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Sample GSM973257 Query DataSets for GSM973257
Status Public on Dec 27, 2012
Title NPC Brain 62d Mouse1
Sample type RNA
 
Source name Brain from 62 days Npc1-/- mouse1
Organism Mus musculus
Characteristics tissue: Brain
genotype: Npc1-/-
age: 62 days
subject: Mouse1
genetic background: BALB/c
Growth protocol Mouse were kept and breeding was done at Freimann Life Scinece Center, University of Notre Dame, IN.
Extracted molecule total RNA
Extraction protocol Total RNA from brain, liver and speleen was isolated using 'Roche MagNa Pure Compact automated System' according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared using 'MessageAmpTM Premier Amplification Kit (Invitrogen)' according to the manufactureres instrcutions.
 
Hybridization protocol Affymetrix mouse 430 2.0 array hybridization were performed by 'UCLA Clinical Microarray Core, UCLA, Los Angeles, CA, USA, according to manufacturer's instrcutions
Scan protocol The acquisition if array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC).
Description Gene expression data from brain of Npc1-/- mouse1 of age 62 days
Data processing The data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. We used a PM/MM difference model for estimating gene expression level and quantile approach for data normalization.
Thresholds for selecting significant genes were set at a relative difference ³1.5-fold, absolute difference ³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.
 
Submission date Jul 24, 2012
Last update date Dec 27, 2012
Contact name Md Suhail Alam
E-mail(s) [email protected]
Phone 574-631-3227
Organization name University of Notre Dame
Department Center for Rare and Neglected Diseases/Biological Sciences
Lab Haldar lab
Street address 103 Galvin, University of Notre Dame, IN
City Notre Dame
State/province IN Indiana
ZIP/Postal code 46545
Country USA
 
Platform ID GPL1261
Series (1)
GSE39621 Expression data from brain, liver and spleen of Npc1-/- mice

Data table header descriptions
ID_REF
VALUE D-Chip signal

Data table
ID_REF VALUE
1415670_at 1286.37
1415671_at 4866.25
1415672_at 3725.67
1415673_at 798.22
1415674_a_at 1001.88
1415675_at 951.42
1415676_a_at 2661.05
1415677_at 1108.59
1415678_at 2730.73
1415679_at 2320.36
1415680_at 589.51
1415681_at 842.42
1415682_at 722.02
1415683_at 2243.94
1415684_at 470.85
1415685_at 555.48
1415686_at 2999.14
1415687_a_at 8263.19
1415688_at 2716.68
1415689_s_at 814.68

Total number of rows: 45037

Table truncated, full table size 784 Kbytes.




Supplementary file Size Download File type/resource
GSM973257_BrainGrayNc62.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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