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• Counts: Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

  These are the log2CPM (log2 counts per million) fragments per gene counts associated with the BAM files in EGAD00001003806, in tab separated format. Counts for 36 postmortem brain samples from 9 non-demented control subjects and 9 Hereditary cerebral hemorrhage with amyloidosis-Dutch type subjects are included (1 Frontal cortex sample and 1 Occipital cortex sample per subject). RNA samples were depleted for ribosomal RNA with the Ribo Zero Gold Human kit (Illumina) and strand specific RNA-Seq libraries were generated. Paired-end sequencing was performed on a HiSeq2500 Illumina system (2x50bp reads). Alignments were performed using GSNAP v2014-12-23 with setting "--npaths 1" on GRCh38 reference genome without the alternative contigs. Fragment per gene counting was performed using HTSeq-count v0.6.1p1 with setting "--stranded reverse". The gene annotation used for quantification were UCSC RefSeq genes for GRCh38 downloaded on 2015-07-13.

  Dataset EGAD00010001457

• UK_RCC_GWAS

  Renal cell carcinoma (RCC) cases comprised adult patients with histologically proven RCC were collected through two sources within the UK. First, 856 cases from SORCE, a MRC collection of surgically treated RCC cases ascertained through UK clinical oncology centres. Second, 189 RCC cases collected through the ICR and Royal Marsden NHS Hospitals Trust. Cases included 590 clear cell carcinomas (CCCs), 42 papillary carcinomas (PCs), 33 chromophobe carcinomas (CCs) and 19 mixed or other histological subtypes. DNA was extracted from EDTA-venous blood samples using the conventional methods and quantified using PicoGreen (Invitrogen). Cases were genotyped using the Human OmniExpress-12 BeadChip according to the manufacturer's recommendations (Illumina Inc, San Diego, CA, USA). After strict QC, 944 cases were retained. Data provided in plink format. Controls used were data from the Wellcome Trust Case Control Consortium 2 (WTCCC2) 1958 birth cohort and the UK Blood Service Control Group (available as EGAS00000000028). 

  Dataset EGAD00010002310

• RNA sequencing from patient-derived intestinal organoids

  uman duodenal tissues for establishing organoid cultures used in this study were sourced from de-identified surgical specimens (n = 3) of the duodenum obtained from patients who had undergone biopsy procedures unrelated to CeD at Tampere University Hospital. The protocol was approved by the Ethics Committee of Tampere University Hospital, Tampere, Finland (ETL code R18082). RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Dataset EGAD50000000492

• Single-nuclei RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

  10x genomics single-nuclei RNA sequencing of 9 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. snRNA-seq was performed using the ‘Frankenstein’ protocol (dx.doi.org/10.17504/protocols.io.bqxymxpw). Briefly, nuclei were extracted from frozen tissues and subjected to fluorescence-activated nuclei sorting (FANS) using 4′,6-diamidino-2-phenylindole (DAPI). Sorting was performed using a BD FACSaria 2 instrument, sorting between 3000 and 10,000 nuclei per sample, capturing both diploid and tetraploid populations. FAN-sorted nuclei were immediately processed using either the 10x Chromium Single Cell 5’ (PN-1000006, 4 samples) or 3’ (PN-1000075, 4 samples) Library & Gel Bead Kit (10x Genomics, USA). Once processed, snRNA-seq libraries were sequenced on the Illumina Nova-Seq 6000 (Illumina, USA) using 150bp paired-end sequencing. This dataset contains raw sequencing reads in FASTQ format.

  Dataset EGAD50000000505

• Cergentis FFPE-TLC sequencing of colorectal carcinoma

  In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. This dataset contains the hg19 reference alignment of the FFPE-TLC sequences for all 29 colorectal cancers and 8 adjacent normals.

  Dataset EGAD50000000618

• Whole genome and transcriptome sequencing of cancer of unknown primary tumours

  Whole genome and transcriptome sequencing of cancer of unknown primary tumours was used to determine yield of clinical biomarkers for a molecular guided trial or for resolving cancer type of origin. This study includes profiling of germline DNA and tumour DNA and RNA by whole genome and transcriptome sequencing. All samples are in BAM format aligned with GRCh38 reference genome. This dataset includes: 1. Whole genome sequencing (WGS) of 78 cancer of unknown primary tumour samples and 73 matched germline DNA. 2. Whole transcriptome sequencing (WTS) of 69 cancer of unknown primary tumour samples (matched to WGS cases) 3. Whole genome sequencing of 22 cell-free DNA samples from cancer of unknown primary patients and matched Germaine DNA(8 samples matched to tumour WGS)

  Dataset EGAD50000000656

• Raw sequencing data from chromosome conformation capture, RNA sequencing and chromatin assays in human primary monocytes

  This dataset contains raw sequencing data from eQTL Capture Hi-C, ATAC-seq and RNA-seq experiments in monocytes isolated from 34 healthy male donors, as well as from Hi-C, 4C-seq and CTCF ChIP-seq in subsets of individuals. The data are released as paired-end Illumina FASTQ files. Hi-C and Capture Hi-C used DpnII digestion and Tn5-based low-input library preparation. In Capture Hi-C, this was followed by targeted capture with custom-designed biotinylated RNA probes targeting ~1100 eQTL regions. ATAC-seq was performed on PFA-fixed cells using a digitonin-based protocol. 4C-seq and CTCF ChIP-seq were performed using standard protocols.

  Dataset EGAD50000001116

• EuroTARGET is a European study on mRCC, collecting clinical data, germline DNA, and tumor samples.

  For patients with metastatic renal cell cancer (mRCC), treatment choice is mainly based on clinical parameters. With many treatments available and the limited response to treatment and associated toxicities, there is much interest in identifying better biomarkers for personalized treatment. EuroTARGET aims to identify and characterize host- and tumor-related biomarkers for prediction of response to tyrosine kinase inhibitor therapy in mRCC. Here, we describe the EuroTARGET mRCC patient cohort.

  Study EGAS50000000798

• Long-read whole genome sequencing as a tool for variant detection in inherited retinal dystrophies

  Advances in whole-genome sequencing (WGS) have significantly enhanced our ability to detect genomic variants underlying inherited diseases. In this study, we performed long-read WGS on 24 patients with inherited retinal dystrophies (IRDs) to validate the utility of nanopore sequencing in detecting genomic variations. We confirmed the presence of all previously detected variants and demonstrated that this approach allows for precise refinement of structural variants (SVs). Furthermore, we could perform genotype phasing by sequencing only the probands, confirming variants were inherited in trans. Moreover, nanopore sequencing enabled the detection of complex variants, such as transposon insertions and structural rearrangements. This comprehensive assessment illustrates the power of long-read sequencing in capturing diverse forms of genomic variation and in improving diagnostic accuracy in IRDs.

  Dataset EGAD50000001238

• Cannabis impacts female fertility as evidenced by an in vitro investigation and a case-control study

  Single immature human oocytes were cultured in vitro (24h) either under control, THC1 () or THC2 (100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC) conditions. Oocytes were collected and subjected to SmartSeq v4 cDNA conversion, library prep (Nextera XT)), and sequencing (NovaSeq S4). The goal of this study was to determine the impact of THC on the human oocyte transcriptome.

  Study EGAS50000001052