Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
5
datasets available to search
ShareScore release 0.9.0
Dataset results
5 results for “PWWP1”
Sampled ΔH/Δλ and ΔH data from ABFE calculations of 12 ligands bound to PWWP1
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 12 ligands to bound PWWP1. These ligands are originally detailed by Böttcher et al. (https://doi.org/10.1038/s41589-019-0310-x).</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Chemoproteomic Analysis of an NSD2-PWWP1 Chemical Probe
<p><strong>Dataset details</strong></p> <p><strong>Project Title: </strong>Chemoproteomic Analysis of an NSD2-PWWP1 Chemical Probe</p> <p><strong>Keywords: </strong>chemoproteomics, epigenetics, chemical probe, histone methyltransferase</p> <p><strong>Project description: </strong>Here we use competitive chemoproteomics pulldowns followed by label-free quantitative LC-MS/MS to assess target engagement and selectivity profiles of UNC6934 and UNC7145, a chemical probe targeting the PWWP1 domain of NSD2 and its negative control counterpart, respectively. To this end, we used a biotinylated probe derivative (UNC7096) for streptavidin pulldowns from KMS-11 multiple myeloma cell lysates, including in the context of UNC7145 or UNC6934 competition.</p> <p><strong>Methods:</strong></p> <p><strong>Chemical Proteomics</strong> </p> <p>To prepare whole cell lysates, KMS11 cells were washed 2 times with 1x PBS, lysed by resuspension in high-salt lysis buffer (20 mM HEPES pH 7.5, 350 mM KCl, 1% Triton X-100 + a protease inhibitor cocktail containing aprotinin, leupeptin, pepstatin A, and E-64) and passed through a 25 gauge needle 5 times followed by a 20 min incubation on ice. Cell lysates were cleared by centrifugation at 18 000 x g for 20 minutes at 4°C. Cleared supernatant was diluted to 150 mM KCl and 0.4% Triton X-100 with 20mM HEPES pH7.5 including fresh protease inhibitors. Sample protein concentrations were determined using the BCA assay (ThermoScientific). For each pulldown, 3 mg of cell lysate was pre-incubated with either DMSO control, 20 µM UNC7145, or 20 µM UNC6934 (final concentration) for 1 hour with rotation at 4°C. For each sample, 25 µl of M270 Dynabeads (ThermoScientific) were prepared by washing three times in low salt wash buffer (10 mM Tris-HCl pH7.9, 100 mM NaCl, 0.1% NP-40), followed by incubation with 1 µM UNC7096 (biotinylated probe) for 1 hour at 4 °C. The unbound biotinylated compound was removed by 3 washes with low salt buffer. UNC7096 bound beads were then added to each sample followed by incubation 1 hour with rotation at 4oC. Beads were then washed 3 times with low-salt wash buffer followed by 2 washes with 50mM ammonium bicarbonate. On-bead digestion was performed by overnight incubation at 37°C with 2 µg of mass spectrometry grade trypsin (Promega). The following morning an additional 2 µg of trypsin was added to each sample and incubated at 37°C for 4-6 hours. The supernatant, containing digested peptides, was collected. Beads were then washed twice with water and supernatant pooled with digested peptides. Samples were then acidified with formic acid to a final concentration of 2% final concentration and flash frozen prior drying under vacuum before being run on a Thermo Scientific LTQ Orbitrap Velos.</p> <p><strong>Label-free quantitative mass spectrometry data analysis </strong></p> <p>Raw MS/MS files were searched and quantified using Maxquant version 1.6.7.0 using the UP000005640 Uniprot human database (containing 20,605 protein entries, last modified November 5, 2019) with label-free quantification enabled and variable modifications oxidized methionine (+15.9949 Da) and deamidated asparagine (+0.9840) set. First search peptide tolerance and main search peptide tolerance were set at 30 and 6 ppm, respectively. For all other parameters default settings were used. </p> <p>Differential enrichment analysis was performed using the DEP package (v1.8.0) in R (v3.5.1). Briefly, samples were filtered for proteins identified in 2 out of 3 replicates of at least one condition, normalized by variance stabilizing normalization and tested for differential enrichment relative to pulldowns competed with DMSO vehicle control. </p> <p><strong>Brief Description of Data Files:</strong></p> <ul> <li><em>.raw & .index files</em> - raw proteomic data files - note: dataset has also been uploaded to ProteomeXchange Consortium via the PRIDE17 partner repository with the dataset identifier PXD017641. </li> <li><em>mqpar.xml </em>- provides parameters used for quantification with Maxquant, which can be found in the combined folder. </li> <li><em>UP000005640_9606.fasta</em> - UniProt reference used for Mazquant quantification of peptides</li> <li><em>NSD2_Chemoproteomics.Rproj & DEP_Analysis.R</em> - R project & script file for differential analysis of Maxquant output with DEP. </li> <li><em>methods.docx</em> - additional details covering experimental method</li> </ul> <p> </p>
Diffraction images for PWWP1 domain of NSD2 in complex with MR837
<p>A set of x-ray diffraction images collected at beam line 08ID of the Canadian Light Source.</p>
Bio NSD3 PWWP1 Expression and Purification Protocol
<p>Bio NSD3 PWWP1 Expression and Purification Protocol</p>
BIO NSD2 PWWP1 Expression and Purification Protocol
<p>Biotinylated NSD2 PWWP1 Expression and Purification Protocol</p>
ScienceDex guides
Understand access before you commit
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.