PCR Screen for 7 chimeric transcripts in 41 pools 5-21-13

2015-01-13

azim58 - PCR Screen for 7 chimeric transcripts in 41 pools 5-21-13

experiment performed 5-21-13 (actually just planned this day) and 5-22-13

refer to this spreadsheet to see which chimeric transcripts were detected
in pools 1-20 and 21-41 (so just 2 pools)
"F:\kurt\storage\CIM Research Folder\DR\2013\5-7-13\chim transc\Chimeric
transcript screen 5-2-13.xls"
Here are some gels that are associated with some of the information in
this spreadsheet. However, this information is not necessarily related to
this experiment
"F:\kurt\storage\CIM Research Folder\DR\2013\5-7-13\chim transc\chimeric
transcript gels 5-2-13.svg"
and here
"F:\kurt\storage\CIM Research Folder\DR\2013\5-7-13\chim transc\chimeric
transcript gels 2 5-2-13.svg"

Chimeric transcript
 Expected size
 Potential positive pools
 Number of pools

10339
 315
 "1-20"
 20

10176
 506
 "1-20"
 20

20131
 246
 "1-41"
 41

20151
 362
 "1-20"
 20

10142
 499
 "21-41"
 20

20026
 229
 "21-41"
 20

10028
 400
 "1-41"
 41

total
 182

182+2*7=196

the 2*7 is for a positive and negative control for each transcript

I should use a water template as a negative control.
I should also use some 4T1 cDNA as a negative control, but I think I will
need to make some more of this. Actually I found some cDNA
4T1 Balb s c tumor cDNA purified 11-27-12

I will dilute this cDNA by 100 so that it can last longer.

For the size range of these fragments I should make a 1.5% gel.
I should make 2 350 mL gels each with 4 24 tooth combs (192 teeth total),
and 1 1.5% 100 mL gel

Shared drive gel images
S:\Research\Cancer_Eradication\Discovering tumor specific antigens\Tumor
cDNA Library\5-23-13

Data for chimeric transcripts found here
a table with which pools contained the chimeric transcript and what the
expected size is (similar to table above)
(This spreadsheet just contains information about which tubes correspond
to which pools that need to be screened with which chimeric transcript)
"F:\kurt\storage\CIM Research Folder\DR\2013\5-24-13\chimeric
transcripts\Data for chimeric transcripts 5-24-13.xlsx"

Diagrams of the gels can be found here
"F:\kurt\storage\CIM Research Folder\DR\2013\5-24-13\chimeric
transcripts\chimeric transcript gels 5-24-13.svg"

Table of results found here
(this spreadsheet has a list of pcrs that I need to retest)
"F:\kurt\storage\CIM Research Folder\DR\2013\5-24-13\chimeric
transcripts\table of results 5-24-13.xlsx"

azim58wiki: