4736 results for "*oma"

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• Genome and transcriptome sequence data from a abdominal sarcoma patient

  Genome and transcriptome sequence data from a abdominal sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004919

• Whole Transcriptome Sequencing

  RNA-seq data of 15 snap-frozen tissue of peritoneal mesothelioma. The strand specific RNA library prepared using TruSeq (Illumina) and pair-end sequencing performed in Illumina HiSeq 4000. The datasets contains paired fastq files for each of 15 tumor samples.

  Dataset EGAD00001004504

• Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Whole Genome Sequencing (WGS) for St. Jude High Grade Glioma (HGG) study

  Dataset EGAD00001000806

• Failure of Differentiation of the Rhombic Lip Constitutes Medulloblastoma

  We used single-cell transcriptomics to study cells from the developing human cerebellum, and show that different molecular subgroups of medulloblastoma resemble distinct glutamatergic progenitors.

  Dataset EGAD00001008381

• Genome and transcriptome sequence data from a squamous cell carcinoma of the alveolar ridge patient

  Genome and transcriptome sequence data from a squamous cell carcinoma of the alveolar ridge patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004934

• scRNA data of neuroblastoma patients

  31 single-cell transcriptomes of neuroblastomas and normal human developing adrenal glands at various stages of embryonic and fetal development

  Dataset EGAD00001006624

• Follicular lymphoma shallow whole genome sequencing and targeted sequencing of lymphoma panel

  Stage I and stage III/IV Follicular lymphoma samples, shallow whole genome sequencing for copy number analysis and targeted capture sequencing for mutation and translocation analysis.

  Dataset EGAD00001008385

• RNA-seq samples

  Raw FASTQ files obtained by RNA sequencing of tumor samples from patients (age 12-29) with newly diagnosed, recurrent intermediate or high-grade sarcoma.

  Dataset EGAD00001008393

• WES tumor samples

  Raw FASTQ files obtained from whole exome sequencing (WES) of tumor samples from patients with newly diagnosed, recurrent intermediate or high-grade sarcoma.

  Dataset EGAD00001008394

• Single-nuclei gene-expression analysis of pheochromocytoma and paraganglioma links tumor subtypes with tumor microenvironment

  This dataset contains raw sequencing reads in FASTQ format from single-nuclei (30 samples) and bulk tissue (40 samples) transcriptome sequencing of pheochromocytoma and paraganglioma tissue specimens. Additionally, data from single-nuclei sequencing of two normal adrenal medulla specimens is included.

  Dataset EGAD00001008403

• GEX CITE-Seq performance dataset

  To understand the impact of enzymatic treatments on gene expression and epitope preservation on major immune cell populations, skin dissociation (SkinD) and solid soft tumor dissociation (TumorD) were tested on three healthy PBMC samples in triplicate (D1, D2, D3), against an untreated control. CITE-seq performance was assessed on a solid biopsy cohort of 11 samples (5 healthy skin samples, 3 primary melanoma samples, 3 melanoma metastasis samples) as well as on a liquid biopsy PBMC cohort consisting of three healthy donors and three immunotherapy-treated melanoma patients. This dataset contains the GEX data for each sample. Data is provided in the form of pooled BAM files. Linkage between samples, BAM files and hashtags is provided in a separate linkage file.

  Dataset EGAD00001008418

• 10x Genomics Single Cell Gene Expression for SA1050EX1XB01442

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1050 passage 1

  Dataset EGAD00001009141

• Mucoepidermoid Carcinoma

  Whole exome sequencing data for 18 mucoepidermoid carcinoma samples. The samples were used for Illumina TruSeq library construction and captured using Agilent V4 exome panel. The PE fastq files are provided.

  Dataset EGAD00001003958

• 2014 Lung squamous cell carcinoma WES analysis result

  This data is belong to 2014 Lung squamous patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 104 paired tumor/normal samples from SMC. All samples has passed QC and re-calibration steps while aligning to reference.

