Additional file 3 of Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

Additional file 3:This Excel file contains the complete PtGen2 master file including annotations and print tip information (3A), the list of duplicate spotted validation cDNAs and buffer blanks that were excluded from statistical analysis (3B), and 251 probes removed from statistical analysis since they mapped to contigs already represented by other cDNAs. 3A (PtGen2 Master Annotation File): Gene ID = unique probe address (metarow, metacolumn, row, column), UniScript = Fungen assembly contig ID, Clone_Name = cDNA clone ID. P_C_R actual = plate, column, and row or source print plates. P_C_R Virtual = plate_column_row with virtual plate 69 (actually a reprint of plate 10). Print Tip = print tip location on 48 pin head. All BlastX results are ordered by database name abbreviation followed by accession (BlastX), description (ID), and E-value (Exp). NCBI = NCBI non-redundant, SP = Swiss Prot, TR = TrEMBL, UREF = UniRef100, TAIR = Arabidopsis, MT2P = Medicago, OSA = rice. 3B (Plate 69 + Buffers) Gene IDs and clone names for duplicate spotted plate 69 (re-spot of source plate 10) used only for validation purposes and removed from statistical evaluation of experimental data. A correlation analysis was done on these 384 probes (see Additional File 5). 3C (251 Duplicate cDNAs): Gene IDs and clone names of 251 cDNAs removed from statistical evaluation of experimental data since these clones were duplicate probes that derived from cDNA clones that mapped to the same Uniscript (contig). (XLS 20 MB)