Box: Oligo A
Location: 451 N Frear, nondefrosting freezer
Notes: Unless this is specifically stated, all of the oligonucleotides are dephosphorylated.  Red number on tube refers to box position.
1) TATA mutation, Oligo 1 2) -2 mutation, Oligo 2 3) Start site C 4) Start site D 5) Start site 1, oligo 221 6) Start site 2, oligo 222 7) hsp70A 8)hsp70 +26/+71
(hsp70A+)		 9) hsp70F
10) hsp70 Ntr -57 to -34 11) hsp70 Ntr -57 to +1 12) hsp70 +16/+71 13) hsp70B 14) hsp70C 15) hsp70D 16) hsp70E 17) hsp70 -89 18) Nuc.Tran.A
19) Nuc.Tran.B 20) 
HSP 70 GAGA-A		 21)
HSP 70 GAGA-B		 22) HA epitope A 23) HA epitope B 24) H1/H3 spacer A 25)
H1/H3 spacer B		 26)
HSE		 27)
Oligo 109
28)
Oligo 110		 29)Seq. primer 
Oligo111		 30) Rev. seq.primer Oligo113 31) Oligo 112 32) Oligo 223 33) Oligo 224 34) Oligo 225 35) Seq. primer 15mer 36) Beta Gal #1
37) Beta Gal #2 38) Histone H4 A 39) Histone H4 B 40) hsp26A 41) hsp26B 42) hsp26C 43) Sal1 linker 44) H3 primer 1 45) H3 primer 2
46) H3 primer 3 47) 
Linker B		 48) Sal linker A 49) Sal linker B 50)Xho1 linker, phosph. 51)Sal1 linker, phosph. 52)Xho1 linker, dephos. 53)Sal1 linker, dephos. 54)Seq.
primer Oligo 111
55) 
Linker A		 56) H1-PCR-A 57)
H1-PCR-B		 58)
+25/+30 mutation		 59)
+14/+19 mutation		 60)-50 GAGA Mutation 61)
+35 to +16 Txn		 62)
Linker A		 63)
Linker B
64)
Linker A'		 65)
TRY-D		 66)
TRY-A		 67)
TRY-B		 68)
TRY-C		 69) SalI linker
Phosphorylated		 70)SalI/NotI
primer 		 71)SalI/NotI
primer		 72) HSE-2
73)GA-I 74)GA-II 75)AvrII 30/35 76)AvrII
35/30		 77) 78)NcoI/NdeI
switch oligo
ID97		 79)Rev. Seq. ID98 80)pUC/M13 Forward
Promega		 81)pUC/M13 Forward
Promega

Description of contents:

Row 1 (return to top)
1)
 TATA mutation, Oligo 1: GCCTCTATTCATACTCCGG
From Wash U. It was used to generate the point mutation that changed TATA to TATG in hsp70. Extension is in the upstream direction.
2)
 -2 mutation, Oligo 2: GAATTGAATTCTCGCTCCGT
From Wash U. It was used to generate the point mutation that created the -2 mutant of hsp70. Extension is in the upstream direction.
3)
 Start site C (SSC, Synthesis file 03100903): TAGCGACGTGTTCACTTTGCTTGTTTGAATTGAATTGTCGCTCTTG
Oligo for affinity chromatography of start site of hsp70 extending from +35 to -10. From Wartik (10/9/90). Combine with oligo SSD to make a start site affinity column. 
4)
 Start site D (SSD, synthesis file 02100902): CTACGGAGCGACAATTCAATTCAAACAAGCAAAGTGAACACGTCG
Oligo for affinity chromatography of start site of hsp70 extending from -13 to +32. From Wartick (10.9.90). Combine with oligo SSC to make a start site affinity column. 
5)
 Start site 1, oligo 221: AATTCAATTCAAACAAGCAAAGTGAACACGTCGCT
Oligo for affinity chromatography of start site of hsp70, to be used in combination with oligo 222.  Extends from -1 to +34. From Wash U.
6)
 Start site 2, oligo 222: AATTAGCGACGTGTTCACTTTGCTTGTTTGAATTG
Oligo for affinity chromatography of start site of hsp70, to be used in combination with oligo 221.  The AATT at the 5' end is not hsp70. From Wash U. 
