Search Results - EGA European Genome-Phenome Archive

RNA sequencing of colon tumor/normal sample pairs

Dataset EGAD00001000215

Deep RNA sequencing in CLL

Dataset EGAD00001000258

HipSci - Monogenic Diabetes - RNA Sequencing - April 2015

Dataset EGAD00001001953

HipSci - Monogenic Diabetes - RNA Sequencing - January 2016

Dataset EGAD00001001955

Single Cell RNA Transcriptomics of Mantle Cell Lymphoma Reveals the Presence of Treatment-Resistant Subclones at the Time of Diagnosis

Mantle cell lymphoma is a chronically relapsing B cell neoplasm characterized by clonal heterogeneity. We implemented single cell RNA sequencing of paired tumor samples from four patients with an aggressive nodal MCL at diagnosis and after failure of standard immunochemotherapy. Clustering the cells based on the inferred CNVs showed small subclones present at diagnosis with a CNV profile similar to the major subclone at relapse. Comparison of these subclones to major subclones present at diagnosis revealed 119 upregulated pathways common for the four patient with an aggressive MCL, including NF-kappaB and PTEN signaling pathways. Additionally, we sequenced a patient with an indolent to blastoid MCL transformation with intestinal tissue involvement. In contrast to other compartments at relapse, the cells in the intestine showed strikingly different CNV profile and presence of new driver mutations including NOTCH1. In conclusion, our study demonstrates that scRNAseq can potentially detect therapy resistant subclones at diagnosis.

Study EGAS50000000825

Differential expression in clear cell renal cell carcinoma

To investigate the levels of gene expression in clear cell renal cell carcinoma (ccRCC), we performed an RNA-seq analysis in 786-O, A-498, UM-RC-2 clear cell renal carcinoma cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq files and csv files with the differential expression results. Differential expression was calculated by the RNAflow pipeline (DEseq2), and log fold changes are calculated with respect to the normal cell line (HK-2), with separate results between normoxic and hypoxic datasets.

Dataset EGAD50000001883

RNAseq of blood, fat and muscle samples from 45,X, 46,XX, 46,XY and 47,XXY

Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. The RNA-seq libraries were multiplexed paired-end sequenced on an Illumina Novaseq 6000 (100 bp) and subjected to initial quality control using FastQC (BAbraham Bioinformatics). In addition to trimming of low-quality ends, adaptor removal was conducted using Trim Galore with default settings (BAbraham Bioinformatics).

Dataset EGAD00001010052

Single cell RNA sequencing of cerebrospinal fluid

Single-cell RNA sequencing of cells isolated from cerebrospinal fluid from 81 individuals with multiple sclerosis (n=33) or other neurological disease (n=48) using 10x Genomics 3’ expression (v2 chemistry).

Study EGAS00001007478

Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

Study EGAS00001000472

HipSci - Primary Immune Deficiency - RNA Sequencing - July 2017

Dataset EGAD00001003536

HipSci - Hereditary Spastic Paraplegia - RNA Sequencing - July 2017

Dataset EGAD00001003537

HipSci - Hereditary Cerebellar Ataxias - RNA Sequencing - July 2017

Dataset EGAD00001003538

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016

Dataset EGAD00001001954

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015

Dataset EGAD00001001952

Colorectal adenomas and carcinomas NKI-AvL TGO series Gut2009

Colorectal cancer (CRC) develops from normal epithelium, through a benign precursor lesion called adenoma, by accumulation of genetic alterations affecting oncogenes and tumour suppressor genes. These CRC-related genomic alterations often result in specific RNA-expression patterns. RNA isolated from fresh frozen specimen of 32 adenomas and 29 CRCs was obtained from the previously published study (Carvalho et al. 2009) and RNA-sequencing was performed with the aim to examine RNA expression changes in colorectal adenoma-to-carcinoma progression.

Study EGAS00001002758

Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

Study EGAS50000000301

Comprehensive Genomic Characterization of Acral Melanoma

In this study, we performed paired tumor/normal long insert whole genome and exome sequencing and tumor RNA sequencing on primary or metastatic acral melanoma tumors collected from 34 patients. Patients were enrolled from either Vanderbilt University or the Memorial Sloan-Kettering Cancer Center. We report an integrated analysis of DNA and RNA sequencing data to describe genomic and transcriptomic characteristics of acral melanoma.

Study phs001036

Multi-omics profiling of PSCCE

We performed whole-exome sequencing, RNA sequencing and immunohistochemistry profiling of primary small cell carcinomas of the esophagus.

