Search Results - EGA European Genome-Phenome Archive

DLP+ Single Cell Genomic Library A98221A

DLP+ Single Cell Genomic Library A98221A for Follicular lymphoma patient sample TFRIPAIR5_FL

Dataset EGAD00001010245

Transcriptome sequencing of hepatocellular carcinoma biopsies

RNA-sequencing of 122 hepatocellular carcinoma biopsies and 15 normal liver biopsies. RNA-seq library prep was performed with 200 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to manufacturer’s specifications. Single-end 126-bp sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry at the Genomics Facility Basel according to the manufacturer’s guidelines. Primary data analysis was performed with the Illumina RTA version 1.18.66.3.

Dataset EGAD00001008205

OSTEOMICS_RNA

RNA sequencing of 79 libraries were prepared, from sample of Osteosarcoma tumors biopsied at diagnosis, with TruSeq Stranded mRNA kit following recommendations: the key steps consist of PolyA mRNA capture with oligo dT beads using 1µg total RNA, fragmentation to approximately 400pb, DNA double strand synthesis, and ligation of Illumina adaptors amplification of the library by PCR for sequencing. Libraries sequencing was performed using Illumina sequencers (NextSeq 500 or Hiseq 2000/2500/4000) in 75 bp paired-end mode.

Dataset EGAD00001008213

10x Genomics Single Cell Gene Expression for SA1162BX1XB03004

10x Genomics Single Cell Gene Expression for High grade serous ovarian carcinoma patient-derived xenograft SA1162 passage 1

Dataset EGAD00001009138

An aggregated vcf file

Germline variants calls were defined using the sequenced reads derived from 230 patients with hepatocellular carcinoma. This dataset is comprised of one aggregated vcf file.

Dataset EGAD00001009410

DLP+ Single Cell Genomic Library A98225

DLP+ Single Cell Genomic Library A98225 for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel

Dataset EGAD00001010246

Pediatric high grade glioma WES

We performed whole exome sequencing in DIPG and hemispheric HGG.

Dataset EGAD00001008279

Human normal esophagus and Barrett's esophagus mtDNA sequencing

BAM files containing paired-end mtDNA sequencing data from human esophageal samples of individuals that had progressed to dysplasia or developed Barrett's esophagus (BE) post-esophagectomy. BE biopsies and the background mucosa were analysed. Each patient (JE*) has associated mtDNA sequencing data from biopsies of stroma, BE and squamous and cardia tissue. Two technical replicates, denoted "A" and "B", were analysed for each biopsy. Libraries were sequenced via the Illumina MiSeq platform v2 (Illumina, San Diego, CA, USA) 300 cycles (150 nt paired-end).

Dataset EGAD00001008310

Esophageal adenocarcinoma plasma cfDNA samples - PERFECT cohort and nCRT cohort

The dataset contains 295 plasma cfDNA samples from various stages of resectable esophageal adenocarcinoma from the PERFECT cohort and the nCRT cohort. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

Dataset EGAD00001008316

DLP+ Single Cell Genomic Library A98297

DLP+ Single Cell Genomic Library A98297 for Follicular lymphoma patient sample TFRIPAIR3_FL

Dataset EGAD00001010248

WES Melanoma subtypes

The dataset include sequencing data from 23 patients diagnosed with metastatic melanoma. The 23 metastatic melanoma subtypes consisted of cutaneous melanoma (CM, n=10); head and neck melanoma (HNM, n=7); uveal melanoma (UM, n=4); acral lentiginous (AM, n=1) and mucosal melanoma (MM, n=1).

Dataset EGAD00001008336

Targeted DNA sequencing dataset for the study "Molecular profiling of EBV associated diffuse large B-cell lymphoma"

We performed deep targeted DNA sequencing with a panel of 74 selected cancer-related genes previously identified to be recurrently mutated in EBV associated DLBCL. Sequencing was performed on a HiSeq platform (Illumina) with 250 bp paired-end reads. There are 68 FFPE samples in this targetedDNAseq-dataset with 46 unpaired tumors and 22 normals used as a panel of normals.

Dataset EGAD00001009396

RNA-seq data from 27 glioblastoma samples

27 Fresh frozen tissue specimens were crushed by mortar and pestle, homogenized using the QIAShredder kit (Qiagen), and genomic DNA and total RNA were extracted using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer’s instructions. RNA libraries were synthesized using 200 ng of total RNA using the Ilumina TruSeq Stranded RNA LT Sample Prep Kit (Illumina), and subsequently sequenced on the NextSeq550 platform to a read depth of 80 million clusters and 160 million paired end reads (75 bp X 75 bp) using V2 chemistry.

