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Sample GSM334280 Query DataSets for GSM334280
Status Public on Nov 26, 2008
Title neocortex, 5 months mouse#4
Sample type RNA
 
Source name neocortex from B6xC3 F1 hybrid mice at 5 months of age
Organism Mus musculus
Characteristics Strain: B6xC3 F1 hybrid
Age: 5 months
Gender: male
Treatment protocol Control Diet: Mice were fed 24 g/wk of AIN-93M diet which has a total energy content of 16740 kJ/kg.
Growth protocol Male B6C3F1 mice were purchased from Harlan-Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidifed water ad libitum.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen tissue using the TRIZOL reagent (Invitrogen, San Diego, CA) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Double-stranded DNA was then synthesized from 1 ug of mRNA using the SuperScript Choice System (Invitrogen) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, LaJolla, CA), purified with phenol-chloroform-isoamyl alchohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA usind the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Chips used in this study were the Affymetrix MOE 430 2.0 arrays which have 45, 037 probe sets (Affymetrix, Santa Clara, CA). cRNA (10 ug) in hybridization cocktail was placed in the chip and hybridized at 45° C for 16 hours with mixing on a rotisserie at 60 rpm. Following hybridization, the hybrization solutions were removed and the gene chips were installed in a fluidics system for washing and staining.
Scan protocol After staining, the gene chips were read at a resolution of 3 um using a Hewlett Packard GeneArray Scanner (Affymetrix). The averaged images collected from two scanned images were used for the analysis.
Description Gene expression data from mouse neocortex
Data processing The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize overall variability in hybridization by a global scaling method.
 
Submission date Oct 16, 2008
Last update date Aug 28, 2018
Contact name Philipp Oberdoerffer
E-mail(s) philober@hms.harvard.edu
Organization name Harvard Medical School
Department Pathology
Lab Sinclair
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1261
Series (2)
GSE13120 Age-related gene expression changes in mouse neocortex
GSE13121 SIRT1 redistribution on chromatin promotes genome stability but alters gene expression during aging
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal calculated by CGOS 1.2 software

Data table
ID_REF VALUE
1415670_at 1043.52
1415671_at 3324.94
1415672_at 2272.5
1415673_at 492.14
1415674_a_at 957.51
1415675_at 1641.31
1415676_a_at 2983.79
1415677_at 1092.25
1415678_at 1567.99
1415679_at 2138.62
1415680_at 523.33
1415681_at 925.61
1415682_at 689.17
1415683_at 1334.39
1415684_at 403.2
1415685_at 308.71
1415686_at 1949.88
1415687_a_at 8000.33
1415688_at 2006.13
1415689_s_at 732.94

Total number of rows: 45037

Table truncated, full table size 780 Kbytes.




Supplementary file Size Download File type/resource
GSM334280.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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