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The genomic DNA associated with ChIP'd samples was then sequenced using a genome analyser (ChIP-SEQ) to identify the C/EBPδ are C/EBPβ binding sites throughout the genome.
All libraries were sequenced in single read mode, using a Genome Analyser instrument (Illumina).
The cDNA libraries were sequenced using a Genome Analyser (GAIIx) in a paired-end approach with 2 × 36 cycles resulting in paired reads with a length of 36 nucleotides per read.
The libraries were sequenced using a Genome Analyser (GAIIx, Illumina, San Diego, CA, USA) in a single read approach with 76 cycles resulting in reads with length of 76 nucleotides.
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Seven pools of RNA samples, representing each treatment and the control sample, which was common for all three treatments, were used to build libraries for high-throughput parallel sequencing using an Illumina Genome Analyser II (GAIIx).
A total of five libraries were multiplexed per sequencing reaction using an Illumina Genome Analyser II next-generation sequencer at the Weill Medicine School Sequencing Facility Cornell Universityy, New York City, NY, USA).
Sequence data: Targeted whole-exome sequencing was carried out for 31 (12 + 19) samples using an Illumina Genome Analyser IIx.
Two separate cDNA libraries were created from 1 μg RNA and sequenced by GATC Biotech AG (Konstanz, Germany) using an Illumina/Solexa Genome Analyser to create single-end reads of 101 bp length (80.5 million reads for T-oaks and 124.8 million reads for S-oaks; Solexa reads available at the SRA at EMBL-EBI [EMBL: ERP002577]).
Both libraries were sequenced by GATC Biotech AG (Konstanz, Germany) using an Illumina/Solexa Genome Analyser to create single-end reads of 36 bp length (12.5 million reads for T-oaks and 12.3 million reads for S-oaks; Solexa reads available at the Short Read Archive (SRA) at EMBL-EBI [EMBL: ERP002577]).
For whole transcriptome sequencing, we used an Illumina Genome Analyser II with 36 bp sequence reads length.
Libraries were sequenced on a Genome Analyser II as 54 bp paired-end reads.
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