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• Redefined indel taxonomy reveals insights into mutational signatures

  Deposited here are whole-genome sequencing bam files from the experimental isogenic cell lines used in the study "Redefined indel taxonomy reveals insights into mutational signatures, Koh, Gene (2023)".

  Dataset EGAD50000000209

• Short-read RNA-seq of doxycycline-inducible DUX4 human myoblast cell lines

  The dataset includes the short-read RNA sequencing data of DUX4i myoblasts (Clone-5 and Clone-7) with and without 16-hour DOX-treatment (n=1 in each condition).

  Dataset EGAD50000000719

• CFTR Gene Variant Detection in Moroccan Individuals via Nanopore Long-Read Sequencing

  This study consists of sequencing the whole CFTR gene (coding and non-coding regions) using Oxford Nanopore on Moroccan CF patients

  Study EGAS50000001423

• ATAC-seq for 2 samples

  This dataset contains ATACseq data from ta primary sample and a patient derived model (PDX) of the novel FOXF1/FENDRR ALL subtype. All the 2 samples are in bam file type.

  Dataset EGAD50000001791

• sWGS of CRC patients

  Paired end (47/98) and single end (51/98) shallow whole genome sequencing (sWGS) data for the identification of somatic copy number alterations (SCNA) and the estimation of tumor fractions in plasma DNA of colorectal cancer (CRC) patients.

  Dataset EGAD00001006101

• The University of Hong Kong Gastric Cancer RHOA Study RNASeq Data

  RNAseq data generated from paired tumor frozen tissues in which the tumor organoids were established for cell-cell or cell-matrix adhesion dependency assay.

  Dataset EGAD00001008830

• Whole exome sequencing

  reference whole exome sequence serving as a reference of individuals. Includes the fastq files of each individual (labelled S1-S5) and the called variants in vcf format merge for all individuals.

  Dataset EGAD00001008728

• Single cell karyotype sequencing of 7 samples from colorectal cancer (CRC) patients

  Contains data for all cells sequenced for this study. Data is organized as one bam-file per sample. Individual cells can be identified through the CB tag in the bam-files.

  Dataset EGAD00001006438

• WGS on patients 1-4, study of metastatic prostate cancer

  Data from the study of subclonal metastatic expansion in prostate cancer. Whole genome shotgun sequencing of fifteen samples, tumour and whole blood, from the four initial patients.

  Dataset EGAD00001001343

• Whole-genome sequencing reveals genomic signatures associated with the inflammatory microenvironments in Chinese NSCLC patients

  We integrate genomic (whole-genome sequencing, WGS) and transcriptome (polyA-enriched RNA-Seq) sequencing from 90 NSCLC cases and comprehensively identified the distinct genomic features of Chinese NSCLC patients.

  Dataset EGAD00001004071

• ctDNA mutation analysis using the SiMSen-seq approach

  Mutation analysis in plasma samples with low ctDNA levels using a molecular barcoding technology, i.e. the single target approach SiMSen-seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing).

  Dataset EGAD00001006104

• RNA-seq on patients 1-4, study of metastatic prostate cancer

  Data from the study of subclonal metastatic expansion in prostate cancer. RNA-seq of twelve samples, tumour and benign tissue, from the four initial patients.

  Dataset EGAD00001001345

• IVF Retrospective Study

  This dataset contains BAM files for 9 samples from individuals involved in a retrospective IVF trial. The BAM files were derived from whole genome sequencing. The 9 individuals consist of three trios containing mother, father and child samples.

  Dataset EGAD00001008147

• NiCOL Study RNA-seq dataset

  15 samples sequenced in RNA-seq. This dataset contains their raw FASTQ data and the raw count table and the TPM count table.

  Dataset EGAD00001010912

• PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

  The dataset includes RNA sequencing data on PRE- treatment biopsies of lymph node metastasis (n=80) The technology used for sequencing is llumina HiSeq 2500

  Dataset EGAD00001012116

• Targeted sequencing of diffuse large B-cell lymphoma tumour samples from the UK's Haematological Malignancy Research Network

  Targeted sequencing was applied to an unselected population-based diffuse large B-cell lymphoma cohort (n=928) diagnosed in the UK's Haematological Malignancy Research Network catchment population of ~4 million (14 centres). DNA extracted from tumour samples was sequenced with a 293-gene panel using the Illumina HiSeq 2500. All data are provided in the CRAM format.

  Dataset EGAD00001008616

• Single-cell RNA-sequencing of peripheral blood mononuclear cells from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000250

• GIST Comprehensive Cancer Panel

  DNA Sequencing of 864 genes from KiCS cancer panel. Multiple family members affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X).

  Dataset EGAD50000000548

• Saliva_Fulani_Database

  In total, 90 DNA samples were genotyped on the Illumina Infinium H3Africa Consortium array (designed for 2,271,503 SNPs; using BeadChip type: H3Africa_2019_20037295_B1). Genotyping was performed at the SNP&SEQ Technology Platform (NGI/SciLifeLab Genomics, Sweden). Saliva Fulani dataset includes individuals from the following populations: 30 individuals from Senegal_FulaniLinguere, 30 individuals from Mauritania_FulaniAssaba, and 30 individuals from Mali_FulaniInnerDelta.

  Dataset EGAD50000000653

• miRNASeq profiles from Indian HFrEF Cohort

  The dataset contains miRNA profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Small RNA libraries were prepared using QIAseq miRNA Library Kit, Qiagen and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001194

• Exome sequencing of tumor DNA samples from patients with BPLL

  DNA extracted from sorted CD19+ tumor cells (16 patients) was used for exome capture with the SureSelect V5 All Exon Kit following the standard protocols. Paired-end sequencing (2 x 100 bp) was performed using HiSeq2000 sequencing instruments. The files are in FASTQ format.

  Dataset EGAD00001004410

• Analysis of circulating miRNAs for the identification of new prognostic and predictive markers in gastro-entero-pancreatic neuroendocrine tumour (GEP-NET)

  NGS profiling of the entire miRNOme conducted on the plasma of 24 samples obtained from well-differentiated, advanced, metastatic and inoperable G1, G2 and G3 GEP-NET patients. Sequencing was performed on NexSeq platform

  Dataset EGAD00001010840

• Megabase-scale Haplotyped Genomic Analysis of Normal and Cancer Genomes

  We experimentally determined Mb-scale haplotypes from germline and cancer genome sequencing. Using a microfluidic process that partitions long DNA fragments into hundreds of thousands of barcoded reactions, we determined haplotype blocks from matched colorectal cancer samples in the delineation of haplotypes of allelic imbalances and other genomic instability events.

  Study phs000898

• BELLINI clinical trial single-cell RNA-Seq and TCR data: cohorts A & B

  Single-cell RNA-Seq data and TCR sequencing data (both by 10X Genomics) of 51 TNBC primary tumors obtained from 29 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (16 patients, 28 samples) received nivolumab for 4 weeks, patients in cohort B (13 patients, 23 samples) received nivolumab + ipilimumab for 4 weeks. The included sequencing data was generated from frozen material for cohort A and from fresh material for cohort B.

  Dataset EGAD50000000807

• ICGC Prostate Cancer Whole Genome Sequencing

  Whole Genome Sequencing Illumina HiSeq data from 20 men with prostate cancer. 20 samples were taken from primary tissue obtained at prostatectomy (target sequencing depth 50X) with matched blood control (target sequencing depth 30X). These were submitted for use in the ICGC Pan-Cancer Analysis of Whole Genomes project. Same raw data submitted in EGAD00001001116. As of September 2020, some of the studies using these data include: Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001000892