11952 results for "cancer rna-seq"

in 13.47 milliseconds.

• Transcriptomic profiling of myeloid cells from secondary lymphoid organs (lymph nodes and tonsils) from lymphoma patients and controls.

  Despite their recognized impact on the pathogenesis and prognosis of B-cell lymphoma, tumor-associated macrophages (TAM) have not been extensively explored in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). We investigated mononuclear phagocyte (MNP) heterogeneity using single cell RNA sequencing (scRNAseq) in B-cell lymphoma lymph nodes compared to reactive secondary lymphoid organs (lymph nodes and tonsils).

  Study EGAS50000001135

• Gene expression by RNAseq in bronchial biopsies of asthmatics, asthma in remission and healthy subjects

  The study focus was differential expression in bronchial biopsies between persistent asthma, asthma in remission and healthy controls using RNAseq. There were 184 samples that passed QC. RNA samples were processed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA), using an automated procedure in a Caliper Sciclone NGS Workstation (PerkinElmer, Waltham, MA). In this procedure, all cytoplasmic and mitochondria rRNA was removed (RiboZero Gold kit). The obtained cDNA fragment libraries were loaded in pools of multiple samples unto an Illumina HiSeq2500 sequencer using default parameters for paired-end sequencing (2 × 100 bp). Data are available as 221 pairs of FASTQ-files. Note that several samples are associated with multiple sequence runs.

  Dataset EGAD00001005112

• RNA_expression_profiling_of_melanoma_patient_derived_xenograft

  Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growthThis 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/

  Study EGAS00001001537

• HG Transcriptome sequencing in the INTERVAL cohort

  We performed bulk RNA-sequencing on peripheral blood collected from 4,732 blood donors recruited as part of the INTERVAL study. Using these data, we mapped gene expression and splicing quantitative trait loci (QTLs). Then, we integrated these data with protein, metabolite and lipid QTLs in the same individuals. The study aimed to identify the shared genetic etiology across transcriptional phenotypes, molecular traits and health outcomes in humans.

  Study EGAS00001003346

• RNAseq Iron-Treated iPSC-derived Microglia

  Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

  Study EGAS00001006112

• Somatic L1 retrotranspositions in normal human cells

  Genomic mutations accumulate in normal cells during lifetime; however, somatic mosaicism generated by mobilization of transposable elements is not well understood. Here, we explored whole-genome sequences of single-cell expanded clones to illustrate the mutational landscape produced by L1. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 and read-through RNA expression profiles to investigate the epigenetic regulation of L1 activity.

  Study EGAS00001006213

• Multiomics Characterization of Low-grade Serous Ovarian Carcinoma

  Low-grade serous ovarian carcinoma (LGSOC) is a rare tumor subtype with high case fatality rates. There is a pressing need to develop effective treatments using newly available preclinical models for therapeutic discovery and drug evaluation. In this study, we use multiomics integration of whole exome sequencing, RNA sequencing, and mass spectrometry-based proteomics on fourteen LGSOC patient derived cell lines to elucidate novel biomarkers and therapeutic vulnerabilities.

  Study EGAS00001004724

• SPECIAL: Dissecting the melanoma ecosystem one cell at the time during immunotherapy

  The aim of this study was to identify potential biomarkers of response to immunotherapy (anti-PD1-based) as well as gain understanding of the biological mechanism of therapy resistance (either intrinsic or acquired) in melanoma patients. Single cell RNA sequencing was performed from pre- and on-treatment (2-3 weeks after immunotherapy) metastatic biopsies from stage III and IV melanoma patients.

  Study EGAS00001006488

• Clinical panel sequencing of cancer of unknown primary using Comprehensive cancer panel (CCP)

  This database includes comprehensive cancer panel (CCP) on paired tumour and germline DNA from cancer of unknown primary samples, all of which are matched to WGS data under this study. This data was used to compare biomarker yield against what was achieved with WGS. This dataset contains n=34 tumour-germline paired samples. All samples are in BAM format aligned with GRCh38 reference genome.

  Dataset EGAD50000000655

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Liquid biopsy to identify taxane resistance in castration-resistant prostate cancer patients

  Taxanes are life-prolonging treatments for patients with advanced prostate cancer. However, treatment resistance and lethal disease invariably develops. We here used liquid biopsies to identify and characterize resistance to cabazitaxel using a targeted sequencing panel (PCF-SELECT).

  Study EGAS50000001292

• Comprehensive analyses of genetic aberrations in gastroenterological tumors

  Intestinal metaplasia (IM) is a risk factor of gastric cancer in gastric mucosa with Helicobacter pylori infection. To explore the susceptibility to the cancer development in pure gastric IM, we investigated landscape of genetic alterations in gastric single-glands with IM.

  Study JGAS000269

• Digital tEchnology For Lung Cancer Treatment

  DEFLeCT metadata: 1) A table containing the mutational profile for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 2) A table containing the expression levels for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 3) A table containing the clinical, histology data and follow-ups of the cohort of 81 PROMOLE lung cancer patients.

  Dataset EGAD00001010838

• Genetic alterations in benign breast biopsies of subsequent breast cancer patient

  This dataset consists of amplicon sequencing of fibrocystic breast tissues, subsequent cancer tissue and germline control of 17 patients. The target genes include all exons of 27 protein-coding genes and 2 non-coding genes, as well as mutation hotspots in three cancer genes, frequently mutated in breast cancer. Ion AmpliSeq libraries were generated and sequenced on the Ion S5 XL system.

  Dataset EGAD00001004874

• A case of colorectal cancer with ERBB2 c.2264T>C (p.Leu755Ser) mutation

  This data set contains next generation sequencing (NGS) data of two serial tumor samples (primary and a metastasis) from a patient with colorectal cancer showing an ERBB2 c.2264T>C (p.Leu755Ser). NGS was performed using the Illumina TruSeq Amplicon Cancer Panel (TSACP, Illumina) covering 212 amplicons in 48 cancer associated genes on the Illumina MiSeq sequencing platform. The dataset contains two BAM files.

  Dataset EGAD00001002252