"Rapid Analysis of the DNA Binding Specificities of Transcription Factors with DNA Microarrays"

Supplementary Information:

Supplementary Data

Supplementary Methods

Supplementary Figure 1. DNA microarray bound by CBP-FLAG-Rpn4, and labeled with Alexa 488-conjugated anti(FLAG) antibody.

Supplementary Figure 2. PBM negative controls. (a) rGST. (b) GST-His6 purified from yeast. (c) GST-His6-Cmd1. (d) No GST-tagged protein in PBM binding reaction (“milk only”).

Supplementary Figure 3. Reproducibility of PBM experiments. (a) SD/mean for triplicate Mig1 PBMs. (b) Cumulative SD/mean for triplicate Mig1 PBMs. (c) Scatter plot of the SD/mean values versus the mean signal intensity for triplicate Mig1 PBMs. (d) SD/mean for triplicate SybrGreen I stained microarrays. (e) Cumulative SD/mean for triplicate SybrGreen I stained microarrays. (f) Scatter plot of the SD/mean values versus the mean signal intensity for SybrGreen I stained microarrays. (g) SD/mean for triplicate Abf1 PBMs. (h) Cumulative SD/mean for triplicate Abf1 PBMs. (i) Scatter plot of the SD/mean values versus the mean signal intensity for triplicate Abf1 PBMs. (j) SD/mean for triplicate Rap1 PBMs. (k) Cumulative SD/mean for triplicate Rap1 PBMs. (l) Scatter plot of the SD/mean values versus the mean signal intensity for triplicate Rap1 PBMs.

Supplementary Figure 4. Effect of varying the p-value threshold for the PBM data on Rap1, Abf1, and Mig1 on the number of spots called “bound”.

Supplementary Figure 5. DNA binding site motifs for PBM data passing 0.01 and 0.05 p-value thresholds.

Supplementary Figure 6. Venn diagrams comparing the PBM data for Rap1, Abf1, and Mig1, respectively, with the ChIP-chip data for these same TFs at 0.01 and 0.05 p-value thresholds.

Figures from the main body of the manuscript:

Figure 1a

Figure 1bc

Figure 2a

Figure 2b

Figure 3

Figure 4a

Figure 4b

Figure 5a

Figure 5b

Figure 5c

Figure 6