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6,171 results for “mutant”
Raw diffraction images of cross-linked cypovirus polyhedra mutant crystals
<p>Diffraction images of cross-linked cypovirus polyhedra mutant crystals related to PDB codes <a href="https://www.rcsb.org/structure/5YR1">5YR1</a>, <a href="https://www.rcsb.org/structure/5YR9">5YR9</a>, <a href="https://www.rcsb.org/structure/5YRA">5YRA</a>, <a href="https://www.rcsb.org/structure/5YRB">5YRB</a>, <a href="https://www.rcsb.org/structure/5YRC">5YRC</a>, and <a href="https://www.rcsb.org/structure/5YRD">5YRD</a> (<a href="http://dx.doi.org/10.1039/c7cc08689j">Negishi et al. 2018, Chem. Commun.</a>).</p> <p>Small-wedge (5° or 10°/crystal) datasets were collected from loop-harvested microcrystals at a wavelength of 1 Å on BL32XU and BL41XU, SPring-8. The datasets for 5YR1, 5YR9, 5YRB, and 5YRC were collected automatically using ZOO system.</p> <p>The crystals belonged to space group I23 with unit cell parameter a~103 Å. All datasets were processed and merged using KAMO pipeline with XDS.</p> <p>This entry includes following data:</p> <ul> <li> <p>1-PhC (5YR1, 1.72 Å)</p> <ul> <li> <p>BL32XU (EIGER X 9M)</p> </li> <li> <p>5°/crystal ×32 (0.1°/frame)</p> </li> </ul> </li> <li> <p>2-PhC (5YR9, 1.70 Å)</p> <ul> <li> <p>BL32XU (MX-225HS)</p> </li> <li> <p>5°/crystal × 127 (1°/frame)</p> </li> </ul> </li> <li> <p>3-PhC (5YRA, 1.79 Å)</p> <ul> <li> <p>BL41XU (PILATUS3 6M)</p> </li> <li> <p>5° or 10°/crystal × 49 (0.25°/frame)</p> </li> </ul> </li> <li> <p>ox1-PhC (5YRB, 1.65 Å)</p> <ul> <li> <p>BL32XU (EIGER X 9M)</p> </li> <li> <p>5°/crystal × 78 (0.1°/frame)</p> </li> </ul> </li> <li> <p>ox2-PhC (5YRC, 1.67 Å)</p> <ul> <li> <p>BL32XU (MX-225HS)</p> </li> <li> <p>5°/crystal × 323 (1°/frame)</p> </li> </ul> </li> <li> <p>ox3-PhC (5YRD, 1.85 Å)</p> <ul> <li> <p>BL41XU (PILATUS3 6M)</p> </li> <li> <p>5°/crystal × 29 (0.25°/frame)</p> </li> </ul> </li> </ul> <p>NOTE that EIGER's master.h5 files were modified; see <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</a>.</p>
Confocal imaging raw data files of autophagy analysis in optn and p62 zebrafish mutants during Mycobacterium marinum infection
<p>Association of fluorescent Mycobacterium marinum bacteria with Ubiquitin immunolabelling and GFP-Lc3 signal in zebrafish larvae carrying mutations in the selective autophagy receptors optnineurin and p62. Data deposited are Leica LIF files belonging bioRxiv 415463; doi: https://doi.org/10.1101/415463</p>
Purification of HTT mutant samples 2019/05/17
<p><strong>Project: </strong>Investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Purification of HTT mutant samples</p> <p><strong>Date completed:­ </strong>2019/05/27</p> <p><strong>Rationale: </strong>To assess HTT function <em>in vitro</em></p>
ROS-Specific Huntingtin Interactions: PAR overlay assay with PBM3 peptide mutant
<p>Poly-ADP ribose overlay assay with huntingtin PBM peptides to test ability of a PBM3 alanine mutant to bind poly-ADP ribose.</p>
Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 1-3)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p> <p>005.md : Production stage</p> <p>006.analysis : Basic energy graphs</p> <p>007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)</p>
Molecular dynamics simulations of the interaction of the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 4-6)
<p><strong>Description of files in this dataset:</strong></p> <p><strong>MD_mutR111A_R117A_CYP2J2_AA_StateX_repeatY.zip</strong> : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the double R111A + R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose). </p> <p>Each directory contains the following sub-directories:</p> <p>001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands</p> <p>002.min : Minimisation stage</p> <p>003.heat : Heating stage</p> <p>004.equil: Equilibration stage</p>
Metabolic fingerprints for suboptimal mycorrhizal colonization in wild-type and the jasmonic acid deficient spr2 tomato mutant
<p>Raw data for metabolic fingerprinting of tomato roots by DLI-ESI-MS and GC-MS to examine the effect of mycorrhizal colonization on the global metabolic profile of WT and <em>spr2</em> mutant plants.</p>
