Direct selection of human genomic loci by microarray hybridization. Nat. Methods 4, 903–905 (2007) | Okou, D. T. et al. Microarray- based genomic selection for high-throughput resequencing. Nat. Methods 4, 907–909 The technological advance that laid the essential groundwork for whole-...
(WGS). Sequencing of the entire genome without using methods for sequence selection. Two-fluorophore system A system in which bases are discriminated by labelling Cs and Ts with a red or green fluorophore, respectively. Each A base is labelled with either a red or green fluorophore, but the ...
Despite the promise of Nanopore sequencing to deconvolute RNA modifications, the standard direct RNA-seq approach of using poly(A) selection during Nanopore library preparations, limits the capture of many ncRNAs that constitute the vast majority of known and conserved editing substrates [23,32,42,43...
Individual cells are the basic substrates for the mechanisms of mutation and selection at work to evolve complex structures known as tumor blocks. For this reason, gaining insights into individual carcinoma cells under the individual condition and, overall, into dynamically related systems of ...
Ewing G, Hermisson J: MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus . Bioinformatics. 2010, 26 (16): 2064-2065. 10.1093/bioinformatics/btq322. Article PubMed Central PubMed CAS Google Scholar Meyer M, Kircher M, Gansauge ...
Furthermore, we created sequencing libraries from the original plasmid templates and using several different RNA selection methods (rRNA depletion, polyA selection, and no selection). We found that both rRNA depletion and polyA selection are responsible for a significant portion of this coverage bias,...
Selection of representative variant-gene pairs used for optimization SURGE optimization (i.e., learning the SURGE latent contexts) requires an input expression matrix and genotype matrix. As specified above, both matrices should be of dimension\(N\)X\(T\), where\(N\)is the number of RNA sam...
Version of inDrop built from the second iteration of the gel beads dsDNA: Double-stranded DNA TruDrop: TruSeq-inDrop library structure that builds upon the inDrop V2 beads i7: Illumina’s acronym for the first index i5: Illumina’s acronym for the second index PhiX: a control libr...
There are also two mutations that lie in two distinct DNA mismatch repair proteins, and two mutations in two outer membrane proteins, OmpV and OmpH. In order to identify purifying or positive selection between the N16961 reference and the Haitian/Dominican Republic V. cholerae strains, we ...
demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and ...