Ethan's Oligos

	A	B	C	D	E	F	G	H	I	J	K	L	M	N
1	Name	oligo ID	Location	Sequence (5' -> 3')	Date created	Date ordered	Order details	Purification	Scale	Notes	Lab notebook	Arrival Date	PCR Product	PCR Product length
2	pFC8tac_tac_promoter_Primer_1	oEH1	E1	GCAGAACGGCACAACAGC	7/29/21	7/29/21	146853411	STD	25nm	Amplifies tac promoter of pFC plasmids	7-29-21.md	8/2/21
3	pFC8tac_tac_promoter_Primer_2	oEH2	E2	GTATTACCGCCTTTGAGTGAGCTG	7/29/21	7/29/21	146853411	STD	25nm	Amplifies tac promoter of pFC plasmids	7-29-21.md	8/2/21
4	pFC9_t7_primer_1	oEH3	E3	CCCGCCGCGCTTAATG	7/29/21	7/29/21	146853411	STD	25nm	Amplfies t7 promoter of pFC plasmids	7-29-21.md	8/2/21
5	pFC9_t7_primer_2	oEH4	E4	GCCCCAATGCGAGCGG	7/29/21	7/29/21	146853411	STD	25nm	Amplfies t7 promoter of pFC plasmids	7-29-21.md	8/2/21
6	pFC8_t7_primer_2	oEH5	E5	GAAGGGGCAGTAGCACAGTCC	7/29/21	7/29/21	146853411	STD	25nm	Amplifies t7 promoter of pFC8 when used with pFC9_t7_primer_1	7-29-21.md	8/2/21
7	VRI_primer_1	oEH6	E6	TACGACTCACTATAGGGCGAATTGG	7/29/21	7/29/21	146853411	STD	25nm	Amplfies any variable region insert fragment	7-29-21.md	8/2/21
8	VRI_primer_2	oEH7	E7	CCTCCTCGCCTCGGTCAC	7/29/21	7/29/21	146853411	STD	25nm	Amplfies any variable region insert fragment	7-29-21.md	8/2/21
9	VR-BglII-targeting	oEH8	E8	CATGAAGGGCGCGCCAAGATC	9/22/21	9/22/21		STD	25nm	Amplifies inserts that contain BglII sites		9/22/21
10	pFC9-T7-C-deam	oEH9	E9	TAATATGATTTATTATAGGGTG	1/3/22	1/3/22		STD	25nm	Targets bisulfite treated (assuming 100% efficient C->T conversion) T7 promoter sequence
11	pFC9-C-deam-rev	oEH10	E10	TATTGTTGTAGGGGTTGTAGAAATG	1/3/22	1/3/22		STD	25nm	Reverse primer to be used with `pFC9-T7-C-deam` for		1/5/22	Do not use, was designed by converting top strand C -> T then making both primers. This method will not work since strands are not complementary after bisulfite treatment
12	pFC9BisP3Fwd	oEH11	F1	GTTTTAAAGTTTTTTGTTTTGGAGAA	1/10/22	1/10/22		STD	25nm	Reverse primer to be used with `pFC9-T7-C-deam` for		1/13/22	GTTTTAAAGTTTTTTGTTTTGGAGAATTAGATTCGGAATGTTTAGAGGTTTGTTGTTGTGTCGTTTTGTTTCGATGGTATTTTGTTCGTTCGTATTGGGGCGCGTTTTTTATTCGTTTTTAATTGTGGTGTCGCGATAGGTTTTATTGCGGGTGTTTGCGGTGGGAAGGGCGGTGGTGATTGGGAGTATGCGGGGTAATCGTAGTGGGTAAGGGATATGGGTGGAGGTGGGTATATTAGGGTGATTGTAGTTTCGTGTGGCGAGGGTACGTGGGGGGATTAGTGTATAGGGATTTTA	298
