|
| Status |
Public on Sep 08, 2011 |
| Title |
6hrKCl_WT_RepB_sc11 |
| Sample type |
RNA |
| |
|
| Source name |
cultured cortical neurons E16+7DIV
|
| Organism |
Mus musculus |
| Characteristics |
condition: 6 hr KCl depolarized
litter: B
genotype/variation: WT
strain: C57BL6
|
| Treatment protocol |
Neuronal cultures were pre-treated with 1 µM tetrodotoxin (TTX) and 100 µM D-APV (Tocris Bioscience) overnight to reduce endogenous neuronal activity prior to stimulation and then left unstimulated or membrane depolarized with 55 mM extracellular KCl by addition of 0.5 volumes of prewarmed depolarization buffer (170 mM KCl, 2 mM CaCl2, 1 mM MgCl2, 10 mM HEPES pH7.5) for 1 hour or 6 hours.
|
| Growth protocol |
Dissociated cortical cultures (E16+7DIV) grown in neurobasal media supplemented with B27, glutamine, and pen/strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by extraction using Trizol (invitrogen) according to the manufactures instructions, and then further purfied using qiagen minelute columns.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Expression Set 430 2.0 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Genechip Scanner 3000.
|
| Description |
E16+7DIV cortical culture neurons
|
| Data processing |
Data were processed using Affymetrix Expression Console Version 1.1 RMA workflow with quantile normalization and general background correction. Differential expression analysis was performed using GeneSpring GX (Agilent technologies) and custom statistical analysis see methods of Cohen et al. neuron 2011 for details.
|
| |
|
| Submission date |
Sep 02, 2011 |
| Last update date |
Sep 08, 2011 |
| Contact name |
Harrison Wren Gabel |
| E-mail(s) |
[email protected]
|
| Phone |
617-512-0289
|
| Organization name |
Harvard Medical School
|
| Department |
Neurobiology
|
| Lab |
Michael Greenberg
|
| Street address |
7 Linden St Apt 3
|
| City |
Brookline |
| State/province |
MA |
| ZIP/Postal code |
02445 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE31849 |
Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function [cultured cortical neurons] |
| GSE31851 |
Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function |
|
