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A DNA probe of 1300 bp was generated using the DIG-PCR amplification kit (Roche, Switzerland) with the primers 5'-GAA GAG CCG AAT CCA CAT and-3' and 5'-CTG GCG CTG CTG CCA CTC-3' and the full length human PLEKHA7 cDNA as template.
All sequences were downloaded from GenBank (Sept , 2004 except for SSR sequences kindly provided by Dr. Ben Burr, Brookhaven National Laboratories, NY). Based on the results, a database of primer sets with predicted product sizes of 600-800 bp was generated using Primer3 [ 41] to design primer pairs in the 3' or 5' termini of unigenes from G. arboreum ESTs [ 42].
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DNA fragments of 500 1,000 bp were generated using PCR.
Paired-end sequences (101 bp) were generated using three lanes of an Illumina HiSeq2000 flow cell (Ilumina Inc. San Diego, CA, USA).
Single end reads with a length of 100 bp were generated using a HiSeq2000 (Illumina) at the Australian National University (Canberra, Australia).
A total of 6,710,574 high-quality paired-end reads of 2 × 36 bp were generated using Illumina GAIIx from the selected cDNA.
An assembly of 66,508 transcripts (>200 bp) were generated using short-read Illumina RNA-Seq libraries constructed from feeding, reproductive, and defensive polyps of H. symbiolongicarpus.
In parallel, a total of 4 602 723 scaffolds and contigs consisting of 1 301 006 845 bp were generated using SOAPdenovo v1.05 and GapCloser 1.10.
For Illumina sequencing, paired-end libraries (2 × 250 bp) were generated using Nextera v2 technology and sequenced by the MiSeq system according to the manufacturer's protocol (Illumina), which resulted in about 180-fold coverage on average.
A total of 8,862,831 single-end reads with an average length of 33 bps were generated using the Solexa Genome Analyzer (Illumina, Little Chesterford, Essex), giving a 63.9× coverage.
Am-tra2 dsRNA-2, encompassing the region from 108 to 499 bp (392 bp long), was generated using oligonucleotides #591 and #592 (Table S1 and Figure S1) from cloned cDNAs of transcript Am-tra2.
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