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PCR products containing inserts of more than 600 bp were sequenced with the Big Dye terminator ver.3 and analyzed using a 3730 ABI automated DNA sequencer (Applied Biosystems, Foster City, CA).
A total of 197,175,220 short reads (75 bp) were sequenced, with an average of 33 million reads per sample.
cDNA transcripts (2 × 100 bp) were sequenced with the Illumina HiSeq 2000 platform by McGill University and Genome Quebec Innovation Center.
Following the conditions detailed in Margulies et al. [ 6], PCR products (the amplicon size is about 1460 bp) were sequenced with the GS 20 platform (454 Life Science-Roche) using a titration 40 × 75 Picotitreplate™ (PTP) with eight regions.
Of these, 220 identified positive clones with a size range of 400 700 bp were sequenced with an ABI BigDye Terminator Cycle Sequencing Kit in an ABI PRISM 3770 automated sequencer (Applied Biosystems, Foster City, California, USA).
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A second, Mate-Paired (MP) DNA library with a mean insert size of 5100 bp was sequenced with 75 bp reads on an Illumina Hiseq2000 (Illumina Inc ., but only the first 50 bp were used to avoid chimeric reads.
A first Paired-End (PE) DNA library with an a mean insert size of 375 bp was sequenced with 50 bp reads on an Illumina Genome Analyzer IIx (Illumina Inc., San-Diego, USA).
A paired-end DNA library with a mean gap length size between 230 and 360 bp was sequenced, with average reads of 100 bp, on an Illumina HiSeq2500 apparatus (Illumina Inc., San Diego, CA, USA).
To characterize this strain, we amplified the RNA region encoding viral protein (VP) 1 by RT-PCR; the amplicon (821 bp) was sequenced with a BigDye Terminator v. 3.1 Cycle Sequencing Kit and an ABI PRISM 3730 DNA Analyzer (Applied Biosystems, Foster City, CA, USA).
Forty primer pairs were used to amplify fragments ranging in size from 351 bp to 1385 bp, which were sequenced with primers also indicated in the table [see Additional file 1].
Paired-end 50 bp reads were sequenced with the Illumina Hi-Seq 2000 platform.
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