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Sample GSM1018510 Query DataSets for GSM1018510
Status Public on Mar 27, 2013
Title Spleen Mock infected 6h Rep 4 (89-1591)
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 89-1591 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)
GSE41520 Genome wide analysis of C57BL-6 mice infected with North-American strain (89-1591) of Streptococcus suis
Relations
Reanalyzed by GSM1018518
Reanalyzed by GSM1018526

Data table header descriptions
ID_REF
VALUE log2 robust spline normalized

Data table
ID_REF VALUE
ILMN_1212607 7.980102203
ILMN_1212612 8.134173307
ILMN_1212636 10.78197644
ILMN_1212637 9.064964097
ILMN_1212645 8.374768982
ILMN_1212648 9.217842929
ILMN_1212653 8.528762645
ILMN_1212672 9.146047542
ILMN_1212682 8.05876576
ILMN_1212692 8.076919016
ILMN_1212693 9.145470313
ILMN_1212695 8.174192796
ILMN_1212702 14.81826706
ILMN_1212703 8.3688998
ILMN_1212717 8.120541901
ILMN_1212720 8.435780365
ILMN_1212759 8.829663107
ILMN_1212791 8.147950897
ILMN_1212794 9.283422333
ILMN_1212828 8.049219058

Total number of rows: 13492

Table truncated, full table size 327 Kbytes.




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

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