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247 results for “CRISPR/Cas9”
SpEDIT: A fast and efficient CRISPR/Cas9 method for fission yeast
<p>Underlying data and extended data for:</p> <p><em>SpEDIT</em>: A fast and efficient CRISPR/Cas9 method for fission yeast</p>
Genome editing of LKB1 gene by CRISPR/Cas9 in lung cancer cells and evaluation of its role in metformin and cisplatin response.
<pre>LKB1 is an important upstream inhibitor of the mTOR/S6Ks pathway. Loss of LKB1 is often associated with cancer, including in A549 lung cancer cell line, boosting the transformation of pre-malignant neoplasic cells. Metformin, a natural compound derived from Galega officinalis, is mainly used as a treatment for diabetes mellitus type 2 (DM2), but recently, it has been associated to lower incidence of cancer. One of the main mechanisms is by activation of AMPK through different pathways, including LKB1 activation. Activation of AMPK inhibits the mTOR pathway, protein synthesis and thus cell growth. The combination of metformin and cisplatin, a main chemothepeutic drug for lung cancer, has shown to improve treatment of cancer cells to cisplatin and also to hinder the cisplatin associated resistance common in lung cancer. Here we aim to use the CRISPR/Cas9 technology to correct the mutation presented in A549 lung cancer cells and improve their response to metformin or to the combination between metformin and cisplatin. Besides, we will assess the mTOR signaling pathway status, as well as cell growth, proliferation, cell cycle and sensitivity to apoptosis induction by cisplatin. This project may be useful as a proof of principle that in the future therapies must consider the genomic background of cancer cells before administration of a specific anticancer drug.<br><br></pre>
Data from: Highly efficient generation of germline mutations using CRISPR/Cas9 in the speckled wood butterfly Pararge aegeria
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Programmable CRISPR/Cas9
<p>To verify certain analyses, the raw data file and replicates of samples were compiled in an Excel document, along with the inclusion of several gel photos</p>
Sequencing data for Flp-In T-Rex HeLa PINK1 CRISPR/CAS9 knock-out (CVCL_D5JI)
<p>PCR and sequencing data (.ab1 and .seq files) for CRISPR-Cas9 PINK1 knockout HeLa cells (clone 3C9) described in <a title="doi link" href="https://doi.org/10.1098/rsob.210264">doi.org/10.1098/rsob.210264</a>. Knock-out generated using the following guides (targeting exone 2), available from MRC-PPU Reagents and Services, University of Dundee: DU52528 and DU52530 (CRISPR Project #CR252). This cell line has been deposited to Cellosaurus: CVCL_D5JI.</p>
Data set - Photosynthetic light harvesting and thylakoid organization in a CRISPR/Cas9 Arabidopsis thaliana LHCB1 knockout mutant.
<p>This data set was produced at the University of Neuchâtel, it cointains the raw data relative to the manuscript entitled "Photosynthetic light harvesting and thylakoid organization in a CRISPR/Cas9 Arabidopsis thaliana LHCB1 knockout mutant."</p> <p>The report presents the difference in terms of protein accumulation, light harvesting, electron transport and thylakoid structure between the WT line (Col0) of <em>Arabidopsis thaliana </em>and a newly generated line that contains multiple mutations in all the genes coding for the light harvesting protein LHCB1, named L1ko.</p> <p>Paper_raw_data.xlsx contains the data utilised to produce the figures presented in the paper.</p> <p>Fluorescence_data.xlsx contains the raw fluorescence traces in excel format for three experiments. The data of the measurments performed with the multispeq are also available here: https://photosynq.org/projects/etr_in_lab_test_protocols</p> <p>Chloroplasts_TEM_WT_L1KO.zip contains all the electron microscopy pictures, at full resolution analysed for the report.</p> <p> </p> <p> </p>
Quantification of transgene expression in GSH AAVS1 with a novel CRISPR/Cas9 based approach reveals high transcriptional variation
<p>Inderbitzin, Loosli and colleagues employ a novel method to construct and extensively characterize DNA barcode libraries and apply CRISPR/Cas9 technology for targeted insertion into the safe harbor gene AAVS1 in Jurkat cells. This technique revealed high fluctuations in gene expression in AAVS1, spanning over two logs.</p>
Protocols for marker-free gene knock-out and knock-down in Kluyveromyces marxianus using CRISPR/Cas9
<p>This file contains the CRISPR targets predicted for every gene in the NBRC1777 genome, you can use it to design primers to target the gene you are interested in. There is one folder per gene. The 'sgRNAcas9_report' file contains a list of all the predicted sites, their position in the gene, and other extra information (e.g. GC content, off targets, etc..). The 'TargetSeq.fa' file contains the sequence of the gene targeted. For more information see <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100448">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100448</a></p>
CRISPR/Cas9 screen for essential endolysosomal genes under free choline limitation
