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Sample GSM789952 Query DataSets for GSM789952
Status Public on Sep 08, 2011
Title 6hrKCl_WT_RepA_sc5
Sample type RNA
 
Source name cultured cortical neurons E16+7DIV
Organism Mus musculus
Characteristics condition: 6 hr KCl depolarized
litter: A
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) 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 9.67202
AFFX-BioB-M_at 10.2247
AFFX-BioB-3_at 9.81474
AFFX-BioC-5_at 10.987
AFFX-BioC-3_at 11.2394
AFFX-BioDn-5_at 12.178
AFFX-BioDn-3_at 13.1356
AFFX-CreX-5_at 14.5632
AFFX-CreX-3_at 14.8357
AFFX-DapX-5_at 8.94471
AFFX-DapX-M_at 10.3064
AFFX-DapX-3_at 10.9372
AFFX-LysX-5_at 6.00928
AFFX-LysX-M_at 6.7045
AFFX-LysX-3_at 7.67251
AFFX-PheX-5_at 7.10237
AFFX-PheX-M_at 6.9978
AFFX-PheX-3_at 7.8943
AFFX-ThrX-5_at 6.98126
AFFX-ThrX-M_at 7.47527

Total number of rows: 45101

Table truncated, full table size 849 Kbytes.




Supplementary file Size Download File type/resource
GSM789952_MG2011041933.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM789952_MG2011041933.RMA.rma.chp.gz 309.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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