12312 results for "cancer rna-seq"

in 15.97 milliseconds.

• 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

• 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

• Single-cell RNA-sequencing of rhabdomyosarcoma tumouroids (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the single-cell RNA sequencing of RMS tumouroids data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015708

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015714

• Bulk RNA-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the bulk RNA sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015718

• scRNA-seq DAC

  Dac EGAC00001001559

• Multi-omics characterisation of immune cells in Long Covid

  We generated 10X Multiomics (paired RNA+ATAC) for Long Covid patients with up to 14 months follow-up.

  Study EGAS50000000142

• Strand-specific RNA Sequencing of initial and recurrent gliomas

  Four RNA-sequencing datasets from two patients with initial low-grade glioma and copy number alteration at IDH1 upon recurrence. Data is provided as bam files.

  Dataset EGAD00001003764

• RNA Sequencing of mCRC xenografts under cetuximab treatment.

  RNA sequencing on cetuximab treated, untreated and release samples of one metastatic colorectal xenograft. 3 cetuximab treated samples, 3 placebo and 3 release - paired fastq.

  Dataset EGAD00001005185

• The Extracellular RNA Quality Control (exRNAQC) study (phase 2)

  mRNA capture sequencing and small RNA sequencing data (FASTQ files) of the exRNAQC study phase 2 (interaction study)

  Dataset EGAD00001009724

• Whole exome and RNA sequencing of 5 samples of patient-derived xenograft (PDX).

  Whole exome and RNA sequencing of 5 samples of patient-derived xenograft (PDX). Available files are raw sequencing fastq files.

  Dataset EGAD00001010102

• Human serum small non-coding RNA sequencing

  Human small non-coding RNA sequencing of serum from sons of PCOS mothers (n=9) and sons of control mothers (n=9), see publication for details.

  Dataset EGAD00001010165

• RNA sequencing of AML with 3q26 rearrangements

  RNA sequencing of 44 AML cases with diverse 3q26 rearrangements. This dataset is complementary to EGAD00001000726 (which only contains t(3;3)/inv(3)) and to EGAD00001006123.

  Dataset EGAD00001015629

• National Cancer Institute (NCI) Biospecimen Pre-analytical Variables (BPV) Analysis

  The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. Data from this study will be used to develop evidence-based biospecimen standard operating procedures and best practices for fit-for-purpose collection, processing, and storage of biospecimens. The BPV Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following sub-studies below or in the "Substudies" box located on the right hand side of this top-level study page phs001304 BPV Cohort. The substudy links will be active once they are released by dbGaP. Preanalytical Impacts on Global Metabolite Profiling - plasma (MassSpec by Metabolon) This study was to evaluate the impact of the storage temperature (s) (-80°C and LN2 vapor) and the length of storage on human plasma quality using LC-MS/MS (liquid-chromatography-mass spectrometry/mass spectrometry) based global metabolite profiling. The study includes 240 plasma samples collected from 40 donors. Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors. Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors. Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors. Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. The study includes 235 samples from 40 donors. Evaluation of frozen conditions on mRNA profiling by TaqMan assay (mRNA expression by Georgetown University). This study was to utilize gene expression profiling, using custom TaqMan arrays, to compare the molecular profiles of RNA from frozen tumor samples collected using two freezing methods (dry ice or LN2), two storage temperatures (-80°C or LN2 vapor), as well as Optimal Cutting Temperature (OCT) compound and non-OCT embedded. The study includes 100 samples from 20 donors. mRNA signature for stratification by cold ischemia time (mRNA expression by IBBL). The study was to determine the effects of cold ischemic time (delay-to-fixation) and formalin preservation (FFPE) on mRNA detection by Taqman assay using tumor tissue specimens from kidney, colon and ovarian cancer patients. There are160 samples from 40 donors. The Biospecimen PV cohort is utilized in the following dbGaP individual studies. To view molecular data, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page phs001304 Biospecimen PV cohort. phs001634 CIT mRNA phs001635 CNV aCGH phs001636 Fixation Delay phs001637 Global Metabolite Profiling phs001638 mRNA TaqMan phs001639 NGS phs001640 Tumor Storage

  Study phs001304

• IBMsnRNAseq

  snRNA-seq and spatial transcriptomic data and analysis of healthy (CTRL) and inflamed (immune-mediated necrotizing myopathy (IMNM) and inclusion body myositis (IBM)) human quadriceps muscle. This data set includes 19 snRNA-seq (7 CTRL, 4 IMNM, 8 IBM) and 8 ST samples (3 CTRL, 2 IMNM, 3 IBM).

  Dataset EGAD50000000449

• ICGC MMML-seq Data Freeze March 2013 whole genome sequencing

  ICGC MMML-seq Data Freeze March 2013 whole genome sequencing

  Dataset EGAD00001000355

• Human T-bet governs innate and innate-like adaptive IFN-g immunity against mycobacteria.

  We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. PBMCs from the patient was analyzed with scRNA-seq.

  Study EGAS00001004504

• Histone Acetylome-wide Association Study of Autism Spectrum Disorder

  H3K27ac ChIP-seq were performed on postmortem samples from autism spectrum disorder and matched control brains. Tissues were chosen from three brain regions: prefrontal cortex, temporal cortex and cerebellum.

  Study EGAS00001001943

• BLUEPRINT September 2016, ATAC-seq for monocyte RPMI_BG_T=24hrs_RPMI_T=5days_LPS_T=4hrs from venous blood, on Genome GRCh38

  ATAC-seq data for 1 sample(s) for monocyte RPMI_BG_T=24hrs_RPMI_T=5days_LPS_T=4hrs from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002915

• BLUEPRINT September 2016, ATAC-seq for class switched memory B cell from venous blood, on Genome GRCh38

  ATAC-seq data for 2 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002908

• ICGC MMML-seq Data Freeze July 2013 whole genome sequencing

  ICGC MMML-seq Data Freeze July 2013 whole genome sequencing

  Dataset EGAD00001000645

• ICGC MMML-seq Data Freeze July 2013 miRNA sequencing

  ICGC MMML-seq Data Freeze July 2013 miRNA sequencing

  Dataset EGAD00001000650

• BLUEPRINT release August 2016, ChIP-Seq for macrophage - T=6days B-glucan, on genome GRCh38

  ChIP-Seq data for 2 macrophage - T=6days B-glucan sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002314

• BLUEPRINT release August 2016, ChIP-Seq for macrophage - T=6days untreated, on genome GRCh38

  ChIP-Seq data for 2 macrophage - T=6days untreated sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002458