Study EGAS00001004889

Kidney_tumour_RNA

This is a bulk DNA and RNA sequencing study of human renal tumours

Study EGAS00001002487

BCG-Flu_Challenge_Study_RNAseq_Human_01

RNA sequencing data generated from human samples collected in the BCG-Flu Challenge study.

Study EGAS50000001677

A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

CITE-Seq (cellular indexing of transcriptomes and epitopes) of 51 lymph node (LN) samples from including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL), and marginal zone lymphomas (MZL, n = 11), in addition to non-malignant reactive lymph nodes (rLN, n = 8). Of the malignant LN samples, 20 were collected at the time of initial diagnosis and 23 were from patients who had previously undergone one or more lines of systemic treatment. Relapse samples were collected at least 3 months after cessation of systemic treatment. This dataset also includes 5 prime RNA sequencing and immune receptor sequencing (10X Genomics) for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL (GCB) and 2 MZL).

Dataset EGAD50000000497

Single cell RNA sequencing of mononuclear cells from synovial fluid of patients with rheumatoid arthritis

Mononuclear cells were collected from synovial fluid of anti-citrullinated positive antibodies (ACPA)-positive rheumatoid arthritis patients (n=8) and ACPA-negative RA patients (n=8). Global cell types (i.e., no enrichment) were obtained from these cryopreserved synovial fluid mononuclear cells (SFMC) samples and immediately fixed and processed using the GEM-X Flex Gene Expression Reagent Kits (10x Genomics) according to protocol. Following Gel Bead-in Emulsion (GEM) generation, samples were processed using the standard manufacturer’s protocol. Once sequencing libraries passed standard quality control metrics, libraries were sequenced on an Illumina NextSeq2000 P4 100 cycle reagent kit with the following read structure: R1: 28, R2: 90, I1: 10, I2: 10. Libraries were sequenced to obtain a read depth greater than 10,000 reads/cell for gene-expression (GEX). FASTQ files are made available. More detailed information can be obtained in Argyriou A. et al, Annals of the Rheumatic Disease, 2025.

Dataset EGAD50000001801

Somatic L1 retrotransposition in normal colorectal epthelium

Throughout an individual’s lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 406 normal colorectal clones, 12 MUTYH-associated adenomatous clones, and 19 matched colorectal cancer tissues. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 (in 139 clones) and read-through RNA expression profiles (in 116 clones) to investigate the epigenetic regulation of L1 activity.

Dataset EGAD00001010183

Multiome sequencing of primary colon tissue and derived organoids

Multiome (ATAC + RNA) sequencing of primary colon tissue and organoids derived from the same donors.

Study EGAS00001008110

HipSci - Monogenic Diabetes - RNA Sequencing - July 2017

Dataset EGAD00001003530

HipSci - Bleeding and Platelet Disorders - RNA Sequencing - July 2017

Dataset EGAD00001003539

HipSci - Monogenic Diabetes - RNA Sequencing - October 2016

Dataset EGAD00001003180

HipSci - Healthy Normals - RNA Sequencing - May 2014

Dataset EGAD00001000897

Modulation of the peripheral blood immune cell transcriptome by vitamin D3 supplementation in people with a first demyelinating event: a randomized placebo-controlled trial

Vitamin D deficiency is a risk factor for developing multiple sclerosis (MS). Both in vitro and animal studies suggest an immunomodulatory effect of vitamin D. The PrevANZ trial, a phase IIb randomized placebo-controlled trial of oral vitamin D3 supplementation in people with a first demyelinating event (FDE), was conducted to determine if supplementation can prevent recurrent disease activity in this cohort at high risk of developing definite MS. As a sub-study of this trial, we used whole blood transcriptomic analyses to investigate the effect of vitamin D3 supplementation on peripheral immune cells in people with an FDE, and to gain insight into potential mechanisms by which vitamin D3 may regulate MS risk and disease activity. The PrevANZ trial randomized participants to 1000 IU, 5000 IU or 10,000 IU daily of oral vitamin D3 or placebo. Peripheral blood was collected at baseline and 12 weeks in PAXgene Blood RNA tubes. Transcriptomic datasets were generated by RNA sequencing.

Study EGAS00001007346

RNA sequencing of high hyperdiploid and ETV6/RUNX1-positive pediatric acute lymphoblastic leukemia

We performed RNA-sequencing of high hyperdiploid and ETV6/RUNX1-positive ALL cases by using the Human Ribo-Zero rRNA Removal Kit to investigate the gene expression in high hyperdiploid ALL.