7)
 hsp70A (synthesis file 02012602): GTTCAGCTGCGCTTGTTTATTTGCTTAGC
+71 to +43. Used for genomic footprinting and selective labelling of +42 to +35. From Wartik (1/25/90).
8)
 hsp70 +26/+71 (hsp70A+, synthesis file 01100901): GTTCAGCTGCGCTTGTTTATTTGCTTAGCTTTCGCTTAGCGACGTG
+71 to +26. Used to selectively label +25 to +18. From Wartik (10-9-90).
9)
 hsp70F (synthesis file 02080802): GCTTGTTCAGCTGCGCTTGTTTATTTGC
+75 to +48. Used in genomic footprinting and for selectively labelling +47 and +46. From Wartik.
Row 2 (return to top)
10)
 hsp70 Ntr -57 to -34 (synthesis file 03052603): ATGTTCGCGAAAAGAGCGCCGGAG
Used to selectively label TATA region of nontranscribed strand. From Wartik. 
11)
 hsp70 Ntr -57 to +1 (synthesis file 01080401): ATGTTCGCGAAAAGAGCGCCGGAGTATAAATAGAGGCGCTTCGTCTACGGAGCGACAA
Used to selectively label initiator region of the nontranscribed strand. From Wartik. 
12)
 hsp70 +16/+71 (synthesis file 03021806): GTTCAGCTGCGCTTGTTTATTTGCTTAGCTTTCGCTTAGCGACGTGTTCACTTTGC
Used to selectively label transcribed strand. From Wartik.
13)
 hsp70B (synthesis file 03012603): GCTTAGCTTTCGCTTAGCGACGTGTTC
+49 to +23. Used for genomic footprinting. From Wartik (1/25/90).
14)
 hsp70C (synthesis file 02050805): CTTTAATCTTTAGAAGCGCAGCAATG
Hybridizes upstream of the hsp70 promoter near the Hpa1 site in the 2nd 132E3 variant. Prepared for genomic footprinting this copy. From Wartik (4/24/90).
15)
 hsp70D (synthesis file 03050803): GCGCAGCAATGTTTTGGCGG
Hybridizes upstream of the promoter near the Hpa1 site in the 2nd 132E3 variant. Prepared for genomic footprinting of this copy. Use with hsp70C. From Wartik (4/24/90).
16)
 hsp70E (synthesis file 01080801): GCAGATTGTTTAGCTTGTTC
Used for genomic footprinting endogenous hsp70 from downstream of the start. Does not pick up gamma elements. From Wartik. +87 to +68.
17)
 hsp70 -89 (synthesis file 03050306): GCCCCCTCGAGGGCTCTCGTTGG
Overlaps the upstream junction between vector and hsp70 in -89 clones. To be used in Pete's scheme for cloning specific 3' deletions. We were going to take products of sequencing reaction and amplify desired fragments with an LMPCR scheme. From Wartik (4/24/90).
18)
 Nuc.Tran.A (synthesis file 03052503): GGCCGACCTTGCGCTTCTTCTTGGGGGGCATTGTGC
Nuclear localization signal for Car20-ß-gal derivative. Idgunji cloned this along with Nuc. Tran. B into Car20 ZT.2
Row 3 (return to top)
19)
 Nuc Tran. B (synthesis file 02052502): GGCCGCACAATGCCCCCCAAGAAGAAGCGCAAGGTC
Nuclear localization signal for Car20-ß-gal derivative. Idgunji cloned this along with Nuc. Tran. A into Car20 ZT.2
20)
 HSP 70 GAGA-A (synthesis file 03071003): TCGATTCGAGGCGCGCTCTC
This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE. Baiyong now has this in his -20 box.
21)
 HSP 70 GAGA-B (synthesis file 03071203): TCGAGAGAGCGCGCCTCGAA
This was going to be used by P.Emanuel to introduce the GAGA sequence upstream of the -50 hsp70 and eliminate the HSE. Baiyong now has this in his -20 box.
22)
 HA epitope A (synthesis file 03041603): TCGACCCGGGTACGACGTCCCAGACTACGCCGGCTAG
Used by Idgunji in making HA epitope tagged histone H1 construct.
23)
 HA epitope B (synthesis file 02041602): TCGACTAGCCGGCGTAGTCTGGGACGTCGTACCCGGG
Used by Idgunji in making HA epitope tagged histone H1 construct.
