Capsicumgenomes contain rich epigenomic signatures, such as DNA methylation, histone modifications, topologically associated domains (TADs) and A/B compartments4. However, little is known about these epigenetic marks in centromeres and telomeres. Therefore, we mapped our own generated (Hi-C and whole...
REVEAL (REcursiVe Exact-matching ALigner) can be used to (multi) align whole genomes. INSTALL REVEAL is written in Python and C code. To build it, it needs Python version 2.7 and a GCC compiler. It uses libdivsufsort for suffix array construction and the probcons code for refinement of ...
To assess how the overall chromosome organization changes during meiosis, we quantified the chromatin contact probability on autosomes as a function of genomic separation (P(s)) for all isolated cell populations (Fig.2a, band Supplementary Figs.6–8). In Sertoli cells, the autosomal chromatin cont...
and only paired quality reads were retained for the subsequent analysis. The filtered reads for all individuals were aligned to the chicken reference genome (GRCg6a) using Burrows‒Wheeler Aligner (BWA) v0.7.17 [29]. The resulting Sequence Alignment Map (SAM) files were converted to Binary Al...
(N’s) and low-quality bases were trimmed from 5’ and 3’ read ends. Overlapping paired-end reads from ancient libraries were collapsed into a single read. Burrows-Wheeler Aligner (BWA) v0.7.15 (bwa-mem algorithm) was used to align reads. Reads were simultaneously aligned to the nuclear...
42 DPA Cnr mutant) (Additional file 8: Table S16-S17), and m6A deposition usually correlated with the decrease in gene expression (Fig. 4). Interestingly, the transcript of SlDML2, a DNA demethylase gene [37], exhibited higher m6A level in the fruit of Cnr mutant, concomitant with a ...
STAR: ultrafast universal RNA-seq aligner Bioinformatics, 29 (2013), pp. 15-21 CrossrefView in ScopusGoogle Scholar Donlin-Asp et al., 2017 P.G. Donlin-Asp, W. Rossoll, G.J. Bassell Spatially and temporally regulating translation via mRNA-binding proteins in cellular and neuronal function ...
(TDP-43)proteinopathy, and the haplotype's large-scaletranscriptomiceffects include the dysregulation of lysosomal genes and alterations in synapticgene splicingthat are also seen in the pathophysiology of TDP-43 proteinopathy. Further, a variant nearGRN, another TDP-43 proteinopathy susceptibility ...
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