d, Representative Sanger sequencing traces of WT and HIC2 motifs edited HUDEP2 single cell clones. Mutations are indicated by red arrows. e, ChIP-qPCR of HIC2-HA in representative WT and HIC2 motifs edited HUDEP2 single cell clones. Results are mean ± s.d. (n = 3). Statistical tests...
8). In fact, since HiC-DC+ covariates such as GC content and mappability account for sources of systematic biases in high-throughput sequencing, we may already be implicitly correcting for a component of ChIP bias. Second, we systematically examined differential HiC-DC+ H3K27ac HiChIP results ...
First, even without a GFA file, HapHiC can still filter out collapsed contigs/unitigs based on the Hi-C sequencing depth. Second, artificially removing Hi-C links between haplotypes by using phasing information from the GFA files might lead to a certain degree of reduction in the anchoring ...
Razin. “Single-Cell Hi-C Bridges Microscopy and Genome-Wide Sequencing Approaches to Study 3D Chromatin Organization.” BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology 39, no. 10 (2017). https://doi.org/10.1002/bies.201700104. - scRNA-seq, review of the ...
Other mutations in MEF2B were discovered after whole genome-sequencing in mantle cell lymphoma [59]. In DLBCL, hot spot mutations of MEF2B occur in aa located within the MADS/MEF2 domains required for dimerization and DNA binding (K4, Y69, D83) (Fig. 1C). Other mutations affect the ...
(e) DNA methylation state of the miR-193a gene from the Methyl-cap-seq analysis, which are indicated as dark peaks. CpG dinucleotides and the BSP primers are also shown. (f) The original sequencing result of both strands of the PCR product of the bisulfite-converted DNA are shown. The...
HapHiC can achieve this without the need for reference genomes. Our evaluations indicate that HapHiC outperforms other Hi-C scaffolding tools with higher tolerance to low contig N50, low Hi-C sequencing depth, and various types of assembly errors. Additionally, HapHiC is super-fast and also su...
site 1-wt (include site 1 binding sequence), site 3-wt (include site 3 binding sequence) and site 4-wt (include site 4 binding sequence) in miR-23 ~ 27 ~ 24 promoter region, were inserted into the promoter region of pGL3 basic (Ambion), and the insertion was confirmed by sequencing...
where assay for transposase-accessible chromatin using sequencing (ATAC-seq), H3K27ac ChIP–seq and RNA sequencing (RNA-seq) data are available17,18. To minimize the effect of cell number variation on the performance of SnapHiC, we randomly selected the same number of cells (N = 261)...
In one embodiment, the analyzing comprises nucleic acid sequencing. In one embodiment, the method further comprises step d) comparing the join sequence to the genome. In one embodiment, the cell comprises a non-mammalian cell. In one embodiment, the non-mammalian cell comprises a cell selected ...