|
| Status |
Public on Oct 15, 2015 |
| Title |
miRNA_E95K mutant IhhN induced cells_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
E95K mutant IhhN induced cells, 750nM for 2 days, replicate 2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C3H10T1/2
induction: E95K mutant IhhN
|
| Treatment protocol |
C3H10T1/2 cells, diluted 1:1 with MEM/EBSS medium supplemented with 10% heat-inactivated fetal bovine serum in the presence of 750nM IhhN protein, were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from cells using Trizol reagent (Invitrogen) according to manufacturer's instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA according to the manufacturer's instructions. (http://www.agilent.com/cs/library/usermanuals/Public/G4170-90011_miRNA_Protocol_3.1.pdf)
|
| |
|
| Hybridization protocol |
Cy3-labelled miRNA sample was hybridized following the manufacturers instructions. Hybridized to Agilent 8x15K miRNA Microarrays for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
miRNA expression after 48hr in C3H10T1/2 cells in the presence of 750nM E95K mutant IhhN
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Oct 14, 2015 |
| Last update date |
Oct 15, 2015 |
| Contact name |
Lu Shen |
| E-mail(s) |
yoyomailer@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
Bio-X Institutes
|
| Lab |
Pharmacogenomics
|
| Street address |
RM 218 Little White House 1954 Huashan RD
|
| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
| |
|
| Platform ID |
GPL10384 |
| Series (2) |
| GSE74020 |
miRNA gene expression signatures for IhhN protein induced cells |
| GSE74023 |
Gene expression and Gli1-ChIP in IhhN protein induced cells |
|
