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Diluted libraries were clustered on two lanes (one library per lane) of a paired-end flowcell using cBot instrument and sequenced using HiSeq2000 sequencer with TruSeq SBS Kit v3-HS (Illumina, USA).
Four libraries were sequenced on one lane each and one library (Hanoverian 1) on two lanes of HiSeq2000 flowcell v3 (Illumina) in paired end mode (2 × 101 bp reads) using TruSeq SBS Kit v3-HS reagents (Illumina).
Each horse was run on one lane except one of the Hanoverians (Hanoverian 1) which was run on two lanes due to its importance for the Hanoverian breed.
Both replicates of the ZT8 and ZT20 time points were sequenced on two lanes and all other samples on one lane.
To generate single-end, 100-bp reads, Library I was sequenced on two lanes and Libraries II and III each in one lane on an Illumina HiSequation 2000 at the Genomic Sequencing and Analysis Facility at the University of Texas at Austin, Texas.
For sequencing by synthesis using the Illumina GA-II platform, cDNA libraries 708ES, 708PES and 773ES were run on two lanes per library while the 773PES library was run on one lane.
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The library was sequenced on three lanes of a flowcell from one end (single read) for 81 cycles on a Genome Analyzer IIx.
Libraries from one chip were pooled, and paired-end 100 bp sequencing was performed on four lanes of an Illumina HiSeq2000.
Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA).
These six samples were then multiplexed and sequenced on three lanes of an Illumina HiSeq 2000.
Sequencing was performed on four lanes of an Illumina NextSeq500, producing >160 million paired-end reads.
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CEO of Professional Science Editing for Scientists @ prosciediting.com