PCRs for new Membranipora and Priapulus primers
Cloning newly collected genes of Membranipora and Priapulus. Selected genes and primers:
Membranipora:
Mm PIWIL1 R1 CCGTTGTTGACCTGATGCCACTTTCG Mm PIWIL1 R2 ACGATGTGATGCTCTCCCTGCTCCATTACC Mm DDX4 R1 TCTCTGTGTCTTGTCTGGCATACCCATCG Mm DDX4 R2 CAGTCACCTTTCTCGGGTTTGGACACTCTC Mm AGO2 F CTTCGCACCTCAGAGGGTAG Mm AGO2 R CTGGCCCTGAAAGCTACAAG Mm MEX3 F CCAGTGAGAGGAGCTGAACC Mm MEX3 R CATCACCACCACACAAGAGG Mm MAGOH F TCCGCCATTCTTTCTCTTTG Mm MAGOH R TGGTTGAATGCAAGATGGAA
Priapulus:
Pc PiwiA F GGGTCTTATTCTTTGTTTGC Pc PiwiA R TTCACGACACCATCGCAG Pc PiwiB R1 TGCGATACTGCCGACCATCTTCTTGTCC Pc PiwiB R2 ACGGGATGTGATGGGCTGTAACCTTTCG Pc Tudor R1 TCCACAAAATAGTAGGCAAGGCAAGGGCTC Pc Tudor R2 ACGCAACAGATGAACACCTCTACGGCTTGG Pc Mael F1 CGTGAAAGAGAGCTGGTCCAGTCAGAATGG Pc Mael F2 CACCGCTTCATAGCTCCAGGTGAAATCC Pc Mael R1 GCGGTGAAATTCCCTCATAATGCCCTTCTC Pc Mael R2 TGGACCAGCTCTCTTTCACGCTTATTTCG Pc Pum F1 ATGAACGCAGTGCCTTGGAACGACTCTCAC Pc Pum F2 GCAGGACGATGCTATGGTCGGCTATTTC
01/03/2012
Regular and first round of RACE with the above primers.
02/03/2012
Second round of RACE. Run a gel with only 5 µL of each to identify bands to be cut from RACE and direct purify the products of the regular PCR. Ran another gel with the remaining product to cut the bands*. Extracted promising bands and set the ligation reaction at 22:30.
- Did not like this procedure. It is better to run the RACE PCR in 10 comb gel with whole 25 µL to get more signal and extract more.
03/03/2012
Heat-shock transformation and plating. Also ligation for remaining bands (Mm PIWIL1, Pc Tudor 2,3,4, Pc PUM).
04/03/2012
05/03/2012
Colony PCR for the remaining bands and repetition for some that there was no positive colonies.
06/03/2012
Plasmid extraction using 1.5 mL of miniprep culture, sequencing reaction, and dropped at the sequencing facility.
08/03/12
Sequences BV25-BV64 returned.
BV25 | Membranipora membranacea | Argonaute2 | T7 | ok | + | SP6 |
BV26 | Membranipora membranacea | Argonaute2 | T7 | ok | + | SP6 |
BV27 | Membranipora membranacea | Mago Nashi | T7 | ok | – | T7 |
BV28 | Membranipora membranacea | Dicer1 | T7 | ok | + | SP6 |
BV29 | Membranipora membranacea | Dicer1 | T7 | ok | + | SP6 |
BV30 | Membranipora membranacea | Germ Cell Less R2 | T7 | ok | – | T7 |
BV31 | Membranipora membranacea | PiwiL1 R2 b2 | T7 | ok | – | T7 |
BV32 | Membranipora membranacea | PiwiL1 R2 b2 | T7 | ok | + | SP6 |
BV33 | Priapulus caudatus | PiwiB R2 b2 | T7 | ok | – | T7 |
BV34 | Priapulus caudatus | Tudor R2 b1 | T7 | ok | – | T7 |
BV35 | Priapulus caudatus | Maelstrom F2 | T7 | ok | + | SP6 |
BV36 | Priapulus caudatus | Maelstrom F2 | T7 | ok | – | T7 |
BV37 | Priapulus caudatus | Tudor R2 b2 | T7 | ok | – | T7 |
BV38 | Priapulus caudatus | Tudor R2 b2 | T7 | ok | – | T7 |
BV39 | Priapulus caudatus | Tudor R2 b3 | T7 | ok | – | T7 |
BV40 | Priapulus caudatus | Tudor R2 b3 | T7 | ok | + | SP6 |
BV41 | Priapulus caudatus | Tudor R2 b4 | T7 | ok | + | SP6 |
BV42 | Priapulus caudatus | Tudor R2 b4 | T7 | ok | + | SP6 |
BV43 | Priapulus caudatus | Pumilio F2 | T7 | ok | + | SP6 |
BV44 | Priapulus caudatus | Pumilio F2 | T7 | ok | – | T7 |
BV45 | Membranipora membranacea | Argonaute2 | SP6 | ok | – | SP6 |
BV46 | Membranipora membranacea | Argonaute2 | SP6 | ok | – | SP6 |
BV47 | Membranipora membranacea | Mago Nashi | SP6 | ok | + | T7 |
BV48 | Membranipora membranacea | Dicer1 | SP6 | ok | – | SP6 |
BV49 | Membranipora membranacea | Dicer1 | SP6 | ok | – | SP6 |
BV50 | Membranipora membranacea | Germ Cell Less R2 | SP6 | ok | + | T7 |
BV51 | Membranipora membranacea | PiwiL1 R2 b2 | SP6 | ok | + | T7 |
BV52 | Membranipora membranacea | PiwiL1 R2 b2 | SP6 | ok | – | SP6 |
BV53 | Priapulus caudatus | PiwiB R2 b2 | SP6 | ok | + | T7 |
BV54 | Priapulus caudatus | Tudor R2 b1 | SP6 | ok | + | T7 |
BV55 | Priapulus caudatus | Maelstrom F2 | SP6 | ok | – | SP6 |
BV56 | Priapulus caudatus | Maelstrom F2 | SP6 | ok | + | T7 |
BV57 | Priapulus caudatus | Tudor R2 b2 | SP6 | ok | + | T7 |
BV58 | Priapulus caudatus | Tudor R2 b2 | SP6 | ok | + | T7 |
BV59 | Priapulus caudatus | Tudor R2 b3 | SP6 | ok | + | T7 |
BV60 | Priapulus caudatus | Tudor R2 b3 | SP6 | ok | – | SP6 |
BV61 | Priapulus caudatus | Tudor R2 b4 | SP6 | ok | – | SP6 |
BV62 | Priapulus caudatus | Tudor R2 b4 | SP6 | ok | – | SP6 |
BV63 | Priapulus caudatus | Pumilio F2 | SP6 | ok | – | SP6 |
BV64 | Priapulus caudatus | Pumilio F2 | SP6 | ok | + | T7 |