14970 results for "cancer studies using rna-seq"

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• RNA-seq dataset of patient and healthy donors

  RNA-seq dataset on a patient (P) presenting with defects of immunity and three healthy donors (C1, C5, C6). This dataset contains raw and processed files from RNA-seq transcriptome analysis performed according to the Smart-seq2. There are 24 single-read (50 bp) fastq files, 6 per patient/donor consisting of 2 cell types and 3 replicates per cell type. There is one count matrix file generated using featureCounts against Ensembl v98 gene models.

  Dataset EGAD00001008371

• Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor infiltrating T cells.

  Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying functional and dysfunctional states of human tumor infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify tissue-specific and general gene-regulatory landscapes in the wide breadth of CD8+ TIL functional states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor entity-matching samples and prioritize key elements by super enhancer analysis. Our analysis reveals a human core chromatin trajectory to TIL dysfunction and identifies key enhancers, transcriptional regulators, and deregulated target genes involved in this process. Finally, we validate enhancer regulation at loci encoding PD1, TCF1, and TIM3 by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study advances the understanding of molecular regulation of TIL (dys-)function and provides a framework for modulating immunotherapeutic relevant TIL genes via their enhancers.

  Dataset EGAD00001008662

• Epigenomes and Transcriptomes of Brain Samples of Schizophrenics and Controls

  We examined the effects of antipsychotic medications on the cell-specific epigenomics and transcriptomics in the frontal cortex of schizophrenic subjects. We performed ChIP-seq (H3K4me3 and H3K27ac) and RNA-seq on neuronal and non-neuronal nuclei of postmortem frontal cortex samples from two cohorts of schizophrenics, either previously treated or not with antipsychotic medications, and control subjects individually matched by sex and age. In total, we tested 29 schizophrenics (15 untreated and 14 treated patients) and their matched control samples. Two replicates were produced on each brain sample for each assay. ChIP-seq data were generated using MOWChIP-seq (Zhu et al., PMID: 31666743) and RNA-seq data were produced using the combination of SMART-seq2 (Picelli et al., PMID: 24385147) and a Nextera XT DNA library preparation kit. The filename contains the information on the experimental group, the number of the sample within the group, the type of the brain nuclei, the epigenomic/transcriptomic data set (either H3K27ac or mRNA), and the number of replicate. For example, “SCZ-1-untreated-neuron-H3K4me3-R1” refers untreated schizophrenic sample #1, replicate 1 ChIP-seq data on H3K4me3.

  Study phs002487

• Aerobiology, Immunology, and Mycobacterium Tuberculosis Transmission

  We submit data from the TB Aerobiology, Immunology and Transmission (TBAIT) study examining clinical and transcriptomic characteristics associated with Tuberculosis cough aerosolization. From a prospective longitudinal cohort of 142 participants with previously untreated pulmonary Mycobacterium tuberculosis (Mtb) infection, we assessed presence of culturable Mtb aerosols using a cough aerosol sampling system (CASS), as well as other clinical, microbiologic, and immunologic characteristics. We performed whole blood transcriptional profiling (submitted here) on a convenience subset of 29 cough aerosol culture (CAC) positive participants and 29 CAC negative participants, using Illumina NextSeq RNA Sequencing (RNA-Seq).

  Study phs003727

• Lung cancer RNA Seq Data Access Committee

  Dac EGAC00001003317

• Breast_cancer_topographs

  Breast cancer topography will be explored using a combination of multi-region whole geome sequencing and in-situ RNA sequencing of fixed tissue specimens.

  Study EGAS00001003698

• Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes

  Study EGAS00001006272

• Multiple Sclerosis risk variants regulate gene expression in innate and adaptive immune cells

  Each of at least 200 single nucleotide polymorphisms (SNPs) have been confirmed to be associated with individually small increases in the risk of Multiple Sclerosis (MS). A key function that could mediate SNP encoded MS risk is their regulatory effects on gene expression or splicing. Transcriptomic profiling was performed using Affymetrix gene-expression microarrays, using RNA extracted from purified human peripheral blood monocytes, CD4 and CD8 positive lymphocyte cells, B-lymphocyte cells and Natural Killer cells from 73 untreated MS cases and 97 healthy controls. Cis expression quantitative trait locus (eQTL) mapping studies were performed in each cell type separately to characterize MS risk loci associated with gene expression change.

  Study EGAS00001004087

• GCP Challenges in Hepatology

  raw RNAseq data from blood plasma of patients diagnosed with liver disease. Total RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq-Kit v3 - Pico Input Mammalian (Takara Bio). Libraries were paired-end sequenced (2x100) o a NovaSeq 6000 instrument using NovaSeq S2 or S1 kit (Illumina).

  Dataset EGAD50000000775

• KNS42 and SF188 H3K36me3 chipSeq

  Chromatin immunoprecipitation (ChIP) was carried out employing antibodies against H3K36me3 and RNA polymerase II using the HistonePath and TranscriptionPath assays by ActiveMotif. Whole genome sequencing was carried out using an Illumina HiSeq2000 and data is provided as 6 BAM files. H3K36me3 chipseq RNA polymerase II chipseq and input coverage for each cell line.