<p>Lysosomes degrade macromolecules and recycle their nutrient content to support cell function and survival. Yet, the machineries involved in lysosomal recycling of many nutrients remain to be discovered, with a notable example being choline, an essential metabolite liberated via phospholipid degradation. Here, we engineered metabolic dependency on lysosome-derived choline in pancreatic cancer cells to perform an endolysosome-focused CRISPR-Cas9 screen for genes mediating lysosomal choline recycling. We identified the orphan lysosomal transmembrane protein SPNS1 as critical for cell survival under choline limitation. SPNS1 loss leads to intralysosomal accumulation of lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE). Mechanistically, we reveal that SPNS1 is a proton gradient-dependent transporter of LPC species from the lysosome for their re-esterification into phosphatidylcholine in the cytosol. Finally, we establish that LPC efflux by SPNS1 is required for cell survival under choline limitation. Collectively, our work defines a lysosomal phospholipid salvage pathway that is essential under nutrient limitation, and more broadly, provides a robust platform to deorphan lysosomal gene function.</p>
Data from: CRISPR/Cas9 knockout of shell matrix protein 1 in the slipper-snail Crepidula atrasolea
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ConvexML: Scalable and accurate inference of single-cell chronograms from CRISPR/Cas9 lineage tracing data
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CRISPR/Cas9 screen for essential endolysosomal genes under free choline limitation
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Combining CRISPR/Cas9 and brain imaging to study the link from genes to molecules to networks
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Mutant Harmonia axyridis raw sequencing data of CRISPR/Cas9 induced mutations in the genes laccase2 and scarlet
<p><em>Harmonia axyridis</em> (Pallas), commonly known as the Asian lady beetle, is a native insect species of Asia that has been intentionally introduced to various regions for biocontrol purposes. However, its widespread presence beyond its original release sites suggests a high degree of invasiveness. In this study, we utilized the CRISPR-Cas9 approach to achieve precise genome editing in <em>H. axyridis</em>. Specifically, we targeted two genes in <em>H. axyridis</em>, <em>laccase2</em> and <em>scarlet</em>, knockdown of which orthologs in other insects showed visible phenotypic changes. The knockout <em>laccase2</em> resulted in an early-detectable phenotype but also in lethality. However, we successfully established a viable and genetically stable mutant colony by disrupting the <em>scarlet </em>gene, resulting in beetles with white eyes. Our findings contribute to the expanding knowledge of genetic manipulation in <em>H. axyridis</em> and provide insights into its potential for future research and practical applications for biocontrol and invasive species management.</p>
CRISPR/Cas9 knock-out sgRNA sequencing in human CaCo2 cells
<p>The data was obtained in course of performing a CRISPR/Cas9 knock-out in human polarized epithelial cells (CaCo<sub>2</sub>). The screen aimed to identify genes relevant for proper epithelial polarization and correct apical transport of the apical transmembrane protein dipeptidyl-peptidase 4. It includes next-generation-sequencing data (raw sgRNA-read-counts) of two experimental (sorted) and corresponding control (ctrl) cell populations. It further contains sequence information on the sgRNAs as represented in the human GeCKOv2-CRISPR library and the corresponding targeted genes.</p>
CRISPR/Cas9 mediated knockout of ABCC1 confers resistance to Bacillus thuringiensis toxin Cry2Ab in Helicoverpa armigera
<p>This data contains the Bt and insecticide bioassay results of ABCC1 knockout and wild-type strain of <em>Helicoverpa armigera</em>. Bioassay results revealed that the HaABCC1-KO strain exhibited >60-fold resistance to Cry2Ab toxin compared with the susceptible XJ strain, while no resistance has been recorded for Cry1Ab, Cry1Ac and Vip3A. Furthermore, the inheritance of <em>H. armigera</em> resistance to Cry2Ab was autosomal and completely recessive, significantly associated with the 4-nt deletion mutation of ABCC1 in the HaABCC1-KO strain. The relative growth of HaABCC1-KO and XJ strain also confirmed the role of <em>HaABCC1 </em>on the toxicity of Cry2Ab.</p>
Small extrachromosomal circular DNA harboring targeted tumor suppressor gene mutations supports intratumor heterogeneity in mouse liver cancer induced by multiplexed CRISPR/Cas9
<p>These files include raw image data from our study titled "Small extrachromosomal circular DNA containing targeted tumor suppressor mutations supports intratumoral heterogeneity in multiplex CRISPR/Cas9-induced mouse liver cancer".</p>
A Safety and Efficacy Study of TALEN and CRISPR/Cas9 in the Treatment of HPV-related Cervical Intraepithelial NeoplasiaⅠ
ClinicalTrials.gov study NCT03057912. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Safety and Efficacy of CRISPR/Cas9 mRNA Instantaneous Gene Editing Therapy to Treat Refractory Viral Keratitis
ClinicalTrials.gov study NCT04560790. IPD Sharing: NO. Countries: 1. Publications: 1.
Data from: Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy
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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.