|
| Status |
Public on Apr 08, 2022 |
| Title |
CaU001: Uninfected Caco-2 cells, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Non-infected Caco-2 cells, biological rep1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon epithelial cells
|
| Treatment protocol |
Cells were serum-starved for 1 hour prior to infection or non-infection. Following infection or non-infection, cells were washed with phosphate buffered saline and replaced with minimum essential medium supplemented with 1% bovine serum albumin. Cells were harvested at 24 hours following infection or non-infection.
|
| Growth protocol |
Caco-2 cells were grown in minimum essential medium supplemented with 20% fetal bovine serum, GlutaMax-I, and 1 mM sodium pyruvate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using Qiagen RNeasy Kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
For samples CaI003, CaI004, CaU001, CaU002: sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671). For samples COR001, C)R002, CSR001, CSR002: sense target cDNA was prepared from 100ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip™ WT Terminal Labeling Kit (Applied Biosystems P/N 900670).
|
| |
|
| Hybridization protocol |
Five micrograms of cDNA was hybridized for 16h at 45C on a Human Gene 2.0 ST GeneChip array.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from non-infected Caco-2 cells
|
| Data processing |
Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1. Signal summarization was performed independently in two groups. Samples CaI003, CaI004, CaU001, CaU002 were summarized in one group, while samples COR001, C)R002, CSR001, CSR002 were summarized in the second group.
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Apr 08, 2022 |
| Contact name |
Geoffrey Neale |
| E-mail(s) |
geoffrey.neale@stjude.org
|
| Organization name |
St Jude Childrens Research Hospital
|
| Department |
Hartwell Center
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE166820 |
Expression data from non-infected and HAstV-1 infected Caco-2 cells |
|
