11762 results for "cancer rna-seq"

in 17.95 milliseconds.

• CIRCLE-seq of PDO

  CIRCLE-seq data of PDAC 1 patient-derived organoid (PDO) - Unmapped reads, libraries were sequenced using the Illumina NextSeq500 with the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles), generating around 10M paired end 150bp reads per sample

  Dataset EGAD50000000281

• Chromatin accessibility profiling of primary human hepatocytes

  The chromatin accessibility profiling of primary human hepatocytes using Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq).

  Study EGAS50000001230

• A distinct monocyte cellular state links systemic immune dysregulation to pulmonary impairment in long COVID

  single cell multiome dataset (snRNA-seq + snATAC-seq) from PBMC of patients with long COVID disease.

  Dataset EGAD50000001729

• ATAC-seq dataset

  This dataset contains ATAC-seq data performed in MM.1S cell line in ETOH (control) or Dexamethasone condition (Treatment)

  Dataset EGAD00001011135

• Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing in Sporadic ALS

  To identify the genetic cause and modifiers of Sporadic ALS, we performed Whole-genome-sequencing, Whole-exome-sequencing and RNA-sequencing of Sporadic ALS patients.

  Study JGAS000393

• ICR_RNASeq_pHGG

  RNA sequencing of paediatric high grade gliomas and diffuse intrinsic pontine gliomas. RNA was sequenced from fresh frozen surgical material or from primary cells cultured under stem cell conditions. RNA was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files

  Dataset EGAD00001004116

• Mayo Clinic and Illumina Collaborative Early Stage Ovarian Cancer (ESOC) Study

  Twenty five patients with early stage carcinoma (Stage I and II) of the ovary were consented for this study. As part of a collaborative agreement with Illumina Inc, Tumor-DNA and patient matched normal DNA from blood underwent whole genome sequencing and microarray genotyping and RNA underwent RNASeq. Tissue also underwent IHC staining for TP53 mutations. The aim of the study was to profile the genomic landscape of these early tumors to discover biomarkers for early detection or subgrouping into different genomic or outcome subgroups. Analyses performed include somatic mutation analysis, RNASeq mutation analysis, LOH analysis, structural variant detection. The current release of this study focusses on 17 patients with serous carcinoma and stage 1 or 2 and with high grade (3 or 4).

  Study phs000897

• ATAC-seq in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  ATAC-seq performed in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives to profile alterations in chromatin accessibility associated with constitutional MLH1 epimutation.

  Dataset EGAD50000000714

• scDNA-seq

  Single cell DNA-seq data (CLL gene panel - Tapestri single-cell DNA CLL panel, Mission Bio)

  Dataset EGAD00001008960

• scRNA-seq of monocultures and co-cultures of PDAC-PDOs and CAFs

  scRNA-seq of monocultures and co-cultures of patient-derived PDAC organoids and matched CAFs. 3 sample sets per patient.

  Dataset EGAD00001009655

• Human tumor scATAC-seq

  We profiled 4 high-grade gliomas patient brain tumor samples by single-cell ATAC-seq using the 10X Chromium 3' technology. The raw fastq and index files are provided.

  Dataset EGAD00001008347

• McGill EMC Release 4 for assay "ATAC-seq"

  McGill EMC Release 4 for assay "ATAC-seq": Sequencing of transposase-accessible chromatin as described by Buenrostro et al. (Nature Methods 10, 1213?1218 (2013) doi:10.1038/nmeth.2688)

  Dataset EGAD00001001300

• BLUEPRINT: WGBS-seq for monocytes and neutrophils

  WGBS-seq for monocytes and neutrophils

  Dataset EGAD00001000673

• Human embryo ATAC+RNA single cell sequencing samples DAC (Linnarsson)

  DAC for human embryo ATAC+RNA single cell sequencing samples

  Dac EGAC50000000657

• RNA sequencing

  For RNA sequencing: All sample numbers starting with 6717 are tumor samples which has been sequenced using transcriptomics (see BAM files). It concerns biopsies of metastatic lesions from patients with BRAFV600 mutated melanoma, obtained before, during and after the study treatment (see samples metadata). RNA sequencing is performed using the Illumina Novaseq 6000 system.

