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• EGAD00010000606

  SNP6 data for matched normal samples

  Dataset EGAD00010000606

• Comprehensive analysis of interaction between human gene expression and environmental metagenomes.

  WGS, 10x scRNA, 10X TCR, 10X BCR and CyTOF analyses were performed using blood samples collected from healthy volunteers aged 18 years or older who worked or lived in the Kashiwa-no-ha area.

  Study JGAS000321

• Genomic and transcriptomic analysis on hepatocarcinogenesis after HCV eradication

  Little is known about the genomic and transcriptomic features of hepatocellular carcinoma developing after HCV eradication (SVR-HCC). In this study, we aimed to unveil the genomic and transcriptomic basis of hepatocarcinogenesis after SVR.

  Study JGAS000234

• 419 Japanese healthy control

  Genotypes of 419 Japanese healthy individuals genotyped by using of SNP arrays (Genome-Wide Human SNP Array 6.0 and Axiom Genome-Wide ASI 1 Array). CEL files and CHP files are included in this data set.

  Study JGAS000120

• Global RNA sequencing data of human iPSC-derived microglia from frontotemporal dementia (FTD) patients

  Global RNA sequencing was performed in RNA samples extracted from human iPSC-derived microglia from healthy controls and sporadic (non-genetic) and genetic C9orf72 hexanucleotide repeat expansion-carrying patients with FTD.

  Study EGAS50000001688

• Single-cell RNA-seq of PBMC from 2 patients iGRAN-Low and 2 patients iGRAN-High

  Single-cell RNA-seq of PBMC from 2 patients iGRAN-Low and 2 patients iGRAN-High [Publication title] CXCL8 secreted by immature granulocytes inhibits wildtype hematopoiesis in chronic myelomonocytic leukemia

  Study EGAS50000000556

• Bulk-RNAseq from human nerve fascicles and Schwann cells

  Bulk-RNAsequencing from human nerve fascicles from patients with polyneuropathies, and human Schwann cell cultures isolated from said nerve fascicles, in comparison to control human Schwann cell cultures and a referential fibroblast culture.

  Study EGAS50000000737

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 208 patients with mUC

  Targeted tissue (n=81), cfDNA (n=319), and WBC (n=208) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000002089

• McQuillin_Global_WES_Schizophrenia

  This research project was a collaboration between University College London, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,623 Schizophrenia, Bipolar and Control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000001316

• Tumor Profiler Project - OV bulk transcriptomics data

  The dataset contains bulk transcriptomics data from 39 samples from 36 different patients with ovarian cancer. 34 samples were collected from the tumor, 5 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001413

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 226 patients with mUC

  Targeted tissue (n=210), cfDNA (n=402), and WBC (n=245) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000001571

• Whole-genome sequencing with complement C1s deficiency linked to systemic lupus erythematosus

  This dataset includes two FASTQ files (R1 and R2) from an Illumina germline nuclear DNA whole-genome sequencing run of a single sample. The sample corresponds to a 34-year-old male with a rare deficiency in complement component C1s, linked to systemic lupus erythematosus (SLE). Genomic analysis revealed two novel mutations in the C1S gene.

  Dataset EGAD50000000988

• WES of precancerous lesions from 10 lynch patients and 3 sporadics

  Raw sequencing data of WES that were obtained from precancerous samples as adenoma and MMR-deficient crypts and paired healthy tissue from MSI CRC patients of which 10 are diagnosed with lynch syndrome and 3 had sporadic cancer. These data were analyzed in order to evaluate microsatellite instability though tumorigenesis and associated to splicing deregulation in MSI tumors RNA.

  Dataset EGAD50000000644

• Tumor Profiler Project - MEL bulk transcriptomics data

  The dataset contains bulk transcriptomics data from 80 samples from 77 different patients with melanoma. Samples were collected from the tumor. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000000851

• Triple_Negative_Breast_Cancer_Whole_Genomes

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000092

• Transcriptome_Sequencing_of_Cancer_Cell_Lines

  In this study we will sequence the transcriptome of Verified Cancer Cell lines. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000261

• RNA seq of MPNST tumour samples

  RNA sequencing of 10 MPNST tumour samples as part of a larger study of MPNST. Article: Lyskjær et al, 2020, J Pathol, "H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours".

  Study EGAS00001004528

• Tumor HTG EdgeSeq from metastatic castrate resistant prostate cancer

  This dataset contains tumor bulk HTG EdgeSeq from patients with metastatic castrate resistant prostate cancer. RNA libraries were prepared following manufacturer's user guide (HTG Molecular Diagnostics). Each library was sequenced in HTG EdgeSeq system.

  Study EGAS00001004852

• RNA sequencing of high hyperdiploid and ETV6/RUNX1-positive pediatric acute lymphoblastic leukemia

  We performed RNA-sequencing of high hyperdiploid and ETV6/RUNX1-positive ALL cases by using the Human Ribo-Zero rRNA Removal Kit to investigate the gene expression in high hyperdiploid ALL.

  Study EGAS00001003079

• Dedifferentiated_Melanoma_RNAseq

  De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up.

  Study EGAS00001003601

• Spectrum and significance of MYC and BCL2 mutations in DLBCL

  We analyzed the spectrum and clinical significance of MYC and BCL2 mutations in 347 DLBCL cases from population-based cohort of BC, Canada.

  Dataset EGAD00001003140

• Somatic mutations in 106 small intestine adenocarcinoma

  106 FFPE tumor samples from small bowel were sequenced with Illumina HiSeq 4000. Exome capture was performed with NimbleGen SeqCap EZ Exome Library v3 Kit. Reads were aligned with BWA–MEM v.0.7.12 to GRCh37 reference genome. Variant calls were produced with GATK HaplotypeCaller. Variant calls were filtered against all data from gnomAD database using allele frequency threshold 0.0001 in order to remove germline variation.

  Dataset EGAD00001003802

• Rare germline variants of acute myeloid leukemia patients

  The dataset (vcf files) consists of rare germline variants of 68 Finnish acute myeloid leukemia patients. We performed exome sequencing and filtered the germline variants against ExAC total MAF<0.01 in two gene panels. The 35 genes in the panels studied here have previously been associated with hematological malignancies and/or solid tumors. The dataset contains only variants of the two gene panels.

  Dataset EGAD00001003894

• Whole-genome sequencing of paired tumor and blood samples from 65 bladder cancer patients

  65 paired tumor and normal whole-genome sequencing samples from urothelial bladder carcinomas (UBC, the most common type of bladder cancer) are used to uncover the whole-genome mutational landscape of UBC. Recurrent mutations in noncoding regions affecting gene regulatory elements and structural variations leading to gene disruptions are prevalent in this type of cancer.

  Dataset EGAD00001004545

• Epigenetic profiling of colorectal cancer initiating cells (CC-ICs) and investigation of changes in transcriptome following EZH2 inhibition using RNA-seq.

  Epigenetic profiling of colorectal cancer initiating cells (CC-ICs) to identify bivalently marked genes (H3K4me3 and H3K27me3 ChIP-seq), and investigation of changes in transcriptome following EZH2 inhibition using RNA-seq.

  Dataset EGAD00001004133