4913 results for "*oma"

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• The UCSF Glioblastoma Genome Project #1

  Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.

  Dataset EGAD00001000777

• Tagged-amplicon deep sequencing

  This dataset contains a collection of tumour samples from high grade serous ovarian carcinoma patients with recurrent disease collected near the point of diagnosis as well as tumour samples collected after patient relapse upon or some time after study entry. Whole blood samples were also collected from patients at study entry for the purpose of germline variant detection. The majority of diagnosis samples were preserved in neutral buffered formalin whereas the majority of post-relapse samples were preserved in universal molecular fixative (UMFIX, Sakura Finetek USA, Inc). DNA was extracted and the tagged-amplicon deep sequencing assay was applied (TAm-Seq, Forshew et al. 2002, Sci Transl Med) with the aid of fluidigm access array technology. Targeted loci were sequenced at very high depths (typically >100X) for the detection of both somatic and germline variants. Sequenced reads were aligned to the GRCh37 reference genome (release hs37d5).

  Dataset EGAD00001011058

• WXS dataset of Ewing and Ewing-like-sarcoma tumoroid biobank reveals distinct drug sensitivities: translocation makes the difference

  Creation of living organoid biobank for ewing and ewing-like sarcomas

  Dataset EGAD00001015417

• MSI2 knockdown and inhibition in mantle cell lymphoma cell lines RNAseq data

  Fastq transcriptomic sequencing files from Z138 mantle cell lymphoma (MCL) cell line upon MSI2 knockdown (KD) with two different shRNAs and after MSI2 inhibition with Ro 08-2750 small molecule. Dataset includes 4 samples of Z138 MSI2-KD, 4 of Z138 control, 3 of Z138 treated with Ro 08-2750 and 3 of Z138 treated with DMSO.

  Dataset EGAD00001009420

• Mantle cell lymphoma primary cases RNAseq data

  Dataset includes fastq transcriptomic sequencing files from 8 conventional (SOX11+) and 4 non-nodal (SOX11-) mantle cell lymphoma (MCL) primary cases. RNA-sequencing has performed from peripheral blood and lymph node diagnostic samples.

  Dataset EGAD00001009422

• HCC.GNE exome dataset

  Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma".

  Dataset EGAD00001000885

• 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

• Single cell characterization of T-cell lymphoma: RNA (2025-07-31)

  Lymphomas are types of blood cancer derived from lymphocytes, and can be classified into two main categories, Hodgkin's lymphomas (HL) and non-Hodgkin lymphomas (NHL). T-cell lymphoma is a type of NHL that develops from T lymphocytes and accounts for 10-15% of total NHL cases. As a rare disease, T-cell lymphoma is functionally, pathologically, and clinically complex and heterogeneous. The 2016 revision of the WHO classification has listed 29 subtypes of mature T/NK-cell neoplasms, among which over 25 are T lymphocyte in origin. These subtypes of T-cell lymphomas have different biological behaviours and clinical prognosis. Clinically, T-cell lymphoma ranges from indolent (slow-growing) to aggressive (fast-growing and spreading) disease. According to the guideline booklet provided by the Lymphoma Research Foundation (https://lymphoma.org/aboutlymphoma/nhl/), indolent T-cell lymphoma subtypes include adult T-cell leukaemia/lymphoma (ATLL), cutaneous T-cell lymphoma (CTCL), and mycosis fungoides (MF), while the aggressive subtypes include anaplastic large cell lymphoma (ALCL), angioimmunoblastic T-cell lymphoma (AITL), peripheral T-cell lymphoma (PTCL), and T lymphoblastic lymphoma (TLBL). PTCL and ALCL represent the most common subtypes of aggressive T-cell lymphoma whereas TLBL is a rare and aggressive subtype mostly diagnosed in children. In this study, we will use single cell RNA sequencing and single cell multiomic methods three aggressive T-cell lymphoma subtypes (ALCL, PTCL and TLBL) and try to gain a deeper insight into the genotypic and phenotypic features of these T-cell lymphomas. . This dataset contains all the data available for this study on 2025-07-31.