  Dataset EGAD00001003960

• Epithelioid sarcoma dataset

  This deposit consists of DNA and RNA sequencing data from 32 EPS patients. 28 samples had tumor DNA sequencing data. 2 had matched normal sequencing data. 27 samples had tumor RNA sequencing data.

  Dataset EGAD00001008515

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

  Data supporting: "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. RNAseq (BAM files) 214 oesophageal adenocarcinoma samples

  Dataset EGAD00001007809

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

  In this dataset there are 55 whole genome sequencing samples of epithelial ovarian carcinoma (bam files).

  Dataset EGAD00001004532

• Pleomorphic invasive lobular carcinoma targeted exome sequencing

  Fifteen pleomorphic invasive lobular carcionoma samples and their matched normal controls were subjected to targeted exome sequencing using the Beijing Genomics Institute TumorCare gene panel. Genomic DNA samples were randomly fragmented and captured libraries of each exome were sequenced on an Illumina Hiseq2000 system. CRAM files are provided for each tumor and normal pair.

  Dataset EGAD00001003995

• FACS sorting of ploidy populations in an undifferentiated soft tissue sarcoma for RRBS

  Groups of cells belonging to different ploidy populations (based on PI staining) were collected from an undifferentiated soft tissue sarcoma. The different ploidy populations underwent RRBS, after which copy number signatures for the ploidy-sorted populations and the bulk population were extracted.

  Dataset EGAD00001008667

• RNA-seq of multiple myeloma patient samples

  RNA from CD138+ plasma cells from patients with a plasma cell dyscrasia were sequenced using the TruSeq Stranded Total RNA Ribo-zero Gold kit (Illumina). Paired-end 75bp reads were generated on a NextSeq500 or HiSeq4000 (Illumina). The dataset consists of 1 MGUS sample, 5 SMM samples, 69 newly diagnosed myeloma samples, 1 relapsed myeloma sample, 1 previously treated myeloma samples, and 4 PCL samples. Matching whole genome sequencing data are available for these samples under study EGAS00001003164.

  Dataset EGAD00001004543

• Whole exome sequencing study of cholesteatoma patients from affected families

  This study used whole exome sequencing on 21 patients with cholesteatoma from 10 families in order to identify variants that may attribute to cholesteatoma aetiology. Exomes were enriched for using hybridisation selection and subject to DNA-sequencing. This datasets is formed of two batches as they were sequencing at different times. Batch-1 exomes were selected for using Nimblegen capture (4-plex) and sequenced on Illumina Hiseq 4000 and batch-2 was exome selected using Agilent SureSelect Human All Exon v6 and sequenced on the Illumina NovaSeq 6000. All samples within the same family were processed within the same batch. This dataset is comprised on BAM files mapped using cgpMAP v3.2.0 (bwa-mem) using the GRCh38.

  Dataset EGAD00001008671

• Whole transcriptome sequencing of 38 follicular lymphoma tumours.

  This data set includes RNAseq from 38 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

  Dataset EGAD00001009650

• HBV-associated hepatocellular carcinoma

  Fastq files of whole-genome bisulfite sequence of tumor tissue of HBV-associated hepatocellular carcinoma

  Dataset EGAD00001004033

• DNA whole-exome sequencing data from patients with metastatic basal cell carcinoma

  Whole-exome sequencing data in fastq format of matched tumour and germline DNA from 8 patients with metastatic basal cell carcinoma. Samples are labeled as Primary, Local or Metastasis: Primary: Sample was obtained from primary tumour. Local: Sample was obtained from local recurrence of primary tumour. Metastasis: Sample was obtained from a metastatic site. Germline: Sample was obtained from normal adjacent tissue. DNA was isolated from FFPE tissue sections of the tumor biopsies using the AllPrep DNA/RNA FFPE Kit (Qiagen) and quality controls conducted using the Qubit fluorometer (Thermo Fisher Scientific). Library preparation was performed using the Agilent SureSelect Human All Exon v7 XTHS2 probes and sequenced on a NovaSeq 6000 S2 2x100bp

  Dataset EGAD00001008675

• Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

  Small RNA sequencing data (TruSeq small RNA library preparation kit v2) from serum samples and tumor tissue of orthotopically injected mice (SH-SY5Y cell line) and unengrafted mice, treated with idasanutlin, temsirolimus and vehicle control.

