Database issue D119–D127doi: 10.1093/nar/gkw1054R-loopDB: a database for R-loop forming sequences(RLFS) and R-loopsPiroon Jenjaroenpun 1 , Thidathip Wongsurawat 1 , Sawannee Sutheeworapong 2 and VladimirA. Kuznetsov 1,3,*1 Department of Genome and Gene Expression Data Analysis, Bio...
Jenjaroenpun P, Wongsurawat T, Sutheeworapong S, Kuznetsov VA. R- loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Res. 2017;45:D119-d127.Jenjaroenpun, P., Wongsurawat, T., Sutheeworapong, S. & Kuznetsov, V. A. R-loopDB: a database for ...
构建了首个集R-loop分布与调控于一体的数据库R-loopBase,从统一不同检测技术的共性以鉴定高置信度的R-loop形成区域,到对R-loop调控蛋白的系统梳理和注释等方面做出了相应的信息整合与可视化呈现,为
(e-f) The expression of SSB1 (e) and SSB2 (f) across tissues using GTEx database. (g) Growth curves of parental and CTR DLD-1 cells. Data are mean ± SD from 4 independent experiments. (h) Western blotting of whole-cell extracts from parental and CTR DLD-1 cells. Tubulin is a...
Data acquisition and processing Three single-cell RNA-seq (scRNA-seq) datasets of patients with LUAD and associated clinical information were collected from the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/: GSE123904, GSE131907, and GSE146100). Moreover, an indep...
(Supplementary Fig.1B). SYCP2 is known to be present in normal tissues except testis, where SYCP2 functions in meiosis18,19. In the TCGA database, SYCP2 expression is significantly higher in breast tumors than in adjacent breast tissue (Fig.1D). We found that DNA hypomethylation at two...
Protein-protein interactions of R-loop-regulated cell-type-specific genes (as shown in Figure 2C) were analyzed by STRING database (version 11.0) (Szklarczyk et al., 2016). Then, the PPI networks were visualized by Cytoscape (version 3.7.2) (Shannon et al., 2003). ChIP-Seq Data Proce...
A genomic annotation for the UCSC mouse genome build GRCm38/mm10 (file knownGene.txt.gz) was downloaded from the site (ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/). Data for 3′UTR regions were added with the UCSC genePredToGtf tool. To assess read coverage distribution ...
(HAT) repeats shared by proteins involved in RNA processing15,16. Disruption of theXab2gene results in pre-implantation lethality in mice17. Thus, there are currently no available data to address the functional role of XAB2 in transcript maturation and the DNA damage response (DDR) in vivo....
Q.S. initiated the project, and supervised the data analysis together with X.Y.; Q.S. and W.X. developed the ssDRIP-seq method and W.X. performed all experiments; W.X., H.X., K.L., Y.L. and Y.F. analysed the data; W.X., H.X., X.Y. and Q.S. prepared the figures...