  Dataset EGAD00001015669

• Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples

  We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Dataset EGAD00001004887

• Single Cell Genome Sequence for DLP+ library A96113A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage on DLP+ library A96113A

  Dataset EGAD00001009453

• Embryonic tumour transmission in monozygotic twins

  We have a case of two siblings (twins) who were born with nodular blue rashes over their body. The first twin had a large periorbital subcutaneous mass which was diagnosed as infantile undifferentiated sarcoma. This baby was too systematically unwell for chemotherapy and died at 12 days of age. The second sibling received two cycles of emergency chemotherapy however died due to disease progression and secondary haemorrhage at 2 months of age. Post-mortem normal and tumour samples have been taken. In addition to placental tissue and parental germline DNA, the goal will be to investigate intra-uterine transfer of sarcoma and the phylogenetic relationship of tumours in both twins.

  Dataset EGAD00001015681

• SF12264 snRNA-Seq Primary GBM

  Single Nuclei RNA-Seq Primary GBM. Gender Female Age 51. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005410

• 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 EGAD00001004916

• 10x Genomics Single Cell Gene Expression for OV2295

  10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma cell line OV2295

  Dataset EGAD00001009143

• Genotype data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the processed data from FMOne.

  Dataset EGAD00001006201

• HIPO blastemal Wilms (nephroblastoma) RNA sequencing samples

  HIPO blastemal Wilms (nephroblastoma) characterisation of tumor driving gene expression events

  Dataset EGAD00001000993

• Single Cell Genome Sequence for DLP+ library A108765A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1181A passage 1 on DLP library A108765A

  Dataset EGAD00001009428

• Single Cell Genome Sequence for DLP+ library A108847B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1182E passage 1 on DLP+ library A108847B

  Dataset EGAD00001009429

• Genomic and Functional Profiling of Acral Melanoma from the admixed Brazilian Population Reveals Disease Drivers and Targetable Vulnerabilities

  Acral melanoma, a subtype of melanoma characterized by its occurrence on palms, soles, and beneath the nails, presents unique challenges in diagnosis and treatment due to its distinct genetic and environmental factors. Despite recent advancements in targeted therapies for melanoma, the efficacy of treatments in acral melanoma remains limited, emphasizing the urgent need for a deeper understanding of its genetic landscape. CRISPR-based functional genomics screening has emerged as a powerful tool for uncovering genetic dependencies and potential therapeutic targets in various cancers. In this project, we present the results of CRISPR screening performed on acral melanoma cell lines to identify genes essential for cell survival and proliferation collectively termed “fitness". Through this screening approach, we aim to elucidate the molecular mechanisms underlying the pathogenesis of acral melanoma and identify novel therapeutic vulnerabilities. Our findings reveal key genetic drivers and pathways implicated in acral melanoma progression, offering potential targets for the development of precision therapies tailored to this aggressive subtype of melanoma

  Dataset EGAD00001015690

• Paired-end RNA-seq analysis of the 3D evolution of glioma cell populations. Part 2.

  Dataset contains paired-end RNA-seq sequencing data from 221 glioma samples.

  Dataset EGAD00001009497

• Whole genome sequencing and somatic mutation profiles and whole genome transcription files of pediatric medulloblastoma

  Fastq, Mutect (SNVs), Platypus (indels), and InfoGenomeR (SVs and CNAs) calls from whole genome sequencing data and fastq files of whole genome transcription data of five patients with pediatric medulloblastoma.

