Tumor Validation primers 1-28-13

2015-01-13

azim58 - Tumor Validation primers 1-28-13

What do these primers bind to? They bind to the beginning and end (or
near beginning and near end) of the associated transcript from the first
exon to the last exon.
An example of an alignment of one of the sets of the primers is found
here:
"C:\kurt\storage\CIM Research Folder\DR\2013\3-18-13\tumor sequence
validation\Rnf130 primer alignment.SPF"

see
"F:\kurt\storage\CIM Research Folder\DR\2013\1-7-13\validation of cDNA
clones\Table of primers 1-7-13.xlsx"

for the table of primers

see
"F:\kurt\storage\CIM Research Folder\DR\2013\1-11-13\primers\Kurt Primer
Order Form 1-11-13.xls"
for the primer order form
also pasted here

see also
PCR conditions that worked well for amplifying some chimeric transcripts
7-2-13

Note that the F and R at the beginning refer to forward and reverse. The
Tr at the end refers to truncated.
Note that the reverse side of the primer binds to the 3' end of the gene
near the poly A region.

===========================================================================

RS61 TTTTTTAAAGCAATTCCAAAGTTTATTAGCCATAG
RS61Tr ATGACAGATGGATGTAGCCCAATC
FS61 AGAGCCTGTATCTACGAGAGTTC
RW17 TTTTTGAATGCTAAGGGTAGTTTATTTTG
RW17Tr GACATATTAGGGCATTGTCACCAC
FW17 aaattatttcatGAGTTCAGCCGAG
FW17Tr GAGCCAACATGAAGACAGCCAC
RCX3 TTTTTAAAGGAATATAAAACTATTTATTGACCAC

RCX3N CTGGCTCATTGAACCATAACCC
RCX3Tr CAACGTCAGCTCCAGCCACG
FCX3 GGGCGGTGCTCCCCCTC

FCX3N cggcggagctgcccg
FCX3Tr CTGGACCGTCGTGTAGTG
RRS8 TTTTTCAGATAGAACAGCAGACACC
RRS8Tr CTACACATGAGGCTCATTTGCC
FRS8 gaaggcggggctgagttttag
FRS8Tr CATCTCTCGGGACAACTGGC
REA TTTTTAAAAAACATTTAGATATTTCTCTAAGTCATTTTAATTC
REATr GAAATGTAGACACTGCAAGCAGG
FEA ggaaaggggcgtggcc
FEATr GTCACTACTCAGGAGGAGAC
RR130 TTTTTGCTTAGCAACACGGTACTTTTATTTTATT
RR130Tr CGCTTGTGTGGCATGATTGG
RR130WT TTTTTATTTTATTATTTATTTATTTTAATACAAAGCTTTGGC
FR130 gccccgcctctcagcac
FR130Tr CTGACTTGCAGCCTGTGGC
RH1 TTTTTCATTTTTTAAAACCATTTTTTAATTAGTTGAAAG
RH1Tr GAGCATACAGTAACATGTGAGTATG
FH1 GCAGTCTGGGCGGAGCTTG
FH1Tr CGACTGTTCGGGCGCTAC
RM1 TTTTTAATAATGAAATAATTTATTTGTTAATGGACGG
RM1Tr GCACCATTCTCCAGTCTCAGCAG
FM1 ggcgagtcgggataaacac
FM1Tr ATGAACATCCAGCTGCTGCTGG
Rco1WT TTTTTCATTGAGAAAGACATATAGGATATGAG
Fco1 tatgttcattaatcgttgattattctcaacc
Fco1Tr CTACTATTCGGAGCCTGAGCG
Rco1 TTTTTACTGAGAAAGACATATAGGATATGAGATTG
Rco1Tr CATAGGTTGGTTCCTCGAATG

===========================================================================

PCR reactions with these primers
RS61+FS61
RS61Tr+FS61
RW17+FW17
RW17Tr+FW17Tr
RCX3+FCX3

RCX3N+FCX3N
RCX3Tr+FCX3Tr
RRS8+FRS8
RRS8Tr+FRS8Tr
REA+FEA
REATr+FEATr
RR130+FR130
RR130Tr+FR130Tr
RR130WT+FR130
RH1+FH1
RH1Tr+FH1Tr
RM1+FM1
RM1Tr+FM1Tr
Rco1WT+Fco1
Rco1+Fco1
Fco1Tr+Rco1Tr

===========================================================================

Primer-BLAST Results

primer blast results FCX3 p RCX3

"C:\Users\kwhittem\Google Drive\DR\2013\8-15-13\primer blast results FCX3
p RCX3.txt"

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These tumor validation primers were received 1-28-13
Technical Datasheet
"C:\kurt\storage\CIM Research Folder\DR\2013\1-28-13\primers\Tumor
Validation Primers 1-28-13.pdf"

Working stock of primers located at 4 C box 1-29-13 KW
-3-21-13 these primers were labelled as 10 nM, but I am very confident
that they are actually 10 uM so I changed the labels on the tubes.

100 uM aliquots of RS8 and EATr primers located at 7-2-13 -20 C box

100 uM aliquots of some primers 9-10-13 (wikipad)

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