15059 results for "cancer studies using rna-seq"

in 21.19 milliseconds.

• MAITS in HCC

  Hepatocellular Carcinoma (HCC) is a leading cause of cancer-related death and can be considered a prototype of inflammation-derived cancer arising from chronic liver injury. The cell composition of the HCC tumor immune microenvironment (TiME) has a major impact on cancer biology as the TiME can have divergent capacities on tumor initiation, progress, and response to therapy. Recent development of multi-omics and single-cell technologies help us to comprehensively quantify the cellular heterogeneity and spatial organization of the TiME and to further our understanding of antitumor immunity. We investigated the cellular composition of liver cancer patient samples (n=8) using single-cell RNA-seq. For this purpose, mononuclear cells were isolated from human liver cancer samples. Three locations within the tumor-bearing liver were used: adjacent liver, rim and tumor core. Then, cells were FACS sorted (either CD45+ cells or MAIT cells) and subjected to 10X Chromium-based scRNA-seq. We investigated immune cell changes and the cellular heterogeneity of the HCC TiME with a focus on MAIT cells. Annotated H5 files are provided. Clinical metadata including TMN stage, sex, gender, ethnicity, pretreatment, and histopathological reports are available for all patient samples. Further details on the study can be obtained in our paper once it’s published.A complementary dataset derived from ultrahighplex CO-Detection by indEXing (CODEX) from paired patient samples can be accessed through The Cancer Imaging Archives (TCIA) under DOI: https://doi.org/10.7937/bh0r-y074.

  Study phs003279

• Single cell RNA-sequencing of tissues from NSCLC patients treated with chemoimmunotherapy

  The goal of this study is to characterize immune cell populations by single cell RNA-sequencing (scRNA-seq) in tumor and uninvolved normal tissues from non-small cell lung cancer (NSCLC) patients with resectable non-small cell lung cancer and who received neoadjuvant chemoimmunotherapy. scRNA-seq was performed on seven pairs of tumor and normal tissues as well as one lymph node (LN) sample. Data set includes pair-end fastq files for single cell RNA sequencing of 7 neo-immuno patients. (Total 15 samples and 50 runs).

  Dataset EGAD00001009778

• 47 urothelial cancer patients WES and 38 RNAseq

  We performed a global mutational landscape analysis using tumor samples from the 47 urothelial cancer patients included in MATCH-R or MOSCATO studies, with advanced metastatic disease and WES available (RNAseq is included for 38 patient samples).

  Dataset EGAD00001011063

• Transcriptional data of human isogenic iPSCs

  This dataset contains bulk RNA-seq data from 12 autosomally isogenic human iPSCs. Three biological replicas from XXY (sample ID 419295-7), XX (sample ID 419298-419300), XY (sample ID 419302, 419305-6), and XO (sample ID 419308, 419310, 419312) hiPSC. RNA for this dataset was collected using Trizol method, and polyA library type was implemented. The libraries were sequenced using Illumina device. The sample reads are deposited as fastq files. Analysis have been done using reference alignment to GRCh38 reference genome.

  Dataset EGAD50000001361

• Idiosyncratic and generic single nuclei and spatial transcriptional patterns in papillary and anaplastic thyroid cancers

  Thyroid cancer is the most common endocrine malignancy. This dataset encompasses two types of thyroid cancer : anaplastic which is the most de-differentiated and aggressive one, and papillary which is the most common one. We profiled 14 patients, including 10 papillary and 4 anaplastic thyroid carcinomas, using both single nuclei RNA sequencing and spatial transcriptomics to link single cell resolution RNA sequencing with tissue morphology and better understand inter and intratumoral thyroid cancer heterogeneity.

  Study EGAS00001007574

• Targeted RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoietic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood. Samples were tested in a clinical diagnostic lab to identify relevant SNVs, indels and gene fusions.

  Dataset EGAD50000000980

• Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_YR03

  Transcriptome Sequencing of Gingivo-buccal Cancer: ICGC-India ProjectAs a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Transcriptome sequencing of paired RNA samples – isolated from the tumor and adjacent normal tissues of 12 patients – have been performed. Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from adjacent normal and tumor tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Sequencing is being performed at the National Institute of Biomedical Genomics, Kalyani.

  Study EGAS00001002851

• Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_Batch05

  Transcriptome Sequencing of Gingivo-buccal Cancer: ICGC-India ProjectAs a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Transcriptome sequencing of paired RNA samples – isolated from the tumor and adjacent normal tissues of 28 patients – have been performed. Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from adjacent normal and tumor tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Sequencing is being performed at the National Institute of Biomedical Genomics, Kalyani.

  Study EGAS00001003285

• Single Cell and Spatial Transcriptomic Profiling of Haemophilus ducreyi Infection

  We investigated the immune response in end-point pustules formed by Haemophilus ducreyi in volunteers using an experimental infection model. Six volunteers were infected in the skin of the upper arm at three sites with 41-85 CFU of H. ducreyi loaded on an allergy testing device; a sham-inoculated (e.g., wound) site was also performed. Five volunteers (4 men and 1 woman; 2 Asians and 3 Whites; aged 27-46 years) formed pustules 6-8 days post infection; 1 volunteer spontaneously resolved all sites. If a volunteer formed pustules, biopsies were performed to collect their pustule and wound sites. Biopsy pairs for all 5 pustule formers were subjected to single cell (sc) RNA-seq. Sequencing libraries were prepared using the 10X Genomics Single-cell 3' RNA-seq kit. Spatial transcriptomics was performed on biopsy pairs from 4 of the 5 pustule formers. Ten micron sections were placed on 10X Genomics Visium slides for fresh-frozen tissue, and libraries were prepared with the 10X Genomics Visium spatial 3' gene expression kit. All samples were sequenced on an Illumina NovaSeq 6000. Count tables were produced with CellRanger and SpaceRanger, respectively, and Seurat was used to analyze the data. We identified 13 major cell types by scRNA-seq; the proportion of some immune cell subsets was increased in pustules compared to wound sites. We also localized the major cell types within the tissue by using the scRNA-seq data to deconvolve the spatial transcriptomic data. The FASTQ files and count tables from CellRanger and SpaceRanger are provided.

  Study phs003754

• Bulk RNA sequencing of Singapore colorectal cancer patients (SG-BULK)

  RNA-seq libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (Kapa Biosystems, Wilmington, MA) and sequenced to a target depth of 200-M reads on the Illumina HiSeq platform (Illumina, San Diego, CA).

  Dataset EGAD00001008512