|
| Status |
Public on Dec 18, 2018 |
| Title |
Sox2 adenovirus infection rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Sox2/GFP adenovirus infected Schwann cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
developmental stage: postnatal day 3 pups
|
| Treatment protocol |
Schwann cells infected with control GFP or Sox2/GFP adenovirus
|
| Growth protocol |
Schwann cells cultured in Defined Medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with miRNeasy mini-kit (Qiagen, 217004) and on-column DNase digestion was also performed
|
| Label |
Biotin
|
| Label protocol |
Biotin-labeled targets for the microarray experiment were prepared using 1µg of total RNA. Ribosomal RNA was removed with the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen), and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Rat Exon 1.0 ST array (Affymetrix) at 45 dergrees for 16 hours. After hybridization, non-specifically bound aterial was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and .CEL intensity files were produced using GeneChip Operating Software version 1.4 (Affymetrix).
|
| Description |
Gene expression data from Sox2/GFP adenovirus infected Schwann cells
|
| Data processing |
The Affymetrix data was analysed using the Affymetrix Power Tools (APT) software. Transcript expression values were normalised using robust multi array (RMA) normalisation and the p-values for each transcript were calculated using the Detection Above Background (DABG) algorithm which indicates whether a probe is significantly expressed or not in comparison to the background noise.
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Xinpeng Dun |
| E-mail(s) |
xin-peng.dun@plymouth.ac.uk
|
| Phone |
00441752583214
|
| Organization name |
University of Plymouth
|
| Street address |
John Bull Building, Research Way
|
| City |
Plymouth |
| State/province |
Devon |
| ZIP/Postal code |
PL6 8BU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6543 |
| Series (1) |
| GSE123915 |
Rat Schwann cell gene expression analysis after Sox2 overexpression |
|