  Dataset EGAD00001009507

• Berlin Neuroblastoma Patient Genomic Data from Targeted Sequencing for Detection of TERT rearrangement breakpoints to monitor neuroblastoma

  Our objective was to establish a liquid biopsy-based monitoring strategy for pediatric high-risk neuroblastomas that are harboring genomic TERT rearrangements at diagnosis. TERT rearrangement breakpoints are detected by a hybrid capture-based neuroblastoma DNA panel sequencing (published in PMID: 34442335) in tumor material and are reflected in cell-free tumor DNA and can serve as robust biomarkers for disease activity. Within the dataset, 5 tumors of 4 pediatric patients with a neuroblastoma were DNA sequenced. Provided are FASTQ data files, bam and bambai files, as well as breakpoint spanning and encompassing read (enspan) bam and bambai files. Sequencing bam data files are aligned to GRCh37.p13 reference genome (processed).

  Dataset EGAD00001011088

• Additional RNASeq files for Roussel MBPRP

  Additional RNASeq files for Roussel paper titled "Combination of CDK4/6 with BET-bromodomain and PI3K/mTOR inhibitors in medulloblastoma in vitro and in vivo"

  Dataset EGAD00001009394

• Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

  This dataset contains different samples from a single patient with SEF. The dataset contains whole genome, whole exome and RNAseq information. Two of the DNA sequencing samples also contain matched normals.

  Dataset EGAD00001007516

• Single-cell RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015713

• Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma more consistent with metastatic melanoma patient

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

  Dataset EGAD00001005831

• UTUC WES data

  Whole exome sequnecing of upper urinary tract urothelial carcinoma

  Dataset EGAD00001007666

• Esophageal Adenocarcinoma Organoid scRNAseq data

  This is 10X single cell RNA-seq data of esophageal adenocarcinoma organoids.

  Dataset EGAD00001007525

• WES of HCC

  WES of HCC by HiSeq 2000,total 71 samples including Hepatocellular carcinoma cell lines and nornal sample(Peripheral Blood or the adjacent tissues of cancer)

  Dataset EGAD00001001249

• 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 EGAD00001005851

• Genome and transcriptome sequence data from a cecum adenocarcinoma patient

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

  Dataset EGAD00001005895

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

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

  Dataset EGAD00001005904

• Genome and transcriptome sequence data from a gastroesophageal junction adenocarcinoma patient

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

  Dataset EGAD00001005910

• Genome and transcriptome sequence data from a peritoneal mesothelioma patient

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

  Dataset EGAD00001001311

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

  Data supporting: "Repurposing of KLF5 activates a cell cycle signature during the progression from Barrett’s Oesophagus to Oesophageal Adenocarcinoma." Rogerson et al. RNA-seq data 2 samples

  Dataset EGAD00001005915

• 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 ICGC Oesophageal Adenocarcinoma tissue samples - barretts_1

  Samples from Ross Innes et. al 2015 - doi:10.1038/ng.3357

  Dataset EGAD00001001394

• USARC 10X Genomics Single Cell DNA Sequencing Data

  We investigated the impact of ploidy heterogeneity on copy number inference at a single cell level using fluorescence-activated cell sorted (FACS) nuclei from an undifferentiated soft tissue sarcoma. FACS revealed the presence of three aberrant subpopulations, including a haploid, a near diploid and a whole genome doubled population. Once sorted, single cell nuclei underwent whole genome sequencing using the chromium CNV single cell DNA library kit (10X Genomics). We sequenced single normal nuclei (2n) and single aberrant / tumour nuclei (1n, 2n and 2n+).

  Dataset EGAD00001008668

• Clinical dataset (new)

  ctDNA guiding adjuvant immunotherapy in urothelial carcinoma (Nature 2021). ABACUS clinical data cut (2020) used in 2021 paper: Clinical data include PCR, RFS_months, RFS_event, and OUTCOME for 40 patients in ABACUS with ctDNA data.

  Dataset EGAD00001007578

• WGS 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 WGS analysis of a panel of mesothelioma cells lines.

