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• Transcriptome profiling of head and neck squamous cell carcinomas with paired patient-derived xenografts

  This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.

  Dataset EGAD50000000995

• WES of head and neck cancer patients refractory to anti-PD-1 therapy

  Whole exome sequencing (WES) was performed on baseline (before low-dose 5-aza treatment) blood and tumor paired samples from 12 participants with head and neck cancer who were refractory to anti-PD-1 therapy. DNA extractions were performed by the Broad Institute of MIT and Harvard using Qiagen AllPrep DNA/RNA kits (Cat. 80204). In total, 24 150-bp pair-end WES data were generated by Illumina.

  Dataset EGAD50000001011

• Indonesian Microbiome Ecology and Evolution v1 - Data Access Policy

  This Data Access Policy sets forth the terms, conditions, and limitations governing access to and use of the raw sequencing data of samples in the Indonesian Microbiome Ecology and Evolution (IndoMEE) v1 dataset by individuals who are not part of the Data Producer. The IndoMEE v1 dataset comprises 126 human faecal samples collected across Indonesia between 2015 and 2021, that was collected to study patterns of human microbiome variation across Indonesia’s diverse geography and lifestyles.

  Dac EGAC50000000587

• Single-cell RNA seq-derived signatures define response patterns to atezolizumab + bevacizumab in advanced hepatocellular carcinoma

  FASTq files and normalised gene expression counts from bulk RNA-sequencing of pre-treatment tumour (n=39) and adjacent non-tumour tissue samples (n=13) from advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab.

  Study EGAS50000000838

• Human Single-Oocyte Transcriptome - Control and Cannabis Treated

  RNAseq data of human single oocytes exposed to THC and its metabolites, (mean concentration measured in the follicular fluid, THC1, n=95, 25 ng/mL Δ9-THC, 5 ng/mL 11-OH-THC, 50 ng/mL 11-COOH-THC) or a supraphysiologic, THC2, n=93, 100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC).

  Dataset EGAD50000001534

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980

• RNA-Sequencing data of Fusobacterium nucleatum treated CAFs and HT-29 tumor spheroid exposed to Fusobacterium nucleatum treated CAFs conditioned medium.

  RNA-Sequencing data of CAFs (patient derived CAF180 and CAF181 as well as the CT5.3 CAF cell line) and HT-29 tumor spheroid samples performed in the context of the study of the interaction of Fusobacterium nucleatum with CRC CAFs. Fusobacterium nucleatum interacts with cancer-associated fibroblasts to enhance colorectal cancer progression

  Dataset EGAD50000001614

• M116 Whole Genome Sequencing

  Whole Genome Sequencing (WGS) was performed using DNA extracted from M116’s blood, saliva, and urine samples. DNA was fragmented to 350 bp, followed by library preparation, paired-end 150 bp WGS, and variant calling, all conducted by Novogene®. Sequencing was carried out with a 10X coverage (approximately 60 Gb and 200 million reads per sample) using the NovaSeq X Plus platform (Illumina). Files types included in this dataset are raw Fastq files.

  Dataset EGAD50000001286

• Visium Spatial tramscriptomics data set

  This data set contains raw FASTQ files and processed files of spatial transcriptomics of 6 EMD samples collected from MM patients. The processed files contain the h5 expression matrices, the Image of the Visium slide, and a TSV of spatial coordinates. Patients included in this data set are PT01A, PT01B, PT02, PT03, PT07, PT08, PT09, PT10, and PT11.

  Dataset EGAD50000000336

• WGS

  A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

  Dataset EGAD50000002026

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• exploration of biomarkers in colorectal cancer

  Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

  Study JGAS000489

• Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors

  We performed whole genome and whole exome sequencing analyses of pancreatic tumors, duodenal tumors and biliary tumors and investigated the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling.

  Study JGAS000359

• The analysis of gene mutations in Hematology malignancy

  We analysed the mutations of target genes regarding malignant lymphoma and myeloma to investigate the relationships between clonal evoutions and disease status. The gene mutation analyses using NGS at the point of diagnosis and relapse or proceeding disease.

  Study JGAS000232

• Analyses of transcriptome and epigenome in cardiac fibroblasts

  We report genome-wide bulk RNA- and ATAC-seq analysis of cardiac fibroblasts isolated from two patients. Cells were pre-treated with either KAT5 inhibitor or vehicle, and their fibrotic responses after TGF-β stimulation was measured.

  Study EGAS50000000835

• scRNA and V(D)J sequencing of WM under ibrutinib

  Single-cell RNA sequencing (5′ gene expression) and single-cell V(D)J sequencing (B-cell receptor and T-cell receptor) were performed on bone marrow mononuclear cells from patients with Waldenström macroglobulinemia treated with ibrutinib monotherapy. Sequential bone marrow aspirate samples were collected at baseline and after treatment. A total of 222 BAM files are included in this dataset.

  Dataset EGAD50000002279

• Case Report: Pre-Clinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma

  We report a rare case of a young patient (VENUS 167) initially diagnosed with grade 1 endometrioid endometrial cancer, which, following endocrine treatment, presented with mixed aggressive carcinoma with three distinct histologic patterns: grade 1 endometrioid, large cell neuroendocrine, and undifferentiated carcinoma. The NGS fastq data are WES, RNAseq and ATAC

  Dataset EGAD50000002397

• Whole Genome Methylation in CLL

  We have extensively characterized the DNA methylome of chronic lymphocytic leukemia (CLL) with mutated and unmutated IGHV as well as several mature B cell subpopulations using whole-genome bisulfite sequencing and high-density microarrays.

  Study EGAS00001000272

• Alternative splicing in Shh-MB

  We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

  Study EGAS00001003220

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Study EGAS00001005151

• Overactivation of the IGF signalling pathway in osteosarcoma

  Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who confirmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

  Study EGAS00001004767

• MiRNome_pituitary_adenoma

  Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a).

  Dataset EGAD00001004998

• Characterization of Leukemic Stem Cells in DNMT3Amut and NPM1mut AMLs

  Using a novel sorting strategy, we performed ultra low input RNAseq from FACS-sorted populations from diagnostic DNMT3Amut and NPM1mut AML patients. Primary samples were retrospectively collected based on their mutational profile. Samples were thawed, stained and FACS sorted using combination of lineage markers, CD34, GPR56 and NKG2DLigands. RNA was extracted and library prepared from 13 samples.

  Dataset EGAD00001009293

• Longitudinal ctDNA in Uveal Melanoma

  This dataset contains data from 11 uveal melanoma patients. Plasma samples were collected at baseline, 2-weeks, 3-, 6-, and 12-months post treatment (surgery/radiation). Samples underwent targeted panel, shallow whole genome, and cfMeDIP sequencing. A total of 46 plasma samples, 7 tumours, 11 buffy coats, and 10 healthy controls are included.

  Dataset EGAD00001008998

• RNA-seq from PDAC samples

  Bam and fastq files from RNA-seq of PDAC samples described in Transcription phenotypes of pancreatic cancer are driven by genomic events events during tumour evolution

  Dataset EGAD00001005799