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Sample GSM1018524 Query DataSets for GSM1018524
Status Public on Mar 27, 2013
Title Spleen Mock infected 6h Rep 2 (SC84)
Sample type RNA
Source name Spleen Mock infected 6h
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
gender: Female
Treatment protocol Mice were infected for 6h with 5 x 10^7 CFU of Streptococcus suis strain SC84 or mock-infected with bacterial growth medium (THB).
Growth protocol Bacterial culture was prepared by transferring 10 μl of 1/1,000 dilutions of 8-h cultures into 30 ml of THB, which was incubated for 16 h at 37°C without agitation. Stationary-phase bacteria were washed twice in PBS (pH 7.3). The bacterial pellet was then resuspended and adjusted to a concentration of 5 × 10^8 c.f.u. ml-1.
Extracted molecule total RNA
Extraction protocol RNA was homogenized from RNAlater-stabilized spleen tissus, extracted and DNAse I treated using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label Biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Replicate 2
Data processing The data were first raw-filtered in order to identify and remove probesets that were not detected and then normalised using robust spline normalization with FlexArray v1.6
Submission date Oct 11, 2012
Last update date Mar 27, 2013
Contact name Claude Lachance
Organization name Bio-Rad
Street address 1329 Meyerside Drive
City Mississauga
State/province Ontario
ZIP/Postal code L5T 1C9
Country Canada
Platform ID GPL6885
Series (1)
GSE41522 Genome wide analysis of C57BL-6 mice infected with Chinese strain (SC84) of Streptococcus suis
Reanalysis of GSM1018508

Data table header descriptions
VALUE log2 robust spline normalized

Data table
ILMN_1212607 8.275556533
ILMN_1212612 8.067585455
ILMN_1212636 11.17036871
ILMN_1212637 9.392205309
ILMN_1212645 8.364721631
ILMN_1212648 9.37079172
ILMN_1212653 8.615157921
ILMN_1212672 9.116411473
ILMN_1212692 8.050665352
ILMN_1212693 8.669094794
ILMN_1212695 8.045663134
ILMN_1212702 14.63134413
ILMN_1212703 8.332283848
ILMN_1212717 8.05643581
ILMN_1212720 8.315705784
ILMN_1212759 8.889920785
ILMN_1212791 8.033982586
ILMN_1212794 9.096648856
ILMN_1212836 8.787561737
ILMN_1212894 8.470391291

Total number of rows: 13325

Table truncated, full table size 323 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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