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• Targeted sequencing

  Paired-end BAM files with associated index files of 15 AML samples were generated using Agilent SureSelect XT library capture system using a custom panel as described before Takahashi et al Blood 2018. Libraries were sequenced using Illumina HiSeq 2500.

  Dataset EGAD00001007671

• Clinical and serum metabolomics data for individuals with ACS

  Full clinical data for a cohort of 199 individuals with acute coronary syndrome. Untargeted serum metabolomics using the Metabolon platform for individuals with ACS (n=156). Serum metabolomics using the Nightingale Health (NMR) platform for individuals with ACS and controls (ACS, n=191; controls, n=961).

  Dataset EGAD00001007724

• WGS samples for multiple myeloma (hipo-067 and hipo-K08K)

  Four PAIRED WGS samples, tumor and control, were sequenced on a HiSeq X Ten and the library preparation kit used was Illumina TruSeq Nano DNA. The tumor was multiple myeloma from bone marrow.

  Dataset EGAD00001008150

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA

  We showed that mice in which Dnase1l3 had been deleted showed aberrations in the fragmentation of plasma DNA. We also observed a change in the ranked frequencies of end motifs of plasma DNA caused by the Dnase1l3 deletion.

  Dataset EGAD00001005071

• Sequencing data for oesophageal and related samples - Rogerson et al (RNA)

  Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples

  Dataset EGAD00001005915

• RNA-seq dataset

  HTG EdgeSeq fastq files of bulk baseline tumors from IMbassdor250: a randomised phase 3 trial comparing atezolizumab with enzalutamide vs enzalutamide alone in patients with metastatic castration-resistant prostate cancer.

  Dataset EGAD00001007685

• RNAseq fastq files of MCL control, NOTCH1 & NOTCH2 samples

  Raw RNAseq paired end fastq files of MCL control samples (3 samples) and MCL samples transduced with a retrovirus expressing mutated NOTCH1 (3 samples) or NOTCH2 (3 samples). Instrument used: Illumina NovaSeq 6000

  Dataset EGAD00001008346

• RNASeq read files of renal cell carcinoma PDX samples

  This dataset contains 56 fastq files of paired-end RNA sequencing of a Illumina® TrueSeq stranded mRNA library of 28 renal cell carcinoma PDX samples.

  Dataset EGAD00001008766

• Matched Pair Cell Line Tumour RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Dataset EGAD00001000630

• Nasal Polyp Whole-transcriptome sequencing

  Whole-transcriptome sequencing (RNAseq) in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and controls. Differential expression patterns in genes involved in cilia, viral defense and NKT-cell specific pathways, suggesting a role of viral immunity in combination with cilia functionality in CRSwNP.

  Dataset EGAD00001010146

• snRNA-seq/snATAC-seq multiome of first and second trimester human gonads - HUGODECA dataset

  Comprehensive map of first- and second-trimester gonadal development in humans using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays, and imaging. ArrayExpress Accession: E-MTAB-11708

  Dataset EGAD00001009388

• Sporadic Parathyroid Carcinoma

  This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.

  Dataset EGAD00001000370

• CYPTAM - PacBio SMRT sequencing

  Dataset contains CYP2D6 sequencing data of 566 individuals who used tamoxifen as adjuvant breast cancer therapy. Phenotype data consists of the ratio between the metabolites endoxifen and desmethyltamoxifen (Metabolic ratio (MR)) as a proxy for CYP2D6 enzyme activity. Each sample is linked to one bam-file containing the CYP2D6 sequence.

  Dataset EGAD00001005972

• Lung Multi-site Targeted Sequence Capture

  DNA extracted from multiple biopsies taken from different areas of primary lung tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

  Dataset EGAD00001001017

• Longitudinal breast cancer cohort in SMC

  Whole transcriptome sequencing (WTS) of a longitudinal breast cancer (BC) cohort consisting of 146 cases (281 tumors, 109 pairs), including 52 (38%) that achieved pathologic complete responses (pCR) and 85 (62%) that harbored residual diseases at time of surgery.

  Dataset EGAD00001004487

• Whole genome sequencing of paired samples from primary and relapsed IDH-wt glioblastomas with matched blood controls

  This dataset contains whole genome sequencing data from 21 primary and relapsed IDH-wt glioblastomas and matched blood controls. Tumors were sequenced at a target coverage of 150x, blood controls at 80x.

  Dataset EGAD00001004563

• Stereotyped subset CLL RNA-seq from 100 patient with CLL

  RNA-sequencing data for 100 stereotypes CLL subset cases. Illumina based short-read sequencing data from a 100 samples from patients with CLL. Oxford Nanopore Technologies long-read sequencing data from 5 samples from patients with CLL.

  Dataset EGAD00001009729

• Genotyping of GM samples

  This dataset contains a vcf file for 99 GM individuals genotyped on the Illumina HumanOmni2.5 array . The vcf file is originated after imputation (IMPUTE2) and filtering for minor allele frequency MAF≥0.05, imputation confidence score INFO of >0.4 and Hardy-Weinberg Equilibrium (HWE) p>1e-06, yielding ~6.3 million variants.

  Dataset EGAD00001010255

• ACC RNASeq data

  Samples prepared using TruSeq Stranded Total RNA library kit. Samples sequenced on a HiSeq 2000.

  Dataset EGAD00001008192

• Maternal plasma data in FetalQuantSD accurate quantification of fetal DNA fraction by shallow-depth sequencing of maternal plasma DNA

  This dataset consist on 70 maternal plasma samples (bam files) used in the FetalQuantSD. The maternal plasma DNA samples were sequenced using the HiSeq 2000 platform (Illumina) with a 50-cycle paired-end mode.

  Dataset EGAD00001004324

• Single-cell Transcriptome for glioblastoma intra-tumoral heterogeneity

  Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).

  Dataset EGAD00001002249

• Whole-exome sequencing of additional thyroid disease cases (2015-08-05)

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001460

• H3Africa ReMAC Shotgun Metagenomic Phenotype

  Phenotype data for shotgun metagenomic sequencing data of nasopharyngeal fluid for studying nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial-resistance in a South African birth cohort. https://www.ebi.ac.uk/ena/data/view/PRJEB37312

  Dataset EGAD00001006244

• Tel Aviv RNA-seq dataset of of BiPSCs and FiPSCs derived cells

  RNA-seq data obtained from directed differentiation of a subset of FiPSCs and BiPSCs cell lines towards islet-like cells. RNA was collected at two key developmental stages: definitive endoderm (DE) and pancreatic progenitors (PP).

  Dataset EGAD00001003780