  Dataset EGAD00001009641

• ctDNA dataset

  ctDNA guiding adjuvant immunotherapy in urothelial carcinoma (Nature 2021). ABACUS ctDNA data used in 2021 paper: ctDNA data include TMB_(mut/Mb), cfDNA_extracted_ng, Plasma_Volume_Used_ml, Sample_Call, Sample_Number_Positive_Calls, Sample_Mean_VAF_In_Plasma (%), Sample_MTM_per_mL_In_Plasma across 40 patients in ABACUS.

  Dataset EGAD00001007579

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 8a)

  Whole genome sequencing data of 26 high-grade serous carcinoma (HGSC) patients (87 samples) sequenced with MGISEQ-2000 and HiSeq X Ten.

  Dataset EGAD00001011304

• 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

• Melanoma post mortem analysis

  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.

  Dataset EGAD00001005072

• Whole genome data for study EGAS00001000824 (Diverse modes of genomic alterations in hepatocellular carcinoma)

  Whole genome data (Complete genomics platform) for the study EGAS00001000824

  Dataset EGAD00001001034

• ChIP sequencing in Cancer Cell Lines

  The project is to evaluate the genomic binding sites of the histone demethylase JARID1C. This gene was recently identified in CGP as a novel recessive cancer gene in human renal cell carcinoma.

  Dataset EGAD00001001453

• Acral Melanoma PDXs from the admixed Brazilian Population - filtered PDX sample BAM files - Whole exome sequencing data

  BAM files containing the whole exome data for the Patient Derived Xenograft samples mapped to build GRCh38. All files have been processed with XenofilteR to remove mouse reads. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015748

• Single Cell Genome Sequence for DLP+ library A95650A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1052J passage 1 on DLP+ library A95650A

  Dataset EGAD00001009325

• Single Cell Genome Sequence for DLP+ library A95652B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage 1 on DLP+ library A95652B

  Dataset EGAD00001009327

• Multi-region RNA-Seq data of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region RNA sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008133

• DLP+ Single Cell Genomic Library A98208

  DLP+ Single Cell Genomic Library A98208 for Diffuse large B-cell lymphoma patient sample TFRIPAIR10_DLBCL

  Dataset EGAD00001010244

• Hospital for Sick Children 2020 Pediatric Low-Grade Glioma RNA and Targeted DNA Sequencing

  Whole transcriptome and targeted dna sequencing (Ampliseq) of pediatric low-grade glioma samples at the Hospital for Sick Children

  Dataset EGAD00001005987

• McGill EMC Community projects Release 7 for cell line "SaOS-2"

  Complete reference epigenome (as defined by IHEC) of a SaOS-2 cell line with osteosarcoma.

  Dataset EGAD00001007678

• Un-mapped RNA-Seq data

  Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.

  Dataset EGAD00001001940

• High-resolution lung adenocarcinoma expression subtypes

  High-resolution lung adenocarcinoma expression subtypes identify tumors with dependencies on MET, CDK4, CDK6, and PD-L1

  Dataset EGAD00001009339

• RNA-seq of human glioblastoma and matched gliomasphere cell lines (BLN panel)

  This dataset contains all RNA-seq runs for the BLN panel of cell lines and matched parental tumors. Tumor/cell line pairs have been authenticated using SNP profiles and all pairs were confirmed. Please note: The dataset also contains raw data from an early primary culture (BLN-1) where no stable cell line could be generated. Please also note different reference genomes.

  Dataset EGAD00001002893

• Myeloma Genome Project Targeted Panel Validation dataset

  372 samples consisting of 185 patient paired CD138+ tumor and non-involved DNA pairs, plus 5 Horizon Diagnostic known mutation standards (HD). Samples were processed using the KAPA HyperCap protocol and hybridized onto a targeted panel for multiple myeloma and associated diseases. Reference Sudha et al Clinical Cancer Research, 2022.

