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Transcriptome libraries of 155 bp were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer's LT protocol.
Paired-end libraries (100 × 2 bp) were prepared using the TruSeq RNA Sample Preparation Kit (Illumina), following the manufacturer's instructions.
richardii (average insert size = 300 bp) were prepared using the Illumina TruSeq library preparation kit (Illumina, San Diego, CA) and run together on a second lane of Illumina HiSeq 2500.
Paired-end libraries with different insert sizes (300 and 800 bp) were prepared using the protocol provided by Illumina.
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A single genomic library with an insert size of approximately 300 bp was prepared using the Illumina Sample Preparation Kit and sequenced for 100 cycles with the Illumina HiSeq 2000 (paired-end) at the UMCG Sequencing Facility in Groningen, The Netherlands.
A strand-specific RNA-seq library with an insert size ranging from 120 to 300 bp was prepared using NEXTflex Directional dUTP-Based RNA-Seq Kit (Bioo Scientific).
DNA-seq paired-end libraries with a 250-bp insert were prepared using the TruSeq DNA Sample Preparation Kit (Illumina) according to the manufacturer's instructions.
For each sample, paired-end libraries with approximately 200-bp inserts were prepared using the Illumina TruSeq DNA Sample Preparation Kit (Illumina Inc., San Diego, CA).
Prior to exome enrichment 300 to 400 bps libraries were prepared using the TruSeq DNA Sample Prep Kit (Illumina, San Diego, CA, USA).
For each endophyte DNA sample, paired-end libraries with inserts c. 400 bp in size were prepared using the standard protocol (TruSeq DNA Sample Prep V2 Low Throughput: Illumina Inc., San Diego, USA) with paired-end adaptors.
250 and 500 bp paired-end libraries were prepared using enzymes from NEBNext Modules and following Illumina TruSeq DNA sample preparation guide.
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