Malaria IDC Comparison Database

PRIMARY AND SUPPLEMENTAL DATA:

Datasets:
All arrays in these datasets have been normalized by a linear scalar (global normalization) to set the total sum of Cy3 intensity equal to the total sum of Cy5 intensity across the entire array. To calculate these sums, only array spots with an R-squared value (coefficient of determination) greater than or equal to 0.75 were included. Timepoints for which there were more than one array first were normalized and then averaged.
These datasets have not been log-transformed or mean-centered as in our expression profile figures.

Table S1. 3D7 Complete set (4.1 MB)
Table S2. Dd2 Complete set (3.4 MB)
HB3 Complete set (3.6 MB)
The complete datasets for each strain as tab-delimited text files. Each file includes all raw data for every oligonucleotide at each time point for each strain.

Table S3. 3D7 QC set (4.3 MB)
Table S4. Dd2 QC set (3.4 MB)
Table S5. HB3 QC set (3.9 MB)
The set of oligonucleotides that passed all quality control filters for each strain. Each file is a tab-delimited text file.

Table S6. 3D7 Overview set (2.8 MB)
Table S7. Dd2 Overview set (2.3 MB)
Table S8. HB3 Overview set (2.9 MB)
The dataset used to generate the IDC phaseogram for each strain as described in Fig. 1. These are a tab-delimited text files.

Primary Data:
To analyze data which has not been normalized or averaged, you will need to reconstruct the timecourse from these files. The gpr files are the output of analysis of the tiff files using GenePixPro 3.0 and contain all information regarding each individual array.

All 3D7 gpr files (32 MB)
All Dd2 gpr files (31 MB)
All HB3 gpr files (29 MB)
All GenePix 3.0 results files (gpr) for each microarray used in this study, by strain. These files have been compressed into a .ZIP file.
Please read the ReadMe file for the 3D7 and Dd2 GPR files.

All 3D7 tiff files (464 MB)
All Dd2 tiff files (454 MB)
All HB3 tiff files (450 MB)
The raw scans as .TIFF files of all microarrays used in this study, by strain. These files have been compressed into a .ZIP file.

Additional Supplemental Data:

Table S9. Pairwise Pearson correlations between strains for all oligonucleotides.
(Tab-delimited text file - 325 KB).

Table S10. Profile variability between strains.
(Tab-delimited text file - 900 KB).

Table S11. Maximal Pearson correlation differences between oligos from the same gene.
(Tab-delimited text file - 173 KB).

Table S12. Average of the sum of the median intensities across the timecourses.
(Tab-delimited text file - 369 KB).