  Dataset EGAD00001009625

• RNAseq of primary mesothelioma cell lines

  Mesothelioma is an aggressive cancer associated with previous exposure to asbestos and dismal prognosis. Since a pemetrexed/cisplatin combination was introduced for treatment of mesothelioma, no new first- or second-line therapies have been discovered. Thus, to better understand what drives mesothelioma carcinogenesis and to identify potential targets for therapy, in this project we aim at performing RNAseq analysis of a panel of mesothelioma cells lines.

  Dataset EGAD00001009642

• CD74-NRG1 study - RNASeq dataset

  RNAseq data, Publication Fernandez-Cuesta et al., 2014, CD74-NRG1 fusions in lung adenocarcinoma

  Dataset EGAD00001000716

• DKFZ-St.Jude Medulloblastoma - 9 SJMB tumor/control pairs, exome

  9 tumor/control exomes, SJMB samples, sequenced on Illumina machines from the paper "Germline Elongator mutations in Sonic Hedgehog medulloblastoma" (Waszak et al. 2020 Nature).

  Dataset EGAD00001006663

• Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the cheek patient

  Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the cheek patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004603

• Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient

  Genome and transcriptome sequence data from a mucinous colloid carcinoma of the pancreas patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004598

• Fecal 16S rRNA gene sequencing

  Human fecal 16S rRNA gene sequencing data from patients treated with combined anti-CTLA-4 and anti-PD-1 immunotherapy for advanced melanoma.

  Dataset EGAD00001006735

• Genome and transcriptome sequence data from a metastatic follicular thyroid carcinoma patient

  Genome and transcriptome sequence data from a metastatic follicular thyroid carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004614

• Genome and transcriptome sequence data from a metastatic adrenocortical carcinoma patient

  Genome and transcriptome sequence data from a metastatic adrenocortical carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004905

• Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma of the breast patient

  Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma of the breast patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004921

• Multi-region sequencing of colon tumour biopsies and matched normals

  Dataset of adenoma and colon cancer multi-region sequencing. Publication: Nat Ecol Evol. 2018 Oct;2(10):1661-1672. doi: 10.1038/s41559-018-0642-z. Epub 2018 Aug 31.

  Dataset EGAD00001004966

• Genome and transcriptome sequence data from a metastatic uveal melanoma patient

  Genome and transcriptome sequence data from a metastatic uveal melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004647

• Genome and transcriptome sequence data from a metastatic leiomyosarcoma of pancreas patient

  Genome and transcriptome sequence data from a metastatic leiomyosarcoma of pancreas patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004662

• Genome and transcriptome sequence data from a non-small cell lung carcinoma patient

  Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004669

• Genome and transcriptome sequence data from a metastatic thymic carcinoma patient

  Genome and transcriptome sequence data from a metastatic thymic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004678

• VCF files of Roma and non-Roma Romanians

  VCF files with whole genome sequencing data of 49 individuals of European/Romanian descent, and 50 individuals of Roma (Romani/Rroma) ethnic background from Romania.

  Dataset EGAD00001004982

• RNA-seq data of 370 high grade ovarian tumors from the ICON7 trial

  Collection of RNA-seq, Illumina, paired-end fastq files for 370 archival tissues from a subset of patients with high grade serous ovarian carcinoma enrolled in the phase 3 ICON7 trial. Clinical data and digital pathology information for CD8 is also available.

  Dataset EGAD00001004988

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004680

• Genome and transcriptome sequence data from a angiosarcoma patient

  Genome and transcriptome sequence data from a angiosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004690

• RNAseq_pituitary_adenoma

  Total RNA was extracted using RNAble (Eurobio), cleaned-up with RNeasy columns (Qiagen) and sequenced. The libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq Stranded mRNA protocol (Illumina), starting from 1 µg of high quality total RNA. Paired end (2 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on hg19 (GRCh37) human reference genome with STAR (v.2.5.2a)

  Dataset EGAD00001004996

• Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004700

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the lung patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004708

• DNA (exome) sequencing of uveal melanoma metastases

  DNA (exome) sequencing of uveal melanoma metastases.

