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Open circle markers of small sizes (558, 930, 1,302, 1,674 bp) were designed using LoxP-directed cloning [ 46].
Gene-specific primers spanning a maximum of 150 bp were designed using Primer Express® software (Applied Biosystems).
Short amplicons (100 200 bp) were designed using the exemplar sequences available from Affymetrix NetAFFX[ 36] to amplify a region surrounding the 25-mer probe.
Primers with melting temperatures of 58 60°C and amplicon lengths of 150 250 bp were designed using Primer3 software (http://frodo.wi.mit.edu/primer3/input.htm).htm
Amplicons (50 to 100 bp) were designed using the program PrimerQuest (Integrated DNA Technologies, Coralville, IO) with parameters adjusted for GC content (40%) and maximum TM difference (1°C).
Expression levels of genes were determined by real-time quantitative RT-PCR and the corresponding primers for the amplification of targets between 75 and 150 bp were designed using Primer3plus software [ 55].
Similar(53)
Primers for amplifying a 100 150 bp product were designed using Primer3 [ 43] and synthesized by Sigma-Aldrich (St . Louis MO, USA).
For the J. curcas transcript data set, 41,651 sequence-specific probes of 60-bp oligonucleotides were designed using the Agilent eArray software (Additional file 5).
Gene-specific primers to generate 140-150 bPCRCR products were designed using the OligoPerfect™ (Invitrogen) software (Table 3).
The gabarapl1 primers used (forward: 5′-TTTGGTGCCCCTTATCTCAC-3′ reverse: 5′-GGCCATCATGTAGCATTCCTT-3′) for amplification of a 241-bp fragment (GenBank ) were designed using the Primer3 software (http://fokker.wi.mit.edu/primer3/input.htm).htm
Amplicons of ~200 bp containing the variants were designed using AssayDesigner software (SEQUENOM Inc., USA) with default parameters.
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