Search Results - EGA European Genome-Phenome Archive

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0187_001A

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0187_001A for Follicular lymphoma patient sample TFRIPAIR10_FL

Dataset EGAD00001010222

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0188_001A

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0188_001A for Follicular lymphoma patient sample TFRIPAIR11_FL

Dataset EGAD00001010223

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0197_001A

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0197_001A for Follicular lymphoma patient sample TFRIPAIR12_FL

Dataset EGAD00001010224

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_001A

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_001A for Follicular lymphoma patient sample TFRI_Pair_13_FL

Dataset EGAD00001010225

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0167_002

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0167_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR2_DLBCL

Dataset EGAD00001010226

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0168_002

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0168_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR3_DLBCL

Dataset EGAD00001010227

Bulk RNAseq of Neuroblastoma patient's tumors

This dataset contains 9 bulk RNAseq of neuroblastoma patient's tumors used to compare with derived PDXs and/or single-cell data in the Thirant C et al, Nature Communications, 2023. They were intially produced for the Berlanga P., Cancer Discovery, 2022.

Dataset EGAD00001010287

Paired diagnostic and relapse medulloblastoma sequencing

Paired diagnostic and relapse medulloblastoma sequencing. Targetted panel sequencing (n=8 relapse, n=7 matched diagnostic). Whole exome sequencing (n=23 relapse, n=18 matched diagnostic). Capture using Agilent SureSelect.

Dataset EGAD00001010321

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 EGAD00001010316

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 EGAD00001010317

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 EGAD00001010318

Processed bam files for the whole exome sequencing of primary lung adenocarcinoma samples

We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

Dataset EGAD00001010320

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

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

Whole Genome Sequencing of Head and Neck Angiosarcoma

This dataset contains 55 Whole Genome Sequencing of the study titled Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.

Dataset EGAD00001010140

Differential methylation positions

This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

Dataset EGAD00001010147

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

Multiple myeloma follow-up Dataset

77 samples collected from 35 multiple myeloma patients. Each patient provided one healthy sample and one primary tumor sample and, in some cases, also samples collected after the progression of the disease.

Dataset EGAD00001010161

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

WES and RNA-seq data of 11 cancer patients with multiple cancer types

This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

Dataset EGAD00001010169

Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

This dataset contains the open chromatin profiles of 8 patient H3-K27M mutant DMGs utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

Dataset EGAD00001010170

Paired RNA-Seq was performed on 125 samples of low grade pediatric glioma

Paired RNA-Seq was performed on 125 samples of low grade pediatric glioma. The sequencing was done with Illumina Novaseq 6000 and the Illumina TruSeq stranded mRNA kit.

Dataset EGAD00001010171

Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC)

Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC). RNA was extracted and sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol. The sequencing was done using Illumina Novaseq 6000.

Dataset EGAD00001010172

Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A

Dataset EGAD00001009964

Genomic Analysis of a Metastatic Fusion-negative Embryonal Rhabdomyosarcoma

Autopsy-derived, later snap-frozen tissue fragments from a 5-year-old female with recurrent metastatic fusion-negative embryonal rhabdomyosarcoma (RMS) primary tumor of the left thigh were analyzed. No quality matched tissue was available. Prior panel analysis identified 2 prominent genetic changes: NRAS Q61K, PIK3CA H1047R, CDKN2A/B loss, and ERBB3 overexpression.

Dataset EGAD00001009973

TK-EP862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - WSG data

In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. WSG data (paired end) provided here correspond to germline DNA, Surgical sample 4 (described in the above manuscript as a cranial metastasis of PFA ependymoma), and a patient-derived xenograft derived from the patient.

Dataset EGAD00001010008

RNA-sequencing data from vitamin C experiment

Fasq-files from 3 unaffected TET2 mutation carriers, 2 mutation carriers diagnosed with lymphoma and 3 family members without TET2 mutation. Time series data collected from 0, 6 and 12 months after daily dose of 1g vitamin C.