  Dataset EGAD00001007911

• BLUEPRINT release January 2015, Bisulfite-Seq for Multiple myeloma

  Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001152

• Myeloid-specific KDM6B inhibition sensitizes Glioblastoma to PD1 blockade

  This data set include FASTQ files for five experiments: Human scRNA-Seq data (6 samples), Human Visium spatial transcriptomic data (3 samples), Mouse scRNA-seq data (4 samples), Mouse scATAC-seq data (2 samples), Mouse ChIP-seq data (8 samples). For the mouse scATAC-seq data (2 samples), there are originally three FASTQ files, R1, R2 and R3 files. The R1 and R2 FASTQ files were merged into one larger file ("R1R2") per sample for submission as paired-end sequencing setting to follow the EGA guidelines. They can be split into individual R1 and R2 files in order to be processed by Cell Ranger software. The files with IC1 suffix are CHIP-seq Input control for anti-KDM6B antibody pull down experiments and the files with IC2 suffix are CHIP-seq Input control for anti-H3K27ME3 antibody pull down experiments in murine model.

  Dataset EGAD00001010073

• Uveal melanoma whole genome sequencing, SNP arrays and RNA-seq

  We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

  Dataset EGAD00001000372

• CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  CM214 - Biomarker Analysis From the Phase 3 CheckMate 214 Trial of Nivolumab Plus Ipilimumab (N+I) or Sunitinib (S) in Advanced Renal Cell Carcinoma (aRCC)

  Dataset EGAD00001007938

• Genome and transcriptome sequence data from a T-cell rich B cell lymphoma patient

  Genome and transcriptome sequence data from a T-cell rich B cell lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003724

• Whole Genome Sequencing of Mutifocal HCC tisue

  The differentiation of distinct multifocal hepatocellular carcinoma (HCC): multicentric disease vs. intrahepatic metastases, in which the management and prognosis varies substantively, remains problematic. We aim to stratify multifocal HCC and identify novel diagnostic and prognostic biomarkers by performing whole genome and transcriptome sequencing, as part of a multi-omics strategy.

  Dataset EGAD00001003348

• UAMS Smoldering Myeloma Timeline Cohort

  To better understand the pattern of genetic changes over time, we performed whole exome sequencing of sequential bone marrow samples from 9 patients taken overtime including some paired SMM/newly diagnosed MM/Relapse MM samples. Samples from 9 patients (9 controls and 53 tumors) underwent whole exome sequencing with an additional capture for the IGH, IHK, IGL, and MYC loci. DNA was obtained from either CD138+ cells from the bone marrow of smoldering myeloma patients through time (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using NimbleGen's MedExome. After PCR amplification hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Dataset EGAD00001005056

• PacBio medulloblastoma datasets

  PacBio data from 5 medulloblastoma tumor-normal pairs. The data consists of BAM files aligned using NGMLR

  Dataset EGAD00001010852

• Genome and transcriptome sequence data from a clear cell adenocarcinoma patient

  Genome and transcriptome sequence data from a clear cell adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008940

• Genome and transcriptome sequence data from a carcinoma of unknown primary patient

  Genome and transcriptome sequence data from a carcinoma of unknown primary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008945

• WGS of T-cell and NK-cell lymphoma for ICGC (NKTL-SG)

  WGS of T-cell and NK-cell lymphoma The tumor samples were sequenced with Illumina HiSeq 2500 platform and the resulting FASTq files have been uploaded.

  Dataset EGAD00001003271

• Melanoma post mortem analysis

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.

  Dataset EGAD00001005073

• Osteosarcoma capture-based RNA sequencing

  This dataset includes 23 specimens from osteosarcoma patients (primary, relapsed, metastatic). It contains bam files from RNA sequencing using a library in which coding regions of cDNA are captured and short-read, paired-end sequencing.