Dataset EGAD00001008362

Single Cell Genome Sequence for DLP+ library A118804A

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1162B passage 1, patient-derived xenograft SA1096B passage 1 on DLP+ library A118804A

Dataset EGAD00001009439

Single Cell Genome Sequence for DLP+ library A118812B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1180C passage 1 on DLP+ library A118812B

Dataset EGAD00001009442

Single Cell Genome Sequence for DLP+ library A95663A

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1053F passage 1 on DLP+ library A95663A

Dataset EGAD00001009446

Single Cell Genome Sequence for DLP+ library A96190B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1051A passage 1 on DLP+ library A96190B

Dataset EGAD00001009466

Single Cell Genome Sequence for DLP+ library A96207B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1052B passage 1 on DLP+ library A96207B

Dataset EGAD00001009474

Single Cell Genome Sequence for DLP+ library A96210B

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient SA1047B on DLP+ library A96210B

Dataset EGAD00001009475

Single Cell Genome Sequence for DLP+ library A98279A

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050A passage 1, patient SA1234 on DLP+ library A98279A

Dataset EGAD00001009486

Paired RNA-Seq for Sarcoma tumors

Paired RNA-Seq of 199 samples of Sarcoma tumors. The sequencing was done mostly on HiSeq 4000 with Illumina TruSeq Stranded mRNA, ist was also done on NovaSeq 6000 using the same kit. Very few samples were sequenced on HiSeq X Ten with Illumina TruSeq RNA or Illumina TruSeq Stranded mRNA.

Dataset EGAD00001010256

Single-cell Transcriptome for glioblastoma intra-tumoral heterogeneity

Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).

Dataset EGAD00001002249

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

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

ADT/SPEX 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 ADT/SPEX 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 EGAD00001008419

Dataset for Sarcoma-WGS linked from study EGAS00001004813

Sequencing data of 77 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

Dataset EGAD00001010257

Dataset HCV positive lymphoma whole exome sequencing

This dataset contains 68 BAM files from matched normal-tumor pairs of HCV positive lymphoma analyzed by exome sequencing on Ilumina platform.

Dataset EGAD00001009786

WGS files for CIC paper data

WGS files for CIC paper titled "Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma"

Dataset EGAD00001009787

RNASeq files for CIC paper data

RNASeq files for CIC paper titled "Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma"

Dataset EGAD00001009788

lymphoma plasma cfRNA

Dataset contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma (DLBCL) and 13 primary mediastinal large B-cell lymphoma (PMBCL) patients, and 22 cancer-free controls. Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

Dataset EGAD00001010259

Raw data for "Spatial and temporal transcriptomics of medulloblastoma with chromothripsis identifies multiple genetic clones that resist to treatment and lead to relapse"

FASTQ files from Illumina sequencing of 10x Visium experiments.

Dataset EGAD00001010260

Single-cell RNA sequencing of anti-LAG3+anti-PD1 treated melanoma patients

Single-cell RNA sequencing of 18 peripheral blood samples from six melanoma patients. The raw data is available as fastq files.

Dataset EGAD00001009807

Hodgkin Lymphoma Whole Genome Sequencing

Whole genome sequencing of 17 paired tumor-normal Hodgkin Lymphoma whole genomes. Bulk tumor (-T) and flow-sorted Reed Sternberg cell (-HRS) samples. Approximately 30x wgs normal depth, 40-50x wgs depth tumor samples.

Dataset EGAD00001009818

Genetic landscape of Extranodal NK/T-cell lymphoma

Whole-exome sequence (WES) data of tumor-normal pairs from 40 ENKTCL patients and RNA sequence (RNA-seq) data of tumors from 20 ENKTCL patients.

Dataset EGAD00001009852

Dataset for Sarcoma RNA sequencing linked from study EGAS00001004813

Sequencing data of 410 sarcoma tumor runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

Dataset EGAD00001010276

Paired WGS samples (tumor and control) of one Sarcoma case

Paired WGS samples (tumor and control) of one Sarcoma case. The paired sequencing was done on Hiseq X Ten with Illlumina TruSeq Nano DNA.

Dataset EGAD00001010277

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

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

Genome and transcriptome sequence data from an adenomacarcinoma of vulva patient

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

Dataset EGAD00001002590

Genome and transcriptome sequence data from a leiomyosarcoma patient

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

Dataset EGAD00001002593

Genome and transcriptome sequence data from a superficial pleomorphic liposarcoma patient

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

Dataset EGAD00001002616

Genome and transcriptome sequence data from a small cell/neuroendocrine carcinoma of the lung patient

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

Dataset EGAD00001002617

Genome and transcriptome sequence data from a metastatic colorectal adenocarcinoma patient

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

Dataset EGAD00001002622

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

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