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Sample GSM1018530 Query DataSets for GSM1018530
Status Public on Mar 27, 2013
Title Spleen S. suis SC84 6h Rep 4 (SC84)
Sample type RNA
 
Source name Spleen S. suis SC84 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 4
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
E-mail(s) claude.lachance@mail.mcgill.ca
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

Data table header descriptions
ID_REF
VALUE log2 robust spline normalized

Data table
ID_REF VALUE
ILMN_1212607 7.997454897
ILMN_1212612 7.901814463
ILMN_1212636 11.53236446
ILMN_1212637 9.073238889
ILMN_1212645 8.037521565
ILMN_1212648 9.280191065
ILMN_1212653 8.231519545
ILMN_1212672 8.710053448
ILMN_1212692 7.903904346
ILMN_1212693 8.22629828
ILMN_1212695 9.243310413
ILMN_1212702 14.54375079
ILMN_1212703 8.177953364
ILMN_1212717 8.600352319
ILMN_1212720 8.334634644
ILMN_1212759 9.224229192
ILMN_1212791 8.133010099
ILMN_1212794 9.026336388
ILMN_1212836 8.551592896
ILMN_1212894 8.968410162

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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