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Sample GSM334278 Query DataSets for GSM334278
Status Public on Nov 26, 2008
Title neocortex, 5 months mouse#2
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
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
Reanalyzed by GSE119085

Data table header descriptions
VALUE Signal calculated by CGOS 1.2 software

Data table
1415670_at 1207.92
1415671_at 3238.28
1415672_at 2408.51
1415673_at 469
1415674_a_at 929.41
1415675_at 1619.99
1415676_a_at 2822.24
1415677_at 1214.09
1415678_at 1588.37
1415679_at 2107.83
1415680_at 536.02
1415681_at 995.97
1415682_at 772.88
1415683_at 1368.51
1415684_at 387.34
1415685_at 322.95
1415686_at 1945.65
1415687_a_at 8345.33
1415688_at 1962.27
1415689_s_at 661.19

Total number of rows: 45037

Table truncated, full table size 779 Kbytes.

Supplementary file Size Download File type/resource
GSM334278.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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