email Hojoon 4-13-13
2013-12-01azim58 - 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