24)
 H1/H3 spacer A (synthesis file 03091702): TTGTCCCGTACGACCTCTTC
Used by Idgunji when PCR amplifying and cloning H1/H3 spacers from different Drosophila cells lines.
25)
 H1/H3 spacer B (synthesis file 02091701): AGACGGACTTGCGATTCCAG
Used by Idgunji when PCR amplifying and cloning H1/H3 spacers from different Drosophila cells lines.
26)
 HSE (synthesis file 01082101/02): CTAGAAGCTT
Julio Coloma used it to make a very effective affinity column for the heat shock factor. There is some confusion concerning the synthesis file but the order # is correct. I think this synthesis was done twice because the first gave low yeild. From Wartik.
27)
 Oligo 109: AGAGAGAGAGAGAGAAAAGAGAGAG
GAGA affinity column, GA strand. Use with oligo 110. From Wash U.
Row 4 (return to top)
28)
 Oligo 110: TCTCTCTCTCTTTTCTCTCTCTCTC 
GAGA affinity column, CT strand. Use with oligo 109. From Wash U. 
29)
 Sequencing primer (Oligo 111): GACGTTGTAAAACGACGGCCAGT
Hybridizes adjacent to the EcoR1 site in pUC13 and extends towards the polylinker. From Wash U.
30)
 Reverse sequencing primer (Oligo 113): AACAGCTATGACCATGATTACG
Hybridizes adjacent to the HindIII site in pUC13 and extends towards the polylinker. From Wash U.
31)
 Oligo 112: GGTAGCAAATGCTCTGATCG
Thomas and Gilmour used it to make strand specific probes for Genomic footprinting. Spans from -23 to -4 on the histone H3 promoter. From Wash U. 
32)
 Oligo 223: AGAGAGAGAGAGAGAAAAGAGAGAG
For making GAGA affinity column, GA strand. Use with oligo 224. This was prepared on a 1umole scale. However, most of it was never purified. That which was not was found to be degraded when examined several years later. That in the box has been purified. From Wash U.
33)
 Oligo 224: TCTCTCTCTCTTTTCTCTCTCTCTC
For making GAGA affinity column, CT strand. Use with oligo 223. This was prepared on a 1umole scale. However, most of it was never purified. That which was not was found to be degraded when examined several years later. That in the box has been purified. From Wash U.
34)
 Oligo 225: CTAGAAGCTT
For making an HSF affinity column. This was prepared on a 1umole scale. Most of it was never purified. That in the box has been purified. However, the affinity column constructed from this oligo did not bind HSF at the high salt concentration expected of HSF. This is in contrast to the Oligo called HSE which was made at Penn State. The two are suppose to be the same sequence. From Wash U.
35)
 Sequencing primer 15 mer: TCCCAGTCACGACGT
Designed after primer from NEB for sequencing pUC and M13. Made at Wash. U., 0.5 pmole/ul. 
36)
 Beta Gal #1 (synthesis file 01011704): TCGACACGCGGCCGCACAATGCCTATTGGAATC
Used with Beta Gal #2 to introduce a linker with a Sal1 site and a translational start site upstream of ß gal in Car20ZT derivatives. From Wartik (1/11/90).
Row 5 (return to top)
37)
 Beta Gal #2 (synthesis file 02011705): GATCGATTCCAATAGGCATTGTGCGGCCGCGTG
Used with Beta Gal #1 to introduce a linker with a Sal1 site and a translational start site upstream of ß gal in Car20ZT derivatives. From Wartik (1/11/90).
38)
 Histone H4 A (synthesis file 03080803): CACTGTTCTATACTATTATACACGC
+50 to +26 of histone H4. Used for genomic footprinting. From Wartik. 
39)
 Histone H4 B (synthesis file 01080804): CACGCACAGCACGAAAGTCAC
+30 to +10 of histone H4. Used in Genomic footprinting. From Wartik. 
40)
 hsp26A: GATTGAAATATTTTTTCTTTGGTTAAG
+145 to +119 of hsp26. Used in genomic footprinting. From Wartik. 
41)
 hsp26B: CTTTGGTTAAGTTGAATGAACTT
+129 to +106 of hsp26. Used in genomic footprinting. From Wartik. 
