|
| Status |
Public on Aug 20, 2013 |
| Title |
TCF4 KD1 rep3 |
| Sample type |
RNA |
| |
|
| Source name |
SH-SY5Y cell line, TCF4 KD1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: neuroblastoma cell line
transfection reagent: present
sirna: present
targeted gene: TCF4
|
| Treatment protocol |
SH-SY5Y cells were transfected with 10nM of siRNA (Eurofinns) or mock transfected (RNAi MAX, Invitrogen). 48hrs after the first transfection, SH-SY5Y cells were re-transfected with the same conditions and left for a further 24hrs before extracting total RNA from the cells.
|
| Growth protocol |
Cells cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% foetal calf serum without antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plus Mini Kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Amersham Cy5 Mono-Reactive Dye (GE Healthcare).
|
| |
|
| Hybridization protocol |
Toray Oligo Chip kit (Toray Industries Inc., Kamakura, Japan).
|
| Scan protocol |
Arrays were scanned at 3 different gain levels with a 3D-Gene™ Scanner 3000 and the resulting data was analysed using the Toray Extraction and 3D-Gene™ Scanner 3000 software (Toray Industries Inc).
|
| Description |
KD1_3
Total RNA was amplified, labelled and hybridized to microarrays. Arrays were then washed and scanned at 3 different gain levels before global normalization.
|
| Data processing |
Hybridized probe spots with signal intensity greater than the mean intensity of plus 2 standard deviations of the background signal were considered to be valid (Flag: OK). The background average was subtracted from the signal intensity and multiplied by the normalisation factor (25 divided by the medium signal intensity of all the subtracted background data) to generate the normalised data.
|
| |
|
| Submission date |
Jun 27, 2013 |
| Last update date |
Aug 20, 2013 |
| Contact name |
Derek Blake |
| E-mail(s) |
[email protected]
|
| Organization name |
Cardiff University
|
| Department |
MRC Centre for Neuropsychiatric Genetics and Genomics
|
| Lab |
Blake Lab
|
| Street address |
Hadyn Ellis Building, Maindy Road
|
| City |
Cardiff |
| ZIP/Postal code |
CF24 4HQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13915 |
| Series (1) |
| GSE48367 |
Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial-to-mesenchymal transition and neuronal differentiation |
|