Dataset EGAD00001010009

Human CCO+ liver mtDNA sequencing

BAM files containing paired-end mtDNA sequencing data from morphologically normal human liver. CCO-proficient hepatocytes acquired from human livers in which clonal CCO-deficient hepatocyte patches had been previously identified. Individual BAM files are named according to their patch, line and sample location, where PT denotes tissue near to the portal triad (PT), central hepatic vein (CV) and midway between these two structures (Mid). "Stroma" control samples were used for identifying germ-line variants. Sequenced on NextSeq 500 platform.

Dataset EGAD00001010016

WGS data for HGSC patient derived organoids and matching tumor and normal samples (Wennerberg)

Sequencing data of 10 high-grade serous carcinoma (HGSC) patients (58 samples including blood derived normal samples as germline controls, fresh frozen tissue samples as tissue controls and organoids) sequenced with HiSeq X Ten / BGISEQ-500 / MGISEQ-2000.

Dataset EGAD00001010019

scRNA-seq of total bone marrow and T cells from multiple myeloma long-term survivors

scRNA This dataset contains 50 scRNA-seq samples from bone marrow aspirates of 11 multiple myeloma patients experiencing long-term survival and 3 healthy donors. For each donor, total bone marrow and CD3+ T cells were sequenced. For multiple myeloma patients, paired samples were collected at initial diagnosis and between 7-17 years after first-line therapy. Bone marrow mononuclear cells were isolated by Ficoll density gradient centrifugation. For sorting of total bone marrow cells singlet, live cells were gated and sorted, for sorting of T cells CD45+, CD3+ cells were gated and sorted on either FACSAria Fusion or FACSAria II. Single-cell RNA sequencing were generated using 10x Genomics single-cell RNAseq technology (Chromium Single Cell 3’ Solution v2) according to the manufacturer’s protocol and sequenced on an Illumina HiSeq4000 (paired end, 26 and 74 bp). Bulk RNA Singlet, live CD3+CD4- CXCR3+CD8+ and CD3+CD4- CXCR3-CD8+ cells were sorted from 7 bone marrow and 3 peripheral blood samples of 7 multiple myeloma patients using a FACSAria Fusion machine. Bulk-RNA sequencing libraries were generated using the SMART Seq Stranded Total RNA-Seq kit (Takara) and sequenced using the Illumina NovaSeq 6000 platform (2 x 100 bp).

Dataset EGAD00001010025

Gut microbiome from melanoma patients

Metagenomics shotgun sequencing was conducted on fecal samples from the Australian patients enrolled in the OpACIN-neo clinical trial (n = 38). Metagenomic shotgun sequencing was performed utilizing the same DNA from the same preparations as for the 16S rRNA gene analysis. Individual libraries were prepared using Nextera XT, and sequencing was performed on the Illumina NovaSeq 6000 S1 (2 x 150bp; Xp workflow).

Dataset EGAD00001010028

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 5)

Whole genome sequencing data of 19 high-grade serous carcinoma (HGSC) patients (47 samples) sequenced with HiSeq X Ten.

Dataset EGAD00001010029

Neuroblastoma WGS dataset

Dataset with whole-genome sequencing tumor and normal samples from 14 neuroblastoma patients.

Dataset EGAD00001010030

Germline variants in childhood melanoma

Whole-exome sequencing was performed on DNA extracted from blood samples of 50 children diagnosed with cutaneous melanoma prior to 18 years of age. Patients were all diagnosed in Queensland, Australia, and self-reported as of European descent. Sequencing was done the Illumina platform using SureSelct V7 Post capture kits.

Dataset EGAD00001010039

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

Ither NB in Organoids RNA-Seq dataset - Exploring high-throughput drug sensitivity testing in neuroblastoma cell lines and patient-derived tumor organoids in the era of precision medicine

Ither NB in Organoids RNA-Seq dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.

Dataset EGAD00001010283

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