Computational analysis GeCKO v2 library (human)

<b>Table 1 - Non-specific sgRNAs GeCKO v2 (human). </b>This table represents the total of 5,664 sgRNAs within the entire GeCKO v2 library (half-libraries A and B combined) that recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. For the analysis, sgRNA target sites were aligned against the human reference genome (GRCh38/hg19 - primary assembly) using BLAT (v36) after optimisation of the algorithm for short length queries (-tileSize=6, -stepSize=3). The resulting alignments were further filtered to only include perfect matches and unique targets (exclusion of hits on alternative assemblies). Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.<br><b>Table 2 - Flagged genes GeCKO v2 (human).</b> This table represents the total of 775 genes for which more than half the corresponding sgRNAs within the entire human GeCKO v2 library (half-libraries A and B combined) are non-specific, i.e. recognise at least two identical target sites (20 bp protospacer + NGG PAM) within the reference genome. A threshold of &gt;50% non-specific sgRNAs per gene (e.g. 4 out of 6 for protein coding genes; 3 out of 4 for miRNA genes) was set in order to flag a group of sgRNAs. Analysis was performed using R (v3.2.3) in R studio (v1.0.136) using Ubuntu.

**表1 人源GeCKO v2文库的非特异性单向导RNA（single guide RNA, sgRNA）**
本表格涵盖了完整人源GeCKO v2文库（合并A、B半文库）中，在参考基因组内可识别至少2个完全相同靶位点（20 bp原间隔序列+NGG PAM，原间隔序列邻近基序，protospacer adjacent motif, PAM）的全部5664条sgRNA。
分析过程中，我们针对短序列查询优化算法（-tileSize=6、-stepSize=3）后，使用BLAT（v36）将sgRNA靶位点与人类参考基因组（GRCh38/hg19 - 主要组装版本）进行比对。所得比对结果将进一步筛选，仅保留完全匹配且为唯一靶位点的序列（排除比对至替代组装版本的序列）。本分析依托Ubuntu系统，在R Studio（v1.0.136）中通过R（v3.2.3）完成。

**表2 人源GeCKO v2文库的标记基因**
本表格涵盖了完整人源GeCKO v2文库（合并A、B半文库）中，对应sgRNA有半数以上为非特异性的全部775个基因，即这些基因的sgRNA可在参考基因组内识别至少2个完全相同靶位点（20 bp原间隔序列+NGG PAM）。我们设定单基因非特异性sgRNA占比＞50%的阈值（例如蛋白编码基因需满足6条sgRNA中≥4条为非特异性；miRNA基因需满足4条sgRNA中≥3条为非特异性），以此完成sgRNA组的标记。本分析依托Ubuntu系统，在R Studio（v1.0.136）中通过R（v3.2.3）完成。