42)
 hsp26C: CTTTGGTTAAGTTGAATGAACTTGTTTG
+129 to +102 of hsp26. Used in genomic footprinting. From Wartik.
43)
 Sal1 linker (synthesis file 01110701): GGTCGACC
Sal1 linker that has been used successfully. Dephosporylated. From Wartik. 
44)
 H3 primer 1 (H3-1, synthesis file 02051102): CTTTCCACCAGTCGATTTGC
+102 to +83 of histone H3. Used for genomic footprinting. From Wartik (5/10/91).
45)
 H3 primer 2 (H3-2, synthesis file 03051103): CGATTTGCGAGCAGTTTGCTTGGTACG
+90 to +64 of histone H3. Used for genomic footprinting. From Wartik (5/10/91).
Row 6 (return to top)
46)
 H3 primer 3 (H3-3, synthesis file 03051303): GCGAGCAGTTTGCTTGGTACGAGCC
+84 to +60 of histone H3. Used for genomic footprinting. From Wartik. (5/10/91).
47)
 Linker B (synthesis file 01012701): GAATTCAGATC
Mate for linker A or A' in ligation-mediated PCR. From Wartik (4/24/90).
48)
 Sal linker A (synthesis file 02050802): GCCAAGCTTGGGCGGTCGAC
Long oligo for ligation mediate PCR that introduces a Sal1 site. Ligate onto the 5' end of a blunted fragment and adds a Sal1 site. Use with Sal linker B. I think this was made for Emanuel to pursue our scheme for making deletions from fragments isolated from a sequencing gel. From Wartik (4/24/90).
49)
 Sal linker B (synthesis file 01050801): GTCGACCGCC
Mate for Sal linker A. I think this was made for Emanuel to pursue our scheme for making deletions from fragments isolated from a sequencing gel. From Wartik (4/24/90). 
50)
 Xho1 linker, phosphorylated (G253A): CCTCGAGG
From Fisher/Promega
51)
 Sal1 linker, phosphorylated (G241A): GGTCGACC
From Fisher/Promega
52)
 Xho1 linker, dephosphorylated (70885): CCTCGAGG
From USB
53)
 Sal1 linker, dephosphorylated (70870): GGTCGACC
From USB
54)
 Sequencing primer (Oligo 111): GACGTTGTAAAACGACGGCCAGT
Hybridizes downstream of the EcoR1 site in pUC13 and extends towards the polylinker. Diluted to 50 pmole/ul. From Wash U.
Row 7 (return to top)
55)
 Linker A (synthesis file 03020903): GCGGTGACCCGGGAGATCTGAATTC
Long oligo for ligation-mediated PCR. Ligates onto the 5' end of a blunted fragment. Adds Xma1, Sma1, BglII, EcoR1. Use with linker B. From Wartik.
56)
 H1-PCR-A (synthesis file 02041002): GGGCAGCGCGCGAGCC
PCR amplify N-terminal half of histone H1. Used by Idgunji to make epitope tagged H1.
57)
 H1-PCR-B (synthesis file 03041003): GGAGGAGACACCAATCTTC
PCR amplify N-terminal half of histone H1. Used by Idgunji to make epitope tagged H1.
58)
 +25/+30 mutation (synthesis file M1082504): AGTGACCTAGGCGCTAAGCGAAAG
Mutates the +25/+30 region of hsp70. Prepared for CloneTech mutagenesis by Kamara Thompson. Yield 1001 ug, mw = 7436.16; dissolved at 0.1 mM. From Wartik (8/31/94).
59)
 +14/+19 mutation (synthesis file M2082505): CAATTCAAACTTACTTAGTGAACACGTCGC
Mutating the +14/+19 region of hsp70. Prepared for CloneTech mutagenesis by Kamara Thompson. Yield 633 ug, mw = 9134.2; dissolved at 0.1 mM. From Wartik (8/31/94).
60)
 -50 GAGA Mutation (synthesis file M3082506): CTCGAGGCGATCGCGACGCCGGAG
Mutating the weak GAGA element at -50 in the -50 deletions of hsp70. Prepared for CloneTech mutagenesis. *Not dissolved. Yield 551 ug, mw = 7405.12. From Wartik (8/31/94).
