Project description: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).
Project description:This dataset contains single cell RNAseq of human iPSCs undergoing cytokine-mediated differentiation alongside targeted CRISPR-mediated endogenous gene activation. For this experiment we sequenced single cells at day 10 of the differentiation protocol, when the cells undergo the endothelial-to-hematopoietic transition described in the paper Petazzi et al, BiorXiv DOI 10.1101/2022.10.04.510611 The dataset contains four libraries: (1) iSAM line infected with non-targeting guide RNA, (2) iSAM line infected with non-targeting guide RNA treated with Dox, (3) iSAM line infected with targeting guide RNAs library, (4) iSAM line infected with targeting guide RNAs library treated with Dox
Project description:We design a porcine genome-scale CRISPR/Cas9 knockout (PigGeCKO) library containing 85,674 single guide RNAs targeting 17,743 protein-coding genes, 11,053 long ncRNAs, and 551 microRNAs. Subsequently, we use the PigGeCKO library to identify key host factors facilitating JEV infection in porcine cells.
2020-09-21 | GSE158247 | GEO
Project description:Whole genome sequencing of guide+donor transformants
Project description:BLaER1 cells are human leukemia pre-B cells able to transdifferentiate into functional and non-tumorigenic macrophages. With the goal of uncovering the genes involved in the transdifferentiation process, we have designed a DECKO (Double Excision CRISPR Knockout) library to knockout lncRNAs and protein coding genes (pc-genes) overexpressed along the seven days the process lasts. We have seen that targeting pc-genes with two gRNAs synergistically enhances the efficiency of knock out, by inducing deletions and/or frameshifts that promote the expression of non-functional proteins. Thus, using the CRISPETa tool, we designed paired guide RNAs targeting either the region surrounding the Transcription Start Site of the 166 lncRNAs or the coding exons of the 874 pc candidate genes. Cas9-expressing BLaER1 cells were infected at low-multiplicity of infection with the combined library and induced transdifferentiation. Delayed and differentiated subpopulations of cells were isolated by Fluorescence-Activated Cell Sorting at 3 days and 6 days after induction, and pgRNAs were sequenced in an Illumina HiSeq2500 instrument. The sequencing reads were mapped and quantified to uncover the enriched pgRNAs found in each subpopulation. Among all genes targeted in the library, we identified twenty pc-genes and six lncRNAs as strong candidates to be involved in the process, as the pgRNAs targeting their loci were enriched in the delayed population compared to the differentiated one, either at 3 days or at 6 days after transdifferentiation induction. From these, we selected two pc-genes and two lncRNAs for deeper characterization.
Project description:We present Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a novel methodology that utilizes barcoded rAAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track the in vivo lineage contribution of gene targeted HSPC clones. By targeting the HBB gene with a rAAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-only, lymphoid-only, and multi-lineage repopulating human HSPC clones in immunodeficient mice.