Search Results - EGA European Genome-Phenome Archive

Single-cell RNA-seq data of bronchoalveolar lavage (BAL) fluid in severe COVID-19 and SARS-CoV-2 stimulated classical blood monocytes

We performed single-cell RNA-sequencing of cells in the bronchoalveolar lavage (BAL) fluid of severe COVID-19. In addition, we performed single-cell RNA-sequencing of SARS-CoV-2 stimulated classical blood monocytes. This study provides detailed insights into the alveolar macrophage response to SARS-CoV-2 infection and reveals a profibrotic macrophage response in severe COVID-19 patients.

Dataset EGAD00001006827

Small-RNA sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

Single-end 75 basepair small-RNA sequencing of 90 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. Samples were prepared using the NEXTFLEX® Small RNA-Seq Kit v3 (Bioo Scientific ). Samples were sequenced at the molecular genomics core (Peter MacCallum Cancer Centre) using 50bp single end sequencing on the Illumina NextSeq 500 (Illumina, USA). This dataset contains raw sequencing reads in FASTQ format.

Dataset EGAD50000000501

Whole Exome and RNA-Sequencing of Germline, Small Bowel Carcinoid Primary Tumor, and Liver Metastasis Trios

This dataset includes trios of germline/constitutional, primary tumor (small bowel carcinoid), and metastatic tumor (liver) trios for 5 patients (i.e. 15 samples total). Constitutional, primary tumor, and metastatic tumor samples all underwent whole exome sequencing (WES or WXS). Primary and metastatic tumor samples underwent RNA sequencing (RNA-seq).

Dataset EGAD00001010036

RNA-Seq dataset of Targeting the dark proteome to expand the lineage-retained antigen landscape in neuroblastoma

This dataset contains bulk RNA-sequencing data generated to enable custom transcriptome assembly and to provide expression context for matched ribosome profiling in the discovery of lineage-retained neuroblastoma tumor antigens. RNA was sequenced from 183 neuroblastoma samples comprising cell lines, patient-derived tumor organoids, and primary patient tumors spanning the adrenergic (ADRN) and mesenchymal (MES) lineage states, with 101 samples prepared as rRNA-depleted (total RNA) libraries and 82 samples prepared as poly(A)-selected libraries. Libraries were sequenced paired-end (2x150 bp) on the Illumina NovaSeq 6000 platform. Raw data are provided as paired-end fastq.gz files.

Dataset EGAD00001016124

MIBC NAC2020 cohort RNA sequencing

The dataset contains RNA sequencing data from N=48 transurethral resections of bladder tumours (TURBTs) from N=48 patients with muscle-invasive bladder cancer. All TURBTs originate from formalin-fixed paraffin embedded tissue. We used the Illumina TruSeq RNA exome kit, previously known as the TruSeq RNA Access Library Prep Kit. This kit converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. All samples were run in an Illumina NovaSeq6000 instrument. Paired FASTQ files from all 48 patients are provided.

Study EGAS50000000741

Low-input RNA-seq libraries from FFPE samples using TaKaRa SMARTer kit

Using the TaKaRa SMARTer Stranded Total RNA-Seq Kit v2, RNA-seq libraries were generated from 5 ng of RNA extracted from FFPE tissue. A low-input workflow was applied with 5 PCR cycles for the first amplification and 16 for the second. Library quality was assessed by Bioanalyzer and Qubit, and libraries were sequenced (2×150 bp) on the Illumina NextSeq 550 platform.

Dataset EGAD50000001552

The transcriptome and DNA methylome profiling of the early human post-implantation embryos

whole genome sequencing data of parent blood samples. Single cell full-length RNA-seq and PBAT-Seq data of in vitro culture D6 to D14 human embryo.

Dataset EGAD00001005137

10x single-nucleus RNA-seq of postoperative human FCD II brain tissues

This dataset contains 10x Genomics single-nucleus RNA sequencing data from postoperative brain tissues of patients with focal cortical dysplasia type II (FCD II). The samples were processed using the Chromium platform.

