User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/07

01/07/13

• Array Star analysis

Array Star analysis

1. Open Array Star. Windows only. This can be run on Parallels from a Mac.
2. Click "Start Chip-Seq project..."
3. Add Experiments to Import: Click [Add File..]
4. Select a ###.bam file from the ChiP seq data folder (shared desktop). Click [Next >].
5. Create binding proteins: Click [Create Binding Protein]. Binding protein label = the name of the protein that was pulled down by the antibody via ChIP. Binding site type = Unknown. Click [OK].
6. Assign Binding Proteins to Experiments: Protein label = the appropriate binding protein (created in previous step). Click [Next >].

PcTF vs. H3K27me3

1. Add Experiments to Import: added 1_aln_sorted.bam (PcTF), 2_aln_sorted.bam (PcTF mock), 6_aln_sorted.bam (H3K27me3), and 7_aln_sorted.bam (H3K27me3 mock)
2. Create binding proteins: created "PcTF" for 1_aln_sorted, and "H3K27me3" for 6_aln_sorted.
3. Set control 2_ and 7_aln_sorted as "yes" for "Is control?"
4. Set 2_aln_sorted as control for 1_aln_sorted. Set 7_aln_sorted as control for 6_aln_sorted.