  Dataset EGAD50000000383

• Paired RNA sequencing of Thymic epithelial tumors - Additional Dataset

  Paired RNA sequencing of additional samples of Thymic epithelial tumors. Uploaded are the paired fastq files, sequencers were Illumina HiSeq 2500, HiSeq 4000, NovaSeq 6000 and HiSeq X Ten. The kits used were Illumina Truseq RNA and Illumina Truseq stranded mRNA.

  Dataset EGAD50000000324

• Cohort A RNA sequencing

  Cohort A includes glioma tumors of varied grading and pathology from male and female individuals. RNA was isolated from fresh frozen glioma tissue of each sample tumor block from Cohort A.

  Study EGAS50000000950

• Cohort B RNA sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. RNA was isolated from FFPE glioma tissue of each sample from Cohort B.

  Study EGAS50000000953

• Identification of Novel Therapeutic Targets for Calcific Aortic Valve Stenosis Using Integrative Genomics

  In order to identify novel therapeutic targets for calcific aortic valve stenosis, we have generated a large transcriptomic dataset from RNA sequencing of human aortic valve tissues from 500 individuals undergoing aortic valve replacement or heart transplant at the Institut universitaire de cardiologie et de pneumologie de Québec – Université Laval (QUEBEC-CAVS-RNA). This dataset represents a unique resource to understand the molecular mechanisms underlying aortic valve diseases.

  Study phs003541

• Circulating Tumor DNA in Intermediate Risk Rhabdomyosarcoma

  In this study, we evaluated circulating tumor DNA (ctDNA) as a biomarker in the serum of 124 patients with newly diagnosed intermediate risk rhabdomyosarcoma (IR RMS) from the Children's Oncology Group (COG) biorepository. In addition to pre-treatment serum, we also analyzed matched tumor tissue and germline in a subset of patients. We profiled samples using ultra-low passage whole genome sequencing (ULP-WGS) and a new custom hybrid-capture sequencing assay, Rhabdo-Seq, to detect copy number alterations, rearrangements, and single nucleotide variants. We found that patients with detectable ctDNA at diagnosis had significantly worse outcomes than those without detectable levels of ctDNA. Our study demonstrates that baseline ctDNA detection is feasible and prognostic in IR RMS. The ULP-WGS and targeted next-generation sequencing (Rhabdo-Seq and TranSS-Seq) data are available in this study.  

  Study phs002866

• 10X snRNA-seq data from human FCDII postoperative brain tissues with mTOR pathway mutations

  Focal cortical dysplasia type II (FCDII) is linked to mTOR pathway mutations and drug-resistant epilepsy. Using 10X snRNA-seq on postoperative FCDII brain tissues, we characterized transcriptional alterations across cell types, revealing mTOR-related dysregulation. These findings provide insights into FCDII pathology and potential therapeutic target

  Study EGAS50000000964

• GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator

  This study introduces a novel scRNA-seq normalization method, which takes unobserved genes into account. To validate GTestimate we designed a cell targeted amplification strategy, enabling us to sequence a small set of cells twice, once at a "typical" sequencing depth and once at a "ultra-deep" sequencing depth.

  Study EGAS50000000915

• Epigenetic analysis of clear cell renal cell carcinoma using ChIP-seq

  To investigate the epigenetic landscape of clear cell renal cell carcinoma (ccRCC), we performed ChIP-seq data for the CTCF, H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, and HIF1A marks in the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as the HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and narrowPeak formats. Data were processed using the nf-core chipseq pipeline.

  Dataset EGAD50000001886

• PhIP-seq of Japanese patients with SLE

  Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) datasets of three eHHV-6B-positive SLE patients (three technical replicates), six eHHV-6B-negative SLE patients (three technical replicates), and a negative control lacking sera or plasma (12 technical replicates; Illumina NextSeq) and sequencing data of HHV-6 peptide phage library (two technical replicates; Illumina NextSeq).

  Study EGAS00001007955

• TARGET-seq+ single-cell transcriptome sequencing

  Single-cell whole transcriptome sequencing data for bone marrow samples from 9 cases with clonal hematopoiesis and 4 control samples. The TARGET-seq+ protocol was used to generate plate-based 3' transcriptome data. For details on cell sorting and the TARGET-seq+ protocol see the methods section of the manuscript. One FASTQ file is provided per cell. Cells are named with their plate and well IDs and the subject ID. Empty wells (no-cell controls) are named "blank". Corresponding genotyping files use the same naming without the "_transcriptome" suffix.

