Project description:To investigate the transcriptomes in colorectal cancer patients, who were diagnosed and treated at Siriraj Hospital, Thailand, we performed gene expression profiling analysis using data obtained from RNA-seq and Nanostring platforms.
Project description:To investigate the transcriptomes in colorectal cancer patients, who were diagnosed and treated at Siriraj Hospital, Thailand, we performed gene expression profiling analysis using data obtained from RNA-seq and Nanostring platforms.
Project description:This dataset contains spatial whole-transcriptome profiles from colorectal cancer (CRC) tissues preserved using formalin-fixed paraffin-embedded (FFPE), fresh frozen (FF), and snap frozen (SF) methods. Samples were obtained from a patient with stage IV CRC during surgical resection at Siriraj Hospital, Mahidol University, Thailand. Each tissue type was sectioned, stained for Pan-cytokeratin (PanCK), CD45, and SYTO13, and analyzed using the NanoString GeoMx Digital Spatial Profiler with the Human Whole Transcriptome Atlas panel. A total of 36 areas of illumination (AOIs) representing epithelial (PanCK⁺), immune (CD45⁺), and stromal (PanCK⁻/CD45⁻) compartments were collected. Sequencing was performed on an Illumina NovaSeq 6000 platform, and raw counts were processed using NanoString DSP Analysis Suite v3.1 and R for normalization and quality control. This dataset provides spatially resolved gene-expression information across different preservation conditions of CRC tissues to support comparative analysis and method evaluation in spatial transcriptomics.
Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Spatial transcriptomics was performed using 10x Genomics Visium on colorectal cancer liver metastatic patient samples.
Project description:The survival rate of patients with colorectal cancer (CRC) declines sharply with recurrence and metastasis. Cancer stem cells play a crucial role in the initiation, progression, recurrence, and metastasis of colorectal cancer. Therefore, in this study, we aimed to identify the CRC-associated genes via spatial analyses of normal colon tissue, colorectal cancer tissue, and colorectal cancer liver metastasis using NanoString GeoMx digital spatial profiling.
Project description:The Nanostring nCounter gene expression assay was used to investigate the molecular signalling of host to Covid-19 infection, from Indian Cohort. The study revealed several biomarkers with strong predictive performance to differentiate Covid-19 infection from healthy controls and markers to differentiate between Covid-19 infection from other flu like symptoms.