Search Results - EGA European Genome-Phenome Archive

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

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

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

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

Dataset for melanoma-RNA

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

Dataset EGAD00001008858

Single cell transcriptomes of of primary tumors and normal endometrial derived organoids treated with DBZ

Endometrial carcinoma, the most common gynecologic cancer, develops from endometrial epithelium which is composed of secretory and ciliated cells. Pathologic classification is unreliable and there is a need for prognostic tools. We used single cell sequencing to study organoid model systems derived from normal endometrial endometrium to discover novel markers specific for endometrial ciliated or secretory cells. We performed single cell sequencing on endometrial and ovarian tumours, and on organoids both treated with DBZ and normal and found both secretory-like and ciliated-like tumour cells.

Dataset EGAD00001006280

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 EGAD00001015717

SF10679

SF10679 snATAC Seq. Oligodendroglioma, Anaplastic (WHO gr. 3). Tumor Location: Frontal Age: 43. Sex: Male.

Dataset EGAD00001006312

Single Cell Genome Sequence for DLP+ library A96142B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1162SA on DLP+ library A96142B

Dataset EGAD00001009455

scRNAseq of neuroblastoma PDX and cell lines

This dataset contains the 22 bam files coresponding to the scRNAseq done in PDX models and cell lines.

Dataset EGAD00001007870

Single-cell RNA-seq of peripheral blood mononuclear cells in classic Hodgkin lymphoma

Abstract: Classic Hodgkin lymphoma (cHL) is a largely MHC class I-negative tumor with recurrent 9p24.1/ PD-L1/ PD-L2 copy gains and the highest reported response rates to PD-1 blockade. We utilized scRNA sequencing to characterize the peripheral immune response to PD-1 blockade and more broadly define non-CD8+ dependent mechanisms of immune evasion in cHL. Peripheral blood mononuclear cells were obtained from 20 patients with relapsed/refractory (R/R) cHL treated with PD-1 blockade (nivolumab) on the CheckMate 205 clinical trial (paired samples from cycle 1 day 1 [C1D1] and cycle 4 day 1 [C4D1]), 11 patients with newly diagnosed, previously untreated cHL and 13 healthy donors.

Dataset EGAD00001011360

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 9 part 2)

Whole genome sequencing data of 35 high-grade serous carcinoma (HGSC) patients (112 samples) sequenced with Illumina Novoseq 6000

Dataset EGAD00001011368

RNAseq data for 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 EGAD00001008458

Whole Exome PC9 and A375 (2019-04-03)

Drug resistant population of PC9(human non-small cell lung cancer) or A375 (human melanoma) cell lines were used for this study. By exome sequencing, we will analyse mutations of cells in drug tolerent state and after drug holiday. . This dataset contains all the data available for this study on 2019-04-03.

Dataset EGAD00001004891

RNA-seq data from paired tumour and germline samples from mesothelioma patients for study EGAS00001005196

Dataset EGAD00001007874

NEC

This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR). Secondary outcomes were safety and objective response rate (ORR). Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. Feasibility of liquid biopsy by ctDNA was assessed.

Dataset EGAD00001010056

Dataset for liposarcoma-EXON

Rare cancer sequencing data of 29 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008886

Exome sequencing of osteosarcoma, blood and saliva

We profiled 31 osteosarcoma tumor patient samples, 18 blood and 1 saliva control samples by exome sequencing, for a total of 50 samples. The raw fastqs are provided.

Dataset EGAD00001011370

Single-cell RNA sequencing generated from 11 glioma patient samples

This dataset includes paired-end fastq files from 6 IDH-mutant, 5 IDH-wild-type glioma patient samples of unmatched initial and recurrent timepoints profiled using single-cell RNA sequencing.