61)
 +35 to +16 Txn (synthesis file M3082703): TAGCGACGTGTTCACTTTGC
Promoter proximal primer for Primer extension analysis of hsp70 in vitro transcription. Yield 1424 ug, mw = 6099.13. Dissolved in TE at 200 uM. Note that the label is rubbing off. From Wartik (8/31/94).
62)
 Linker A (synthesis file M2082702): GCGGTGACCCGGGAGATCTGAATTC
Long oligo for ligation-mediated PCR, New prep to supplement that in slot 55. Ligates onto the 5' end of a blunted fragment. Use with linker B. *Not dissolved. Yield 874 ug, mw = 7723.3 From Wartik (8/31/94).
63)
 Linker B (synthesis file M1082901): GAATTCAGATC
Short oligo for ligation mediated PCR, New prep to supplement that in slot 47. Mate for linker A in ligation-mediated PCR. *Not dissolved. Yield 348 ug, mw = 3340.33 From Wartik (8/31/94).
Row 8 (return to top)
64)
Linker A' primer: GCGGTGATTTAAAAGATCTGAATTC
Alternative linker primer for genomic footprinting. Tm differs from Linker A primer. A mate for Linker B. From Midland (4/6/93).
65)
 TRY-D: CGAAAATATAAGCTCAATC
Genomic footprinting, 5' to 3' transformed hsp70, matches rosy region. From Midland (7/30/93). 
66)
 TRY-A: GCTCAATCAAAAGAAGC
Genomic footprinting, 5' to 3' transformed hsp70, matches rosy region. From Wartik (10/28/92).
67)
 TRY-B: CAAAAGAAGCTTGGCTGC
Genomic footprinting, 5' to 3' transformed hsp70, matches rosy region. From Wartik (10/28/92). 
68)
 TRY-C: GAAGCTTGGCTGCAGGTCG
Genomic footprinting, 5' to 3' transformed hsp70, matches rosy region. From Wartik (10/28/92).
69)
  
70)
   SalI/NotI primer: CGAAGCTTGCGGCCGCGTGTCGACCGATTGTTTAGCTTG. From Ana-Gen Technologies, Inc (8/25/97).  This anneals to the junction between the hsp70 and ß gal sequences in our fly transformation constructs.  Kate Cilli used it in conjunction with the sequencing primer to amplify promoter inserts from an hsp70 XBS derivative and subclone as an XhoI/NotI fragment.  100 pmole/ul
71)
   SalI/NotI primer: CGAAGCTTGCGGCCGCGTGTCGACCGATTGTTTAGCTTG. From Ana-Gen Technologies, Inc (8/25/97).  This anneals to the junction between the hsp70 and ß gal sequences in our fly transformation constructs.  Kate Cilli used it in conjunction with the sequencing primer to amplify promoter inserts from an hsp70 XBS derivative and subclone as an XhoI/NotI fragment.  33 pmole/ul
72)
  HSE-2: CTAGAAGCTTCTAGAAGCTT.  From Wartik D2636 (5/20/94).  Self-anneals for producing HSF affinity column.
Row 9 (return to top)
73)
  GA-I: GATCGAAACAGAGAGCCAG.  From Wartik D2637 (5/20/94).  For use with a complementary DNA in making GAGA affinity column.
74)
  GA-II: GATCCTGGCTCTCTGTTTC.  From Wartik D2638 (5/20/94).  For use with a complementary DNA in making GAGA affinity column.
75)
  AvrII 30/35: AGTGAACACGCCTAGGAGCGAAAGCTAAGCA. From Ana-Gen Technologies, Inc. 100pmoles/ul.  For mutation +30 to +35 of hsp70
76)
  AvrII 35/30: AGCTTTCGCTCCTAGGCGTGTTCACTTTGCT. From Ana-Gen Technologies, Inc. 100pmoles/ul.  For mutation +30 to +35 of hsp70
77)
78)
  NcoI/NdeI switch oligo: GAGTGCACCATATGCGGTGTGAAAT.  From Wartik (9/11/95) ID 97
79)
  Rev. Sequencing primer: AACAGCTATGACCATGATTACG. From Wartik (9/12/95).
115 pmole/ul. ID 98
80)
  pUC/M13 Forward (Promega Q560B): CGCCAGGGTTTTCCCAGTCACGAC
81)
  pUC/M13 Forward (Promega Q560A): CGCCAGGGTTTTCCCAGTCACGAC
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