Gene expression for suboptimal mycorrhizal colonization in wild-type and jasmonic acid deficient spr2 tomato mutants
<pre>Data were obtained from mycorrhizhal colonized roots of wild-type and and spr2 mutants tomato plants, at 32 and 45 days after mycorrhizhal inoculation. Amplifications were performed using SYBR Green detection chemistry and run in triplicate in 96-well reaction plates with the CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). The data was analyzed by the delta delta ct method. </pre>
ABI sequencing files for mouse Prex2 mutant sequence verification
<p>File HWZD44_3A_1-P0058.ab1 is an ABI sanger sequencing trace showing the presece of the mutation E22A in exon 1 of mouse Prex2,</p> <p>File 59_2h-P0060.ab1 is an ABI sanger sequencing trace showing the presece of the mutation N204A in exon 6 of mouse Prex2.</p>
Assembly of wild type and mutant variants of Enterohemorrhagic type IVa pili
<p>To analyse pilus assembly, bacteria of <em>E. coli</em> strain BW25113 F’<em>lacI</em><sup>Q</sup> were transformed with plasmid pMS41 encoding the EHEC pilus assembly genes and pCHAP8565 or its mutant derivatives encoding PpdD variants (Luna Rico et al. 2019). Bacteria were cultured for 48-72 hours on M9 minimal agar plates (Miller 1972) containing carbenicillin (100 mg.mL-1) and chloramphenicol (25 mg.mL-1). Bacteria were harvested and resuspended in LB medium at OD<sub>600nm</sub> of 1. The suspension was vortexed vigorously for 1 min to detach pili from bacteria. Bacteria were pelleted by 5-min centrifugation at 16000 g at 4°C and resuspended in SDS sample buffer at a concentration of 10 OD<sub>600nm</sub> per 1 mL. The supernatant containing pili was subjected to another round of centrifugation for 10 min. Pili were precipitated with 10% tri-chloroacetic acid on ice for 30 min and pelleted by a 30-min centrifugation at 16000g at 4°C. Pili pellets were washed twice with ice-cold acetone, air-dried and resuspended in SDS-sample buffer at a concentration equivalent to that of the bacteria. The equivalent volumes (5 ul) of each fraction were analysed by denaturing SDS polyacrylamide gel electrophoresis (SDS-PAGE) on 10% polyacrylamide Tris-Tricine gels (Schägger and Von Jagow 1987). Proteins were transferred on nitrocellulose by Western blot and probed with anti-PpdD antibodies and secondary anti-rabbit antibodies coupled to HRP as described (Luna Rico et al. 2019). The fluorescent signal was recorded with a Typhoon FLA-9000 scanner (GE).</p>
EvolvingSTEM Bioinformatics mutant colony sequencing
<p>Mutant colony sequencing for EvolvingSTEM Bioinformatics</p>
eor-1 and pag-3 mutants crossed to NeuroPAL
<p>Image volumes and annotations for eor-1 and pag-3 mutants crossed to NeuroPAL. Excel files are included with annotations for each image.</p> <p>The following image volumes and their annotations are provided for the NeuroPAL publication, "NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans". The publication is available here:<br> https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2</p> <p>Please cite this work when using the images and their annotations.</p> <p>The image volumes are organized in 6 folders:</p> <p>- "eor-1 Control" = wild-type NeuroPAL[otIs669] controls<br> - "eor-1 cs28 x otIs669" = eor-1(cs28);NeuroPAL[otIs669] mutants<br> - "eor-1 ok1127 x otIs669" = eor-1(ok1127);NeuroPAL[otIs669] mutants</p> <p>- "pag-3 Control" = wild-type NeuroPAL[otIs669] controls<br> - "pag-3 n3098 x otIs669" = pag-3(n3098);NeuroPAL[otIs669] mutants<br> - "pag-3 ok488 x otIs669" = pag-3(ok488);NeuroPAL[otIs669] mutants</p> <p>These image files can be viewed with the NeuroPAL ID software, available at:<br> https://www.hobertlab.org/neuropal/<br> OR<br> https://github.com/amin-nejat/CELL_ID</p> <p> </p>
Single molecule tracking videos: SOX18 and its dominant-negative mutant SOX18RaOp
<p>Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18<sup>RaOp</sup>) responsible for both the classical mouse mutant <u>Ra</u>gged <u>Op</u>ossum and the human genetic disorder Hypotrichosis-Lymphedema-Telangiectasia-Renal Syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18<sup>RaOp</sup> disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.</p>
A dominant-negative SOX18 mutant disrupts multiple regulatory layers essential to transcription factor activity
