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Sample GSM1322449 Query DataSets for GSM1322449
Status Public on Oct 23, 2014
Title AP5.6hr.5
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.5
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 0.080511516
A_52_P96028 0.057221602
A_52_P413492 -2.466088069
A_51_P351598 -0.212969641
A_52_P700056 -2.444475908
A_51_P199778 0.511626129
A_52_P660466 0.022751203
A_52_P62011 1.17101521
A_51_P134184 -0.066663942
A_52_P265820 0.075827607
A_51_P469476 0.284630769
A_52_P61833 0.533985784
A_51_P375631 0.760469576
A_51_P432011 -0.181465767
A_52_P160057 4.15114326
A_52_P633785 0.795779893
A_52_P329881 -0.859378126
A_52_P1053160 -0.237118084
A_52_P677891 3.471312283
A_52_P352541 1.791866028

Total number of rows: 20674

Table truncated, full table size 510 Kbytes.




Supplementary file Size Download File type/resource
GSM1322449_Agilent_251486825546_S01_GE2-v5_95_Feb07_1_1.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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