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1,977 results for “CRISPR”
Single-cell RNA-seq of the embryonic zebrafish heads from wild-type siblings and betaPix CRISPR mutants at 1 dpf and 2 dpf
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Data from: A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1
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Strains and constructs for: A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites
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Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance
<p>CRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR-Cas9 screens using <i>TP53</i> wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and <i>TP53</i> knockout human retinal pigment epithelial cells using a focused dual guide RNA library targeting 852 DDR-associated genes. Our work demonstrates that although functional p53 status negatively affects identification of significantly depleted genes, optimal screen design can nevertheless enable robust screen performance. Through analysis of our own and published screen data, we highlight key factors for successful screens in both wild-type and p53-deficient cells.</p>
Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK
<p>One of the most foundational aspects of ecological studies and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype-based identification. The CRISPR-Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently developed CRISPR-Cas13a platform SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) enables highly accurate taxonomic identification and has all the characteristics needed to transition to ecological and environmental disciplines. Here we conducted a series of proof of principle experiments to characterize SHERLOCK's ability to accurately, sensitively, and rapidly distinguished three fish species (two with protected status and one non-native) co-occurring in the San Francisco Estuary which are easily misidentified in the field. We improved SHERLOCK's ease of field deployment by combining its rapid isothermal amplification and CRISPR genetic identification with a minimally invasive and extraction-free DNA collection protocol as well as the option of instrument-free lateral flow detection. This approach opens the door for redefining how, where and by whom genetic identifications occur in the future.</p>
Data from: CRISPR-Cas9 mediated CD133 knockout inhibits colon cancer invasion through reduced epithelial-mesenchymal transition
We previously reported that CD133, as a putative cancer stem cell marker, plays an important role in cell proliferation and invasion in colon cancer. To understand the role of CD133 expression in colon cancer, we evaluated the inhibitory effect of CD133 in colon cancer cells. In this study, we generated CD133knockout colon cancer cells (LoVo) using the CRISPR-Cas9 gene editing system. CD133+ colon cancer cells (LoVo) were infected with the lentiviral vector carrying CD133 gRNA and purified cell by culturing single cell colonies. CD133knockout cells was validated by western blot and flow cytometry analysis. In functional study, we observed a significant reduction in cell proliferation and colony formation in CRISPR-Cas9 mediated CD133 knockout cells in compare with control (P < 0.001). We also found the anticancer effect of stattic was dependent on CD133 expression in colon cancer cells. Although CD133knockout cells could not completely block the tumorigenic property, they showed remarkable inhibitory effects on the ability of cell migration and invasion (P < 0.001). In addition, we examined the epithelial mesenchymal transition (EMT)-related protein expression by western blot. The result clearly showed a loss of vimentin expression in CD133knockout cells. Therefore, CRISPR-Cas9 mediated CD133knockout can be an effective treatment modality for CD133+ colon cancer through reducing the characteristics of cancer stem cells.
CRISPR-Cas12a-integrated transgenes in genomic safe harbors retain high expression in human hematopoietic iPSC-derived lineages and primary cells
<p>We identified and characterized potential integration safe harbor sites (SHS) in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these genomic sites in iPSC, primary T and NK cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation capabilities of engineered iPSC towards CD34+ hematopoietic stem and progenitor cells (HSPC), lymphoid progenitors (LPC), and natural killer (NK) cells, and showed that transgene expression was retained in these lineages. </p>
Datasets for: CRISPR-TE designing for mouse L1Md Families
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Phenotypically active ORF and CRISPR consensus profiles
This hosts the files on phenotypically active genes for JUMP, derived from https://zenodo.org/records/14025602 after filtering samples with no matches above a given threshold (see filenames for thresholds).
CRISPR-Cas9 dataset of isogenic cell lines
<p>A collection of CRISPR-Cas9 isogenic (RB1, BRCA1, BRCA2) cell lines screens.</p>
NGS Data from: Improved gRNA secondary structures allow editing of target sites resistant to CRISPR-Cas9 cleavage
<p><span><span>We engineered gRNAs with highly stable hairpins in their constant parts and further enhanced their stability by chemical modifications. The 'Genome-editing Optimized Locked Design' (GOLD)-gRNA increases genome editing efficiency up to around 1000-fold (from 0.08% to 80.5%) with a mean increase across different other targets of 7.4-fold. The related NGS data is deposited </span></span>here.</p>
Mitochondrial and ER membrane protein trafficking CRISPR screens
<p><span>The trafficking of specific protein cohorts to the correct subcellular location at the correct time is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or FACS. To broadly empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identify genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. </span>We show that loss of the SUMO E1 component SAE1 results in the mislocalization and destabilization of mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.</p>
Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: viruses, plasmids, and more
<p>Supplementary Table 2-1. Samples and assembly summary <br> Supplementary Table 2-2. CRISPR-targeted TR sequence summary</p>
Data for Eirew et al Accurate determination of CRISPR-mediated gene fitness in transplantable tumours
<p>Derived counts files and experimental metadata for Eirew et al Accurate determination of CRISPR-mediated gene fitness in transplantable tumours.</p>
PRISMA Checklist for for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
<p>PRISMA Checklist for for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.</p>
PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
<p>PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.</p>
PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
<p>PRISMA Checklist for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.</p>
StArt Protocol for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
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Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Microscope images - Xist act KDs]
<p>Microscope images related to Figure 5 in Schwämmle et al. 2025. </p> <p>The cells are day 2 differentiated TX1072 XX SP427 mESCs with the indicated knockdowns. (-2iLIF)</p> <p>Exonic Xist is stained using Cy5 Stellaris probes. The nuclei are stained using DAPI.</p> <p>These files were used to perform automated image analysis to detect and quantify Xist clouds (https://github.com/EddaSchulz/TFiScreen_Paper).</p>
Data from: Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum
Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ~2% of ancestral poultry strains and a nucleotide substitution rate of 0.8 – 1.2 X 10-5 per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches, there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ~50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.