Useful Links

​SLD  (Stamm lab plasmid and reagent collection)

​NEB Builder (Gibson cloning)

BLAT (sequence analysis at UCSC browser)

Primer 3 (design primers)

Oligocalc (oligonucleotide properties calculator)

NEB Tm calculations (Q5 annealing temperatures)

Human Splicing Finder (find splice sites, branch points and regulatory motifs, contains links to other prediction sites)

RNA precipitation

Salt                          Concentration of stock solution       Final concentration
NaOAc, pH 5.2                              3M                                                    300 mM
NH4Ac                                         5M                                                    500 mM
KAc, pH 5.2                                  3M                                                    300 mM
LiCl                                              8M                                                    800 mM

Alcohol volume for precipitation after salt addition
Ethanol (100%)               2.2 –2.5 volumes
Isopropanol                     0.6-1 volumes

Glycogen addition for low RNA concentrations: 100 µg/ml (1/100 Volume of a 10 mg/ml stock soln.)

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Minimum RNA Polymerase Promoter Sequences (5’->3’)

The first nucleotide of the RNA (+1) is in capital letter
T7: taatacgactcactataGgg
T3: aattaaccctcactaaaGgg
SP6: atttaggtgacactataGaa