  Dataset EGAD00001011175

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for mature neutrophil, on genome GRCh37)

  ChIP-Seq data for 182 mature neutrophil sample(s). 2847 run(s), 366 experiment(s), 355 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002670

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

  ChIP-Seq data for 1 sample(s) for class switched memory B cell from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001002951

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  This dataset comprises two mtscATAC-seq libraries (customized 10X ATAC-seq) generated from donor M80 and donor H05, and one DOGMA-seq library (customized 10X multiome) generated from donor H05, all derived from primary human peripheral blood mononuclear cells. Patient M80 is an 80-year-old male with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), while donor H05 is a healthy 5-year-old pediatric donor. The raw FASTQ files have been provided.

  Dataset EGAD50000001489

• Single-Cell Multi-Omic Analysis of the Vestibular Schwannoma Ecosystem Uncovers a Nerve Injury-Like State

  Vestibular schwannomas are benign tumors that can lead to significant morbidity, including hearing loss, facial nerve paralysis and obstructive hydrocephalus. The genomic landscape of vestibular schwannomas is relatively bland and the molecular pathophysiology of vestibular schwannomas is poorly understood. Therefore, we performed single cell RNA sequencing on 15 sporadic vestibular schwannomas, with paired single cell ATAC sequencing (n = 6) and whole exome sequencing (n = 12) to perform a detailed characterization of the vestibular schwannoma tumor microenvironment at the transcriptional and epigenetic level. We validated our results by analyzing bulk RNA sequencing data from 22 newly sequenced vestibular schwannomas and 173 previously sequenced bulk RNA sequencing data from 195 vestibular schwannomas. Data available in dbGaP include whole exome sequencing of 12 tumors and matched blood samples. Matching single cell RNA sequencing and single cell ATAC sequencing data is available via NCBI GEO.

  Study phs003318

• CRC cell line ATAC-seq

  ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line

  Dataset EGAD50000000296

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• BLUEPRINT: WGBS-seq of B cells

  Whole Genome Bisulfite-seq of four B cell samples

  Dataset EGAD00001000710

• CLL ATAC Seq of Untreated and IBET762 treated samples

  CLL PBMC cells were isolated using ficoll gradient. They have been treated with IBET762 or DMSO as solvent control and ATAC Seq has been performed on them.

  Dataset EGAD00001008723

• Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Dataset EGAD00001008645

• BLUEPRINT September 2016, ATAC-seq for bone marrow, on Genome GRCh38

  ATAC-seq data for 4 sample(s) from bone marrow, on Genome GRCh38. 4 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002710

• Dataset to study clonal evolution in iAMP21 patient SJBALL021901 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJBALL021901 with 71 high quality cells sequenced (67 blast and 4 normal)

  Dataset EGAD00001009755

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A

  Bolleboom-Gao peri-tumoral snRNA-seq glioblastoma dataset 2022/A

  Dataset EGAD00001009964

• ctDNA mutation analysis using the SiMSen-seq approach

  Mutation analysis in plasma samples with low ctDNA levels using a molecular barcoding technology, i.e. the single target approach SiMSen-seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing).

  Dataset EGAD00001006104

• release_2: ICGC PedBrain: whole exome sequencing and Target-Seq

  release_2: ICGC PedBrain: whole exome sequencing and Target-Seq

  Dataset EGAD00001001624

• Single-cell ATAC-Seq (Chromium Next GEM Single Cell ATAC kit v1.1 from 10X Genomics )

  Human data for chromatin accessibility (scATAC-Seq) in CD34+ B cell precursors.

  Dataset EGAD00001010910

• Epigenetic profiles of neuroblastoma PDXs

  This dataset contains bam files for ChIP-seq experiments for 6 neuroblastoma PDXs (Patient Derived Xenograft). It includes the bam files for the H3K27ac mark as well as the bam files of the corresponding input DNA for each sample.

  Dataset EGAD00001003394

• Genomic and Transcriptomic sequencing of neuroblastoma cell lines

  Genomic and Transcriptomic sequencing of neuroblastoma HSR and ecDNA cell lines. Data represents five 96-well plates that were processed with G&T sequencing, resulting in genomic and transcriptomic data from the same single cells. Dataset contains 95 bam files containing the DNA sequencing data and 95 bam files containing the RNA sequencing data of CHP212 cells, 380 bam files (190 DNA and 190 RNA) for TR14 cells, 188 bam files (94 DNA and 94 RNA) for Kelly cells and 192 bam files (96 DNA and 96 RNA) for IMR5/75 cells.

