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Sample GSM486968 Query DataSets for GSM486968
Status Public on Dec 18, 2009
Title Spleen_uninfected_control_rep1
Sample type RNA
 
Source name Spleen homogenate, uninfected
Organism Mus musculus
Characteristics strain: C57BL/6
gender: Female
age: 6 weeks
tissue: Spleen
infection/agent: none
Treatment protocol Mice were euthanized and spleen tissue was collected and stored in RNAlater for microarray analysis
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from spleen tissue by phase separation with Trizol (Invitrogen, USA) and column chromatography using an Rneasy Mini kit (Qiagen Inc, USA), RNA quantity was measured using a Nanodrop (Nanodrop Technologies, USA) and quality was assessed using an Agilent Bioanalyzer Nanochip (Agilent Technologies, USA)
Label Cy3
Label protocol cRNA was synthesised from 250ng of pooled total RNA with an Illumina Total Prep RNA Amplification Kit (Ambion Inc., USA) according to the manufacturers instructions
 
Hybridization protocol cRNA was hybridised to Illumina mouse-6 v1.1 expression beadchips according to the manufacturers instructions
Scan protocol Microarrays were scanned using a Beadstation 500 at Green factor level 2
Description Gene expression in the spleen of normal C57BL/6 mice
Data processing Data was analysed using BeadStudio and Genespring GX; Values reported were derived using Illumina BeadStudio v3 and represent relative signal intensity normalized to background, Genespring GX was used to normalise each chip to the 50th percentile and each gene to the median and uninfected controls, measurements less than 0.01 were set to 0.01
 
Submission date Dec 17, 2009
Last update date Dec 17, 2009
Contact name Melissa Louise Burke
E-mail(s) melissa.burke@qimr.edu.au
Organization name Queensland Institute of Medical Research
Department Division of Infectious Diseases and Immunology
Lab Molecular Parasitology
Street address 300 Herston Road
City Herston
State/province QLD
ZIP/Postal code 4006
Country Australia
 
Platform ID GPL6481
Series (1)
GSE19525 Gene expression in the Schistosoma japonicum infected spleen

Data table header descriptions
ID_REF
VALUE normalized data
Detection Pval_Uninfected_4003444051_E

Data table
ID_REF VALUE Detection Pval_Uninfected_4003444051_E
10243 0.9556791 0.98752
10280 0.96960247 0.82034
10575 1.0645454 0.99251
20048 0.9426412 0.86775
20296 0.8953134 1
20343 1.0343902 0.82034
20373 0.882991 0.59389
20431 0.9497871 1
50014 1.0735934 0.59638
50017 0.9144613 0.65502
50019 0.9692428 1
50020 0.9033107 0.9844
50022 0.999586 0.08359
50025 1.0138371 0.30942
50026 1.1024659 0.51653
50035 1.0543419 0.61634
50037 1.0997162 0.99938
50039 1.0234417 1
50040 0.87638825 0.98378
50041 0.95578486 0.99938

Total number of rows: 46643

Table truncated, full table size 1182 Kbytes.




Supplementary file Size Download File type/resource
GSM486968.txt.gz 937.0 Kb (ftp)(http) TXT
Processed data included within Sample table

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