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107 results for “Caco-2 cells”
Data and Analysis from "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells"
<p>Data, data processing and data analysis for manuscript "Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells". (Preprint available <a href="https://doi.org/10.1101/2022.08.15.503960">here</a>)</p> <p><strong>Analysis of AP-MS data</strong>: analysis.zip</p> <p>Contains the following scripts as well as their outputs:</p> <ul> <li>01_preparation.R R script for filtering and processing our mass spec data.</li> <li>02_diffbinding.R R script for differential analysis followed by gene set enrichment.</li> <li>03_funcstats.R R script for statistical analysis over different ontology terms.</li> <li>04_semantic_analysis.R R script for the GO semantic analysis for the output of 02 and 03.</li> <li>05_1_random_walks.py Python script for performing random walks for specific functional terms.</li> <li>05_2_random_walks_analysis.R R script for the analysis and visualization of the output of 05_1.</li> </ul> <p>The required input data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD035399">entry</a>.</p> <p>Interactive visualization of the results of most of this analysis is available on <a href="https://github.com/PhilippJunk/kras_apms_vis">GitHub </a>as a Shiny app.</p> <p> </p> <p><strong>Analysis of whole cell lysate</strong>: analysis_wholecelllysate.zip</p> <p>Contains the following script, as well as its output:</p> <ul> <li>01_analysis.R R script for loading the data and extracting/visualizing KRAS and effector abundances.</li> </ul> <p>The required data is deposited in the "data" sub-folder, taken directly from the linked PRoteomics IDEntification database (PRIDE) <a href="https://www.ebi.ac.uk/pride/archive/projects/PXD039404">entry</a>.</p>
['Comparative proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells']
['Microgravity is one of the most important features in spaceflight. Previous evidence has shown that significant changes to the musculoskeletal and immune systems occurred under microgravity. The present study was undertaken to explore the change in protein abundance in human colon colorectal cells that were incubated for 48 or 72 h either in normal conditions and µG simulated conditions. The comparative proteomic method based on the 18O labeling technique was applied to investigate the up-regulated proteins and down-regulated proteins in SH-SY5Y under simulated microgravity.']
qPCR array study for cell cycle related genes in Caco-2 cells treated with human lectin ZG16p
GEO Series GSE84321. Homo sapiens. 6 samples. Type: Expression profiling by RT-PCR.
Escherichia coli alpha-hemolysin HlyA induces host cell polarity changes, epithelial barrier dysfunction and cell detachment in human colon carcinoma Caco-2 cell model via PTEN-dependent dysregulation
GEO Series GSE169213. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Modulation of gene expression induced by cylindrospermopsin in human intestinal Caco-2 cells
GEO Series GSE55723. Homo sapiens. 11 samples. Type: Expression profiling by array.
Differences in Toxic Response induced by three Variants of the Diarrheic Shellfish Poisoning Phycotoxins in Human Intestinal Caco-2 Cells
GEO Series GSE159293. Homo sapiens. 24 samples. Type: Expression profiling by array.
Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells
GEO Series GSE114909. Campylobacter jejuni. 12 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile in Caco-2 cells upon co-treatment with lovastatin and selective AHR ligands
GEO Series GSE130234. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Different responses of Caco-2 and MCF-7 cells to silver nanoparticles are based on highly similar mechanisms of action
GEO Series GSE84982. Homo sapiens. 73 samples. Type: Expression profiling by array.
Transcriptome analysis of Caco-2 Cells upon deoxynivalenol and its acetylated exposure
GEO Series GSE164334. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Comparison of iPSC-derived human intestinal epithelial cells with Caco-2 cells and human in vivo data after exposure to Lactiplantibacillus plantarum WCFS1
GEO Series GSE276364. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome and Translatome Profiling of Caco-2 cells
GEO Series GSE48603. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq data from human Caco-2 cells co-incubated with Giardia intestinalis WB cyst cells
GEO Series GSE172213. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Integrated mRNA/miRNA-seq of Caco-2 and HT-29 cells under chemical hypoxia (cobalt chloride, oxyquinoline)
GEO Series GSE158632. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Transcriptomic points of departure for 6PPD-Quinone derived from human Caco-2 and HepG2 cells
GEO Series GSE302559. Homo sapiens. 72 samples. Type: Expression profiling by high throughput sequencing.
Microarray analysis of Salmonella-infected or uninfected in vitro M cells and Caco-2 cells
GEO Series GSE73880. Homo sapiens. 12 samples. Type: Expression profiling by array.
Dynamic Gene Network Analysis of Caco-2 Cell Response to Shiga Toxin-Producing Escherichia coli-Associated Hemolytic–Uremic Syndrome
GEO Series GSE104488. Homo sapiens. 25 samples. Type: Expression profiling by array.
RNA-seq data from Giardia intestinalis WB trohozoites infecting human Caco-2 cells
GEO Series GSE144004. Giardia duodenalis; Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Caco-2 cells: cultured in conventional vs apical anaerobic conditions
GEO Series GSE43049. Homo sapiens. 6 samples. Type: Expression profiling by array.
Gene expression in Caco-2 cells co-cultured with bacteria in an apical anaerobic environment
GEO Series GSE49900. Homo sapiens. 24 samples. Type: Expression profiling by array.
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