11769 results for "cancer rna-seq"

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• BLUEPRINT release August 2015, ChIP-Seq for adult endothelial progenitor cell, on genome GRCh38

  ChIP-Seq data for 1 adult endothelial progenitor cell sample(s). 8 run(s), 7 experiment(s), 7 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001554

• BLUEPRINT release August 2015, ChIP-Seq for macrophage, on genome GRCh38

  ChIP-Seq data for 12 macrophage sample(s). 49 run(s), 49 experiment(s), 49 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001576

• BLUEPRINT release August 2015, ChIP-Seq for segmented neutrophil of bone marrow, on genome GRCh38

  ChIP-Seq data for 4 segmented neutrophil of bone marrow sample(s). 20 run(s), 19 experiment(s), 19 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001588

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - T=10day_RANK_M-CSF, on genome GRCh38

  ChIP-Seq data for 1 monocyte - T=10day_RANK_M-CSF sample(s). 2 run(s), 2 experiment(s), 2 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 EGAD00001002420

• BLUEPRINT release August 2016, ChIP-Seq for naive B cell, on genome GRCh38

  ChIP-Seq data for 15 naive B cell sample(s). 67 run(s), 59 experiment(s), 59 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 EGAD00001002466

• BLUEPRINT release August 2016, ChIP-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  ChIP-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 13 run(s), 13 experiment(s), 13 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 EGAD00001002488

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• Whole-genome and transcriptome versus panel sequencing in precision oncology: A translational-clinical comparison

  Precision oncology offers new cancer treatment options. While the use of whole-genome (WGS) and transcriptome (TS) sequencing remains often confined to specific clinical programs, molecular analysis with gene panels is more common clinical practice. Methods: Twenty patients with rare or advanced tumors sequenced by WGS/TS within the DKFZ/NCT/DKTK-MASTER program from 2015 to 2020 (MASTER 1) were additionally sequenced with the TSO500 DNA and TST170 RNA Assay by Illumina. Original Molecular Tumor Board (MTB) therapy recommendations (TR) were juxtaposed with TR from NGS panel data analysis (comparison 1). To mitigate temporal differences between the two sequencings, WGS/TS was bioinformatically reanalyzed (MASTER 2), and new TR were again compared (comparison 2). Results: In comparison 1, 47.1% of the MASTER 1’s TR and 62.8% of the panel’s TR were identical, as were 45.9% of the TR of MASTER 2 and 54.9% of the panel in comparison 2. In both MASTER 1 and MASTER 2, 26.5% and 36.1% of TR, respectively, relied on Biomarkers (BM) which were not covered by the panel. Eight of the ten MTB-derived therapy implementations were also supported in the panel, the two remaining ones being based on BM absent from the panel. Conclusions: About half of the TR in WGS/TS and panel sequencing were identical. Around a third of TR issued by WGS/TS were based on BM which are not covered by the panel, leading to therapy implementations. The presented data underscores the clinical value of comprehensive molecular analyses in individuals with advanced cancers.

  Study EGAS50000000431

• Whole exome and RNA sequencing of organoid samples derived from TRACERx patients

  Immune checkpoint blockade in non-small cell lung cancer (NSCLC) rarely leads to complete tumour remission, suggesting that tumours harbour subpopulations of cancer cells that can escape immune predation. However, while tumours consist of multiple genetically distinct clones, the extent to which separate tumour subclones differ intrinsically in their functional capacity for immune evasion remains largely unexplored. This has been challenging to address due to an inability to isolate and propagate individual tumour subclones from human cancers. Here, we leverage the multi-region TRACERx lung cancer evolution study to generate a patient-derived platform that allows the functional analysis of immune escape at single clone resolution. We generated libraries of >20 separate NSCLC organoid lines per patient by isolating individual (clonal) organoids established from multiple spatially separated tumour regions. Each organoid subline was co-cultured with autologous tumour infiltrating lymphocytes (TIL) to evaluate their capacity to elicit a T cell response. Organoid lines derived from separate tumour regions, or from single clones within individual regions, differ vastly in their capacity to elicit a T cell response, showing the coexistence of intrinsically immune evading (‘hot’) and non-evading (‘cold’) clones in the same primary tumour. Organoid lines escaping T cell recognition represent genetically and transcriptionally unique subclones with a distinct evolutionary history, showing that evolutionary sculpting of subclonal diversity can have functional consequences for anti-tumour immunity. Notably, the identification of immune-evasive subclones would not have been possible using computational approaches alone, highlighting the unique value of functional co-culture platforms. This patient-derived functional co-culture platform reveals that tumour evolution can give rise to distinct cancer clones with intrinsic differences in immune evasion capacity and provides an approach to prospectively identify, isolate and characterise immune evading subclones from patients with cancer.

  Study EGAS00001008092

• 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

• Dataset for desmoplastic small round cell tumor - RNA

  This dataset contains 32 RNA sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq RNA and TruSeq Stranded RNA Kit. The sequencing was always paired.

