Search Results - EGA European Genome-Phenome Archive

Primary_DIPG_expression_profiles

In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG. Seventeen primary tumor samples stereotactically biopsied at diagnosis by neurosurgeons in the Necker-Enfants Malades hospital (Paris, France) and snap-frozen for RNA extraction and subsequent poly-A mRNA purification.

Dataset EGAD00001011080

Long-read data (PacBio)

The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

Dataset EGAD00001006597

Bulk RNA-seq data of isogenic wild-type RPE1

Deposited here are time series (6, 24 and 48hrs) bulk RNA-seq data generated from isogenic wild-type (WT) RPE1 untreated or treated with Brequinar (and other dNTP-pool disruptor compounds)

Dataset EGAD50000001544

SF11644 scRNA-Seq primary GBM

SF11644 Primary GBM Gender Male age 57. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

Dataset EGAD00001005393

SF11956 scRNA-Seq GBM IDHR132H Wildtype Male

SF11956 IDHR132H WT GBM. Male, 63. Single Cell RNA seq from high grade glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

Dataset EGAD00001005392

RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells

RNA-Seq data on multiple myeloma CD138positive bone marrow plasma cells, 11 samples, sequenced on HiSeq 4000 and HiSeq X-Ten, using mostly the TruSeq stranded mRNA Kit.

Dataset EGAD00001008619

UIC HNSCC RNA-Seq and miRNA-Seq Data

This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

Dataset EGAD00001004489

RNA bam files of Renal Cell Carcinoma patients

the dataset contains RNA bam files of Renal Cell Carcinoma patients, which belongs to "An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors"

Dataset EGAD00001003895

RNA-seq data of patients with glioblastoma IDH-wt (CNS WHO grade 4) with matched primary and relapse samples.

Between January 1st, 2016, and December 31th, 2021, patients with glioblastoma IDH-wt (CNS WHO grade 4) were included. RNA-seq was performed in a subset of patients.

Dataset EGAD00001015683

SF11979 snRNA-Seq Primary GBM IDHR132H Wildtype Female

Single Nuclei Primary GBM IDHR132H Wildtype. Female 76. 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 EGAD00001005430

Human tumour and matched-normal single-cell RNAseq

We profiled 16 high-grade gliomas patient tumour samples by single-cell and single-nuclei RNA-seq and 3 normal-matched single-cell RNA-seq using 10X Chromium 3'. The fastq files are provided.

Dataset EGAD00001006097

Gene expression analysis for nasal polyps

The aim of the study is to identify the gene expression profile and biomarkers related with chronic rhinosinusitis with nasal polyps (CRSwNP). RNA-sequencing was performed to identify differentially expressed genes between nasal polyps (NP) and inferior turbinate mucosa from 6 patients with CRSwNP. We validated the RNA-seq results by quantitative real-time PCR.

Study JGAS000153

Dataset for RNA sequencing of Glioblastoma samples

This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

Dataset EGAD50000000081

Alveolar Rhabdomyosarcoma sequencing data

This dataset comprises DNA sequencing for tumor and matched normal from an Alveolar Rhabdomyosarcoma patient. It also include RNA sequencing data from the tumor sample.

Dataset EGAD00001006622

README-for-EGAS00001004349-linking-HIPO-K09R-RNA-files

Dataset EGAD00001006785

RNA-sequençing of 21 inflammatory hepatocellular adenomas and 1 non-tumoral sample

Dataset EGAD00001005284

ADARIO Dataset

RNA editing analyses of BRCA-isogenic cell lines and patient-derived xenografts (PDX)

Dataset EGAD50000000739

Normal CD19

Bulk RNA-seq on normal human CD19+ cells

Dataset EGAD00001011105

Repeated Sampling experiment

Repeated Sampling Experiment containing 135 fastq files of RNA sequencing. These represent time series of different organ areas sampled during autopsies.

