While we have demonstrated the utility of 3D-seq for population-level and single-cell mapping of DPIs involving bacterial transcription factors under standard laboratory growth conditions, we envision that its unique features will catalyze additional applications. In particular, the ability to modulate Dd...
Integration of single-cell transcriptomes and diffusion map analysis of HSPCs fromTP53-sAML patients showed thatTP53multihit HSPCs clustered separately fromTP53-WT pre-LSCs in two distinct populations with enrichment of LSC and erythroid-associated transcription, respectively (Fig.2aand Supplementary Table3...
A transcription factor, PbWRKY24, contributes to russet skin formation in pear fruits by modulating lignin accumulation Letter to the Editor|15 Oct 2024|OPEN Disruption ofClOSD1leads to both somatic and gametic ploidy doubling in watermelon ...
The evaluation considers aspects such as the extent of mixing between different omics, cell type conservation, single-cell level alignment accuracy, trajectory preservation, scalability, and ease of use. Tools/methods compared: scMVP, MOFA+, MultiVI, Cobolt, scDART, UnionCom, MMD-MA, scJoint, ...
We sorted cells into two populations (top and bottom 10%) based on the expression level of pluripotency markers (TRA-1-60 and SSEA4), as a proxy for differentiation, and sequenced the TF barcodes. Despite even TF distributions in the initial libraries (skew = 5), the distributions became...
No classical TATA-box sequence was found, but a number of other potential transcription factor binding sites could be identified (Fig.2 B), suggesting that the TGX promoter is a TATA-less promoter. Interaction of CCAAT/enhancer-binding protein (may bind to CAAT box), nuclear factor I (NF1...
(3) advanced analysis at the level of peaks, motifs, nucleosomes, and TF footprints, and (4) integration with multiomics data to reconstruct regulatory networks. These steps will allow researchers to conduct robust analysis on ATAC-seq data and generate more biological meaningful results. Finally...
(Fig.2E, Venn diagram). We observed that the RPM per L1 locus detected using scRNA-Seq positively correlates with L1 FPKM determined using bulk RNA-Seq (r = 0.51,P < 0.0001, Fig.2E). Comparing the bulk RNA-Seq FPKM level of the 11 L1 loci that were not detected to be ...
These counts were similar to those reported by other studies [1, 2] suggesting that our results are consistent at chromosome level. We hypothesize that these multifractal behaviors might be explained by different repetitive DNA contents in the human genome, similar to the results found in C. ...
(1:1). In addition,CbuSPLhad more isoforms in Tb than in Vb in both the EF and NF buds. The above results imply that AS events may have an important role in floral transition inC. bungei. These observations indicate that AS greatly increases the complexity of gene transcription inC. ...