User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/05

Current revision

Pc-TF Genomics

H3K27me3 enrichment

Workflow

Open SeqMan Pro. File > Open > ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
In an internet browser, go to the UCSC genome browser. Select Feb. 2009 GRCh37/hg19.
Enter a gene name. Click [Submit].
Take note of the chromosome number.
Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
Select Contig > Strategy View to view the enrichment histogram.
Select Features > Show Feature Table. Find the gene name. Click on it and the strategy view window will jump to that gene.
Click the gene symbol. Zoom in. Tak emote of the maximum depth of coverage (max. DOC).

Based on Carly's control gene list [1]; CDKN2A and MMP12 added by me

@@ Line 12: / Line 12: @@
 * ChIP seq analysis: bird's eye view of H3K27me3 enrichment
-* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes
 ----
 '''H3K27me3 enrichment'''<br>
-* Completed H3K27me3 (lane 3) "BAM --> assembly" workflow
+* Completed H3K27me3 (lane 6) "BAM --> assembly" workflow
 * Open in SeqMan pro to explore known silenced vs. active genes
@@ Line 51: / Line 50: @@
 | B2M || chr 15 || active || 0
 |-
-| G6PD || chr X || active || ---
+| G6PD || chr X || active || ~130
 |-
-| HPRT1 || chr X (24) || active || ---
+| HPRT1 || chr X (24) || active || ~150
 |-
-| PGK1 ||  chr X (24) || active || ---
+| PGK1 ||  chr X (24) || active || ~240
 |-
-| CDKN2A || chr9 || silent (H3K27me3+) || ---
+| CDKN2A || chr9 || silent (H3K27me3+) || ~90
 |-
-| MMP12 || chr11 || silent (H3K27me3+) || ---
+| MMP12 || chr11 || silent (H3K27me3+) || ~18
 |-
-| MYT1 || chr20 || silent (H3K27me3+) || ---
+| MYT1 || chr20 || silent (H3K27me3+) || '''~270'''
 |-
-| OLIG1 || chr21 || silent (H3K27me3+) || ---
+| OLIG1 || chr21 || silent (H3K27me3+) || 0
 |-
-| OLIG2 || chr21 || silent (H3K27me3+) || ---
+| OLIG2 || chr21 || silent (H3K27me3+) || ~130
 |}