  Dataset EGAD50000000912

• RNA-sequencing

  RNA-sequencing for a cohort of B-ALL samples : 5 Down Syndrome (DS), 16 Hyperdiploid (HeH), 6 iAMP21, 9 other. RNA-sequencing for B-cell progenitors from 3 healthy. It also contains RNA-sequencing datasets of Patient-Derived Xenografts (X) developed from the B-ALL samples : 4 Down Syndrome (DS), 4 Hyperdiploid (HeH), 1 iAMP21, 3 other.

  Dataset EGAD00001005426

• scRNA-seq reveals alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

  Dac EGAC00001001547

• The paired FF/FFPE colon set, Exome-Seq

  Dataset EGAD00001000834

• AML scRNA-seq

  Dataset EGAD00001006537

• Bulk RNA sequencing of SARC PDOs and UroCa PDOs.

  This dataset contains raw FASTQ files from bulk RNA sequencing of SarBC-01 organoids at different passages (Passage 6, Pssage 19, Passage 59), UroBC-01 organoids (Passage 70), UroBC-16 organoids (Passage 19) and UroBC-22 organoids (Passage 8). RNA was isolated using the Quick-DNA/RNA Miniprep kit (Zymo Research, Irvine, CA, USA, D7001) and subjected to bulk RNA sequencing. TruSeq Stranded mRNA kit (Illumina, 20020594) was used for the library preparation according to manufacturer’s guidelines. Sequencing was performed on Illumina NovaSeq 6000 using paired-end 100-bp reads.

  Dataset EGAD00001011156

• RNA sequencing of 12 NSCLC samples from 4 patients at MDACC

  Multi-region RNA sequencing of 12 NSCLC samples from 4 patients at MDACC

  Study EGAS00001005951

• ChIP_2PEAKS

  Second batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2

  Dataset EGAD00010002051

• scRNA-seq analysis Identifies Hepatic IL-13-Producing ILC3-Like Cells Potentially Linked to Liver Fibrosis

  Study EGAS00001007207

• Human oligodendroglial progenitor cells (hGPCs/OPCs) derived from induced pluripotent stem cell (iPS) scCRISPRi/a-seq

  Dac EGAC50000000804

• Functional Multiomics of Cellular Therapy and Immune Checkpoint Blockade Therapy for Solid Tumors

  Tumor samples were collected from a patient with synovial sarcoma, which acquired resistance to ACT targeting NY-ESO-1. Biopsies (n=3; primary, metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Bulk tumor whole exome and RNA sequencing corresponding to all three tumor specimens and whole exome sequencing from patient-matched normal blood are made available through this accession.

  Study phs002762

• Extracellular microRNA Biomarkers for Diagnostic and Prognostic Assessment of Preeclampsia at Triage

  This study is comprised of samples from 123 donors (71 cases and 52 controls) undergoing evaluation for preeclampsia. All samples were collected between 20 and 40 weeks of gestation. Small RNA sequencing was done on serum RNA obtained from donors. We were able to identify 3 bivariate extracellular miRNA biomarkers that can enable early diagnosis of preeclampsia. The raw fastq small-RNA sequencing fastq files will be submitted to dbGaP.

  Study phs003169

• RNA-sequencing on thyroid samples from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality

  The current data pertains RNA-sequencing reads obtained from thyroid samples acquired from fetuses with Down syndrome and fetuses with no genetic/developmental abnormality. Total RNA was isolated from left lobe from thyroid samples using a hand-held homogenizer and the Promega ReliaPrep RNA Miniprep System (Thermo Fisher Scientific). RNA yield was determined with the NanoDrop Microvolume Spectrophotometer (Thermo Fisher Scientific). Fragmentation and mRNA library preparation was performed using the Kapa mRNA Hyperprep Kit (Roche, Basel, Switzerland). Libraries were equimolar pooled and quality was checked on a TapeStation system using the DNA1000 ScreenTape (Agilent Technologies, Santa Clara, CA, USA). Libraries were sequenced with poly(A) selection to sequence all messenger RNA for gene expression analysis on the NovaSeq6000 PE150 (Illumina, San Diego, CA, USA), producing at least 40M 150-bp paired-end reads per library.

  Dataset EGAD50000000387

• RNA sequencing from patient-derived intestinal organoids

  uman duodenal tissues for establishing organoid cultures used in this study were sourced from de-identified surgical specimens (n = 3) of the duodenum obtained from patients who had undergone biopsy procedures unrelated to CeD at Tampere University Hospital. The protocol was approved by the Ethics Committee of Tampere University Hospital, Tampere, Finland (ETL code R18082). RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Dataset EGAD50000000492

• Bulk RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"

  This dataset includes 14 bulk RNA sequencing data (28 fastq files) in the study entitled "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2". RNA sequencing library was generated with Truseq stranded total RNA Gold kit.

  Dataset EGAD00001006241