fastq.gz format. For the original study, the variant allele fractions of these somatic mutations were compared with the Tumor Methylation Scores calculated from Northstar Response in the same samples.

  Dataset EGAD50000001016

• Transcriptome of memory B cells with autoproliferation in MS

  Transcriptional profile of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 5 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Transcriptome libraries were constructed from the same samples, except for one sample pair, which was excluded due to limited input material (5 donors as for Methylome, D1; D2, D3, D5, D6; samples from donor D4 unfortunately technically failed). SMARTer Total Stranded RNA-seq library construction with ribosomal depletion was performed and then sequenced on NovaSeq S4 lane.

  Dataset EGAD50000001270

• Genotyping microarray data of molecular tumorboard patients in the context of the HRD-manuscript published in IJC

  Intensity files (.idat) derived from the Infinium CytoSNP-850K BeadChip microarray (Illumina) were used to analzye a possible Homologous-Recombination-Repair Deficiency (Molecular Rationale for a PARP-Inhibitor therapy) of n= 39 tumor patients (each n= 39 .idat files of the green and red chanel respectively) presented in the Molecular Tumorboard at the University Hospital Erlangen. Using these files a Genomic Instability Score was bioinformatically deducted (R-based scripts, e.g. ASCAT, scarHRD) based upon the presence of three parameteres "Loss of Heterozygosity, LOH", "Large Scale Transitions, LST" and "Telomeric Allelic Imbalances, TAIs". The associated manuscript is published in International Journal of Cancer, IJC.

  Dataset EGAD00010002736

• TSO500 sequencing of ovarian tumour samples

  This dataset consists of 8 ovarian cancer DNA sample libraries prepared using the Illumina TruSight Oncology 500 Kit (Illumina, cat no. 20076480) following the manufacturer's protocol. Library quality and quantity were assessed with High Sensitivity/D5000 Screentape Assay (Agilent Technologies, cat no. 5067-5592) on 4150/4200 Tapestation Quant-IT/Qubit dsDNA HS (Qiagen, cat no. Q32851) assay according to the supplier’s recommendations. Libraries were then pooled together in equal ratios and sequenced using PE-150bp mode on NovaSeq S1 flow cell 300 cycles kit (Illumina, 20028317) or S4 flow cell 300 cycles kit (Illumina, 20028312) aiming for 100 million reads per sample. The dataset contains sequence reads in fastq file format.

  Dataset EGAD50000001451

• RNA seq of intestinal biopsies and blood cells from patients with celiac disease and controls

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Dataset EGAD50000001597

• Single-cell profiling reveals monocyte mitochondrial dysfunction in patients with cirrhosis progressing to acute-on-chronic liver failure

  We performed single-cell RNA-seq and CITE-seq in PBMC samples derived from patients with acutely decompensated cirrhosis at risk of developing ACLF, as well as from Healthy Donors. We identified a population of monocytes associated with disease progression. We also explored the presence of this cell population in blood samples by bulk RNA-sequencing.

  Study EGAS50000001127