13	pFC9BisP4Rev	oEH12	F2	TAAAATCCCTATACACTAATCCCC	1/10/22	1/10/22		STD	25nm	amplification of deaminated produc		1/13/22	GTTTTAAAGTTTTTTGTTTTGGAGAATTAGATTCGGAATGTTTAGAGGTTTGTTGTTGTGTCGTTTTGTTTCGATGGTATTTTGTTCGTTCGTATTGGGGCGCGTTTTTTATTCGTTTTTAATTGTGGTGTCGCGATAGGTTTTATTGCGGGTGTTTGCGGTGGGAAGGGCGGTGGTGATTGGGAGTATGCGGGGTAATCGTAGTGGGTAAGGGATATGGGTGGAGGTGGGTATATTAGGGTGATTGTAGTTTCGTGTGGCGAGGGTACGTGGGGGGATTAGTGTATAGGGATTTTA	298
14	tac_init_fwd_primer	oEH13	F3	AATCATCGGCTCGTATAATGGGTACCCAAACACTCCCTCGG	See https://github.com/EthanHolleman/plasmid-VR-design/releases/tag/v2.0	1/10/22		STD	25nm	Forward primer for amplification of inserts from T7 init series for Gibson into pFC8(53)TacT1T2		1/12/22
15	tac_init_rev_primer	oEH14	F4	TCGTTTTATTTGATGCCTGGAAGCTTCTGATGCCCCCTCCTCTACA	See https://github.com/EthanHolleman/plasmid-VR-design/releases/tag/v2.1	1/10/22		STD	25nm	Reverse primer for amplification of inserts from T7 init series for Gibson into pFC8(53)TacT1T2		1/21/22
16	pFC9_Nt.BspQI_nick	oEH20	F9	TACGACTCACTATAGGGCGAATTGG	1/24/22	1/24/22		STD	25nM	Sanger sequencing primer for testing Sanger seq validation of nicks. Targets ~150 bp downstream of Nt.BspQI site present in pFC9 and other pFC plasmids.		1/27/22
17	oEH15_Cas9_validator	oEH21	F10	GCCGCCAAAGTCCACCAC	1/24/22	1/24/22		STD	25nM	Sanger sequencing primer for validating nicks produced by Cas9 nickase enzyme using oEH15 as the sgRNA.		1/27/22
18	oEH16_Cas9_validator	oEH22	G1	GCCGCCAAAGTCCACCAC	1/24/22	1/24/22		STD	25nM	Sanger sequencing primer for validating nicks produced by Cas9 nickase enzyme using oEH16 as the sgRNA.		1/27/22
19	oEH17_Cas9_validator	oEH23	G2	GCGCAGCGAGTCAGTGAGC	1/24/22	1/24/22		STD	25nM	Sanger sequencing primer for validating nicks produced by Cas9 nickase enzyme using oEH18 as the sgRNA.		1/27/22
20	oEH19_Cas9_validator	oEH24	G3	CGATAGTTACCGGATAAGGCGC	1/24/22	1/24/22		STD	25nM	Sanger sequencing primer for validating nicks produced by Cas9 nickase enzyme using oEH19 as the sgRNA.		1/27/22
21	oEH_61_Cas9_validator	oEH64		CCAATACCCACTGTCGCCG
22	RT-qPCR-p0	oEH65		AATTCGTCGCAGTGACCGAG	3/14/22	3/14/22		STD	25nM	RT-qPCR primer designed against pFC9VR1 for Cas9 nickase transcription efficiency tests		3/23/22
23	RT-qPCR-p1	oEH66		GCGACCACCAACACAACCC	3/14/22	3/14/22		STD	25nM	RT-qPCR primer designed against pFC9VR1 for Cas9 nickase transcription efficiency tests		3/23/22
24	RT-qPCR-p2	oEH67		GGAGGCTATGGCAGTGGACC	3/14/22	3/14/22		STD	25nM	RT-qPCR primer designed against pFC9VR1 for Cas9 nickase transcription efficiency tests		3/23/22
