|
| Status |
Public on Oct 23, 2014 |
| Title |
AP5.6hr.3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA purified from cultured neurons
|
| Organism |
Mus musculus |
| Characteristics |
cell type: neurons
treatment: 100 uM AP5 for 6 hrs
|
| Growth protocol |
DIV 21 dissociated mouse hippocampal neurons in 6 well plates were treated by Vehicle, 100 μM AP5, 100 nM NVP-AAM077 or 1 μM Ro25-4891 for 6 hours in a cell culture incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy plus kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
Briefly, total RNA sample was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. The labeled cRNA was purified using RNeasy mini kit (Qiagen, San Diego, CA). cRNA yield and Cy-dye incorporation was determined using ND-1000 spectrophotometer (Thermo Scientific)
|
| |
|
| Channel 2 |
| Source name |
universal mouse reference (Stratagene, La Jolla, CA)
|
| Organism |
Mus musculus |
| Characteristics |
sample type: reference
|
| Growth protocol |
DIV 21 dissociated mouse hippocampal neurons in 6 well plates were treated by Vehicle, 100 μM AP5, 100 nM NVP-AAM077 or 1 μM Ro25-4891 for 6 hours in a cell culture incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy plus kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Briefly, total RNA sample was converted to double-stranded cDNA and then to Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. The labeled cRNA was purified using RNeasy mini kit (Qiagen, San Diego, CA). cRNA yield and Cy-dye incorporation was determined using ND-1000 spectrophotometer (Thermo Scientific)
|
| |
|
| |
| Hybridization protocol |
750 ng of the labeled cRNA was fragmented and hybridized to arrays as described in manufacturer’s hybridization kit
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
AP5.6hr.3
|
| Data processing |
Agilent’s Feature Extraction software 11.0 was used to analyze acquired array images
|
| |
|
| Submission date |
Feb 05, 2014 |
| Last update date |
Oct 23, 2014 |
| Contact name |
Josh Kaminker |
| Organization name |
Genentech
|
| Department |
Bioinformatics and Computational Biology
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE54708 |
Regulation of neuronal gene expression and survival by basal NMDA receptor activity: a role for Histone Deacetylase 4 |
|
