ArticlePloS one2013
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication.Genome biology and evolution · 2023Article
- CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.Genome research · 2023Article
- The acidic amino acid-rich C-terminal domain of VanabinX enhances reductase activity, attaining 1.3- to 1.7-fold vanadium reduction.Biochemistry and biophysics reports · 2022Article
- Article
- Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family.Plant physiology · 2021Article
- Article
- Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower.Genetics · 2020Article
- The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome.Frontiers in genetics · 2019Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- The genetic architecture of UV floral patterning in sunflower.Annals of botany · 2017Article
- Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.Nature communications · 2017Article
- Rapid gene isolation in barley and wheat by mutant chromosome sequencing.Genome biology · 2016Article
- The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.RNA (New York, N.Y.) · 2015Article
- Biological invasions, climate change and genomics.Evolutionary applications · 2015Review
- Elucidating the genetic basis of antioxidant status in lettuce (Lactuca sativa).Horticulture research · 2015Article
- Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts.BMC genomics · 2014Article
- Article
- Separating homeologs by phasing in the tetraploid wheat transcriptome.Genome biology · 2013Article
- Article
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7 authors.
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Abstract
Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
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