  Dataset EGAD00001008689

• WGS and RNA-Seq data of 2 additional patients of newly diagnosed multiple myeloma (NDMM)

  For WGS DNA of tumor or control samples was prepared for paired sequencing using the Illumina TruSeq DNA Nano Kit and sequenced on NovaSeq 6000. For RNA-Seq the sequencing Kit Illumina TruSeq stranded mRNA was used with the same sequencer. There are 4 samples for WGS (18 runs) and 4 samples for RNA (4 runs) available.

  Dataset EGAD00001009627

• Whole genome sequencing of Osteosarcoma clonal evolution

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Dataset EGAD00001011285

• Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient

  Genome and transcriptome sequence data from an odontogenic ghost cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001658

• Single Cell Genome Sequence for DLP+ library A96205B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1049A passage 1 on DLP+ library A96205B

  Dataset EGAD00001009471

• Whole Genome Sequencing of low-grade ovarian serous carcinoma

  Whole genome sequencing of 14 cases of low-grade ovarian serous carcinoma with matched normal DNA

  Dataset EGAD00001009626

• Paired RNA-Seq of four patients with advanced Parathyroid carcinoma (PC)

  Paired RNA-Seq of four patients with advanced Parathyroid carcinoma (PC). The library was prepared using the Illumina TruSeq stranded mRNA Kit, the sequencing was done either on an Illumina HiSeq 4000 or on Illumina NovaSeq 6000.

  Dataset EGAD00001009730

• Dataset GBM 2022

  The cellular origin and differentiation status of glioblastoma by scRNA-seq

  Dataset EGAD00001008745

• INSPIRE multi-timepoint cfMeDIP dataset

  This dataset contains raw sequencing data from multi-timepoint cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) of plasma samples from the INSPIRE study (NCT02644369). Details about the study, including inclusion/exclusion criteria and interventions are available at https://clinicaltrials.gov/study/NCT02644369. Briefly, five cohorts were included, INS-A (head & neck squamous cell carcinoma), INS-B (triple-negative breast cancer), INS-C (high-grade serous ovarian cancer), INS-D (melanoma), and INS-E (mixed solid tumors). All patients in the study were diagnosed with advanced cancer and received treatment with pembrolizumab. Plasma samples were collected at baseline and every 3 cycles until disease progression, death, loss of follow-up, or completion of the study. Plasma samples were first processed for cell-free DNA mutations and remaining samples were then processed by cfMeDIP-seq, prioritizing baseline and post-cycle 3 samples. In total, data from 204 timepoints from 87 distinct patients are deposited.

  Dataset EGAD00001011312

• Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens

  Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor “purity.” Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.

  Dataset EGAD00001008344

• Whole genome sequencing of 78 follicular lymphoma tumours and matched normals

  Whole genome sequencing for tumour/normal matched pairs from 78 samples

  Dataset EGAD00001011343

• BLUEPRINT release August 2016, RNA-Seq for Multiple Myeloma, on genome GRCh38

  RNA-Seq data for 14 Multiple Myeloma sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002401

• Transcriptome: chondrosarcoma

  Transcriptome sequencing of nine patients diagnosed with chondrosarcoma. cDNA was generated using the NuGEN Ovation RNA-Seq FFPE system. Total RNA was randomly primed and thermally sheared and the resulting cDNA fragment was amplified. The cDNA was then mechanically sheared using sonication to generate ~250 bp fragments. Sequencing libraries were generated using the NuGEN Ovation Ultralow System V2 library prep kit and sequenced on HiSeq2500 TruSeq v3.

  Dataset EGAD00001008699

• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

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

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

  Dataset EGAD00001002038

• scRNA-seq, WES, and bulk RNA-seq on longitudinal samples from 7 Lymphoma patients treated with CD20xCD3 bispecific antibodies

  We performed scRNA-seq on 15 fresh lymph node core biopsies from 7 Lymphoma patients treated with CD20xCD3 bispecific antibodies. We also performed whole-exome sequencing (WES) and bulk RNA-seq on formalin-fixed paraffin embedded (FFPE) tumor samples from these patients. WES was additionally performed on matched germline samples (blood) for each patient.