Study EGAS00001003079

Integrated Exome and RNA Sequencing of Dedifferentiated Liposarcoma

Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

Study JGAS000177

Characterization of High-Grade Serous Ovarian Cancer Subtypes via Single-Cell and Spatial-Transcriptomics Profiling

We measured gene expression in single-cell RNA sequencing samples from patients with high-grade serous ovarian cancer (HGSOC), for a study on improving HGSOC subtype definition by taking into account varying cell type proportions within tumors. The initial dataset (added October, 2020) contains 3 samples (3 individuals). The next dataset (added November, 2022) contains 34 samples from 8 individuals. The samples in the second dataset were sequenced in five different ways: 1) rRNA depletion and bulk RNA sequencing of tumor chunks, 2) rRNA depletion and bulk RNA sequencing of dissociated cells, 3) poly-A capture and bulk RNA sequencing of dissociated cells, 4) poly-A capture and scRNA sequencing of dissociated cells, 5) barcoding and pooling cells and scRNA sequencing (2 pools of 4 samples each). The third dataset (added June, 2024) contains data from one spatially resolved transcriptomics experiment (4 samples, one per Visium capture area, describing one tumor from one individual) and scRNA sequencing on 5 samples (5 individuals).

Study phs002262

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - October 2016

Dataset EGAD00001003181

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - July 2017

Dataset EGAD00001003531

RNA-seq of CD34+ HSPCs from LRMDS patients

To profile transcriptional alterations of HSPCs in LR-MDS patients, 7AAD−CD45+Lin-CD235a−CD34+ cells were isolated from healthy donors and LR-MDS patients for RNA sequencing.

Study EGAS00001008182

Genomic Analysis of Diffuse Large B Cell Lymphoma

Tumors from 383 newly diagnosed diffuse large B cell lymphoma were included in this study. Tumor DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue sections, germline DNA was extracted from blood, and whole exome sequencing (WES) of all samples (n=340 tumor normal pairs) was performed using the Agilent SureSelect XT AllExon v5 + UTR kit and sequencing was carried out on an Illumina NovaSeq, 100 x 2 paired end reads. Tumor RNA (n=321) was extracted from formalin-fixed, paraffin embedded (FFPE) tissue sections and RNA sequencing was performed using the Illumina TruSeq RNA Exome Kit (Illumina) for library preparation, sequencing platform HiSeq 4000, 100 x 2 paired end reads.

Study phs003634

Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis

This dataset contains raw sequencing files associated with the paper "Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis" (https://doi.org/10.1038/s41590-023-01490-5). It is composed of two experiments, which are as follows: 1. Single-cell profiling of whole blood leukocytes: This experiment comprises sequencing files generated using the BD Rhapsody single-cell multi-omics profiling (RNA + protein) platform. This platform was used to profile the whole blood leukocyte population in a cohort of sepsis patients, cardiac surgery controls and healthy controls. There are 48 samples and four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the protein profiling (ADT-based AbSeq) library. 2. Single-cell profiling of circulating HSPCs: This experiment comprises sequencing files generated using the 10X single-cell multi-omics (RNA-seq + ATAC-seq) profiling platform. This platform was used to profile circulating HSPCs in a cohort of sepsis patients and healthy controls. There are 5 samples (or plexes), each of which consists of a pool of individuals for whom cells were multiplexed and sequenced as a single sample. There are four files per sample: two paired-end FASTQ files (R1 and R2) corresponding to the RNA-seq library, and two paired-end FASTQ files (R1 and R2) corresponding to the ATAC-seq library. Because these samples consists of multiplexed pools, index files are also provided. These can be used for sample deconvolution using the Cell Ranger pipeline. NOTE: Due to EGA's constrains in the number of files permitted per sample, index files (I1 and I2) for the HSPC data set are provided as a separate experiment named "FASTQ index files (I1 and I2) for deconvolution of 10X single-cell multiomics libraries".