  Dataset EGAD50000000729

• 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 .

  Study EGAS00001007182

• small RNA-sequencing and RNA-sequencing of human brain tissue with temporal lobe epilepsy

  This data set contains the raw .fastq files from two RNA-sequencing experiments and two small RNA-sequencing experiments. Both control brain tissue and tissue from sufferers of mesial temporal lobe epilepsy were sequenced. Two different brain regions were sequenced; the cortex and the hippocampus. For more details please see: Mills, James D., et al. "Coding and non-coding transcriptome of mesial temporal lobe epilepsy: Critical role of small non-coding RNAs." Neurobiology of disease 134 (2020): 104612.

  Dataset EGAD00001005735

• RNA-seq analysis of transcriptome variation with human ESC subclones

  Many studies over the past 10 years, culminating in the recent report of the International Stem Cell Initiative (ISCI, 2011) have shown that hPSC acquire genetic and epigenetic changes during their time in culture. Many of the genetic changes are non-random and recurrent, probably because they provide a selective growth advantage to the undifferentiated cells. Some are shared by embryonal carcinoma cells, the malignant counterparts of ES cells. The origins of these growth advantages are poorly understood, but may come from altered cell cycle dynamics, resistance to apoptosis or altered patterns of differentiation. Less is known about the nature and consequences of epigenetic changes, but it is likely that these similarly affect hPSC behaviour; e.g., enhanced expression of DLK1, an imprinted gene, is associated with altered hPSC growth (Enver et al 2005). Inevitably, these genetic and epigenetic changes will impact on our ability to use hPSC for regenerative medicine, either because malignant transformation of the undifferentiated cells or their differentiated derivatives to be used for transplantation compromises safety, or because they impede the function of those differentiated derivatives, or because they affect the efficiency with which the undifferentiated cells can be expanded and differentiated into desired cell types. Focusing initially upon the existing clinical grade hESC lines, later moving to iPSC, we will Consolidate and extend knowledge of the rate, type and functional impact of the genetic variations that occur during hPSC culture. We will use whole genome and exome sequencing as well as SNP arrays, together with clonal analysis and other cytogenetics techniques. Common changes will be compared with those found in the normal human population, at low frequency in the original cell population or observed during iPSC generation in the HIPSCI project currently based at the WTSI. These studies will provide a better understanding of the range of genetic changes that occur in hPSC beyond the CNVs already identified. In conjunction with cancer genome resources and expertise at WTSI, bioinformatic analyses of these hPSC data will allow us to assess potential impact on hPSC behaviour pertinent to applications in regenerative medicine, notably the likelihood that specific changes arising in undifferentiated PSC cultures may be associated with potential malignant transformation of differentiated progeny This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001004266

• TSO500 on RNA

  TruSight Oncology 500 RNA probes panel on case 521

  Dataset EGAD50000000271

• Therapy and RNA group Ghent DAC

  This is a Data Access Committee for datasets of the Therapy and RNA group Ghent (TaRGeT, Belgium).

  Dac EGAC50000000491

• TST170 Pilot RNA BAM

  TST170 Pilot RNA BAM files

  Dataset EGAD00001006044

• Single-cell RNA-seq of peripheral blood mononuclear cells in classic Hodgkin lymphoma

  Classic Hodgkin lymphoma (cHL) is a largely MHC class I-negative tumor with recurrent 9p24.1/ PD-L1/ PD-L2 copy gains and the highest reported response rates to PD-1 blockade. We utilized scRNA sequencing to characterize the peripheral immune response to PD-1 blockade and more broadly define non-CD8+ dependent mechanisms of immune evasion in cHL. Peripheral blood mononuclear cells were obtained from 20 patients with relapsed/refractory (R/R) cHL treated with PD-1 blockade (nivolumab) on the CheckMate 205 clinical trial (paired samples from cycle 1 day 1 [C1D1] and cycle 4 day 1 [C4D1]), 11 patients with newly diagnosed, previously untreated cHL and 13 healthy donors.

  Study EGAS00001007569