495 results for "cancer rna-seq"

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• RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Fresh peripheral blood mononuclear cells of four human donors were cultured together with either lung adenocarcinoma A549 cancer cells or A549-expressing H1N1 Sialidase cancer cells. These treatments induced the differentiation of donor cells into immunosuppressive MDSC-like cells, which were further subjected to bulk RNA sequencing. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode on 4 lanes of an Illumina NextSeq 500 flow-cell

  Dataset EGAD00001012437

• Genomic Changes in Breast Cancer Among Chinese Women in Hong Kong

  Recently, tumor sequencing and profiling analyses have improved molecular classification and refined existing breast cancer subtypes. However, epidemiologic data are absent in most somatic profiling studies even in extensively studied Western populations. The expansion of genomic studies to understudied populations with the integration of etiologic factors will allow the capture of a much wider range of genetic structure and mutagenic exposures associated with breast cancer risk. We therefore conducted a detailed molecular characterization of paired breast tumor/normal tissues using fresh frozen tissues collected from breast cancer cases in an ongoing breast cancer case-control study in Hong Kong. These analyses included whole genome (WGS)/exome sequencing (WES), targeted DNA panel sequencing, RNA sequencing (RNA-Seq), and genome-wide methylation profiling analyses.

  Study phs001870

• Multiregional single nuclei RNA-seq and WGS of prostate cancer

  This study investigates the clonal evolution and metastatic dissemination of prostate cancer using multiregional single-nuclei RNA sequencing (snRNA-seq) and low-pass whole-genome sequencing (WGS) data from 43 spatially distinct tumor areas in five patients with locally advanced prostate cancer, including both primary and regional lymph node samples. We employed the Chromium Next GEM Single Cell 3’ Kit (v3/3.1, 10x Genomics) for single-nuclei transcriptome profiling and constructed bulk WGS libraries using the NEBNext Ultra II FS DNA Library Prep Kit (New England Biolabs) from the same pool of nuclei extracted from each area. snRNA-seq data were aligned to the human genome (GRCh38-1.2.0_premrna) using 10x Genomics Cell Ranger v5.0.0, while WGS reads were aligned to the human reference genome (GRCh38) with BWA MEM, achieving an average sequencing depth of 0.3X for low-pass WGS and 16X after resequencing.

  Dataset EGAD50000001357

• RNA-seq data from 7 CAF-S1 primary cell lines isolated from breast Cancer

  Dataset EGAD00001006144

• Raw transcriptomic sequencing data from peritoneal metastasis of gastric cancer

  This controlled-access dataset contains raw FASTQ files generated from single-cell RNA sequencing (scRNA-seq) and 10x Genomics Visium spatial transcriptomics. The dataset includes scRNA-seq data from four human lesions of peritoneal metastasis of gastric cancer (PMGC) and Visium spatial transcriptomics data from one human PMGC lesion. It also includes scRNA-seq data from nine PMGC lesions from humanized mouse models engrafted with human gastric cancer cells under different treatment conditions. These data are provided to support transcriptomic analysis of tumor and immune microenvironment features in PMGC.

  Dataset EGAD50000002714

• MOSAIC Window - Bladder dataset

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 15 Muscle-invasive Bladder Cancer patients, treated with upfront cystectomy. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000000967

• Sequencing data from the study "Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer"

  This dataset consists of 71 whole-genome samples and 47 RNA-seq samples. All WGS samples are provided in .bam format and RNA-seq samples are provided as .fq.gz (paired-end). Next-generation sequencing data on whole genomes were processed by aligning sequencing reads to a reference genome (NCBI build 37/hg19) using bwa-mem (0.7.13-r1126).

  Dataset EGAD50000001978

• MOSAIC Window Bladder Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 15 Muscle-invasive Bladder Cancer patients, treated with upfront cystectomy. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001251

• FFPE cohort with RNA-seq data of tumor samples

  This dataset contains RNA-seq raw data in fastq format from 14 tumor samples. The samples are from primary tumors or metastasis and represent various cancer entities. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006781

• PanCurX Translational Research Initiative - RNA-Seq mapped and unmapped reads

  Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases - RNA-Seq mapped and unmapped reads

  Dataset EGAD00001004548