Dataset EGAD50000000330

RCRF release 2

RNA sequencing of a Chromophobe renal cell carcinoma, Non-clear cell chromophobe renal cell carcinoma, Neuroendocrine PDAC and clear cell sarcoma

Dataset EGAD50000000872

Glioblastoma single cell RNAseq

Glioblastoma single cell RNA sequencing from two patient, sampled at different positions in tumor and outside tumor

Dataset EGAD50000001423

Single-nucleus RNA-sequencing of normal adrenal cortex and adrenocortical tumors

BAM generated using Cell Ranger v3.1.0 and Space Ranger v1.3.1 and anonymized using BAMBoozle

Dataset EGAD50000000835

10x Genomics VDJ single cell sequencing and 10x Genomics sc RNA-Seq (5 individuals/17 VDJ runs,19 scRNA runs))

single cell RNAseq and TCR sequencing data of 5 individuals. 10x Genomics VDJ single cell sequencing (17 runs) and 10x Genomics sc RNA-Seq (19 runs). The VDJ sequencing was done on a Nextseq 550 using the Chromium Single Cell VDJ Reagent Kit. The RNA-Seq was done either on HiSeq4000 or NovaSeq 6000 using the Chromium Single Cell 5 Reagent Kit.

Dataset EGAD00001009986

RCC Infiltrated Macrophages and Monocytes

Tumor infiltrated Macrophages and Monocytes were sorted on Aria II (Becton Dickinson) into TRIzol LS and flash frozen. RNA was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Total RNA (0.649–1 ng) with RNA integrity numbers 6.8 to 10 underwent amplification using the SMART-Seq v4. Ultra Low Input RNA Kit (Clontech; cat. #63488). Amplified cDNA (15 ng) was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8504) using 8 cycles of PCR.

Dataset EGAD00001009393

Host pathogen interaction long read transcriptome

Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECT’s utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

Study EGAS00001006779

Replication data for RNA-SEQUENCING: A RELIABLE TOOL TO UNVEIL TRANSCRIPTIONAL LANDSCAPE OF PAEDIATRIC B-OTHER ACUTE LYMPHOBLASTIC LEUKAEMIA

This dataset contains the raw data of the RNA-seq experiments described in the paper "RNA-Sequencing: a reliable tool to unveil transcriptional landscape of pediatric B-other acute lymphoblastic leukemia" It contains the raw data from 60 pediatric patients diagnosed with B cell progenitor acute lymphoblastic leukemia lacking the main genetic alterations. RNA material was extracted from bone marrow or periphereal blood and RNA libraries were prepared using Illumina® TruSeq™ stranded mRNA kit following manufacturer's instructions and were sequenced in a NextSeq 550 using a v2 HighOutput 150 cycle kit 2x75bp. Funding: Instituto de Salud Carlos III (ISCIII), PI21/00213

Dataset EGAD50000000981

RNA-seq data: Histone mutations in human Pre-Leukemic HSC and AML

RNA-seq data from TEX cells transduced with HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2 control in triplicate. In addition, RNA-Seq was performed on untransduced TEX cells. Libraries [rRNA-depleted stranded (HMR)] were sequenced on an Illumina Hiseq 4000 platform to generate 100 bp paired-end reads.

Dataset EGAD00001004437

RNA Seq of 25 spheres derived from lymph nodes of lung cancer patients

To further decipher the cell type composition within single spheres we performed RNA-Seq of 25 selected spheres of 4 different categories (including 8 signature-/balanced, 9 signature+/balanced, 1 signature-/aberrant, 7 signature+/aberrant). Samples were sequenced using Illumina NextSeq 2000.Fastq reads were processed using inhouse RNA-Seq workflow.

Dataset EGAD00001011099

RNA-sequencing of 82 pleural mesothelioma samples

The dataset contains RNA-sequencing data (bam files) for 82 pleural mesothelioma samples. All the samples were sequenced on an Illumina NovaSeq 600 sequencer in paired-end mode, generating 100 nt length reads, to obtain an average of 60 million clusters for RNA. Demultiplexing was performed using Illumina bcl2fastq2. Fastq quality was assessed using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and low-quality reads were discarded. Sequence reads were aligned to Human reference genome (UCSC genome assembly GRCh38/hg38) using STAR (v. 2.7.0b).

Dataset EGAD50000002131

RNA sequencing of BCP-LBL and EM B-ALL patients samples

In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL and extramedullary (EM) manifestations of B-ALL patients, we performed RNA sequencing of 16 tissue samples from BCP-LBL and EM B-ALL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

Dataset EGAD50000002047

Healthy human B-lymphopoiesis RNA-Seq reference using FACS sorted bone marrow aspirates

To define a transcriptomic reference of human B lymphopoiesis, bone marrow aspirates were obtained from n=4 healthy donors (study registration DRKS00023583). After immunodensity cell separation, samples were FACS-sorted into 7 established lymphopoietic differentiation stages. RNA was extracted from 5,000-320,000 cells per differentiation stage and subjected to ultra-low-input RNA sequencing after generation of stranded sequencing libraries.

