|
| Status |
Public on Dec 05, 2012 |
| Title |
TimKO rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Tim-3 knockdown
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Tim-3 knockdown
cell line: RAW 264.7
|
| Treatment protocol |
RAW264.7 cells were transfected with pRNAi-U6H1vector containing Tim-3 siRNA or control siRNA. The siRNA duplex giving maximal knockdown was selected. Raw264.7 cell clones stably express Tim-3 SiRNA were selected after continued culture with selecting drugs (G418, Sigma-Aldrich), and were analyzed for Tim-3 expression.
|
| Growth protocol |
Tim-3 knockdown and control RAW264.7 cells were maintained in DMEM supplemented with 10% heat-inactivated FBS, 100 units/ml of penicillin, and 100 units/ml of streptomycin in a humidified 5% CO2 atmosphere at 37 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of Tim-3-siRNA transfected RAW264.7 cells. It is the first of three Tim-3 knockdown biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5 (Roche NimbleGen, Inc.). All gene level files were imported into Agilent GeneSpring GX software(version 11.5.1) for further analysis. Genes that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 100.0 were chosen for differentially expressed gene screening.
|
| |
|
| Submission date |
Dec 04, 2012 |
| Last update date |
Dec 05, 2012 |
| Contact name |
Gencheng HAN |
| Organization name |
Beijing Institute of Basic Medical Sciences
|
| Department |
Department of Immunology
|
| Street address |
27 Taiping Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100850 |
| Country |
China |
| |
|
| Platform ID |
GPL10192 |
| Series (1) |
| GSE42729 |
Expression analysis of Tim-3 knockdown RAW264.7 cell |
|
