|
| Status |
Public on Mar 16, 2013 |
| Title |
HT-29, stimulated with NaB, replicate #1 |
| Sample type |
RNA |
| |
|
| Source name |
HT-29 cells stimulated with 2 mM NaB
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT-29
cell type: colonic epithelial cell line
treatment: NaB
|
| Treatment protocol |
Culture media was discarded, cells were rinsed with PBS and stimulated with 2 mM NaB (Sigma) alone or in combination with 125/150 ug/ml ciprofloxacin (Sigma) in culture medium in the absence of fetal calf serum and penicillin-streptomycin for 24 hours at 37C in 5% CO2. Cells incubated with only culture medium served as an unstimulated control.
|
| Growth protocol |
HT-29 (ATCC, HTB-38) was grown up to 80-90% confluence in culture medium (RPMI-1640 supplemented with 10% fetal calf serum, 25 mM HEPES, 2 mM L-glutamine amd penicillin-streptomycin [Invitrogen]) in 6-well tissue culture plates (Corning) at 37C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of RNA from cells was performed utilizing the RNeasy RNA purification kit according to the manufacturer's instructions (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Total RNA was converted to sense strand cRNA using the Ambion WT expression kit. For fragmentation and labeling, the GeneChip WT Target Labeling kit was used.
|
| |
|
| Hybridization protocol |
Hybridization to Human Gene 1.1 ST array plates was carried out overnight with biotin-labeled cRNA according to the Affymetrix protocol.
|
| Scan protocol |
Array plates were scanned using a GeneTitan scanner.
|
| Description |
PS02_NaB
Gene expression data from HT-29 cells stimulated with 2 mM NaB.
|
| Data processing |
Preprocessing in Affymetrix Expression Console (v 1.1) using the following methods. Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.
|
| |
|
| Submission date |
Mar 15, 2013 |
| Last update date |
Mar 16, 2013 |
| Contact name |
Protim Sarker |
| E-mail(s) |
protim@icddrb.org
|
| Phone |
+8801772683211
|
| Organization name |
icddr,b
|
| Street address |
Mohakhali
|
| City |
Dhaka |
| ZIP/Postal code |
1212 |
| Country |
Bangladesh |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE45220 |
Expression data from HT-29, a human colonic epithelial cell line |
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