25	RT-qPCR-p3	oEH68		CCCAGCCACTTCCTACGGA	3/14/22	3/14/22		STD	25nM	RT-qPCR primer designed against pFC9VR1 for Cas9 nickase transcription efficiency tests		3/23/22
26	RT-qPCR-T8-0-F	oEH69		GCTTCAGCTTTTGTTCCCTTT	3/19/22	3/21/22		STD	25nM	RT-qPCR primer downstream of sgRNA8 site.		3/23/22
27	RT-qPCR-T8-1-R	oEH70		AATACGCAAACCGCCTCTC	3/19/22	3/21/22		STD	25nM	RT-qPCR primer downstream of sgRNA8 site.		3/23/22
28	RT-qPCR-T8-2-F	oEH71		GCTTCCTCGCTCACTGACTC	3/19/22	3/21/22		STD	25nM	RT-qPCR primer downstream of sgRNA8 site.		3/23/22
29	RT-qPCR-T8-3-R	oEH72		AACCGTATTACCGCCTTTGA	3/19/22	3/21/22		STD	25nM	RT-qPCR primer downstream of sgRNA8 site.		3/23/22
30	RT-qPCR-T11-0-F	oEH73		GGGGTTGTGTTGGTGGTC	3/19/22	3/21/22		STD	25nM			3/23/22
31	RT-qPCR-T11-1-R	oEH74		CCGCCAATACCCACTGTC	3/19/22	3/21/22		STD	25nM			3/23/22
32	RT-qPCR-T11-2-F	oEH75		GTGGTGGGGGTTGTGTTG	3/19/22	3/21/22		STD	25nM			3/23/22
33	RT-qPCR-T11-3-R	oEH76		CCGCCAATACCCACTGTC	3/19/22	3/21/22		STD	25nM			3/23/22
34	RT-qPCR-T9-0-F	oEH77		AGGCCAGGAACCGTAAAAAG	3/19/22	3/21/22		STD	25nM			3/23/22
35	RT-qPCR-T9-1-R	oEH78		TTGAGCGTCGATTTTTGTGA	3/19/22	3/21/22		STD	25nM			3/23/22
36	RT-qPCR-T9-2-F	oEH79		AGGCCAGGAACCGTAAAAAG	3/19/22	3/21/22		STD	25nM			3/23/22
37	RT-qPCR-T9-3-R	oEH80		AGGCCAGGAACCGTAAAAAG	3/19/22	3/21/22		STD	25nM			3/23/22
38	RT-qPCR-T4-0-F	oEH81		ATACCTGTCCGCCTTTCTCC	3/19/22	3/21/22		STD	25nM			3/23/22
39	RT-qPCR-T4-1-R	oEH82		CGAACGACCTACACCGAACT	3/19/22	3/21/22		STD	25nM			3/23/22
40	RT-qPCR-T4-2-F	oEH83		GGATACCTGTCCGCCTTTCT	3/19/22	3/21/22		STD	25nM			3/23/22
41	RT-qPCR-T4-3-R	oEH84		CGAACGACCTACACCGAACT	3/19/22	3/21/22		STD	25nM			3/23/22
42	RT-qPCR-T7-0-F	oEH85		ACTGTGGTGGTGGTGCTTTT	3/19/22	3/21/22		STD	25nM			3/23/22
43	RT-qPCR-T7-1-R	oEH86		GCTTATCGATACCGTCGGATT	3/19/22	3/21/22		STD	25nM			3/23/22
44	RT-qPCR-T7-2-F	oEH87		TACTGTGGTGGTGGTGCTTT	3/19/22	3/21/22		STD	25nM			3/23/22
45	RT-qPCR-T7-3-R	oEH88		GCTTATCGATACCGTCGGATT	3/19/22	3/21/22		STD	25nM			3/23/22
46	RT-qPCR-AMP-1-F	ttgttgccgggaagctagag		ttgttgccgggaagctagag	6/12/23	6/12/23
47	RT-qPCR-AMP-1-R	gtgacaccacgatgcctgta		gtgacaccacgatgcctgta	6/12/23	6/12/23
48	RT-qPCR-AMP-2-F	aataaaccagccagccggaa		aataaaccagccagccggaa	6/12/23	6/12/23
49	RT-qPCR-AMP-2-R	ctctagcttcccggcaacaa		ctctagcttcccggcaacaa	6/12/23	6/12/23
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69	RT-qPCR-AMP-1-F	ttgttgccgggaagctagag
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