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Dataset results
97 results for “DNA editing”
Next-generation Sequencing Data Associated with "Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches"
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NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
<p>We developed a method to detect copy number variation and loss of heterozygosity in genome-edited cell lines by only sequencing the edited site. We introduced different substitutions on both chromosomes of diploid H9 human embryonic stem cells using CRISPR/Cas9 and a mixture of homology-directed repair donor DNAs carrying different substitutions. Here, we deposit the associated sequencing data (BAM-files) generated by extracting genomic DNA from genome-edited H9 cells, PCR amplifying the region of interest and sequencing on a MiSeq platform. We sequenced the edited site of cell bulks to investigate the editing efficiencies of individual donors from the donor mixtures. For proof of concept, we isolated over 850 cellular clones from the edited cell bulks and sequenced the edited site and heterozygous positions flanking the edited site to determine the number of alleles at the edited site and detect copy-neutral loss of heterozygosity. Additionally, we sequenced the DNA donors to assess, the distribution of individual donors in the mixtures.</p>
NGS data from: Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic mutations
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NGS data from: Predominant HDR-dependent genome editing and prevention of byproducts by DNA repair pathway choice
<p>CRISPR-Cas9 genome editing has been widely adapted to cleave genomic DNA sequences of interest. Cellular repair of the CRISPR induced DNA double-strand breaks is dominated by error prone end joining pathways that outcompete inefficient homology-directed repair (HDR) that would allow precise introduction of a mutation present in a supplied synthetic DNA donor. To achieve predominant HDR, we studied the combinatory effect of inhibitory mutations in genes that are central to competing repair pathways.</p>
NGS data from: Predominant HDR-dependent genome editing and prevention of byproducts by DNA repair pathway choice
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5′ modifications improve potency and efficacy of DNA donors for precision genome editing
<p><span>Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit HDR efficacy. Here, we explore chemical modifications to both double-stranded and single-stranded DNA-repair templates. We describe 5′-terminal modifications, including in its simplest form the incorporation of triethylene glycol (TEG) moieties, that consistently increase the frequency of precision editing in the germlines of three animal models (<i>Caenorhabditis elegans</i>, zebrafish, mice) and in cultured human cells. </span></p>
Prediction of designer-recombinases for DNA editing with generative deep learning
<p>Sequence data from "Prediction of designer-recombinases for DNA editing with generative deep learning" publication.<br> Tyrosine site-specific recombinase gene sequences with the corresponding target sequences from already published projects. Recombinases were produced with directed evolution and sequenced with PacBio HiFi.</p> <p>The evolution of the recombinases sequences in this dataset were published in the following publications:</p> <ul> <li>https://doi.org/10.1126/science.1141453</li> <li>https://doi.org/10.1038/nbt.3467</li> <li>https://doi.org/10.1093/nar/gkz1078</li> <li>https://doi.org/10.1038/s41467-022-28080-7</li> </ul>
5′ modifications improve potency and efficacy of DNA donors for precision genome editing
Open the record for dataset details and reuse information.
Precise editing of pathogenic nucleotide repeat expansion in iPSCs without inducing DNA double-strand breaks using a prime editor [RNA-Seq]
GEO Series GSE248085. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Expanding the editable genome and CRISPR-Cas9 versatility using DNA cutting-free gene targeting based on in trans paired nicking
GEO Series GSE135064. Homo sapiens. 12 samples. Type: Other.
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A
GEO Series GSE97816. Homo sapiens. 29 samples. Type: Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing [RNA-seq, IL1B treatment]
GEO Series GSE270873. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [Modifications - screen]
GEO Series GSE121666. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
CRISPR-Cas9-based editing of histone H3 arginine 17 reveals its methylation-dependent regulation of Yap signaling and early mouse embryo development (genomic DNA-seq data set)
GEO Series GSE112539. Mus musculus. 8 samples. Type: Other.
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RNA-Seq]
GEO Series GSE97815. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Cas12a base editors induce efficient and specific editing with low DNA damage response
GEO Series GSE145552. Mus musculus; Homo sapiens. 265 samples. Type: Expression profiling by high throughput sequencing; Other.
Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways [RNA-seq]
GEO Series GSE247589. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Removal of promoter DNA methylation by epigenome editing reverses HBG silencing [RNA-seq]
GEO Series GSE284289. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing.
DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A [RRBS]
GEO Series GSE97813. Homo sapiens. 4 samples. Type: Methylation profiling by high throughput sequencing.
Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [RNA-seq]
GEO Series GSE144903. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
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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.