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Sample GSM1216847 Query DataSets for GSM1216847
Status Public on Aug 28, 2013
Title 712_cKO.rep3
Sample type RNA
 
Channel 1
Source name Universal mouse reference (UMR) from Stratagene
Organism Mus musculus
Characteristics reference: Universal mouse reference (UMR) from Stratagene
Treatment protocol DLK knockdown was induced by placing mice on a tamoxifen diet for 3 weeks. All wild type animals were on the tamoxifen diet as well. Animals were taken down and hippocampus was dissected out and processed for RNA extraction.
Growth protocol Mice were bread to give the specific genotypes.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNAesy mini kit following the manufacturer's instructions and including on column DNAse digestion. RNA quality was verified by running samples on Agilent Bioanalyzer 2100.
Label Cy3
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
 
Channel 2
Source name cKO.rep3
Organism Mus musculus
Characteristics tissue: adult hippocampus
genotype: DLK conditional knockout
Treatment protocol DLK knockdown was induced by placing mice on a tamoxifen diet for 3 weeks. All wild type animals were on the tamoxifen diet as well. Animals were taken down and hippocampus was dissected out and processed for RNA extraction.
Growth protocol Mice were bread to give the specific genotypes.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNAesy mini kit following the manufacturer's instructions and including on column DNAse digestion. RNA quality was verified by running samples on Agilent Bioanalyzer 2100.
Label Cy5
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
 
 
Hybridization protocol Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.
Scan protocol Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 11.
Data processing Agilent Feature Extraction software version 11 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.
 
Submission date Aug 27, 2013
Last update date Aug 28, 2013
Contact name Jessica Lynn Larson
E-mail(s) larsonj5@gene.com
Phone 6502251802
Organization name Genentech
Department Bioinformatics and Computational Biology
Lab Larson
Street address 1 DNA Way
City South San Francisco
State/province California
ZIP/Postal code 94080
Country USA
 
Platform ID GPL11202
Series (1)
GSE50245 Dual leucine zipper kinase is required for excitotoxicity induced neuronal degeneration

Data table header descriptions
ID_REF
VALUE Normalized log transformed ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_55_P1989846 0.286975221
A_55_P1991598 -0.287624267
A_55_P2022211 3.847830734
A_55_P1980764 -0.510525577
A_55_P1964375 -0.083811136
A_51_P128876 -2.22044546
A_55_P2121042 -0.179552997
A_52_P219230 0.032545636
A_51_P207591 -3.407173038
A_55_P2131920 -3.252538674
A_55_P2404223 -0.513898046
A_55_P2101944 0.934142371
A_52_P358860 -0.59162072
A_51_P119031 0.510618419
A_51_P309854 5.701404463
A_51_P343900 -1.097656528
A_51_P234359 0.479846482
A_51_P487813 0.042884683
A_52_P613977 0.135748016
A_55_P1957209 1.456624286

Total number of rows: 39429

Table truncated, full table size 1000 Kbytes.




Supplementary file Size Download File type/resource
GSM1216847_Agilent_252665514835_S001_GE2_1100_Jul11_1_4.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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