|
| Status |
Public on Oct 02, 2014 |
| Title |
HT29 cell treated by control for nutrient starvation |
| Sample type |
RNA |
| |
|
| Source name |
HT-29 cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT-29
cell type: colorectal carcinoma cells
|
| Treatment protocol |
For 5-FU treatment, HT29s were treated with 5 μM of 5-FU for 24 h. For nutrient starvation, HT29s were incubated in Krebs-Ringer buffer (120 mM NaCl, 5 mM KCl, , 24 mM NaHCO3, 5.6 mM glucose, 2mM CaCl2, pH 7.6) at 37 °C for 7 h.
|
| Growth protocol |
HT29 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere of 5% CO2/ 95% air with medium changes every two days. Cells in mid-log phase were used in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
|
| Label |
Hy3
|
| Label protocol |
The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling
|
| |
|
| Hybridization protocol |
The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual
|
| Scan protocol |
The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).
|
| Description |
Ctrl
|
| Data processing |
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Four replicated spots of each miRNA probe were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering (>=2).
|
| |
|
| Submission date |
Oct 01, 2014 |
| Last update date |
Oct 02, 2014 |
| Contact name |
Ni Hou |
| E-mail(s) |
houni.0627@hotmail.com
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
Department of Genetics and Molecular Biology
|
| Street address |
76 Western Yanta Road
|
| City |
Xi'an |
| State/province |
Shaanxi Province |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL19128 |
| Series (1) |
| GSE61943 |
Expression of miRNAs in human colorectal carcinoma cells upon autophagy induction |
|