  Dataset EGAD00001008434

• CRISPR/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase

  Here we report successful gene knock-in (KI) in the eggs of Schistosoma mansoni by combining CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs). We targeted the acetylcholinesterase (AChE) gene of S. mansoni using two synthetic guide RNAs (gRNAs), X5 and X7, respectively. Liver eggs of S. mansoni were exposed to CRISPR-vector containing X5 or X7 by electroporation. Simultaneously, eggs were transfected with a ssODN donor encoding a stop codon in all six frames. Next generation sequencing analysis revealed that CRISPR/Cas9-mediated editing in S. mansoni eggs resulted in Homology-Directed Repair (HDR) when template DNA ssODN provided. Furthermore, soluble egg antigen (SEA) from AChE-modified eggs exhibited markedly reduced AChE activity compared with controls, indicative that programmed Cas9 cleavage mutated the AChE gene. Following injection of modified schistosome eggs into the tail veins of mice, a significant decrease in granuloma size in the lungs of these animals. Notably, an enhanced Th2 response induced by eggs in lung, and splenocytes small intestine-draining mesenteric lymph node cells was also generated in mice injected with X5-KI eggs in different methods. These findings further demonstrate the power and utility of CRISPR/Cas9-based genome editing for undertaking functional genomics studies in schistosomes.

  Dataset EGAD00001006573

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Dataset EGAD00001010156

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Patient-derived GBM cultures TMZ+BMP4 treated

  Batch RNA sequencing of passages 5-7 of three patient-derived monolayer glioblastoma cultures in which TMZ and BMP4 synergize. 3 biological replicates, either untreated, only temozolomide, only BMP4 or temozolomide + BMP4

  Dataset EGAD00001010163

• Targetable NOTCH1 rearrangements in reninoma - RNA

  Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

  Dataset EGAD00001010889

• RBtargetedSeq

  Retinoblastoma is a rare childhood cancer of the retina. We studied retinoblastoma by Targeted Sequencing.

  Dataset EGAD00001008004

• Human tumor single-nuclei RNA-seq

  We profiled 4 patient neuroblastoma-FORX2 tumor samples by single-nuclei RNA-seq using 10X Chromium 3'. The raw fastqs are provided.

  Dataset EGAD00001010903

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• Transcriptome (RNA-seq) data for the validation of the glioblastoma progression study (GBMatch).

  37 transcriptomes derived from fresh-frozen glioblastoma tumor samples. These transcriptomes have been produced for validation purposes and match the corresponding RRBS and WGS profiles in that DNA and RNA was extracted from the same tumor samples.

  Dataset EGAD00001004076

• Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of neuroblastoma xenograft models.

  Dataset EGAD00001010905

• Exome-sequencing of H3-K27M glioma.

  Fastq or bam files are deposited for 28 patient H3-K27M diffuse midline gliomas. UMPEDD65 was profiled by targeted exome-sequencing using the TSO500 Illumina assay, while all other samples were sequenced by whole-exome sequencing.

  Dataset EGAD00001009269

• Whole exome and RNA sequencing data from urothelial bladder cancer patients treated with anti-PD-(L)1

  We have generated and analyzed genomic data from a cohort of metastatic urothelial carcinoma patients treated with ICI such as anti-PD-(L)1 monoclonal antibodies. The dataset contains whole exome sequencing data of 27 whole blood samples and 27 FFPE tumor samples. Further, it includes RNA sequencing data from 21 tumor samples. Following the RECIST criteria, 10 patients were classified as non-responders to the treatment, and 17 were responders. The dataset also contains a merged vcf file containing somatic mutations called by Strelka2 and Mutect2 following the gatk best practice pipeline.

