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Sample GSM789959 Query DataSets for GSM789959
Status Public on Sep 08, 2011
Title 6hrKCl_S421A_RepA_sc12
Sample type RNA
 
Source name cultured cortical neurons E16+7DIV
Organism Mus musculus
Characteristics condition: 6 hr KCl depolarized
litter: B
genotype/variation: MeCP2 S421A
strain/background: ES cells derived from a 129 background and injected into C57BL6 mice to generate chimeras. The resulting strain was extensively backcrossed into C57BL6(>10 generations) before cortical cultures were derived.
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) harrison_gabel@hms.harvard.edu
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

Data table header descriptions
ID_REF
VALUE log2 RMA

Data table
ID_REF VALUE
AFFX-BioB-5_at 9.15913
AFFX-BioB-M_at 9.65273
AFFX-BioB-3_at 9.17472
AFFX-BioC-5_at 10.4006
AFFX-BioC-3_at 10.2829
AFFX-BioDn-5_at 11.7637
AFFX-BioDn-3_at 12.6857
AFFX-CreX-5_at 14.2572
AFFX-CreX-3_at 14.5868
AFFX-DapX-5_at 8.71054
AFFX-DapX-M_at 10.1077
AFFX-DapX-3_at 10.7451
AFFX-LysX-5_at 5.73423
AFFX-LysX-M_at 6.50187
AFFX-LysX-3_at 7.46788
AFFX-PheX-5_at 6.76154
AFFX-PheX-M_at 6.52332
AFFX-PheX-3_at 7.7571
AFFX-ThrX-5_at 6.86097
AFFX-ThrX-M_at 7.20012

Total number of rows: 45101

Table truncated, full table size 850 Kbytes.




Supplementary file Size Download File type/resource
GSM789959_MG2011041940.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM789959_MG2011041940.RMA.rma.chp.gz 309.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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