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• RNAseq of pre- and post-5AZA-treated head and neck cancer patients refractory to anti-PD-1 therapy

  RNA sequencing (RNA-seq) was performed on baseline (before low-dose 5-aza treatment) and on-treatment (low-dose 5-aza treatment for 5 or 10 days) tumor samples from eight participants with head and neck cancer who were refractory to anti-PD-1 therapy. RNA library preparations, sequencing reactions, and initial bioinformatics analyses were conducted at GENEWIZ, LLC. In total, 16 150-bp pair-end RNAseq data were generated.

  Dataset EGAD50000001010

• RNA-seq FASTQ files studied in Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application

  This data set contains 12 paired fastq files (RNA-seq) from one wild-type iPS cell, two HLA-KO iPS clones and three CD14+ monocytes differentiated from them. The RNA-seq libraries were generated with Illumina TruSeq Stranded Total RNA library prep kit. The libraries were sequenced with Illumina NovaSeq 6000 in paired-end mode.

  Dataset EGAD50000001700

• Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

  Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

  Dataset EGAD50000001709

• Single-cell RNA sequencing of metastatic colorectal cancer patient-derived xenografts treated with cetuximab

  Tumor implantation and expansion were performed in two 6-week-old NOD/SCID mice. Once tumors reached an average volume of approximately 700 mm³, mice were randomly assigned to one of two treatment arms: vehicle (physiological saline, intraperitoneally, twice weekly) or cetuximab (20 mg/kg, intraperitoneally, twice weekly). After 1 week of treatment, mice were sacrificed, and tumors were harvested and preserved in sCelLiVE® Buffer for downstream single-cell RNA sequencing analysis.

  Dataset EGAD50000002103

• Log2-CPM (voom)-normalised read-count matrix of the RNAseq Datasets of CLUSTER JIA pre-MTX cohort

  Samples were sequenced with NovaSeq6000 and the sequencing files were processed using the RSSnextflow workflow (https://gitlab.com/b8307038/rssnextflow). The raw read counts from all batches were combined. Analysis-ready batch-corrected read counts were generated using ComBat-seq. Read counts normalisation for DGE analysis was performed with limma-voom function (log2 CPM) as seen in the pipeline.

  Dataset EGAD50000002170

• Single-cell RNA sequencing of Small Intestinal Neuroendocrine Tumors (SI-NET)

  Single-cell RNA sequencing (scRNA-seq) was performed on cells isolated from intestinal mucosa and small intestinal neuroendocrine tumors (SI-NETs) to compare their transcriptomic profiles. Tumor and adjacent normal tissues were collected from two SI-NET patients, enzymatically dissociated, and processed into single-cell suspensions. Single-cell libraries were generated using the Chromium Single Cell 3′ Reagent Kit v3 and sequenced on an Illumina platform to produce FASTQ files for downstream analysis.

  Dataset EGAD50000002265

• Raw and processed snRNAseq data of Choroid Plexus Tumors

  This dataset contains raw sequencing and processed data of single nuclei transcriptomes. The data were generated with 10x chromium probe-based single-nucleus assay on FFPE tissues of 43 Choroid Plexus Tumour resections and 12 non-neoplastic fetal and adult ChP resections. Raw data contain BAM files of the sequencing. Processed data contain count matrices as generated by 10x CellRanger for raw and filtered running options.

  Dataset EGAD50000002320

• Somatic copy number alterations profiling in non-small cell lung cancer and their correlation with clinical efficacy in first-line treatment

  Genomic data from FFPE tumor samples of 258 patients with non-small cell lung cancer (NSCLC), profiled by shallow whole-genome sequencing (sWGS) at 1x. The study aimed to characterize somatic copy number alterations (SCNAs) and SCNA burden to assess their clinical relevance for patient stratification across different first-line treatments.

  Dataset EGAD50000002322

• TenK10K Phase 1: scRNA-seq fastq format sequencing data

  Single cell RNA-sequencing data for PBMCs from the Tenk10k Phase 1 cohort (1925 individuals post-QC). Libraries were prepared using the 10x Genomics 3’ Chromium Next GEM Single Cell HT V3.1 kit and sequenced on the NovaSeq 6000 platform. This analysis consists of 4,768 fastq format files in 1,192 runs, and an analysis which provides the relationship of 298 library pool samples to 1,925 individual samples.