  Dataset EGAD00001004119

• CMV infection during pregnancy

  This study aims to characterize the transcriptional diversity, clonal composition, and viral target antigens of CMV-specific CD8 T cells among pregnant women with different anti-CMV serological patterns. Single-cell RNA sequencing (scRNA-seq) combined with MHC-peptide dextramers were performed using CD8 T cells from pregnant donors.

  Study JGAS000728

• Combined Tumor and Immune Signals From Genomes or Transcriptomes Predict Outcomes of Checkpoint Inhibition in Melanoma

  Cancer immunotherapy with checkpoint blockade (CPB) leads to improved outcomes in melanoma and other tumor types, but a majority of patients do not respond. High tumor mutation burden (TMB) and high levels of tumor-infiltrating T cells have been associated with response to immunotherapy, and integrative models using DNA and RNA have improved predictions of clinical benefit. However, identification of immune and tumor-intrinsic features in models using DNA or RNA alone have not been comprehensively explored in melanoma. In this study, we sequenced DNA and RNA of tumors from 67 melanoma patients receiving CPB, and aggregated this cohort with previously published data, yielding whole exome sequencing (WES) data for 189 patients and bulk RNA sequencing data for 178 patients. Using these datasets, we derived genomic and transcriptomic factors that predict overall survival (OS) and response to immunotherapy. Using whole exome DNA data alone, we calculated T cell burden (TCB) and B cell burden (BCB) based on rearranged TCR/Ig DNA sequences, and found that melanoma patients with high TMB and either high TCB or high BCB survived longer and had higher response rates, as compared to patients with low TMB and either low TCB or low BCB. Next, using bulk RNA-Seq data, differential expression analysis identified 83 genes which are associated with high or low OS. By combining pairs of immune-expressed genes with tumor-expressed genes, we identified three gene pairs which are associated with response and survival (Bonferroni P<0.05). All three gene pair models were validated in an independent cohort (n=180) (Bonferroni P<0.05). The best performing gene pair model included the lymphocyte-expressed MAP4K1 (Gene ID: 11184) and the transcription factor TBX3 (Gene ID: 6926) which is overexpressed in poorly differentiated melanomas. We concluded that RNA-based (MAP4K1 and TBX3) or DNA-based (TCB and TMB) models combining with immune and tumor measures improve predictions of outcome after checkpoint blockade in melanoma.

  Study phs002683

• RNAseq of human breast cancer tumors from the PEARL study

  Formalin fixed, paraffin-embedded human breast cancer tumor samples had RNA extracted using the Thermo Scientific KingFisher Flex instrument and the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit; Total RNA libraries were created using the Bravo Automated Liquid-Handling Platform and the TruSeq Stranded Total RNA Library Prep Gold Kit; libraries were sequenced on the Illumina NovaSeq 6000 machine using a 2x50 bp paired-end configuration to target a read depth of 120 million clusters per library.

  Dataset EGAD00001015613

• RNA-seq FASTQ files from newborn screening dried blood spot samples

  Paired-end RNA-seq FASTQ files from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). Each sample was sequenced in 4 lanes, leading to 8 FASTQ files per sample and a total of 21x8=168 FASTQ files. There is an additional number of 8 FASTQ files corresponding to sample BS13, which was downsampled to 1/4 of its original depth (see BS13_README file for details).

  Dataset EGAD00001004991

• single cell RNA-seq and ATAC-seq of human fetal forebrain tissue

  Oligodendrogenesis in the human central nervous system has been mainly observed at the second trimester of gestation, a much later developmental stage compared to mouse. Here we characterize the transcriptomic neural diversity in the human forebrain at post conceptual weeks (PCW) 8 to 10, using single-cell RNA-Seq. We find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level with single-cell ATAC-Seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of fifty key genes using In Situ Sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mouse and human and describe regulatory mechanisms involved in human OPC specification.

  Study EGAS00001006136

• HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling

  Single-cell DNA-sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propose HIPSD&R-seq (HIgh-throughPut Single-cell Dna and Rna-seq), a scalable yet simple and accessible assay to profile low-coverage DNA and RNA in thousands of cells in parallel. Our approach builds on a modification of the 10X Genomics platform for scATAC and multiome profiling. In applications to human cell models and primary tissue, we demonstrate the feasibility to detect rare clones and we combine the assay with combinatorial indexing to profile over 17,000 cells.

  Study EGAS50000000691

• 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

• RNA-seq from time-course experiment treating cells for 72h

  RNA sequencing from MSTO-211H cell line cultures treated for 72h with vehicle solution, palbociclib 250nM, or abemaciclib 250nM (N = 3, each). RNA-seq prepared using TruSeq Stranded mRNA libraries and sequenced with Illumina HiSeq 4000. Data is in raw fastq format, paired end. Some samples have been split in two lanes, with a final count of 24 fastq files.

