A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-opted by Multiple HIV-1 Strains. A Virus-Packageable CRISPR System Identifies Host Dependency Factors Co-opted by Multiple HIV-1 Strains

The goal of this CRISPR-based screen (HIV-CRISPR) is to identify HIV-1 dependency factors by evaluating multiple pathways simultaneously. Here are Illumina sequencing data and counts files from HIV-CRISPR screens using a guide RNA library targeting the whole genome (TKOv3), a custom guide RNA library targeting human epigenome genes (HuEpi), a custom guide RNA library targeting interferon-stimulated genes (PIKA), and a custom guide RNA library of genes containing of a subset of each of the aforementioned libraries designed to target human dependency factors (HIVDEP). The HIV-CRISPR screens described here were performed in clonal ZAP knockout Jurkat cell lines as ZAP inhibition of the HIV-CRISPR vector has been previously described (PMID: 30520725). Overall design: These HIV-CRISPR screens were performed by generating a pool of ZAP-knockout Jurkat cells engineered to stably overexpress CCR5 and that are each knocked out for human genes using the TKOv3, HuEpi, PIKA, or HIVDEP guide RNA libraries. Each screen was performed in two biological replicates. Afterwards, for each condition, the cell pellets were harvested, genomic DNA (gDNA) was extracted, and sequencing was performed to evaluate the single guide RNA (sgRNA) representation of the library. Simultaneously, the viral supernatant was harvested, viral RNA (vRNA) was extracted, and sequencing was performed. By comparing the sgRNA representation of the viral RNA to the library representation of the genomic DNA, the sgRNAs that are depleted in the viral population are associated with potential HIV-1 dependency factors. The plasmid library of the HIV-CRISPR HIVDEP guide RNA library was also sequenced and included here. The plasmid guide libraries of the guide RNA libraries TKOv3, PIKA, and HuEpi have been sequenced before and are not included here.

本基于CRISPR（成簇规律间隔短回文重复序列）的筛选（HIV-CRISPR）旨在通过同时评估多条通路，鉴定HIV-1依赖因子。本数据集包含使用四类向导RNA（guide RNA, gRNA）文库开展HIV-CRISPR筛选得到的Illumina测序数据与计数文件：其一为靶向全基因组的TKOv3文库，其二为靶向人类表观基因组基因的自定义HuEpi文库，其三为靶向干扰素刺激基因的自定义PIKA文库，其四为靶向人类依赖因子、源自上述各文库子集的基因的自定义向导RNA文库（HIVDEP）。本次HIV-CRISPR筛选在克隆化ZAP敲除Jurkat细胞系中完成，因ZAP对HIV-CRISPR载体的抑制作用此前已有报道（PMID: 30520725）。
实验整体设计如下：本研究通过构建稳定过表达CCR5且分别利用TKOv3、HuEpi、PIKA或HIVDEP gRNA文库对人类基因进行敲除的ZAP敲除Jurkat细胞池，开展全部HIV-CRISPR筛选实验，每个条件均设置2次生物学重复。筛选完成后，针对每个实验组收集细胞沉淀、提取基因组DNA（gDNA）并进行测序，以分析文库中单向导RNA（single guide RNA, sgRNA）的占比；同时收集病毒上清液、提取病毒RNA（vRNA）并完成测序。通过对比病毒RNA中的sgRNA占比与基因组DNA中的文库sgRNA占比，可将病毒群体中丰度降低的sgRNA与潜在HIV-1依赖因子关联起来。
本研究还对本次HIV-CRISPR筛选所用的HIVDEP gRNA文库的质粒文库进行了测序并纳入本数据集；而TKOv3、PIKA及HuEpi gRNA文库的质粒文库此前已完成测序，故未重复纳入本次数据集。