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183 results for “Base editing”
XML Data for "Four Early Chan Texts from Dunhuang - A TEI-based Edition"
<p>This zip archive contains the XML data, schema, stylesheets, and associated material that are the basis for a print edition of 48 Dunhuang manuscript witnesses of four early Chan Buddhist texts. The print edition is:</p> <p>Marcus Bingenheimer 馬德偉, Chang Po-Yung 張伯雍 (eds.): <em>Four Early Chan Texts from Dunhuang – A TEI-based Edition</em> 早期禪宗文獻四部 —— 以TEI標記重訂敦煌寫卷:楞伽師資記,傳法寶紀,修心要論,觀心論. Taipei: Shin Wen Feng 新文豐, 2018.<br> (Vol. 1: Facsimiles and Diplomatic Transcription 摹寫版 (ISBN: 978-957-17-2274-0), Vol. 2: Parallel, Punctuated and Annotated Edition 對照與點注版 (ISBN: 978-957-17-2275-7), Vol. 3: Calligraphy Practice 抄經版 (ISBN: 978-957-17-2276-4).)</p> <p>See the included README.txt for further information.</p>
IN02004 Changu Narayana Base of Pillar Inscription. Sanskrit XML file, draft epidoc edition
<p>IN02004 Changu Narayana Base of Pillar Inscription. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02021 Lagantole Avalokitesvara base. Sanskrit XML file, draft epidoc edition
<p>IN02021 Lagantole Avalokitesvara base. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02020 Sivalinga base near the Aryaghat bridge. Sanskrit XML file, draft epidoc edition
<p>IN02020 Sivalinga base near the Aryaghat bridge. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02019 Pasupati Sivalinga base of Abhiri. Sanskrit XML file, draft epidoc edition
<p>IN02019 Pasupati Sivalinga base of Abhiri. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02011 Trident Base Inscription of Jayalambha. Sanskrit XML file, draft epidoc edition
<p>IN02011 Trident Base Inscription of Jayalambha. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02012 Changu Narayana Base of Effigy Inscription. Sanskrit XML file, draft epidoc edition
<p>IN02012 Changu Narayana Base of Effigy Inscription. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
IN02095 Changu Narayana Gate Sivalinga Base Inscription. Sanskrit XML file, draft epidoc edition
<p>IN02095 Changu Narayana Gate Sivalinga Base Inscription. Sanskrit XML file (without metadata). Draft epidoc edition to be incorporated into 'Siddham' archive</p>
A photo-switchable gold nanoformulation based on the dCas9 protein for spatiotemporal controlled gene editing activation in vivo
Open the record for dataset details and reuse information.
Data from: Repairing a deleterious domestication variant in a floral regulator of tomato by base editing
<p>This repository contains the data necessary to run the analysis described in the publication "Repairing a deleterious domestication variant in a floral regulator of tomato by base editing" by Glaus et al., 2024. A preprint is available on bioRxiv (doi: <a href="https://doi.org/10.1101/2024.01.29.577624" rel="nofollow">https://doi.org/10.1101/2024.01.29.577624</a>)</p> <p> </p> <p>82_acc_Spim0.1_filtered.vcf.gz -- variant call results for 82 genomes with LA1589 as reference</p> <p>82_acc_Spim0.1_filtered_SIFT_out.tar.gz -- sift4g prediction results for 82 genomes with LA1589 as reference (SIFTannotations.xls and SIFTpredictions.list)</p> <p>sift_lib_LA1589.tar.gz -- sift4g library for the LA1589 genome</p> <p>SolpimLA1589_liftoff.tar.gz -- liftoff annotation of LA1589 genome</p> <p> </p> <p>In case of any questions, please contact Sebastian Soyk (sebastian.soyk@unil.ch)</p>
A human genome editing-based MLL-AF4 acute lymphoblastic leukemia model recapitulates key cellular and molecular leukemogenic features. (Processed data)
<p>The prognosis of infant B-cell acute lymphoblastic leukemia (iB-ALL) remains dismal, especially in patients harboring the MLL-AF4 (KTM2A-AFF1) rearrangement, which arises prenatally in early hematopoietic stem/progenitor cells (HSPCs) and accounts for 80% of iB-ALL and 10% of non-infant cases. MLL-AF4+ B-ALL shows a bimodal localization of the MLL gene breakpoint within the MLL break cluster region, and two subgroups of patients based on the gene expression pattern of the HOXA/MEIS cluster have been identified. The pathogenic mechanisms in MLL- AF4+ B-ALL are challenging to study functionally due to the absence of faithful human cellular models recapitulating the disease phenotype and latency. Here, we assess the molecular contribution and leukemogenic capacity of MLL breakpoints occurring in either intron 10 (MLL i10 , centromeric) or intron 12 (MLL i12 , telomeric) in ontogenically-different human HSPCs sourced prenatally (fetal liver) and neonatally (cord blood). CRISPR-Cas9-induced MLL-AF4 (MA) targeting either MLL i10 (M i10 A) or MLL i12 (M i12 A) causes MA-driven in vitro myeloid immortalization in both fetal liver- and cord blood-CD34+ HSPCs. The centromeric location of the MLL breakpoint, but not the cellular ontogeny, determined the expression of HOXA/MEIS1 genes in MLL-edited cells. Centromeric MLL breakpoints endowed enhanced myeloid clonogenic replating to MLL- edited CD34+ HSPCs. The cellular ontogeny and the location of the MLL breakpoint also influenced the capacity of MLL-edited CD34+ HSPCs to initiate pro-B-ALL in vivo, which faithfully recapitulated the molecular, transcriptomic and methylome profiles of patients with primary MA+ iB-ALL. Our data provide key insights into the cellular and molecular leukemogenic determinants of MA+ iB-ALL. This dataset contains processed RNAseq and DNA methylation data from the abovementioned study.</p>
Code repository for: Base editing mutagenesis maps functional alleles to tune human T cell activity
<p>Jupyter notebook and supplemental datasets required to created critical figures for the publication.</p>
Safer and efficient base editing and prime editing via ribonucleoproteins delivered through optimized lipid-nanoparticle formulations
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Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease
<p>An expanded CAG repeat in the huntingtin gene (<em>HTT</em>) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and gRNAs efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering <em>HTT</em> mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.</p>
Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease
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Data from: Improved specificity and efficiency of in vivo adenine base editing therapies with hybrid guide RNAs
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A Transfection-Free Approach of Gene Editing via a gold-based nanoformulation of the Cas9 protein
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FIGURE. Map of the region and sampling area showing the relative position of Livingston Island to Antarctic Peninsula (A), and the main sampling locations (B): 1—Hannah Point, 2—Mongolian (Reserve) Port, 3—Caleta Argentina. Map outlines are based on OpenStreetMap© contributors (www.openstreetmap.org), edited and arranged using Adobe Illustrator© and Adobe Photoshop®. Scale bars = 35 km (A); 2 km (B). in The genus Craspedostauros E.J.Cox (Bacillariophyta) on the coasts of Livingston Island, Maritime Antarctica
FIGURE. Map of the region and sampling area showing the relative position of Livingston Island to Antarctic Peninsula (A), and the main sampling locations (B): 1—Hannah Point, 2—Mongolian (Reserve) Port, 3—Caleta Argentina. Map outlines are based on OpenStreetMap© contributors (www.openstreetmap.org), edited and arranged using Adobe Illustrator© and Adobe Photoshop®. Scale bars = 35 km (A); 2 km (B).
Sequencing data from validation experiment for base editing of SCN2A
<p>It is challenging to apply traditional mutational scanning to voltage-gated sodium channels (NaVs) and functionally annotate the large number of coding variants in these genes. Using a cytosine base editor and a pooled viability assay, we screened a library of 368 guide RNAs (gRNA) tiling NaV1.2 to identify more than 100 gRNAs that changed NaV1.2 function. We sequenced base edits made by a subset of these gRNAs to confirm specific variants that drove changes in channel function. Electrophysiological characterization of these channel variants validated the screen results and provided functional mechanisms of channel perturbation. The majority of the changes caused by these gRNAs were classified as loss-of-function along with two missense mutations that led to gain-of-function in NaV1.2 channels. This two-tiered strategy to functionally characterize ion channel protein variants at scale identifies the largest set of loss-of-function mutations in a single NaV1.2 study to date.</p>
Clinical Validation Study for EDIT-B Test: an Aid for Differential Diagnosis of Bipolar Disorder, Based on RNA Editing Blood Biomarkers
ClinicalTrials.gov study NCT05603819. IPD Sharing: NO. Countries: 3. Publications: 29.
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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.