  Dataset EGAD00001007737

• Systematic comparative analysis of single-nucleotide variants detection methods from single-cell RNA sequencing data

  Systematic interrogation of single nucleotide variations (SNVs) is one of the most promising approaches to delineate the cellular heterogeneity and phylogenetic relationships at the single cell level. While SNV detection from abundant single cell RNA sequencing (scRNA-seq) data is applicable and cost-effective in identifying expressed variants, inferring sub-clones, and deciphering genotype-phenotype linkages, there is a lack of computational methods specifically developed for SNV calling in scRNA-seq. Although variant callers for bulk RNA-seq have been sporadically used in scRNA-seq, the performances of different tools have not been assessed. Here, we performed a systematic comparison of seven tools including SAMtools, the GATK pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, using both simulation and scRNA-seq datasets, and identified multiple elements influencing their performance. Our study provided the first benchmarking to evaluate the performances of different SNV detection tools for scRNA-seq data.

  Study EGAS00001003883

• H005 RNA-seq CLL

  Paired-end RNA sequencing using total RNA from 136 primary lymphoma samples. Sequencing was performed on the Illumina HiSeq2000 with 300bp insert size. The dataset contains FASTQ files.

  Dataset EGAD00001002056

• Transcriptome sequencing of gingivo-buccal oral squamous cell carcinoma for integrative analysis: alterations in expression of genes attributable to methylation changes

  Gingivo-buccal oral squamous cell carcinoma (OSCC-GB) is the most common cancer among men in India and is associated with high mortality. Although OSCC-GB is known to be quite different from tongue cancer in its genomic presentation and its clinical behavior, it is treated identically as tongue cancer. Predictive markers of prognosis and therapy that are specific to OSCC-GB are, therefore, required. To achieve this, we have carried out transcriptome (n=72) profiling of paired tumor-normal tissues collected from OSCC-GB patients from India. RNA sequencing was performed on tumor and paired adjacent normal samples from 72 OSCC-GB patients. From each patient, total RNA was extracted from tumor and normal tissue samples using AllPrep DNA/RNA Mini Kit (QIAGEN). The quality and concentration of isolated total RNA were checked using Agilent 2100 Bioanalyzer and NanoDrop 2000 (Thermo Fisher Scientific). The OD260/OD280 ratio was ≥ 2 and RNA Integrity Number (RIN) was ≥ 7.0 for all sequenced samples. Ribosomal RNA (rRNA) was removed from the RNA samples, using Ribo-Zero Magnetic Kit (Epicentre). Sequencing libraries were prepared from rRNA depleted samples using TrueSeq RNA Sample Preparation Kit (Illumina). Each triplex cDNA library pool was sequenced as 100bp paired-end on HiSeq-2000 or HiSeq-2500 (Illumina). Protocols suggested by the manufacturers were used for all assays.

  Study EGAS00001003893

• Epigenomics of Prostate Cancer from Cell Free Plasma

  We sought to perform epigenomic characterization of prostate cancers by profiling circulating nucleosomes isolated from patient plasma using cell free chromatin immunoprecipitation followed by sequencing (cfChIP-seq). Our major findings include identification of prostate-cancer specific regulatory elements using a novel statistical method accounting for variable tumor DNA fraction in plasma, inferring transcription factor activity based on binding motif enrichment within regulatory elements, and epigenetically phenotyping patients based on clinical and genomic features. Data available in dbGaP will include cfChIP-seq and targeted sequencing from approximately 50 patients with a known diagnosis of cancer and healthy patient controls.

  Study phs003482

• Single cell RNA-seq and ATAC-seq of human fetal forebrain tissue, weeks 8 to 11.

  Single cell RNA-seq from 6 and single nuclei ATAC-seq from 3 human fetal tissue samples. Samples from 8 to 11 weeks. Includes a 8.5 weeks samples with matching both ATAC-seq and RNA-seq runs. Data was sequenced using 10X Genomics chromium technology, for scRNA-seq samples belong to v2 and v3.

  Dataset EGAD00001008653

• Cohort-Based Genome-Wide Association Study of Glioma (GliomaScan)

  We conducted a new independent GWAS of adult glioma using 1,856 cases and 4,955 controls from 14 cohort studies belonging to the Cohort Consortium, 3 case-control studies, and 1 population-based case only study. Cases were newly diagnosed glioma [ICDO-3 codes 9380-9480 or equivalent], and controls were cancer-free at the time of glioma diagnosis. We found evidence of strong replication for three of the seven previously reported associations at 20q13.33 (RTEL), 5p15.33 (TERT), and 9p21.3 (CDKN2BAS), and consistent association signals for the remaining four at 7p11.2 (EGFR both loci), 8q24.21 (CCDC26) and 11q23.3 (PHLDB1). The direction and magnitude of the signal were consistent for samples from cohort and case-control studies, but the strength of the association was more pronounced for loci rs6010620 (20q,13.33; RTEL) and rs2736100 (5p15.33, TERT) in cohort studies despite the smaller number of cases in this group, likely due to higher grade tumors being captured in the cohort studies. Our findings suggest that larger studies focusing on novel approaches as well as specific tumor subtypes or subgroups will be required to identify additional common susceptibility loci for glioma risk.

  Study phs000652

• bulk RNA-Seq of colorectal cancer patient samples

  Study EGAS00001006666