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• Long read mRNA sequencing of human neural retinal samples

  Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Files are raw BAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.

  Dataset EGAD50000000101

• LCM isolated buccal epithelial cell WGS of chimeric twins

  Buccal epithelial cells of chimeric twins were isolated using laser-capture microdissection. Cells were pooled (13-60 cells) per batch to create a genomic DNA library using an NEB low-input kit.

  Dataset EGAD50000000131

• Pacbio_methylation_cases

  The PacBio cases dataset for differential methylation analysis included 10 case samples with known KMT2A loss-of-function variants, 2 VUS samples. All samples were sequenced using PacBio Revio® HiFi reads at a matched coverage of 15X, and methylation was called using pb-cpg-tools on aligned BAM files.

  Dataset EGAD00010002807

• Siberia.Pakendorf

  The tar archive contains a) the txt file with the genotypes, b) illumina annotation file with info on SNPs, c) sample info file unfiltered illumina data, autosomes only data from Pugach et al MBE 2016 The Complex Admixture History and Recent Southern Origins of Siberian Populations

  Dataset EGAD00010002304

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors.

  Dataset EGAD00001000641

• Identification of drug resistance genes in melanoma by Exome Sequencing

  The cell lines in this study are a combination of internally sequenced (cosmic) and externally sequenced cell lines known to be “double-wild-type” (lacking BRAF and NRAS somatic mutations). These sequences were realigned in this data set for consistency.

  Dataset EGAD00001003260

• Whole Exome Data of RFWD3 Fanconi anemia patient

  Dataset contains one sample derived from gDNA of human fibroblasts. Files are in FASTQ format and were generated using the Agilent SureSelect Human All Exon 50Mb Kit and followed by Next Generation Sequencing on a HighSeq2000 instrument (Illumina).

  Dataset EGAD00001003311

• Whole exome sequencing of SU- DIPG-XIII from different sites

  Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)

  Dataset EGAD00001003563

• SLC9A3R1 variant associated with age-related hearing loss

  The dataset contains one BAM file that includes a SLC9A3R1 variant identified in two Italian patients affected by age-related hearing loss. Data have been produced by targeted re-sequencing, using Ion Torrent PGM platform.

  Dataset EGAD00001004171

• Exome sequencing files for "Minimal functional driver gene heterogeneity among untreated metastases"

  Files from whole exome sequencing of 14 tumors from two cancer patients (endometrial and lung cancer) along with a matched normal tissue per patient.

  Dataset EGAD00001004212

• Whole exome sequencing of melanomas from a Braf mutant mouse model UV radiation study

  Whole exome sequencing of 41 melanomas and normal DNA from Braf mutant mice: 15 tumours from UV exposed mice, 15 tumours from non-exposed mice and 11 from UV exposed, sunscreen-protected mice.

  Dataset EGAD00001000775

• Whole Genome (WG) sequencing data files for H_NO-JB001

  DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.WG sequencing produced ~30-fold (primary tumour, spleen normal)-50-fold (lung metastasis) coverage

  Dataset EGAD00001001253

• mFAST-SeqS of plasma-DNA

  Sequence data from L1-amplicon libraries prepared from plasma-DNA from a set of 24 female controls and 18 male controls without malignant disease and samples from patients breast (n= 28) and prostate cancer patients (n=61).

  Dataset EGAD00001001314

• Longitudinal RNA-seq in a twin cohort

  The dataset consists of 232 RNA-seq samples (whole blood) obtained from healthy female from the TwinsUK adult registry cohort. The samples were obtained at two time points separated on average by 22 months.

  Dataset EGAD00001002068

• MGRB dataset. GATK joint called variants of 2570 phase 2 samples.

  This dataset comprises a 2572 sample joint called vcf from the Medical Genome Reference Bank.

  Dataset EGAD00001005228

• DESIGN-NKI low coverage WGS

  Low-coverage whole genome sequencing data of 37 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for WGS to a depth of approx. 0.5X.

  Dataset EGAD00001005718

• DESIGN-VUMC low coverage WGS

  Low-coverage whole genome sequencing data of 37 HPV-negative HNSCC specimens from patients treated at the VU Medical Centre, Amsterdam. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for WGS to a depth of approx. 0.5X.

  Dataset EGAD00001005719

• RNAseq data

  Whole genome transcriptome poly-A selected strand specific 100bp paired-end RNA sequencing of post-mortem brain tissue from prefrontal cortex and orbitofrontal cortex were performed. Brain tissue samples were collected from four different biobanks in England and USA.

  Dataset EGAD00001005948

• RNA-seq analysis of megakaryocytes and granulocytes in Quebec platelet disorder

  RNA-seq was performed on cultured megakaryocytes and peripheral-blood derived granulocytes from individuals with QPD and a unaffected controls. Each group consisted of n=3 biological replicates.

  Dataset EGAD00001006053

• plasma dna fragmentations

  Data were generated by next-generation sequencing (Illumina) in a fastq format. This dataset involved sequencing data from pregnant women and patients with hepatocellular carcinoma (HCC). For HCC samples, the paired buffy coat and tumor DNA tissue samples were also sequenced.

  Dataset EGAD00001006054

• Metastases of a cancer of unknown primary (CUP)

  RNA seq analysis of 6 CUP metastases (each in triplicate), analysed by paired sequencing with NextSeq 500. Whole exome sequencing of 15 CUP metastases, analysed by paired sequencing with NextSeq 500.

  Dataset EGAD00001005963

• Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles

  SMARTer Stranded Total RNA-Seq method of human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. Including a titration experiment with spikes.

  Dataset EGAD00001006150

• Matched FF and FFPE WGS from a metastatic prostate tumor

  This dataset contains three bam files. One normal blood sample and two matched FF and FFPE samples from the same metastatic prostate tumor.

  Dataset EGAD00001006180

• Epigenetic subtypes of neuroblastoma - ChIPseq

  In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 60 primary neuroblastoma samples.

  Dataset EGAD00001006285

• Dataset of whole-exome sequencing of clonally related neuroblastoma and teratoma

  This dataset includes bam files of WES of clonally related neuroblastoma and teratoma as well as peripheral blood samples as a control. Neuroblastoma and teratoma samples were formalin-fixed paraffin embedded.

  Dataset EGAD00001007039