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Sample GSM1018509 Query DataSets for GSM1018509
Status Public on Mar 27, 2013
Title Spleen Mock infected 6h Rep 3 (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 3
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)
GSE41520 Genome wide analysis of C57BL-6 mice infected with North-American strain (89-1591) of Streptococcus suis
Reanalyzed by GSM1018517
Reanalyzed by GSM1018525

Data table header descriptions
VALUE log2 robust spline normalized

Data table
ILMN_1212607 8.031841931
ILMN_1212612 8.157926054
ILMN_1212636 11.49126558
ILMN_1212637 9.426237883
ILMN_1212645 8.084411249
ILMN_1212648 9.139188181
ILMN_1212653 8.440032883
ILMN_1212672 9.090869106
ILMN_1212682 7.936161574
ILMN_1212692 8.103638681
ILMN_1212693 8.559111087
ILMN_1212695 8.55371539
ILMN_1212702 14.2486177
ILMN_1212703 8.313157721
ILMN_1212717 8.19101022
ILMN_1212720 8.24049486
ILMN_1212759 9.18708695
ILMN_1212791 8.25013589
ILMN_1212794 8.830544065
ILMN_1212828 8.045931559

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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