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Sample GSM1322459 Query DataSets for GSM1322459
Status Public on Oct 23, 2014
Title control.6hr.1
Sample type RNA
 
Channel 1
Source name RNA purified from cultured neurons
Organism Mus musculus
Characteristics cell type: neurons
treatment: vehicle control 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 control.6hr.1
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

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_52_P298165 -0.004453754
A_52_P96028 0.157775336
A_52_P413492 -2.563986736
A_51_P351598 -0.136698501
A_52_P700056 -2.280164984
A_51_P199778 0.16240639
A_52_P660466 0.098364969
A_52_P62011 1.118900924
A_51_P134184 0.08893262
A_52_P265820 0.076634653
A_51_P469476 0.270350338
A_52_P61833 0.374259631
A_51_P375631 0.495003816
A_51_P432011 -0.074584183
A_52_P160057 3.35593817
A_52_P633785 0.404344075
A_52_P329881 -0.731869208
A_52_P1053160 -0.587417956
A_52_P677891 3.145763133
A_52_P352541 1.046922338

Total number of rows: 20674

Table truncated, full table size 510 Kbytes.




Supplementary file Size Download File type/resource
GSM1322459_Agilent_251486825549_S01_GE2-v5_95_Feb07_1_2.txt.gz 14.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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