Dataset EGAD50000001403

RNA-seq dataset of salivary gland tumor samples

This dataset contains paired-end RNA-seq data of salivary gland tumor samples from 94 patients. Sequencing was performed on Illumina HiSeq 2500, HiSeq 4000, HiSeq X Ten or NovaSeq 6000.

Dataset EGAD50000001191

Multi-omics analysis of cocaine use disorder in postmortem brain tissue of the ventral striatum

The dataset contains raw sequencing data from miRNA-seq, RNA-seq and single-nuclei RNA-seq experiments to investigate transcriptomic changes in cocaine use disorder.

Dataset EGAD50000000881

RNA-Seq of non-canonical t(7;12) AML

We performed WGS on AutoMACS-separated BM leukemic blasts (CD34 + CD33+) to characterize the breakpoint and genes involved in the translocation. Additionally, we performed RNA-seq of the bone marrow blast cells to explore the functional consequences of the t(7;12) translocation

Dataset EGAD50000000268

IBS-D RNA-seq raw data

The data set consists of fastq raw files from RNA-seq of seven mucosal biopsies of the colon from seven patients, among them three patients with irritable bowel syndrome with diarrhea-predominant symptoms. Paired end sequencing on Illumina NovaSeq 6000 was used.

Dataset EGAD50000000063

COLONOMICS small RNA sequencing

This dataset consists of SOLiD small RNA-seq of 250 colorectal samples: 100 tumor tissue samples, 100 normal tissue samples (adjacent to tumor sites) and 50 matched control samples of healthy individuals. CSfasta and qual files converted to single fastq files prior to uploading.

Dataset EGAD00001004827

A molecular atlas of the human postmenopausal fallopian tube and ovary from single-cell RNA

This datasets contains raw sequencing fastq data of 17 samples from 7 donors of single cell RNA using10x genome technology of human postmenopausal fallopian tube and ovary tissues.

Dataset EGAD00001010076

Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation

Small RNA sequencing data (TruSeq small RNA library preparation kit v2) from serum samples and tumor tissue of orthotopically injected mice (SH-SY5Y cell line) and unengrafted mice, treated with idasanutlin, temsirolimus and vehicle control.

Dataset EGAD00001009625

Single Nuclei RNA sequencing batch 1

This dataset includes the first 9 PTC samples and 6 ATC samples profiled on the same sequencing flowcell.

Dataset EGAD00001011366

Single cell sequencing of mild and critical COVID19 PBMC

Single-cell RNA sequencing of 13 ‘mild-moderate’ and 10 ‘critical’ COVID19 PBMC samples

Dataset EGAD00001006997

Characterization of Immune-Related Gene Expression in Lung Cancer

We performed a comprehensive analysis of inter- and intratumor heterogeneity of immune gene expression in 160 lung cancer patients from the Environment And Genetics in Lung cancer Etiology (EAGLE) study. The transcriptome was profiled with RNA sequencing in 269 tumor samples and 110 normal tissue samples from 160 subjects.

Study phs002346

BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

Dataset EGAD50000000808

Studying the single cell characteristics of pancreatic cancer

Pancreatic cancer is a dangerous malignancy in the pancreas. In this study we use single-cell RNA sequencing technique to help understand the transcriptome characteristics of pancreatic tumor cells. This study help understands the complex microenvironment of pancreatic tumors and will likely to benefit clinical research of pancreatic cancer treatments.

Study EGAS00001003889

Bulk RNA-sequencing data of advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab.