  Dataset EGAD50000002517

• RNA-seq data

  This dataset contains 200 RNA-seq bam files (142 SLE, 58 healthy individuals). RNA libraries were prepared with the Illumina TruSeq sample preparation kit and were sequenced on Illumina HiSeq2000. 49 bp paired-end reads were mapped to the GRCh37 reference human genome using the GEM mapper.This dataset was generated as part of the following study: Panousis et al (2019). Combined genetic and transcriptome analysis of patients with SLE: Distinct, targetable signatures for susceptibility and severity

  Dataset EGAD00001005037

• GELATO clinical trial RNA-Seq data (metastatic lesions)

  RNA-Seq data of 46 matched lobular breast cancer metastatic samples obtained from 21 unique patients from GELATO clinical trial assayed at three timepoints: at baseline (directly after patient randomization), pre-atezolizumab (after induction treatment with carboplatin for two weeks) and on atezolizumab (after two cycles of atezolizumab combined with carboplatin). The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009834

• Haplotype Reference Consortium Release 1.1

  Haplotype Reference Consortium Release 1.1 - subset for release via the EGA

  Dataset EGAD00001002729

• Somatic mutation and clonal evolution in premalignant lung disease

  In this study we aim to characterise the landscape of mutation and clonal selection in normal lung and premalignant lung disease. The study combines targeted sequencing and whole-genome sequencing of microbiopsies of lung and bronchial epithelium. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with premalignant lung disease. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010122

• Somatic mutation and clonal evolution in the human bladder WES-NOVASEQ (2020-05-05)

  n this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006117

• Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

  Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

  Dataset EGAD00001006170

• Metagenomic sequences from human stool samples

  ​DNA extraction from human stool samples was performed at the Center for Microbiome Innovation (CMI) at University of California, San Diego. DNA sequencing libraries were prepared using Nextera XT (Illumina). Shotgun DNA sequencing was performed on the Illumina HiSeq4000 platform. Raw fastq reads were quality-checked. Skewer (version 0.2.2) was utilized with the paired-end mode. Human reads were identified and removed by Bowtie2 mapping against the human genome reference (hg19), followed by bam2fastq with --unaligned --no-aligned --force options.

  Dataset EGAD00001006364

• Sequencing data for oesophageal and related samples - Ng, Contino et al (WGS)

  Data supporting "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. WGS (BAM files) 383 oesophageal adenocarcinoma samples 383 normal samples

  Dataset EGAD00001007808

• Somatic mutation and clonal evolution in the human pancreas - WGS (2019-12-17)

  In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma. This dataset contains all the data available for this study on 2019-12-17.

  Dataset EGAD00001005751

• Lymphocyte Gut WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006934

• LSC RNA-Sequencing

  To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

  Dataset EGAD00001008488

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• Genetic vulnerability of knockout cancer lines (2019-04-01)

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage. . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004881

• Somatic mutation and clonal evolution in the human bladder_TGS (2020-05-05)

  In this study, we aim to characterise the landscape of mutation and clonal selection in the human bladder. The study includes targeted sequencing of laser-dissected microbiopsies from the bladder. The samples utilised in this study will include urothelium from transplant donors with no history of bladder cancer and cystectomy specimens from patients with bladder cancer. . This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006114

• Fastq and reference alignment of 19 samples for defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Dataset EGAD00001008690

• Exome Sequencing of Poor Prognosis Acute Myeloid Leukaemia (2019-08-19)

  We plan to sequence the exomes of 4 AML cases (tumour and germline) in an effort to discover new mutations in this disease that could improve our understanding of leukaemogenesis and guide the development of new targeted therapies. The Sanger Institute will sequence the exomes of 4 Acute Myeloid Leukaemia cases including tumour and germline DNA so that somatically-acquired, AML-specific mutations can be accurately designated. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005265