screen of tumor library antibody binding sequences 7-19-13

2014-08-29

Original gel images found here
S:\Research\Cancer_Eradication\Discovering tumor specific antigens\Tumor cDNA Library\7-16-13

Inkscape file found here
"F:\kurt\storage\CIM Research Folder\DR\2013\7-19-13\annotated gels 7-19-13.svg"
also
annotated gels tumor and normal at each condition compared side by side
"F:\kurt\storage\CIM Research Folder\DR\2013\7-19-13\annotated gels tumor and normal at each condition compared side by side7-19-13.svg"

and
annotated gels tumor and normal at each condition compared side by side
"F:\kurt\storage\CIM Research Folder\DR\2013\7-19-13\annotated gels tumor and normal at each condition compared side by side7-19-13.svg"

Table of detected transcripts found here
"F:\kurt\storage\CIM Research Folder\DR\2013\7-22-13\Transcript Detection Table 7-22-13.xlsx"
Notes about file ids
"F:\kurt\storage\CIM Research Folder\DR\2013\7-19-13\file ids 8-12-13.txt"
Notes about bands detected
When I could detect the wild type size in the normal I could usually detect this size in the tumor sample as well unless the size was very large.  I also tried to look for alternative smaller bands present in the tumor, but not the normal.  Such bands may indicate that some mis-splicing occurred.  I may have detected such mis-splicing with the Cbx3 transcript.
Cbx3 investigation
{
I would like to investigate Cbx3 further to determine whether there are known Cbx3 frameshifted or chimeric transcripts upstream of the sequence I detected in my library.

Cbx3 sequence detected in library
"F:\kurt\storage\CIM Research Folder\DR\2013\8-12-13\cbx3 investigation\cbx3_sequence_in_library.txt"
found from here
"F:\kurt\storage\CIM Research Folder\DR\2012\11-19-12\sequence analysis\8-26-12 plasmid details.xlsx"

I blasted this Cbx3 sequence with Mus Musculus (taxid: 10090).  I searched for highly similar sequences (megablast)

There is just 1 match with the refseq_rna database
There were 56 matches with the nr database.
There were 253 matches with with the est database

Ideally, I would like to align the full sequence of each of the matches with the wild type transcripts, and my library sequence to determine if any of them would produce the same frameshifted protein.
I'm not sure if there is a program or tool to help me do such an analysis.
}

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Backlinks
"F:\kurt\storage\CIM Research Folder\DR\2012\11-7-12\PCR Screen Portal 11-7-12.txt"

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