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• WES raw data set for the study "Genomic profiling of localized (lFL) and systemic follicular lymphoma (sFL) reveals novel insights into FL pathogenesis"

  221 patient samples including 164 initial tumor (TI) samples (53/164 fresh frozen TI samples, and 111/164 formalin-fixed paraffin-embedded (FFPE) TI samples), 22 paired matched normal samples, and 35 unpaired normal samples from healthy donors; FASTQ file format, Agilent SureSelect Human All Exon V6 Kit (Agilent Technologies, Inc., Santa Clara, California, USA)

  Dataset EGAD00001011369

• Dataset for synovial_sarcoma-RNA

  Rare cancer sequencing data of 23 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008844

• sWGS of OV cell lines for ACN rascal study

  This dataset contains 60 .bam files of shallow WGS data (~0.1X) from ovarian cancer cell lines. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008118

• Dataset for bone_cancer-EXON

  Rare cancer sequencing data of 87 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008865

• Dataset for hematopoietic_malignancy-WHOLE_GENOME

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008881

• Dataset for leiomyosarcoma-WHOLE_GENOME

  Rare cancer sequencing data of 66 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008887

• Dataset for upper_gastrointestinal_tumor-EXON

  Rare cancer sequencing data of 85 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008902

• Whole-genome and transcriptome sequencing files obtained in monozygotic twins discordant for Mayer-Rokitansky-Küster-Hauser syndrome

  Raw, unfiltered, paired-end fastq files obtained through whole-genome and RNA-sequencing, respectively. RNA-seq of affected individuals in three twin pairs. WGS of blood in five twin pairs as well as uterine rudiment tissue of selected affected individuals.

  Dataset EGAD00001008992

• The University of Hong Kong Colon Cancer Ganciclovir Study WGS Data

  Human clonal intestinal organoids were treated with 1µM MMF (Roche), 20 μM GCV (Hainan Poly Pharm Co Ltd), or in combinations (1 µM MMF + 20 μM GCV or 1 µM MMF + 40 μM GCV) continuously for 4-6 weeks. DNA was extracted after drug treatment. WGS was performed with 150 bp PE sequencing at 30X using an Illumina Novaseq sequencer.

  Dataset EGAD00001009667

• Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer

  The dataset for Multimodal Genomic Features Predict Outcome of Immune Checkpoint Blockade in Non-small Cell Lung Cancer includes 106 bam files from whole exome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include matched tumor/normal samples from non-small cell lung cancer patients treated with immunotherapy.

  Dataset EGAD00001005796

• Papua New Guinean Genome Altitude Project Dataset 1

  The PGAP dataset 1 includes 81 whole genome sequences for Papua New Guinean individuals sampled in Daru (N=38) and Mount Wilhelm (N=43). DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD00001010143

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (scRNA)

  Data supporting: “Single-cell RNA sequencing unifies developmental programs of Esophageal and Gastric Intestinal Metaplasia.” Nowicki-Osuch, Zhuang et al. scRNAseq (FASTQ files) 59 samples

  Dataset EGAD00001010074

• Strand-seq data of primary acute myeloid leukemia patient samples with complex karyotype

  In this study, we aimed to identify somatic structural variation of acute myeloid leukemia with complex karyotype (CK-AML) at the single-cell level and to investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of two patient-derived xenografts (PDXs).

  Dataset EGAD00001011172

• Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

  This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

  Dataset EGAD00001008632

• Human Embryonic Multi-tissue ChIP-seq (Manchester)

  Histone ChIP-seq of 13 human embryonic tissues from weeks 6-8 of gestation. H3K4me3, H3K27me3 and H3K27ac. Biological replicates (n=2) for 11 tissues. Tissues (n): Brain (2); Retinal Pigmented Epithelium (eye)(2); Palate(2); Tongue (1); Left ventricle (heart)(2); Lung(2); Liver(2); Pancreas (2*); Stomach(1); Upper limb (2); Lower limb (2); Adrenal gland (2); Kidney (2)

  Dataset EGAD00001004335

• Dataset for other_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 49 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008895

• Genomic abnormalities of TP53 define distinct risk groups of paediatric B-cell non-Hodgkin lymphoma

  Whole exome sequencing data from 90 diagnostic lymphoma samples run and published as part of the Leukemia manuscript. 133 total exomes were sequenced including tumour and normal controls. Copy number array data was also generated for 95 patients.

  Dataset EGAD00001008162

• Gut microbiome from melanoma patients

  Metagenomics shotgun sequencing was conducted on fecal samples from the Australian patients enrolled in the OpACIN-neo clinical trial (n = 38). Metagenomic shotgun sequencing was performed utilizing the same DNA from the same preparations as for the 16S rRNA gene analysis. Individual libraries were prepared using Nextera XT, and sequencing was performed on the Illumina NovaSeq 6000 S1 (2 x 150bp; Xp workflow).

  Dataset EGAD00001010028

• BLUEPRINT September 2016, ChIPmentation Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  ChIPmentation data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002930

• BLUEPRINT September 2016, ChIPmentation Lymphoma_Follicular from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Lymphoma_Follicular from lymph node, on Genome GRCh38. 7 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002931

• BLUEPRINT September 2016, ChIPmentation Burkitt Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002939

• RNA sequencing of multiple tumor biopsies and patient-derived spheroids from five colorectal cancer patients (BAM files)

  Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.

  Dataset EGAD00001003820

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - mobile_elements

  Samples from Edwards et al 2015 - doi:10.1186/s12864-015-1685-z

  Dataset EGAD00001001048