  Dataset EGAD00001011350

• Sporadic multiple meningioma Genomics

  Wes for 15 multiple meningioma samples from 6 individual

  Dataset EGAD00001008710

• 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

• Vcf RNA-Seq data

  Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.

  Dataset EGAD00001001941

• Exome sequencing VCF files for glioma progression

  Exome sequencing VCF files describing mutations during glioma progression.

  Dataset EGAD00001001887

• Genomics of acral lentiginous melanoma

  Melanoma is the most aggressive type of skin cancer, causing about 75% of dermatological cancer deaths. Acral lentiginous melanoma (ALM) is the most common subtype of melanoma in admixed Latin American populations, but very few tumour genomes and exomes, all from European-descent individuals, have been analysed across several studies. Because of this, the genomic landscape of ALM is mostly unknown. Our aim in this project is to define this landscape and identify driver somatic alterations by whole-exome sequencing a collection of ALM germline/tumour paired FFPE samples from the National Cancer Institute of Mexico. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010126

• Genome and transcriptome sequence data from a glioblastoma tumor patient

  Genome and transcriptome sequence data from a glioblastoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

  Dataset EGAD00001015288

• mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel and secondary fusion transcripts in formalin-fixed paraffin-embedded tissue: a sarcoma showcase

  mRNA capture sequencing data (FASTQ files) of 28 FFPE sarcoma tumors

  Dataset EGAD00001007696

• Genomic analysis for intrahepatic cholangiocarcinoma

  Intrahepatic cholangiocarcinomas (iCCs) are characterized by their rarity, difficulty in diagnosis, and overall poor prognosis. We performed comprehensive genomic characterization of treatment-naive iCC. This study reports a large-scale genomic analysis of iCC. The findings could assist in patient stratification with iCCs and in developing rational therapeutic strategies.

  Dataset EGAD00001008557

• Ancestry and somatic profile predict acral melanoma origin and prognosis – WXS

  Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

  Dataset EGAD00001015755

• Ancestry and somatic profile predict acral melanoma origin and prognosis – RNA

  Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

  Dataset EGAD00001015756

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 0)

  Whole genome sequencing data of 5 High-grade serous carcinoma (HGSC) patients (6 samples) sequenced with BGI.

  Dataset EGAD00001009738

• Dataset for transcriptomic sequencing of Merkel cell carcinoma(MCC) samples

  This dataset contains transcriptome sequencing for 5 samples of MCC tumors . The sequencing was performed on Illumina NextSeq 6000 . The sequencing was always paired.

  Dataset EGAD00001015702

• Genome and transcriptome sequence data from a recurrent glioma patient

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

  Dataset EGAD00001002043

• A developmental cell atlas of the human thyroid gland

  Thyroid hormones are essential for health, but human thyroid development and cellular heterogeneity are poorly understood. We generated a high-resolution, spatiotemporal transcriptional atlas of human fetal thyroid, and examined its perturbations in trisomy 21 (T21), where aberrant thyroid development is associated with congenital hypothyroidism, and in papillary thyroid carcinoma (PTC). Normal tissue revealed two functional follicular cell states (fTFC1, fTFC2) with divergent PAX8 expression levels, persisting into adulthood. Additionally, the rare C-cell population was comprehensively profiled at single-cell resolution for the first time. T21 fetal thyroid was hypoplastic, with disrupted follicular morphology and altered expression of genes mediating cellular topology and extracellular matrix interactions. Finally, the transcriptional signals of both fetal follicular cell states were found to be perturbed in PTC. Overall, we defined a reference atlas for normal human fetal thyrocyte heterogeneity and provided novel insights into thyroid disorders.