Dataset EGAD00001010927

Profiling RNA Translation in Pediatric Medulloblastoma

This study provides RNA-sequencing and ribosome profiling data for patient-derived cell lines and patient tissue samples for children with medulloblastoma. Ribosome profiling is a variant protocol of RNA-sequencing that directly sequences ribosome-bound RNA fragments only. Associated RNA-seq and Ribo-seq data obtained separately for some cancer cell lines can be found on the NCBI SRA as PRJNA957428. Samples were processed for poly-A mRNA sequencing using the Roche Kapa Kit. Ribosome profiling was performed as described in the manuscript referenced below (Hofman et al.) and based on the article by McGlincy et al., Methods (2017). Ribo-seq data were analyzed for sample quality using RiboseQC (Calviello, Nat Struct Mol Biol, 2020). These data were used to quantify P-sites of open reading frames. RNAseq and ribo-seq data were integrated and compared to determine translational efficiency values using TPM (Ribo-seq) over TPM (RNA-seq) as the metric. Ribo-seq data on 14 samples and RNAseq data on 21 samples derived from 16 fresh-frozen surgical samples for medulloblastoma and 5 autopsy samples are available through dbGaP. A second cohort of 4 medulloblastoma samples (RNAseq, Ribo-seq) related to this study can be found on the EGA at EGAS00001007426.

Study phs003446

ICGC PedBrain: RNA sequencing

Dataset EGAD00001000328

HipSci - Healthy Normals - RNA Sequencing - May 2015

Dataset EGAD00001001438

FBSeq: RNA sequencing of human fetal brain.

RNA sequencing of 120 human fetal brains (aged 12-19 post-conception weeks) was performed as part of a Medical Research Council (U.K.) funded project (MR/L010674/2) to investigate genetic effects on gene expression in the developing human brain and their role in neuropsychiatric disorders. Human fetal brain tissue from elective terminations of pregnancy was provided by the Human Developmental Biology Resource (HDBR) (http://www.hdbr.org), with ethical approval (#08/H0712/34), and with consent for use of fetal material for medical research provided by female donors. Total RNA was extracted from half of the available brain tissue from each fetus using Tri-Reagent and treated with TURBO DNase. RNA-Seq libraries were prepared using 1µg of purified total RNA and the Illumina TruSeq Stranded Total RNA Library Prep kit, following ribosomal RNA depletion. Libraries were sequenced on the Illumina HiSeq 2500 or HiSeq 4000 systems, generating at least 50 million read pairs per sample.

Study EGAS00001003214

Control samples, breast cancer clinical samples and matched patient-derived tumour xenografts (PDTXs) to develop and test a computational approach to discriminate human and mouse sequences in PDTXs

Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. In this study we generated Whole Exome Sequencing (WES) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA.

Study EGAS00001002445

metastatic uveal melanoma tumour biopsies

Tumour biopsies were obtained from uveal melanoma patients pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

Study EGAS50000000864

metastatic uveal melanoma tumour biopsies (n=35)

Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

Study EGAS50000000836

RNA004 Nanopore DRS of peripheral blood

Direct RNA Sequencing offers the capability of standard transcriptomic analyses + RNA modification analysis, which holds promising applications for future clinical workflows. To this end, we tested the newly available RNA004 kit on human peripheral blood and provide orthogonal GLORI measurement for benchmarking of m6A-detection.

Study EGAS50000001201

Immune Determinants of Resistance to PD-1 Blockade in Renal Cell Carcinoma

We performed an integrated bulk and single-cell transcriptomic analysis of tumors from 102 advanced renal cell carcinoma patients enrolled in a phase II clinical trial of frontline nivolumab (NCT03117309) to investigate determinants of response to anti-PD1 monotherapy. The present study includes 112 archival or pre-treatment tumors of clear cell and non-clear cell histologies from 90 patients that underwent bulk RNA sequencing (RNA-seq). For 76 patients, 74 of whom had matched RNA-seq, whole exome sequencing (WES) was also performed on tumor samples as well as matched peripheral blood. Additionally, 19 fresh tumor samples from 17 patients, including pre and post-treatment samples and mixed histologies, were locally cryopreserved and centrally processed for single cell RNA (scRNA-seq) and TCR (scTCR-seq) sequencing. 7 patients had matched scRNA/scTCRseq, RNAseq, and WES.

Study phs003618

RNA-Seq

RNA Sequencing

Dataset EGAD00001001121

Genomic and transcriptomic analysis of baseline PDAC patients' tumors from the OXIRI phase 1b clinical trial

This study was aimed at investigating the genomic and transcriptomic features associated with response to the OXIRI regimen (oxaliplatin, irinotecan, capecitabine) in pancreatic ductal adenocarcinoma (PDAC) tumors. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) on baseline tumor samples obtained from 8 patients recruited in the OXIRI phase 1b clinical trial (NCT02368860).

Study EGAS00001006073

RNA-seq and WGS data of MB-0152

Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152)

Dataset EGAD00001003342

GermCellTumour

DNA and RNA sequencing across a number of different germ cell tumours, included mixed components within the same tumour.

Study EGAS00001003457

3786 results for "RNA AND sequencing OR transcriptome"

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