How to Check Master Block DNA for PGA Project

 

            For pga, BKRB20030/0031 is used to check the master block DNA plate each time when the master plate is made. In order to be consistent with our pga oracle database and not to confused with the original BKRB2 data, a new entry ( called MSTRB --- standing for ?master block? ) has been created in PGA database.

 

            MSTRB is only about 1 kb long and have a pair of primers called MSTRB0030 and MSTRB0031 ( For the technicians, please take some of BKRB20030/BKRB20031

primer stock and re-label them as MSTRB0030/ MSTRB0031 accordingly)

 

            From now on, technicians should log in pcr events, sequencing events, and generating sample sheets under MSTRB ?gene? in pga database like what you  do for any normal genes. The data for checking master block DNA should be transferred into

            /c16/mstrb/new_chromats

 

            To check the master block data, analysts may follow the protocol as described below in proper directories under /c16/mstrb

 

1) Make sure you  have no chromats in chromat_dir, no phd / poly files in phd_dir and poly_dir.

 

2) Run moveChromats.pl in new_chromats to move all chromats to proper directories.

 

3) cp   /c16/mstrb/fasta_dir/MSTRB.REF.phd.1   /c16/mstrb/phd_dir/

 

4) Assemble the data in edit_dir and do the analysis just like what you do for a normal gene, such as running the pAnalysiTables.pl and the ga.pl programs. The goal is to get a prettybase file.

 

5) Compare the prettybase file you get with the original prettybase file called bkrb2.pretty.orig.txt in /c16/mstrb/prettybase_dir. If the genotypes for those snps are consistent, the master block DNA is confirmed to be fine.

 

6) cp  /c16/mstrb/edit_dir/xxxxx.prettybase.txt

         /c16/mstrb/prettybase_dir/plate_name.prettybase.txt

 

            The plate_name can be obtained from technicians. For pga, the plate name is like ?PGA.010802.M?.

 

7) mv    /c16/mstrb/chromat_dir/*    /c16/mstrb/saved_chromats/

 

8) Any files left in edit_dir, phd_dir and poly_dir can be deleted.