  Dataset EGAD00001015783

• Genomic Analysis of Focal Nodular Hyperplasia with Associated Hepatocellular Carcinoma Unveils its Malignant Potential

  Whole exome sequencing of FNH and two HCC compartments from a single patient, along with matched germline.

  Dataset EGAD00001007702

• Neuroblastoma WGS samples used for detection of seismic amplification

  Paired-end WGS data of 27 neuroblastoma patient samples (10 obtained at diagnosis, 6 at relapse and 11 matched blood samples as controls) used for detection of complex "seismic" amplification. Mean coverage is 24-55x per sample. The remaining patient samples of the dataset can be found under accession number EGAS00001001308.

  Dataset EGAD00001007807

• Myeloma Genome Project Targeted Sequencing Panel - Oxford Data

  This dataset comprises the BAM files from targeted genome sequencing of CD138+ selected myeloma tumour samples from 21 individuals. In 5 cases there is only one tumour sample, but in the other 16 cases there are sequential samples, spanning treatment relapses. There are denoted Tumor A, B C etc. Therefore there are a total of 48 myeloma tumour samples. For each individual there is also a germline control samples, obtained either from peripheral blood or from CD138-selected bone marrow cells.

  Dataset EGAD00001008735

• Pheochromocytoma paraganglioma single nuclei RNA-seq

  Single nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients (SDHB and RET). Files are fastq files of 10x-5'scRNAseq libraries.

  Dataset EGAD00001008739

• RNAseq dataset for MALT1 in MCL

  Manuscript Title: Co-targeting of BTK and MALT1 overcomes resistance to BTK inhibitors in mantle cell lymphoma Journal: Journal of Clinical Investigation Authors Vivian Changying Jiang1, Yang Liu1, Junwei Lian1, Shengjian Huang1, Alexa Jordan1, Qingsong Cai1, Fangfang Yan3, Joseph Mitchell McIntosh1, Yijing Li1, Yuxuan Che1, Zhihong Chen1, Jovanny Vargas1, Maria Badillo1, JohnNelson Bigcal1, Heng-Huan Lee1, Wei Wang1, Yixin Yao1, Lei Nie1, Christopher Flowers1, and Michael Wang1, 2* Abstract Bruton’s tyrosine kinase (BTK) is a proven target in mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma. However, resistance to BTK inhibitors is a major clinical challenge. We here report that MALT1 is one of the top overexpressed genes in ibrutinib-resistant MCL cells, while expression of CARD11, which is upstream of MALT1, is decreased. MALT1 genetic knockout or inhibition produced dramatic defects in MCL cell growth regardless of ibrutinib sensitivity. Conversely, CARD11 knockout cells showed anti-tumor effects only in ibrutinib-sensitive cells, suggesting that MALT1 overexpression could drive ibrutinib resistance via bypassing BTK-CARD11 signaling. Additionally, BTK knockdown and MALT1 knockout markedly impaired MCL tumor migration and dissemination, and MALT1 pharmacological inhibition decreased MCL cell viability, adhesion, and migration by suppressing NF-κB, PI3K-ATK-mTOR, and integrin signaling. Importantly, co-targeting MALT1 with safimaltib and BTK with pirtobrutinib induced potent anti-MCL activity in ibrutinib-resistant MCL cell lines and patient-derived xenografts. Therefore, we conclude that MALT1 overexpression associates with resistance to BTK inhibitors in MCL, targeting abnormal MALT1 activity could be a promising therapeutic strategy to overcome BTK inhibitor resistance, and co-targeting of MALT1 and BTK should improve MCL treatment efficacy and durability as well as patient outcomes. Dataset description: The bulk RNA-seq dataset was generated for the cell lines below and used for two major purposes: 1. DEG analysis and GSEA analysis comparing IBN-R and IBN-S cells 2. DEG analysis and GSEA analysis comparing MCL cells with/without MI-2 treatment. sample Cell MI-2 Ibrutinib (IBN) Venetoclax (VEN) Used for IBN-R vs IBN-S comparison Used for MI-2 vs untreated (DMSO) H9 Granta519 - R S yes H21 Granta519 - R S yes H33 Granta519 - R S yes H10 Granta519-VEN-R - R R yes H22 Granta519-VEN-R - R R yes H34 Granta519-VEN-R - R R yes H3 JeKo BTK KD_1 - R R yes yes H15 JeKo BTK KD_1 - R R yes yes H27 JeKo BTK KD_1 - R R yes yes H5 JeKo BTK KD_2 - R R yes yes H17 JeKo BTK KD_2 - R R yes yes H29 JeKo BTK KD_2 - R R yes yes H1 JeKo-1 - S R yes yes H13 JeKo-1 - S R yes yes H25 JeKo-1 - S R yes yes H7 Mino - S S yes H19 Mino - S S yes H31 Mino - S S yes H8 Mino-VEN-R - S R yes H20 Mino-VEN-R - S R yes H32 Mino-VEN-R - S R yes H11 Rec-1 - S S yes H23 Rec-1 - S S yes H12 Rec-VEN-R - S S yes H24 Rec-VEN-R - S R yes H36 Rec-VEN-R - S R yes H35 Rec-1 -- S R yes H4 JeKo BTK KD_1 + MI-2 + yes H16 JeKo BTK KD_1 + MI-2 + yes H28 JeKo BTK KD_1 + MI-2 + yes H6 JeKo BTK KD_2 + MI-2 + yes H18 JeKo BTK KD_2 + MI-2 + yes H30 JeKo BTK KD_2 + MI-2 + yes H2 JeKo-1 + MI-2 + yes H14 JeKo-1 + MI-2 + yes H26 JeKo-1 + MI-2 + yes

