我们进一步表明,与标准ATAC-seq相比,Tn5切割位点频率保留在ATAC-STAR质粒文库中,从而能够从ATAC-STARR数据中确定TF结合。通过这种方法,我们发现激活子和沉默子通过不同的转录因子footprint combinations聚集在一起,这些活性组类代表了免疫细胞功能的不同基因调控网络。总之,这些数据突出了ATAC-STARR-seq从单一DNA片段来源...
③ SCENIC+还通过计算基于STARR-seq信号的前10%排名的恢复曲线下面积(AUC),评估了Signac、pycisTopic和ArchR识别的DARs,以及pycisTopic识别的细胞系特异性主题区域的增强子恢复能力。④ SCENIC+的基序数据库构建流程包括从29个基序集合中收集34,524个独特基序,并通过两步策略进行聚类。使用隐马尔可夫模型(HMMs)对输入区...
Most gene regulatory activity occurs within accessible chromatin, and recently described methods have combined assays that capture these regions鈥攕uch as assay for transposase-accessible chromatin using sequencing (ATAC-seq)鈥攚ith self-transcribing active regulatory region sequencing (STARR-seq) to ...
To do this, we combined assay for transposase-accessible chromatin using sequencing (ATAC-seq) with self-transcribing active regulatory region sequencing (STARR-seq); we call this method ATAC-STARR-seq. With ATAC-STARR-seq, we identify both active and silent regulatory elements in GM12878 B ...