Microarray Raw data for IAI Manuscript

This site contains the 12-chipe microarray data for the manuscript submitted to the journal Infection and Immunity. The information listed here can be used for the reviewers to look into the detailed intensity data for all the genes in the 12-chip experiment.

Manuscript Information: Brucella melitensis triggers time-dependent modulation of apoptosis and down-regulation of mitochondria-associated gene expression in mouse macrophages. Yongqun He, Sherry Reichow, Sheela Ramamoorthy, Xicheng Ding, Raju Lathigra, Johanna C. Craig, Bruno W.S. Sobral, Gerhardt G. Schurig, Nammalwar Sriranganathan, Stephen M. Boyle. Revised manuscript submitted to Infection and Immunity. 2006.

Three data types are included:

1. Cell Intensity File (.CEL): The .CEL data file contains fluorescence intensities for each microarray probe. When the .CEL file is opened in either GCOS or MAS 5.0, these probe-specific intensity values are used to reconstruct the scanned image of the hybridized array. The probe-specific intensities in the .CEL file are also used to calculate the probe-set-level Signals and Presence Calls recorded in the .CHP file. It is noted that the data format is not text format and cannot be readed directly. Each file is about 10 MB. The .CEL data will be submitted to the public microarray gene expression data repository NCBI GEO as microarray raw data.
   
   

   	Replicate1	Replicate2	Replicate3
   Control	C-1.CEL	C-2.CEL	C-3.CEL
   4 h p.i.	M-4-1.CEL	M-4-2.CEL	M-4-3.CEL
   24 h p.i.	M-24-1.CEL	M-24-2.CEL	M-24-3.CEL
   48 h p.i	M-48-1.CEL	M-48-2.CEL	M-48-3.CEL

   
   
2. Report File (.RPT): The .RPT Report File summarizes background noise, housekeeping information, and spiked-in controls for each chip in text format. It is noted that the intensity signal data in the report file are obtained from the fluorescence intensities without data normalization.
   
   

   	Replicate1	Replicate2	Replicate3
   Control	C-1.RPT	C-2.RPT	C-3.RPT
   4 h p.i.	M-4-1.RPT	M-4-2.RPT	M-4-3.RPT
   24 h p.i.	M-24-1.RPT	M-24-2.RPT	M-24-3.RPT
   48 h p.i	M-48-1.RPT	M-48-2.RPT	M-48-3.RPT

   
   
3. Microarray signal pivot data: The .CEL file can be used to produce Chip (.CHP) File using the Affymetrix GCOS software. The Signal values and Presence Calls in the .CHP file are organized by probe set in a pivot table called Pivot. We have also created a Microsoft Excel file that includes all the 12-chip pivot dat. Please download the file HERE. The size of this file is about 28 MB.

Reference: Affymetrix manual: Affymetrix microrray data analysis fundamental, which is publicly available at affymetrix.com.

Notes:

1. More supplemental data for the manuscript are available at here. Those supplemental data are availble for the public to view.
2. Once accepted for publication, the raw data listed here will be submitted to public gene expression data repository NCBI GEO. After that, these files in this website will probably be moved since it becomes redundant to keep these files that occupy large storage space..

Suggestions and Comments? Please contact Dr. Yongqun He at the University of Michigan. Thank you.