email+Hojoon+4-13-13

Hi Hojoon,

Unfortunately I have another thing to ask you as well. Dr. Johnston wants me to screen my tumor cDNA library for the presence of your validated mouse chimeric transcripts (Table 3.3 of your dissertation). I know that you have the primers and sequences of these primers. I'll probably just order the primers fresh. I have a problem though. I can't find all of the primer sequences I need.

You have a list of primers with some type of ID like TR_E10404 in this file C:\kurt\storage\CIM Research Folder\DR\2013\4-11-13\genefusion info\Mouse_Human_primers_for_mouse.xls I don't know if this is an ID that matches with something in a public database, or if this is a custom ID that you assigned for these chimeric transcripts yourself.

You have a list of chimeric transcripts that match with some of these ids here: C:\kurt\storage\CIM Research Folder\DR\2013\4-11-13\genefusion info\Total_FG_peptide_annotation2-1.xlsx

However, about 1/2 of the chimeric transcripts in your Table 3.3 are not in this file. I searched the entire shared drive for files containing the names of some of the other transcripts and found a few more in this file: S:\Research\Cancer_Eradication\Candidate_List\96Pep_chip_0820_2009.txt

However, I still need to find the ids (so that I can find the primer sequences) of a few more chimeric transcripts from your Table 3.3 listed below. Tmem170 + Cfdp1 Slc35a3 + Hiat1 Noslap + EG665574 Samd5 + Sash1

I'm not sure why these chimeric transcripts were not grouped with some of the other files I already looked at. Do you know where I might find these? I need to get the "TR_...." id so that I can get the primer sequence.

Once again thanks for your help!

Best, Kurt