  Dataset EGAD00001009771

• Melanoma microRNA profiling

  This dataset includes microRNA profiling of 61 early-passage metastatic melanoma cell lines. The data are provided as single-end small RNA seq fastq files.

  Dataset EGAD00001006269

• Comprehensive RNA repository of tissue and plasma from patients with esophageal cancer or precursor lesions

  A comprehensive RNA repository (both coding and non-coding) from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were collected. This dataset includes both mRNA and small RNA sequencing data (fastq.gz files) of all tissue and plasma samples. In total,102 RNA-seq libraries from 51 samples (17 plasma and 34 tissue samples) were sequenced (plasma mRNA libraries were sequenced twice).

  Dataset EGAD00001006857

• RNA-seq analysis of transcriptome variation with human ESC subclones

  Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001004266

• Whole exome sequencing of primary mediastinal large B-cell lymphoma

  This dataset contains raw .fastq files of a whole exome sequencing experiment on primary mediastinal large B-cell lymphoma and contains 8 tumor-normal pairs and 14 unpaired tumor samples.

  Dataset EGAD00001008744

• Whole genome sequencing of osteosarcoma and blood

  We profiled 2 patient osteosarcoma tumor samples as well as the blood of the same patients by whole genome sequencing, for a total of 4 samples. The raw fastqs are provided.

  Dataset EGAD00001011372

• Single Cell Genome Sequence for DLP+ library A118784A

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050B passage 1, patient-derived xenograft SA1050E passage 1 on DLP+ library A118784A

  Dataset EGAD00001009436

• Cohort of NGS lymphoma samples used as control

  Control cohort of lymphoma samples sequenced with a hybrid capture panel designed to be able to detect translocations and mutations in lymphoma samples. used in the paper "Robust detection of translocations in lymphoma FFPE samples using Targeted Locus Capture-based sequencing"

  Dataset EGAD00001007711

• Single Cell Genome Sequence for DLP+ library A118808B

  Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1096C passage 1 on DLP+ library A118808B

  Dataset EGAD00001009441

• Dataset for liposarcoma-RNA

  Rare cancer sequencing data of 40 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008854