|
| Status |
Public on Jul 01, 2007 |
| Title |
GFP control 3 |
| Sample type |
RNA |
| |
|
| Source name |
Homo sapiens
|
| Organism |
Homo sapiens |
| Characteristics |
Cell line: SH-SY5Y from ATCC, Vector: pEGF-C2, cDNA insert: none
|
| Treatment protocol |
Transfected SH-SY5Y cells were selected in the presence of 500 ug/ml genetecin. On post-transfection day 7, total RNA from GFP vector and DN-TRF2 transfected cells was prepared for transcriptome analyses using the NIA MGC1 9,600 human gene array. Samples were collected from three independent experiments and were processed in parallel.
|
| Growth protocol |
SH-SY5Y human neuroblastoma cell were grown in Advanced-Dulbecco's modified Eagle's medium (Gibco life Technologies, Gaithersburg, MD), supplemented with 5% fetal Clone III bovine serum (HyClone, Logan,UT), 2 mM L-glutamine, 100U/ml penicillin G sodium, and 100 ug/ml streptomycin sulfate. Cell cultures were maintained in 37°C in a humidified 5% CO2/95% air atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit protocol
|
| Label |
33P-dCTP
|
| Label protocol |
~5 ug of total RNA was radiolabeled with 33P-dCTP using Superscript II from Invitrogen. Labeled cDNA was separated from unincorporated probe and small nucleotides using a Bio-Rad size exclusion column, Bio-Spin 30 with SSC. 1ul of each sample was counted in a scintillation counter and the remainder was used for hybridization.
|
| |
|
| Hybridization protocol |
Radiolabeled cDNA was denatured at 95 degrees C for 7 minutes and added to 12 mls of Invitrogen microhyb containing 10% dextran sulfate with Cot-1 DNA (Invitrogen) and Poly-A DNA oligos, (Sigma) added as blocking agents. Arrays were hybridized overnight at 55 degrees C to human MGC cDNA filters. The hybridized filters were quickly rinsed once and then washed twice at 65 degrees placed onto steel plates covered with plastic wrap and exposed to Kodak storage Phosphorimaging screens for 3-4 days.
|
| Scan protocol |
Imaging screens were scanned at 50um resolution in a Storm Phosphorimager.
|
| Description |
C1
|
| Data processing |
All data was extracted using ArrayPro Software and processed in Excel spreadsheets using Z normalization of each array. Differently expressed genes were identified between the different sample groups by z-ratio analysis using an in-house microarray analysis program.
|
| |
|
| Submission date |
Feb 07, 2007 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL1211 |
| Series (1) |
| GSE6983 |
TRF2 Inhibition-Mediated Degradation Derepresses the Neuronal Differentiation Program |
|
