14970 results for "cancer studies using rna-seq"

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• GBM cancer stem cell lines -RNA-seq and WGS data

  Glioblastoma stem cell lines have been profiled for RNA-seq and WGS

  Study EGAS00001003700

• scRNA-seq using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data for 15 samples from patients with ovarian cancer, 5 samples for each of the 3 tumor immune phenotypes (Infiltrated, Excluded and Desert). Dissociated cells from each tumor sample have been sorted to isolate live cells from the 3 compartments: tumor, immune and stromal. Each of the compartments has been analyzed separately by scRNAseq, excluding some desert tumors for which cells from the stromal and immune compartments have been pooled. Sequencing was performed using 10X Genomics Chromium Single Cell platform (v2 Chemistry).

  Dataset EGAD00001006974

• Longitudinal RNA-seq datasets from patients after abdominal surgery

  This dataset consists of RNA-seq data of 126 whole-blood samples derived from patients after abdominal surgery. Total-RNA collected preoperatively and at 3-time points postoperatively (2-6, 24 and 48hrs) were analysed using RNA-sequencing. RNA was collected in PAXGene (Qiagen) tubes and extracted using the PAXGene RNA extraction kit, with a DNase step to remove contaminating DNA. Globin and ribosomal RNA were removed via a Ribo-zero kit (Illumina) and library preparation was carried out using the TruSeq Stranded Total RNA Library Prep Kit (Illumina). Next generation sequencing was performed on the NovaSeq sequencing platform (Illumina) at the Wellcome Centre for Human Genetics (WCHG) in Oxford.

  Dataset EGAD00001011102

• Breast Cancer - immune clusters - RNA-seq

  In this study we use expression data from breast cancer tumors to define immune clusters in breast cancer. Immune clusters have gradual levels of immune infiltration. In the intermediate immune infiltration cluster, we found a worse prognosis which is independent of known clinicopathological features. We also found the immune clusters associated with treatment response. Further using gene expression data and deconvolution algorithms to dissect the immune contexture of the clusters.

  Dataset EGAD00001004985

• Whole exome sequencing of advanced gastric cancer

  To define the cellular characteristics of malignant ascites of advanced gastric cancer patients and search for therapeutic strategies, we obtained 5 malignant ascites and 1 cerebrospinal fluid from five patients with gastric cancer. We analyzed single-cell RNA-seq data of 180 cells from 4 malignant ascites and 1 cerebrospinal fluid metastasis using Fluidigm® C1™ System. Whole exome sequencing data was also generated from blood or tumor tissue.

  Dataset EGAD00001005740

• RNA-seq

  RNA-seq (Illumina HiSeq 2500) of 142 Human Breast Cancer samples

  Dataset EGAD00010002478

• The MD Anderson Colorectal Cancer Case Control Study

  Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the US. Driven by common disease common variants hypothesis, genome-wide association studies only identified a number of common susceptibility loci that explained a small portion of CRC heritability. We conducted a case-control study using whole exome sequencing to identify rare genetic variants with intermediate effect size that predispose individuals to colorectal cancer.

  Study phs002691

• single cell RNA-seq data of circulating tumor cells from three small cell lung cancer patients

  This dataset contains raw 10x Genomics single-cell RNA sequencing data from a total of eight runs of circulating tumor cells from three small cell lung cancer patients. Each run represented by four FASTQ files (R1, R2, I1, I2) generated using the Illumina NextSeq 2000 platform. These files include read pairs as well as sample and cellular barcode indices. Circulating tumor cells were enriched from the blood of three SCLC patients using the CTC-iChip followed by magnetic depletion of RBCs. The enriched samples were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system.

  Dataset EGAD50000002035

• Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Dataset EGAD00001005097

• Complex-I stratification of Parkinson's disease - single nucleus RNAseq

  Single nucleus RNA seq dataset for CI stratification of Parkinson's disease Single nucleus RNA seq dataset of prefrontal cortex tissue from a total of N=18 samples. Tissue samples correspond to patients with idiopathic Parkison's disease (PD) with varying levels of Complex-I activity (N=12) and neurologically healthy controls (N=6). Single nucleus RNA seq was carried out using 10X Genomics Chromium. This dataset corresponds to a subset of the samples sequenced using conventional bulk tissue RNA seq and available within this Study as a separate Dataset.

  Dataset EGAD50000000432

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: NOVA1 gain and loss of function systems

  We produced NOVA1 and EGFP over-expression RNA-seq datasets in three healthy control individuals using lentivirus-mediated gene transfer to model NOVA1 gain of function. Additionally, we produced a NOVA1 loss of function RNA-seq dataset by generating iPSC-MN with NOVA1 knock out produced by CRISPR/Cas9 in the CV-B iPSC line.

  Study EGAS00001005881

• Whole exome sequencing and RNA-seq of esophageal squamous cell carcinoma

  We perform integrative genome-wide analyses such as whole-exome sequencing, copy number variant(CNV) analysis, and gene expression analysis using next-generation sequencing and other methods to elucidate driver genes and signaling pathways causing tumorigenesis and cancer progression, leading novel molecular diagnostics and molecular therapies.

  Study JGAS000367

• NKI-AvL CRC-OVC RNA-seq

  The dataset “NKI-AvL CRC-OVC RNA-seq" includes 4 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004341

• RNA seq data of 2 lung cancer samples prepared using 2 different RNA-seq library preparation protocols

  Raw data used for generation of the results in the Vardetector manuscript – “.bam” files of RNA-seq data of tumor samples of 2 patients prepared with 2 different library preparation protocols (exome-capture and ribodepletion –> 4 “.bam” files in total). The submission also contains the somatic mutations “.vcf” files (4 in total, however 2 unique). Moreover, also an output of the Vardetector module (“.csv” file with the number of reads above the mutations of interest) is present in the submission (4 “.csv” files in total).

  Study EGAS50000001419

• RNA-seq

  Bulk RNA-seq data of 8 RNA samples were generated. Libraries were prepared using the Stranded mRNA Library Prep, Ligation Kit (Illumina) following manufacturer’s recommendations and sequenced on a NextSeq 2000 (2x50 bp, Illumina).

  Dataset EGAD00001010308

• Functional Analysis of Genetic Variants in African Americans with Breast Cancer

  The goal of this study is to identify and characterize novel genetic variants associated with a predisposition to breast cancer (BCa) in African Americans (AAs) using a family case-family control study design. Variants of unknown clinical significance (VUS) were characterized using bioinformatics tools. Future studies will further characterize select VUSs using in vitro genomic editing methods and functional assays to determine the functional consequences. The targeted sequencing data is made available for 85 actionable cancer genes. These genes have been previously classified with deleterious mutation(s) and whose phenotype results in a specific, defined medical recommendation(s).

  Study phs002977

• Genomic characterization of Malignant Pleural Mesothelioma.

  Genomic characterization of Malignant Pleural Mesothelioma using RNA-seq, Exome and Illumina 2.5 M array.

  Study EGAS00001001563

• Targeted gene fusion sequencing (Fus-seq) in mesothelioma

  This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract.

  Dataset EGAD00001000361

• Single nucleus RNA-seq of human epiglottis and subglottis

  This dataset contains single nucleus RNA-seq of human epiglottis and subglottis tissue performed using the 10X platform

  Dataset EGAD50000001279