主要是从GEO数据库搜集目前已发表的STARR-seq和MPRA数据,然后分别进行Enhancer peak calling ,鉴定具有enhancers和Epromoters活性的序列。 链接:https://www.jianshu.com/p/98ce9a3f3fe5 STARR-seq目前广泛应用于增强子活性检测。但传统的STARR-seq的准确性严重依赖于从报告基因reporter gene启动子开始的自转录mRNA的...
STARR-seq enterpriseNature Structural & Molecular Biology 20, 308 (2013). doi:10.1038/nsmb.2539Author: Beth MoorefieldNature Structural &
一种高通量的验证方法例如self-transcribing active regulatory region-sequencing(STARR-seq)能够对基因组范围内的CRMs进行大规模的评估。在STARR-seq中,基因组片段被打断并添加barcode,打断后的片段被克隆到报告基因的3’UTR区域,从而创建了一个报告基因库中衍生的RNA片段表明了CRMs的活性(图5B)。 https://zhuanlan.z...
STARR-seq enterprise. Nat Struct Mol Biol 20, 308 (2013). https://doi.org/10.1038/nsmb.2539 Download citation Published05 March 2013 Issue DateMarch 2013 DOIhttps://doi.org/10.1038/nsmb.2539 Springer Nature America, Inc. Access this article Log in via an institution Buy article PDF 39...
Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable” (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from...
In STARR-seq, each candidate therefore serves as its own barcode, and this direct coupling of candidate sequence and activity allows the parallel screening of highly complex candidate libraries (Arnold et al., 2013; Fig. 1, left). Figure 1 Open in figure viewerPowerPoint Step-wise schematic ...
D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074–1077 (2013). 6. Arnold, C. D. et al. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory ...
(http://kipoi.org/models/DeepSTARR/). Genome browser tracks showing genome-wide UMI-STARR-seq and DeepSTARR predictions inDrosophilaS2 cells, including nucleotide contribution scores for all enhancer sequences, together with the enhancers used for mutagenesis, mutated motif instances and respective ...
seq The index of header set in the input. input_length The sum of the length of the name/value pairs in the input. output_length The length of the compressed header block. percentage_of_original_size output_length / input_length * 100 wire The compressed header block as a hex string....
Activity Maps Identified by STARR-seqArnold, Cosmas DRath, MartinaStark, Alexander