  Dataset EGAD00001010324

• Spatial targeted gene sequencing of metastatic melanoma

  We performed deep targeted DNA sequencing for a panel of 265 cancer-related genes. This included subsampling 35 different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor. Samples with cancer cell purity greater than 80% based on pathologic assessment were used for cancer gene panel DNA sequencing. Mean sequencing coverage was 861x and paired-end reads in FASTQ format were generated by the Illumina pipeline and aligned to the reference human genome hg19 build using the Burrows-Wheeler Alignment Tool (BWA, v0.7.5) with default settings. Aligned reads were further processed using GATK with best practices for removing duplicates, indel removal and recalibration.

  Dataset EGAD00001005821

• 10x Genomics Single Cell Gene Expression for SA1049CX1XB01422

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1049 passage 1

  Dataset EGAD00001009140

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

  Genome and transcriptome sequence data from a lung adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005880

• Genome and transcriptome sequence data from a metastatic epitheloid angiomyelolipoma patient

  Genome and transcriptome sequence data from a metastatic epitheloid angiomyelolipoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003689

• Single Cell Genome Sequence for DLP+ library A118797B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1184D passage 1 on DLP+ library A118797B

  Dataset EGAD00001009438

• Gene panel sequencing of paired samples from primary and relapsed IDH-wt glioblastomas

  This dataset contains gene panel sequencing data from 43 sample pairs of primary and relapsed IDH-wt glioblastomas. The gene panel covers 50 glioma-associated genes. 14 of the sequenced sample pairs were sequenced with whole genome sequencing also and are accessible under EGAD00001004563.

  Dataset EGAD00001004565

• Genome and transcriptome sequence data from a metastatic gallbladder adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic gallbladder adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005903

• Genome and transcriptome sequence data from a breast ductal carcinoma patient

  Genome and transcriptome sequence data from a breast ductal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010946

• Genome and transcriptome sequence data from a endometrial adenocarcinoma patient

  Genome and transcriptome sequence data from a endometrial adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010949

• Genome and transcriptome sequence data from a breast ductal carcinoma patient

  Genome and transcriptome sequence data from a breast ductal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010950

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010951

• Genome and transcriptome sequence data from a carcinoma of unknown primary patient

  Genome and transcriptome sequence data from a carcinoma of unknown primary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010962

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of pancreas patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of pancreas patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010973

• Sequencing data for oesophageal and related samples - Abbas et al (RNA)

  Data supporting: "Mutational signature dynamics shaping the evolution of oesophageal adenocarcinoma" Abbas et al (RNA for 197 samples)

  Dataset EGAD00001011269

• Genome and transcriptome sequence data from a Ewing sarcoma patient

  Genome and transcriptome sequence data from a Ewing sarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003738

• Genome and transcriptome sequence data from a metastatic melanoma patient

  Genome and transcriptome sequence data from a metastatic melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004599

• Genome and transcriptome sequence data from a metastatic follicular lymphoma patient

  Genome and transcriptome sequence data from a metastatic follicular lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010978

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010984

• Genome and transcriptome sequence data from a prostate adenocarcinoma patient

  Genome and transcriptome sequence data from a prostate adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010988

• Genome and transcriptome sequence data from a non-small cell adenocarcinoma patient

  Genome and transcriptome sequence data from a non-small cell adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004600

• Genome and transcriptome sequence data from a follicular lymphoma patient

  Genome and transcriptome sequence data from a follicular lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004611

• Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

  Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004601

• Molecular Characterization for Nasopharyngeal Carcinoma (NPC)

  Total RNA was isolated from 50 formalin-fixed paraffin-embedded nasopharyngeal cancer (NPC) specimens using the RecoverAll Total Nucleic Acid Isolation kit (Ambion). Tumor RNA libraries were prepared with 200ng RNA using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Gold, and sequenced with >80 million 100 bp paired-end reads.

  Dataset EGAD00001009047

• Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004612

• Genome and transcriptome sequence data from a double-hit lymphoma patient

  Genome and transcriptome sequence data from a double-hit lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004624

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the salivary gland patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the salivary gland patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010992

• Genome and transcriptome sequence data from a metastatic basal cell carcinoma of frontal scalp patient

  Genome and transcriptome sequence data from a metastatic basal cell carcinoma of frontal scalp patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004621