Dataset EGAD00001010917

RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

Fresh peripheral blood mononuclear cells of four human donors were cultured together with either lung adenocarcinoma A549 cancer cells or A549-expressing H1N1 Sialidase cancer cells. These treatments induced the differentiation of donor cells into immunosuppressive MDSC-like cells, which were further subjected to bulk RNA sequencing. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode on 4 lanes of an Illumina NextSeq 500 flow-cell

Dataset EGAD00001012437

Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

HCHWA-D is an early onset hereditary form of Cerebral Amyloid Angiopathy (CAA) caused by a point mutation resulting in an amino acid change (NP_000475.1:p.Glu693Gln) in the Amyloid Precursor Protein (APP). Post-mortem brain tissue (9 patients and 9 age-related controls; frontal and occipital cortex) was used for next generation sequencing of RNA (RNA-Seq with ribosomal RNA depletion).

Study EGAS00001002730

scMultiomics of ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

This dataset contains scMultiomics (scRNAseq + scATACseq) data of human telencephalic organoids, at day 120, from 3 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication): 1. Library 233269(RNA)/235293(ATAC): Pat.1 ARID1B+/- clone 1a (9 pooled organoids). 2. Library 233270(RNA)/235294(ATAC): HD.1 ARID1B+/+ clone 3a (9 pooled organoids). 3. Library 233271(RNA)/235295(ATAC): HD.1 ARID1B+/- clone 3b (8 pooled organoids).

Dataset EGAD50000000499

RNASeq profiles of ROBUST clinical trial and processed WGS mutation calls output

The dataset contains RNAseq profiles of 1040 patients from the ROBUST clinical trial (NCT02285062). The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (75PE, 50M) were constructed using Illumina TruSeq RNA Access method. Fastq files are included. Also includes processed WGS mutation calls output.

Dataset EGAD50000000482

Small RNA-Seq of MicroRNA's in extracellular vesicles of Ushers Syndrome patients

Small RNA-Seq dataset of MicroRNA's found in tear extracellular vesicles (EVs) and hiPSC-derived retinal pigment epithelium (RPE) cells of Ushers Syndrome patients and control samples. 14 samples were isolated and assessed for quality before preparing libraries using the miReasy and TruSeq Small RNA Library Preparation Kit. Sequencing was performed on the Illumina NextSeq 2000 platform, generating paired end FASTQ files.

Dataset EGAD50000001709

Single-cell RNA sequencing of 16 NPM1 mutated AML patients

This dataset contains paired-end fastq files for single-cell RNA-seq of 16 NPM1 mutated AML patients. 19 fastq pairs are included, with two samples split into two lanes and a second (technical) replicate for one patient. Libraries were constructed using 10x Genomics Chromium Next GEM Single cell 3’ v3.1 and sequencing was performed using Illumina NovaSeq6000.

Dataset EGAD50000000478

The study on genomic profiling using clinical specimens (tissue, blood, etc.) form patients with lung and thymic tumors

The objective is to generate a comprehensive immunogenomic profiling in thymoma using RNA sequencing and TCR repertoire analysis and to evaluate the potential of immunotherapy in thymoma from multiple perspectives.

Study JGAS000552

5' single cell RNA sequencing

Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.

Dataset EGAD00001007672

Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

Dataset EGAD00001006332

RNA-sequencing data of post-mortem brain tissue taken from individuals with SCA3 and controls

Spinocerebellar ataxia type 3 (SCA3) is the most common autosomal dominant inherited ataxia worldwide, caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyglutamine (polyQ)-expansion in the corresponding protein. Here we have RNA-sequencing data from the cerebellum of individuals with SCA3 and matched controls.

Dataset EGAD00001009317

Integrated analysis of whole genome and RNA sequencing in 22 HBV-associated HCCs

RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.

Dataset EGAD00001001035

Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

Dataset EGAD00001008971

Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

Dataset EGAD50000001098

RNAseq and T cell receptor (TCR) profiling of PBMC cells 3 months post Omicron exposure

This dataset contains RNA-seq and T cell receptor (TCR) sequencing files from a cohort (n=20) 3 months post positive PCR for SARS-CoV-2. A total of 10 hospitalised (samples H1-10) and 10 non-hospitalised (samples NH1-10) are contained within this dataset. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs.

Dataset EGAD50000001356

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