|
| Status |
Public on Jan 11, 2020 |
| Title |
Caco-2 cell without interaction - control (2h), replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Caco-2 cell, control
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Cellular culture
|
| Treatment protocol |
Caco-2 cells (human intestinal epithelial cells) were cultivated in DMEM complemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA), 1mM L-glutamine (Sigma-Aldrich), penicillin (100U mL-1) (Sigma-Aldrich) and streptomycin (100mgmL-1) (Sigma-Aldrich) and 1% non-essential amino acids. All cell were cultivated in a humidified 5% CO2 atmosphere. The cells were grown until confluent monolayers in a six-well tissue culture plate at a density of 1x106 cells. This cells haven’t infection, but was incubated for 1,5h at 37°C in 5% CO2 as well as infected cells. DMEM containing 10% FBS and 50 mg mL-1 gentamicin was added and cells were cultured for 30 min. The cells were then washed with a fresh medium containing 10% FBS, and re-incubated for up to 3h at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from Caco-2 cells (without any interaction) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression from Caco-2 cells without interaction - control
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering any NA per group and the expression values in Log (base 2).
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| |
|
| Submission date |
Jan 13, 2017 |
| Last update date |
Jan 12, 2020 |
| Contact name |
Hadassa Cristhina Azevedo Soares Santos |
| E-mail(s) |
hadassa.cass@gmail.com
|
| Phone |
55 11 959921111
|
| Organization name |
University of São Paulo
|
| Department |
Department of Clinical Chemistry and Toxicology
|
| Lab |
Lab of Microbiology
|
| Street address |
Avenida Professor Lineu Prestes, 580
|
| City |
São Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
05508-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE93587 |
Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells II |
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