The dataset includes FASTq files and normalised gene expression counts from bulk RNA-sequencing of pre-treatment tumour (n=39) and adjacent non-tumour tissue samples (n=13) from advanced hepatocellular carcinoma (HCC) patients treated with atezolizumab plus bevacizumab. Specifically, RNA was extracted from the FFPE tumour tissue using RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quality and quantity were evaluated using Agilent RNA 600 Pico Chips (Agilent Technologies). Sequencing libraries were prepared using the SMARTer Stranded Total RNA-seq kit v3 (Takara Bio). Sequencing was performed on an Illumina NovaSeq 6000 system. After obtaining the Fastq files, read 2 UMIs and adapters were trimmed using seqtk (v1.2), reads were aligned using STAR (v2.7.7a) to the human reference genome (GRCh38) and quantified with HTSeq (v2.0.2).

Dataset EGAD50000001227

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

Bulk RNA-Seq

Human data for transcriptome (bulk RNA-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

Dataset EGAD00001010906

Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

Bulk RNA Sequencing of 33 epithelioid sarcomas (EpS) and 3 extracranial extra-renal rhabdoid tumors (EERT) Whole-exome sequencing of 30 EpS and 3 EERT Single-cell RNA Sequencing of 8 EpS Visium Spatial Transcriptomics of 3 EpS

Dataset EGAD50000001419

Analysis of Treg gene expression patterns by RNA-Seq in patients with rheumatoid arthritis (RA) and healthy controls (HCs) : Comparison between young and elderly individuals

We compared the gene expression of CD4+CD45RA-CD25hiCD127lo Treg cells from PBMCs between young and elderly RA patients and HCs by RNA-seq

Study JGAS000693

Single cell RNA seq component of ATAC-RNA multiome analysis of a four weeks post conception embryo head

Four single-cell RNA libraries were generated from an unbiased sample of cells of a human four weeks post conception embryo using the 10X Chromium Single-Cell Instrument and NextGEM Single Cell Multiome ATAC+Gene Expression kit (10X Genomics) according to the manufacturer’s protocol.

Dataset EGAD50000001501

Dataset for "HPV integration induces gene fusions" (RNA)

RNA-seq data for "HPV integration induces gene fusions" We performed RNA-seq analysis of five HPV+ head and neck cancer samples using Illumina short reads. Sequenced are submitted in bam format. We also sequenced one samples with pacBio long reads, and the reads are submitted in fastq format.

Dataset EGAD50000001303

RNA-seq data from hypothalamic tissue from individuals with Prader-Willi syndrome and age-matched controls.

RNA-seq data (bam files) from the hypothalamus of 4 individuals with Prader-Willi syndrome and 4 age-matched control individuals. Detailed information about the study design, case-control matching and RNA-seq data processing is provided in the accompanying publication [Bochukova et al (2018) Cell Reports].

Dataset EGAD00001004034

NGS-ProToCol prostate cancer RNA-seq data.

NGS-ProToCol RNA-seq dataset contains 41x normal adjacent prostate and 51x prostate cancer samples taken from fresh frozen radical prostatectomies, sequenced using random-hexamer priming. RNA-seq was performed on the Illumina HiSeq 2500 platform, 2 x 126 bp stranded paired-end reads at a depth of 70 mln reads.

Dataset EGAD00001004215

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

CellRanger counts processed with the Cell Ranger software v3.1.0.

Dataset EGAD50000000836

Whole transcriptome sequencing of pheochromocytoma and paraganglioma arising from germline SDHB mutations

Paired-end 150 basepair whole transcriptome sequencing of 91 SDHB-deficient non-metastatic and metastatic pheochromocytoma and paraganglioma. Samples were prepared using the NEB-Next directional RNA-Seq kit (NEB, USA) and underwent 150bp paired-end sequencing on the Illumina NovaSeq 6000 (Illumina, USA) according to manufacturer’s instructions. This dataset contains raw sequencing reads in FASTQ format.

Dataset EGAD50000000504

sc-RNA-Seq soft tissue sarcoma tumoroid biobank

Dataset EGAD00001009002

RNA-seq data from diagnosis and relapse samples of Down Syndrome acute lymphoblastic leukemia.

