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Sample GSM871674 Query DataSets for GSM871674
Status Public on Feb 08, 2012
Title ac_bulb at T1
Sample type RNA
 
Source name bulbourethral glands, biopsied, 60 min, acute
Organism Ovis aries
Characteristics gender: male
breed: Santa Inês
age: 12 months
tissue: bulbourethral glands
treatment: Brucella ovis ATCC 25840 infection
phase of infection: acute
Treatment protocol The rams were kept in an isolated pen and experimentally challenged with a rough (R) virulent B. ovis PA strain (ATCC 25840).
Growth protocol Twelve 12-month-old healthy Santa Inês rams, previously diagnosed as negative for brucellosis/visna maedi/toxoplasmosis/neosporosis, were selected for the study.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissue samples collected at 0, 60, 120, 240 dpc using the Invisorb® Spin Tissue RNA Mini Kit (Invitek Gmbh, Germany) according to the manufacturer’s instructions, and purified with the RNeasy Mini-kit (Qiagen, Mississauga, ON, Canada). Total RNA was quantified by absorbance at 260 nm. The quality of all RNA preparations was controlled by electrophoresis on agarose gels. They were also evaluated on an Agilent Bioanalyser instrument (Agilent Technologies, Palo Alto, CA, USA). Only samples with a preserved rRNA ratio (28S/18S), no evidence of RNA degradation, and values ≥ 8 at the Bioanalyser were used in the microarray hybridization and qPCR.
Label Cy3
Label protocol RNA labeling was performed as recommended by the manufacturer.
 
Hybridization protocol Expression measurements were performed using the Affymetrix GeneChip® Bovine Genome Array (Affymetrix, USA), which interrogates 23,000 genes, following the hybridization protocol recommended by the manufacturer.
Scan protocol After array scanning, quality control was performed with GCOS software (Affymetrix, USA) according to the manufacturer’s recommendations.
Description ac_bulb.cel
Gene expression data from rams infected with B. ovis.
Data processing The quality control also was verified using Expression Console (http://www.affymetrix.com/browse/level_seven_software_products_only.jsp?productId=131414&categoryId=35623#1_1). The unwanted variables (batch effects) were removed using ComBat methodology (http://jlab.byu.edu/ComBat/Abstract.html) (Johnson et al., 2007). The IQR (Inter-Quartile-Range) filter available at R/Bioconductor (Irizarry et al., 2003) was applied. Gene expression values were obtained using the three-step Robust Multi-array Average (RMA) pre-processing method, implemented in the Affy package from R/Bioconductor (Irizarry et al., 2003). We employed the RankProd method for the selection of differentially expressed genes (DEGs), considering a p-value cut-off of 0.05 adjusted for FDR (False Discovery Rate) (Benjamini & Hochberg, 1995). RankProd is a rank-based nonparametric procedure (Hong et al., 2006). The method used HCL (Hierarchical Clustering) for the grouping of data with the Pearson correlation coefficient for the calculation of within-group distance and complete linkage between groups for the calculation. The method is available in the program Expander (http://acgt.cs.tau.ac.il/expander/index.html) (Shamir et al., 2005). We performed functional annotation analysis of the differentially expressed genes with the IPA (Ingenuity Pathway Analysis, http://www.ingenuity.com) tools. In IPA, we considered the default parameter Molecules per Network=35, Networks per Analysis=25, only direct relationships between genes and the “Ingenuity Expert Information” Data Source, including the new option of “Ingenuity ExpertAssist Findings”, in which the information has been manually reviewed and curated from full-text scientific publications.
 
Submission date Feb 07, 2012
Last update date Feb 08, 2012
Contact name João Marcelo Azevedo de Paula Antunes
E-mail(s) joaomarceloufes@hotmail.com
Organization name UNESP
Department Higiene Veterinária e Saúde Pública
Street address FMVZ, Distrito de Rubião Júnior
City Botucatu
State/province São Paulo
ZIP/Postal code 18618-970
Country Brazil
 
Platform ID GPL2112
Series (2)
GSE35612 Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis (acute phase)
GSE35615 Microarray analysis of gene expression in rams experimentally infected with a rough virulent strain of Brucella ovis

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.70915931476718
AFFX-BioB-5_at 7.56699774214782
AFFX-BioB-M_at 8.29707842903454
AFFX-BioC-3_at 9.16379353368229
AFFX-BioC-5_at 8.80680551935157
AFFX-BioDn-3_at 11.0252072605646
AFFX-BioDn-5_at 9.90256157633415
AFFX-Bt-A00196-1_s_at 3.64064962160046
AFFX-Bt-AB076373-1_at 3.81839467959327
AFFX-Bt-AF292559-1_at 2.1965600197248
AFFX-Bt-AF292559-2_s_at 1.76283414415664
AFFX-Bt-AF292559-3_s_at 1.89312557739812
AFFX-Bt-AF292559-4_s_at 3.77800334397773
AFFX-Bt-AF292560-1_s_at 2.14368872521332
AFFX-Bt-AF298789-1_at 3.49036073892366
AFFX-Bt-AF323980-1_at 2.32570400135445
AFFX-Bt-AJ002682-1_s_at 2.99739448877154
AFFX-Bt-AJ002682-2_s_at 3.46812734798825
AFFX-Bt-AJ132968-1_at 2.4909198153919
AFFX-Bt-AY056050-1_at 3.98361870515173

Total number of rows: 24128

Table truncated, full table size 794 Kbytes.




Supplementary file Size Download File type/resource
GSM871674_ac_bulb.cel.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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