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• Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases. Cancer Discovery doi: 10.1158/2159-8290. PMID: 30787016 PMCID: PMC6497554

  The BAM files for WES and RNA seq used in the article "Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases." on cancer Discovery 2019. PMID: 30787016 PMCID: PMC6497554. Authors : Grant M Fischer, ..., Michael A Davies.

  Dataset EGAD00001005046

• Megabase scale methylation phasing using Nanopore long reads and NanoMethPhase

  This paper describes the work by Akbari V,. et al. on detection of allele specific methylation using oxford nanopore sequencing data. They have developed set of tools, SNVoter and NanoMethPhase, and workflow which enable the detection of allele specific methylation even in samples with sparse coverage of nanopore sequencing data.

  Dataset EGAD00001007920

• Transcriptome profiling of prostate tissue samples from early onset prostate cancer patients and normal controls by RNA-seq

  The dataset contains RNA-seq data of 96 EOPC patients and 9 controls. For some patients multiple tissue samples were sequenced ("multi-area" samples). The RNA extraction and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001004791

• Prognostic and immunomodulatory consequences of ERV expression in ovarian cancer

  The dataset contains transcriptional data obtained using total RNA sequencing on a Illumina machin. 59 samples are from the Hammersmith Hospital (HH) cohort of human primary ovarian tumours and 20 samples are from ovarian cancer cell lines Kuramochi (3 replicates) and Ovsaho (2 replicates) treated with 1 uM DNMTi guadecitabine or vehicle, at an early (day 5) or late (day 8) timepoint.

  Dataset EGAD00001006589

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• Whole genome bisulfite sequencing data of human monocyte sample 43_Hm01_BIMo_Ct from healthy male donor.

  Human monocytes from a healthy male blood donor were obtained after written informed consent and anonymised. Library preparation was performed essentially as described in the “Whole‐genome Bisulfite Sequencing for Methylation Analysis (WGBS)” protocol as released by Illumina. The library was sequenced on an Illumina HiSeq2500 using 101 bp paired-end sequencing. Read mapping was done with BWA.

  Dataset EGAD00001001390

• AHA Uganda Study RNAseq Dataset

  This dataset was generated as part of the AHA Uganda Study, an Acute Rheumatic Fever case-control prospective study conducted in Uganda. This dataset consists of raw fastqs from RNA sequencing for 266 samples (226 cases, 40 controls) from 162 individuals over five timepoints. RNA was extracted from Paxgene blood samples using the Sureselect HS2 library preparation kit. Sequencing was performed on Illumina NovaSeq 6000, yielding ~30-40 million raw paired reads per sample.

  Dataset EGAD00001015810

• RNASeq Whole Transcriptome Expression Profiles of NFE2 and PF4 as Translational Biomarkers for BET Inhibition-Induced Thrombocytopenia in Preclinical and Clinical Studies

  Longitudinal blood samples for exploratory biomarker analysis were collected from 51 out of 83 patients enrolled in CA011-001 (NCT02419417) study of BMS-986152, totaling 425 samples collected on three different dosing schedules (A, B, and C). Whole transcriptome expression profiling was performed on the collected blood samples using RNASeq, with Illumina TruSeq library preparation and paired sequencing. Gene expression data was quantified as transcripts per million (TPM).

  Dataset EGAD50000001659

• Genomic and Transcriptomic Profile of Paired Primary-Metastasis Colorectal Tumors

  Samples encompass primary colorectal tumors, adjacent normal colonic mucosa and metastasis of 12 patients, collected by Medical Pathologists from surgically removed specimens. Normal mucosa samples were taken more than 2 cm away from the tumor. Tissues were embedded in optimal cutting temperature (OCT) medium, snapshot frozen in liquid nitrogen within 40 minutes of collection and preserved at -80ºC. Samples were collected between June 2010 and October 2017 as part of a prospective biobanking project.

  Dataset EGAD00001007686

• Oral microbiota composition assessed with 16S rRNA sequencing from adults aged over 65 years old.

  This is a oral microbiota amplicon dataset derived from adult participants aged over 65 years old. It consists a total number of 491 samples, stored in 982 paired-end FASTQ files with sequence lengths of 200 nucleotides generated with a Illumina MiSeq. Of those 491 samples, 347 were used in analysis, the remaining 144 samples are control samples.

  Dataset EGAD00001007705