Dataset EGAD00001007772

Dataset for leiomyosarcoma-EXON

Rare cancer sequencing data of 96 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

Dataset EGAD00001008885

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

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

Dataset EGAD00001011369

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

Small-molecule inhibitors in melanoma - Kenski / Kong - WES (2019-04-11)

Small-molecule inhibitors targeting the most commonly activated pathway in melanoma, MAPK pathway (either alone or in combination) are already given to melanoma patients for few years, and initially reduce tumour burden dramatically, eventually melanomas become resistant and tumours progress while on treatment. Resistance to this treatment occurs by acquisition of additional mutations or other alterations that affect the mitogen-activated protein kinase (MAPK) pathway by either direct or indirect signalling. Many resistance mechanisms somehow lead to reactivation of extracellular signal-regulated kinase (ERK), thereby restoring signalling of the oncogenic BRAF/MEK/ERK pathway. In addition, PI3K pathway activation contributes to resistance to BRAF inhibition. Less frequent but equally important to the phenomenon of targeted drug resistance is the observation that B15-20% of BRAF mutant melanoma patients fail to respond to BRAF inhibition already early on treatment, owing to intrinsic resistance. These patients have little therapeutic options, unless immunotherapy can be given. To better understand the resistance mechanisms in MAPK inhibitor-treated melanoma patients and melanoma biology, our lab generated a big panel of MAPK inhibitor resistant melanoma cell lines by continuous drug exposure. The understanding of the genetic landscape and gene expression as well as cross resistance to other treatment regimens, and other aspects of melanoma biology such as phenotype switch, will allow us to better exploit new therapeutic strategies for melanoma patients. . This dataset contains all the data available for this study on 2019-04-11.

Dataset EGAD00001004952

Genome and transcriptome sequence data from a melanoma patient

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

Dataset EGAD00001011022

WGS, RNA-seq and methyl-seq data for multiple tumour clones from a single glioblastoma case.

10 bams of WGS data from HiSeqXTen platform; 10 bams of RNA-seq data from HiSeq2500 platform; 7 bams of TruSeq Methyl Capture EPIC sequencing data from HiSeq4000 platform

Dataset EGAD00001004773

RNASeq read files of renal cell carcinoma PDX samples

This dataset contains 56 fastq files of paired-end RNA sequencing of a Illumina® TrueSeq stranded mRNA library of 28 renal cell carcinoma PDX samples.

Dataset EGAD00001008766

BLUEPRINT release August 2016, ChIP-Seq for Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma, on genome GRCh38

ChIP-Seq data for 3 Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma sample(s). 10 run(s), 10 experiment(s), 10 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_chipseq_analysis_ebi_20160816

Dataset EGAD00001002506

Embryonal Rhabdomyosarcoma sequencing data

This dataset contains samples from 9 patients with embryonal rhabdomyosarcoma. 9 samples have whole exome tumor data (one has multiple). 7 samples have tumor RNAseq data. 1 sample has matched normal dna sequence data

Dataset EGAD00001007939

20190219_EGA_MelanomaOnTreatment

Illumina platform sequencing data for matched tumour-normal DNA samples from 77 melanoma patients participating in a study investigating response to immunotherapy. Selected cases also have RNA sequencing of the tumour.

Dataset EGAD00001004869

Genome and transcriptome sequence data from a liposarcoma patient

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

Dataset EGAD00001002541

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 EGAD00001002563

Genome and transcriptome sequence data from an adenocarcinoma of lung patient

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

Dataset EGAD00001002564

Genome and transcriptome sequence data from a right breast carcinoma patient

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

Dataset EGAD00001002580

Single Cell Genome Sequence for DLP+ library A95717B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050D passage 1 on DLP+ library A95717B

Dataset EGAD00001009489

Genome and transcriptome sequence data from a metastatic myxofibrosarcoma patient

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

Dataset EGAD00001002581

Genome and transcriptome sequence data from a squamous cell carcinoma of vulva patient

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

Dataset EGAD00001002586

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 EGAD00001002594

Functional dissection of inherited non-coding variation influencing multiple myeloma risk

This dataset contains ATAC sequencing of plasma cells from multiple myeloma (MM) patients. The data was used to investigate genotype-specific chromatin accessibility quantitative trait locus (caQTL) using caQTLseg (https://github.com/abhisheknrl/caQTLseg). This dataset contains 161 bam files.

Dataset EGAD00001007814

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