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DBD-thiocarbamoyl (TC -amino acids generaTC -aminoe modified sequencing method were sepacidsd on the reversed phase or Pirkle type chiral stationary phase column and then oxidized to DBD-CA-amino acids with hydrogeneratedide as a post-column reagent and detected fluorimetrically.
Samples were digested overnight with modified sequencing grade trypsin (Promega, Madison, WI), Glu-C (Worthington, Lakewood, NJ), or chymotrypsin (Roche, Switzerland).
The 16 and 40 gel pieces were distained, washed and after treatment with DTT and iodoacetamide alkylation, Protein-containing gel slices were treated with trypsin (modified sequencing grade; Promega) and extracted according to the manufacturer's instructions (Promega).
Purified asMIP ligation products were amplified with modified sequencing primers (described above).
The modified sequencing grade trypsin was from Roche (Mississauga, ON, Canada).
Endopeptidase trypsin (modified, sequencing grade) was purchased from Promega (Madison, WI, USA).
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Immunization with selected modified sequences lowered immunogenicity for particular peptides and revealed residual immunogenicity of incompletely de-immunized modified peptides.
Four modified sequence specific primers (SSP) pairs were designed for the selective amplification of coeliac disease associated alleles (DQA1*05, DQB1*02, DQB1*03 02 alleles), and human growth hormone (positive control).
Gel pieces were then subjected to a modified in-gel trypsin digestion procedure [30], followed by washing and dehydration with acetonitrile for 10 min. After removal of acetonitrile, gel pieces were completely dried in a speed-vac, and rehydrated with 50 mM ammonium bicarbonate solution containing 12.5 ng/µl modified sequencing-grade trypsin (Promega, Madison, WI) at 4°C.
Other modified sequences, CA-TG and modified sequences I and II, are also listed under the basic sequence.
We prepared two modified DNA sequences in which 5'-CA-3' and 5'-GT-3' were removed from the 6x segment: modified sequence I and modified sequence II (Fig. 1, modified I and II).
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