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Sample GSM840267 Query DataSets for GSM840267
Status Public on Dec 01, 2012
Title A. pleuropneumoniae__serotype2_48h__rep1 [78-1]
Sample type RNA
 
Source name Actinobacillus pleuropneumoniae 4226 from pig lung 48h
Organism Actinobacillus pleuropneumoniae
Characteristics serotype: 2
strain: 4226
Treatment protocol Prior to RNA extraction, 100 to 300 mg lung tissue with visual lesions was finely chopped by scalpel, transferred to 5 ml Phenol:Guanidinthiocyanat lysis buffer (provided in the Qiagen kit) in which it was divided further by a Tissue shearer for 2 min.
Growth protocol Immediately post mortem, infected lung tissue was isolated, cut into pieces smaller than 0.5×0.5 cm and preserved in RNAlater stabilization reagent (Ambion, Cambridgeshire, United Kingdom) at -20°C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Lipid kit (QIAGEN, Hilden, Germany). Genomic DNA was eliminated by RNase-free DNase I treatment during the isolation procedure. After RNA extraction, the material was further treated by TURBO™ DNase, according to the protocol provided by the manufacturer (Ambion). The RNA concentration and quality were measured by NanoDrop (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively. For each sample, 30 µg of total RNA was enriched for bacterial RNA applying the MicrobEnrich Kit according to the supplied protocol (Ambion). Subsequently, one µg of the enriched RNA was amplified using a MessageAmp II-Bacteria kit (Ambion) according to the manufacturer's instructions.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc. (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc. (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc. (Madison, WI USA*) following their standard operating protocol. See www.nimblegen.com.
Description This sample is of A. pleuropneumoniae strain 4226. It is the first of three biological replicates for pig no. 78, each isolated from separate lung lesions.
Data processing The Robust Multichip Average (RMA)function was applied for normalization of the microarray data (Irizarry et al. Biostatistics 4(2):249). For RMA normalization we have used RGui version 2.9.2 (2009-08-24) (http://cran.r-project.org/bin/windows/base/), using the package Oligo.
 
Submission date Nov 29, 2011
Last update date Dec 01, 2012
Contact name Kirstine Klitgaard
E-mail(s) kksc@vet.dtu.dk
Phone 0045 35886265
Organization name National Veterinary Institute, Technical University of Denmark
Street address Bulowsvej 27
City Copenhagen
ZIP/Postal code 1790
Country Denmark
 
Platform ID GPL11003
Series (1)
GSE33999 Genome wide transcriptional portrait of Actinobacillus pleuropneumoniae during invasive disease reveals new strategies for survival and persistence in the host

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 ratio, median gene-level signal intensity.

Data table
ID_REF VALUE
AP2_cds_1 7.37640959
AP2_cds_10 7.527033373
AP2_cds_106 9.153956155
AP2_cds_11 7.210896111
AP2_cds_1101 9.916698916
AP2_cds_1191 11.5265059
AP2_cds_1199 11.54263881
AP2_cds_12 9.651235801
AP2_cds_1207 9.689544101
AP2_cds_1249 8.70669744
AP2_cds_1250 8.206995459
AP2_cds_13 10.55191882
AP2_cds_1353 9.258693904
AP2_cds_1356 12.73504693
AP2_cds_1357 11.50887067
AP2_cds_1392 11.84400895
AP2_cds_1393 10.43148187
AP2_cds_14 10.69059452
AP2_cds_1406 8.597586375
AP2_cds_1441 11.07544434

Total number of rows: 4876

Table truncated, full table size 140 Kbytes.




Supplementary file Size Download File type/resource
GSM840267_398422A12_2010-07-08_10-53_Area1_532.xys.gz 779.0 Kb (ftp)(http) XYS
Processed data included within Sample table
Processed data are available on Series record

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