Dataset EGAD00001003280

RNA sequencing datasets from isolated human subcutaneous and visceral adipocytes from obese and lean people

94 human adipocyte samples isolated from whole adipose tissues using collagenase digestion of tissue and flotation of lipid-laden adipocytes, followed by RNA isolation and RNA sequencing (SMARTer Stranded Total RNA-Seq library preparation, HiSeq 4000 100-bp paired-end reads). Adipocyte samples comprise subcutaneous and visceral adipocytes isolated from obese and lean people (N=24 obese-subcutaneous, N=24 obese-visceral, N=22 control-subcutaneous, N=24 control-visceral). Human adipocyte RNA sequencing data are provided as BAM files.

Dataset EGAD00001010195

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de-novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondaryrearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.

Study EGAS00001000659

RNA sequencing of untreated head and neck cancer patient-derived xenografts (PDXs) and matched patient tumor tissue.

RNA sequencing was performed on untreated patient tumor tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC). The aim of this analysis was to characterize the transcriptional landscape of the tumors in the in vivo setting.

Study EGAS50000001595

RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 2)

The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four ETV6::RUNX1 patients (ALLT-388, ALLT-392, ALLT-394, ALLK-114) and from a second relapse sample of one ETV6::RUNX1 patient (ALLK-104). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic and relapse tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

Dataset EGAD50000002589

RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 4)

The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of 10 B-other ALL patients (ALLT-389, ALLT-391, ALLT-393, ALLK-101, ALLK-109, ALLK-110, ALLK-113, ALLK-115, ALLK-123, ALLK-124). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

Dataset EGAD50000002599

WGS and RNA-Seq data of 2 additional patients of newly diagnosed multiple myeloma (NDMM)

For WGS DNA of tumor or control samples was prepared for paired sequencing using the Illumina TruSeq DNA Nano Kit and sequenced on NovaSeq 6000. For RNA-Seq the sequencing Kit Illumina TruSeq stranded mRNA was used with the same sequencer. There are 4 samples for WGS (18 runs) and 4 samples for RNA (4 runs) available.

Dataset EGAD00001009627

Single-cell bam files and RNA sequencing of viral RNA stocks

244 infected single-cell alveolar bam files, 48 empty well bam files, and 52 RNA sequencing of amplicons (4 SARS-CoV-2 variants with 12 batches and 4 viral variants pool samples). 244 alveolar single cells were captured over 12 experimental batches and experimental condition is written in metadata uploaded as "infected_cells_final_revision.csv". on github (https://github.com/twkim-0510/SARS-CoV-2_viral_competition). Each bam file name corresponds to the sample_name column of the metadata.

Dataset EGAD00001009711

Medulloblastoma dataset

This dataset contains a tumor + normal DNA sequence data and tumor RNA seq data for a medulloblastoma patient.

Dataset EGAD50000000384

raw fastq file from 10x genomics sequencing

RNA samples of bone marrow and cord blood were sequenced by 10x genomics platform.

Dataset EGAD00001004200

Results of RNA sequencing from all patients/samples

Results of sequencing the targeted RNA-seq panel of breast cancer patients and controls. This dataset comprises of FASTQ files of 295 samples (both breast cancer patients and controls) and the results of mapping the FASTQ files to the reference human genome (hg38) available in a form of raw gene expression matrix.

Dataset EGAD50000000017

3D-GSC_expression_profiles

In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG-derived glioma stem cell (GSC) models. Twenty-two primary GSC models derived from biopsies collected at diagnosis were cultured in an ECM-mimicking compound before for RNA extraction and subsequent rRNA-depletion and sequencing .

Dataset EGAD00001011079

RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C)

RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C). Samples used were Whole Blood. Febrile illness controls include children with bacterial and viral infections and healthy controls. This dataset contains samples from patients recruited into the DIAMONDS study.

Dataset EGAD00001011134

3924 results for "RNA AND sequencing OR transcriptome"

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