Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1161603 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mammalian genomes host a diverse array of RNA that includes protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using massively parallel RNA-targeting CRISPR Cas13 screens, we probed how loss of ~6,200 lncRNAs impacts cell fitness across five human cell lines and identified 778 lncRNAs with either context-specific or broad essentiality. We observe a high level of consistency between distinct guide RNAs targeting the same lncRNA in the pooled screens and confirm their essentiality with individual perturbations. We find that the overwhelming majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that essential lncRNAs modulate key cellular pathways for proliferation and that their loss can impair cell cycle progression and drive apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development and, using ~9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.
2024-11-15 | GSE281460 | GEO
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).
2023-01-26 | GSE223326 | GEO
Project description:To profile the cell states of interacting natural killer (NK) cells and blood cancer cells, we cultured 26 different cell lines representing diverse hematologic neoplasms either alone or with NK cells derived from three healthy human donors. After 24 h co-culture, we labeled the cells from each monoculture or co-culture condition with oligonucleotide-conjugated antibodies against ubiquitously expressed surface proteins (with different oligonucleotide for each mono- or co-culture), enabling multiplexing in the scRNA-seq using the cell hashing method. We additionally performed pooled CRISPR screens with a single-cell transcriptome readout using the CROP-seq platform in blood cancer cells cultured either alone or in the presence of NK cells to study the effects of perturbing genes that influenced sensitivity to NK cell killing in genome-scale CRISPR screens.
2023-07-24 | E-MTAB-13204 | biostudies-arrayexpress
Project description:The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases such as cancer. To extend the catalog of human core and context- dependent fitness genes, we have developed a high-complexity second-generation genome-scale CRISPR-Cas9 gRNA library and applied it to fitness screens in five human cell lines. Using an improved Bayesian analytical approach, we consistently discover 5-fold more fitness genes than were previously observed. We present a list of 1,580 human core fitness genes and describe their general properties. Moreover, we demonstrate that context-dependent fitness genes accurately recapitulate pathway-specific genetic vulnerabilities induced by known oncogenes and reveal cell-type-specific dependencies for specific receptor tyrosine kinases, even in oncogenic KRAS backgrounds. Thus, rigorous identification of human cell line fitness genes using a high-complexity CRISPR-Cas9 library affords a high-resolution view of the genetic vulnerabilities of a cell. Additional data can be found at tko.ccbr.utoronto.ca RNAseq of five human cell lines with Cas9 knock-ins.
2015-11-25 | E-GEOD-75189 | biostudies-arrayexpress
Project description:Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted multiple genome-scale CRISPR screens for essential CTCF loop anchors in the human K562 erythroid cell line. Surprisingly, the primary drivers of apparent ``hits'' in this screen were single guide RNAs (sgRNAs) with low sequence specificity. After removing these confounders, we found that no CTCF loop anchors among the ones we screened are essential for cell growth in culture. We also observed analogous effects in independent non-coding screens densely tiling regulatory elements and genomic neighborhoods near previously known essential genes. Strikingly, we found that low-specificity guides also result in strong confounding growth effects in screens employing epigenetic perturbations that do not cause DNA damage, such as CRISPRi and CRISPRa. Remarkably, the set of confounded guides is distinct for each perturbation mode. Promisingly, strict filtering of CRISPRi libraries using GuideScan-aggregate specificity scores removed these confounded sgRNAs and allowed for the identification of essential enhancers, which we validated extensively. Our stduy presents the first genome-scale functional characterization of CTCF binding sites in the human genome, while also identifying the limitations on and outlining the future prospects for the detailed functional dissection of regulatory elements in the genome using Cas9.
2019-07-01 | GSE131349 | GEO
Project description:Genome-wide CRISPR screens identified lncRNAs that promote cell proliferation in HeLa, Huh7, and MCF7 cells
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Project description:Resistance to the first approved BCL-2 inhibitor venetoclax is emerging in lymphoid malignancies. The study aimed to identify the genetic determinants of such resistance. From genome-scale screens we determined the genes influencing the sensitivity to BCL-2 inhibition. The present set of data is related to expression changes (assessed by RNA sequencing) observed in the resistant OCI-Ly1 lymphoma cell line as well as those resulting from genetic perturbation (using CRISPR-Cas9) targeting the genes highlighted in our genome-scale screen.
2019-09-25 | GSE128563 | GEO
Project description:Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging essential genes (EGs) that are indispensable for hPSC fitness, defined as cell reproduction in this study. To map essential genetic determinants of hPSC fitness, we performed genome-scale loss- of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and laminin to identify EGs. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSC EGs are substantially different from other human model cell lines, and EGs in hPSCs are highly context dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated genetic regulators of hPSC biology.
2020-08-15 | GSE156284 | GEO
Project description:Pooled CRISPR screens in human intestinal organoids [CRISPR screens]
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Project description:All bulk CRISPR based screens CD2 and B2M CRISPRi tiling screens (primary human CD8 T cells), IL2RA CRISPRa tiling screens (Jurkats), CRISPRi/a TF screens (primary human CD8 T cells), and CRISPR TFome KO (primary human T cells)
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