<p>Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18<sup>RaOp</sup>) responsible for both the classical mouse mutant <u>Ra</u>gged <u>Op</u>ossum and the human genetic disorder Hypotrichosis-Lymphedema-Telangiectasia-Renal Syndrome. Combining three single-molecule imaging assays in living cells together with genomics and proteomics analysis, we found that SOX18<sup>RaOp</sup> disrupts the system through an accumulation of molecular interferences which impair several functional properties of the wild-type SOX18 protein, including its target gene selection process. The dominant-negative effect is further amplified by poisoning the interactome of its wild-type counterpart, which perturbs regulatory nodes such as SOX7 and MEF2C. Our findings explain in unprecedented detail the multi-layered process that underpins the molecular aetiology of dominant-negative transcription factor function.</p>
Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron
<p>Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in the early stages of development. This dataset contains the raw data associated with the statistics and figures reported in an accompanying paper which describes the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe <em>Bacteroides</em> <em>thetaiotaomicron</em> VPI-5482 that we created as a resource for the research community.</p>
Locomotor Responses of Utricular Mutants to High Magnetic Field Exposure
<p>Wild-type mice or head-tilt (het) or tilted (tlt) mutant mice were exposed to static 14.1 T magnetic field, or sham-exposed, for 30 min; locomotor activity was recorded for 2 minutes after exposure. The het and tlt mice lack otoconia in the inner ear, and are unresponsive to vestibular linear acceleration. After magnetic field exposure, wild-type mice and tlt mice show suppressed rearing and tight counter-clockwise circling. The het mutant mice do not show circling nor is their rearing suppressed. This suggests that otoconia, or a function that depends on otoconia, are required for full vestibular responsiveness to magnetic fields.</p>
BLM overexpression as a predictive biomarker for CHK1 inhibitor response in PARP inhibitor–resistant BRCA-mutant ovarian cancer
<p>PARP inhibitors (PARPis) have changed the treatment paradigm in BRCA-mutant high-grade serous ovarian carcinoma (HGSC). However, most patients eventually develop resistance to PARPis, highlighting an unmet need for novel therapeutic strategies. Using high-throughput drug screens, we identified ATR/CHK1 pathway inhibitors as cytotoxic, and further validated monotherapy activity of the CHK1 inhibitor (CHK1i), prexasertib, in PARPi-resistant BRCA-mutant HGSC cells and animal models. As a proof-of-concept trial, we conducted a phase II study of prexasertib in BRCA-mutant HGSC patients. The treatment was well-tolerated but yielded an objective response rate of 6% (1/17; 1 PR) in patients with prior PARPi treatment. Exploratory biomarker analyses revealed that replication stress and fork stabilization were associated with clinical benefit to CHK1i. In particular, overexpression of BLM, and CCNE1 overexpression or copy number gain/amplification were seen in patients deriving durable benefit from CHK1i. Our findings suggest replication fork–related biomarkers should be further evaluated for CHK1i sensitivity in HGSC.</p>
SAXS data of GDAP1 delta319-358 CMT-mutants
<p>SEC-SAXS data of GDAP1 delta319-358 CMT-mutants. The compressed files contain a directory containing the buffer and sample frames. The directory should open in ATSAS chromixs for data reduction.</p>
SAXS data of GDAP1 delta303-358 CMT-mutants
<p>Unsubtracted and subtracted SEC-SAXS frames from GDAP1 delta303-358 CMT-linked mutants. The compressed files contain a directory (directories) containing the buffer and sample frames. The directory should open in ATSAS chromixs for data reduction. </p> <p> </p>
(SNP Array) Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of TP53 mutant Leukaemic Evolution
<p>Single nucleotide polymorphism (SNP) array data files related our publication titled "Single-Cell Multi-Omics Identifies Chronic Inflammation as a Driver of <em>TP53 </em>mutant Leukaemic Evolution".</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.