gRNA database of the <i>Capsella bursa-pastoris </i>accession PGL0001 (alias ‘msu-wt’) and list of homoeolog gene pairs (1-to-1) for analyzed genome.

The database contains a comprehensive set of characteristics for gRNA spacer sequences, including calculated metrics for on-target (DeepSpCas9 and DeepHF) and off-target (CFD and MIT) activity for the knockout of genes from the <i>C. bursa-pastoris</i> accession PGL0001 (alias 'msu-wt') genome (GCA_001974645.2 GenBank). The sequences have been prefiltered according to the specified set of thresholds:The spacer's GC composition should be between 20-80%The spacer should be located within the 5-65% of the CDS of the geneThe spacer should not contain polyT sequences (four or more T sites)The spacer should not have sequence complementarity with the sgRNA hairpin backbone of SpCas9 or itselfThe spacer should not be located at overlapping sites of coding regions of different genesThe spacer cut site should be located in CDS region of all coding isoforms of a target gene;DeepSpCas9 and DeepHF on-target scores should be at least more than 0.2 and aggregated CFD off-target score (for all targets with maximum 3 mismatch) should be at least more than 0.2.Homoeolog pairs were identified with orthofinder software.本数据库包含一套针对gRNA间隔序列（gRNA spacer sequences）的全面特征集，涵盖了针对播娘蒿（<i>C. bursa-pastoris</i>）品系PGL0001（别名‘msu-wt’）基因组（GenBank登录号GCA_001974645.2）中基因敲除实验的靶标活性（on-target activity）与脱靶活性（off-target activity）的计算指标，其中靶标活性指标包括DeepSpCas9与DeepHF，脱靶活性指标包括CFD与MIT。 该数据集的序列已按照下述预设阈值完成预筛选： 1. 间隔序列的GC含量需处于20%至80%区间内； 2. 间隔序列需位于靶基因编码区（Coding Sequence, CDS）的5%至65%区域内； 3. 间隔序列不得包含连续4个及以上胸腺嘧啶（T）的polyT序列； 4. 间隔序列不得与SpCas9的单向导RNA（single-guide RNA, sgRNA）发夹骨架或自身存在序列互补性； 5. 间隔序列不得位于不同基因编码区的重叠区域； 6. 间隔序列的切割位点需处于靶基因所有编码同工型的CDS区域内； 7. DeepSpCas9与DeepHF的靶标活性评分均需不低于0.2，且针对所有错配数不超过3的靶位点的汇总CFD脱靶活性评分同样需不低于0.2。 同源同祖基因对（homoeolog pairs）通过OrthoFinder软件完成鉴定。