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1,123 results for “Cis”
Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus [Extra tables + files]
<p>This zenodo contains extra files and tables necessary to run code specified in https://github.com/EddaSchulz/TFiScreen_Paper/.</p> <p>These files are associated with analysis in Schwämmle et al., 2025.</p>
Integrated maize cis-regulatory elements (iCREs)
<p>Files containing the genomic coordinates of the conserved non-coding sequences (BLSSpeller, msa_pipeline, funTFBS, and Song-2021), the accessible chromatin regions (ACRs) and the unmethylated regions (UMRs) in the maize genome version 5 employed to generate the integrated cis-regulatory-elements (iCREs), both the all and maxF1 sets.</p> <p>Version 1.1 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene.</p> <p>Version 1.2 includes an extra version of the same files as the previous one but with the genome coordinates in the maize genome version 4 (AGPv4)</p> <p>Version 1.3 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene in the coordinates of the maize genome version 4 (AGPv4).</p> <p>Version 1.4 includes Supplementary Table 3 and 4 (which in the reserach chapter version of the article, included in the doctoral dissertation of Nicolás Manosalva, they correspond to Supporting Datasets 5 and 6):</p> <ul> <li>Table S3/Dataset S5: Gene ontology (GO) enrichment of the genes associated with different repetitive element types and transposable element (TE) superfamilies that are found within iCREs. </li> <li>Table S4/Dataset S6: Number of, median value of the transcripts per million, and p-value of the genes associated with TEs within, outside, and within and outside iCREs. The computations were binned per distance to the closest gene.</li> </ul>
An integrative characterisation of proline cis and trans conformers in a disordered peptide
<p>These metadynamic molecular dynamics simulations, nuclear magnetic resonance spectroscopy (NMR), and small-angle X-ray scattering (SAXS) data support the findings of the manuscript entitled 'An integrative characterisation of proline cis and trans conformers in a disordered peptide' by Pettitt et al. DOI: <a href="https://doi.org/10.1016/j.bpj.2024.09.028" target="_blank" rel="noopener">10.1016/j.bpj.2024.09.028</a></p> <h1>Metadynamic molecular dynamics simulations</h1> <p>The <code>Metadynamic_simulations_Zenodo.tar.xz</code> directory contains data for an N-terminally acetylated disordered peptide. The peptide is the C-terminal region of open reading frame 6 (ORF6-CTR) from SARS-CoV-2. The data were produced by metadynamics simulations in 3 force fields: AMBER03WS (a03ws), AMBER99SB-disp (a99sb), and CHARMM36m (C36m). We used PLUMED version 2.7.1 and GROMCS 2021.2. All the data and PLUMED input files required to reproduce the simulation results are available on PLUMED-NEST. This data should be used with the code provided on GitHub at <a href="https://github.com/hansenlab-ucl/orf6-ctr_cis_trans_conformers/tree/master/Metadynamic_simulations"><code>https://github.com/hansenlab-ucl/orf6-ctr_cis_trans_conformers/tree/master/Metadynamic_simulations</code></a></p> <p>Once downloaded, this directory should be extracted using the following command:</p> <p>tar -xzvf Metadynamics_simulations_Zenodo.tar.xz</p> <p>The directory should be saved with the name <code>Metadynamic_simulations_Zenodo</code> and placed in the same directory as the GitHub <code>README_metadynamic_simulations.md</code> file.</p> <h2>This dataset contains:</h2> <ul> <li>{system}.pdb - atomic coordinate files for the NAc-ORF6-CTR in the a03ws, a99sb, and C36m force fields.</li> <li>{system}_traj.trr - single concatenanated trajectory files for the a03ws run 1, a03ws run 2, a99sb, and C36m simulations.</li> <li>{system}_weights_corr.dat - weights for each frame in _traj.trr for the a03ws run 1, a03ws run 2, a99sb and C36m simulations. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 0.95 nm for C36m, and 1.2 nm for the other force fields.</li> <li>{system}_weights_saxs_bme.dat - SAXS Bayesian/Maximum Entropy (BME) reweighted weights for each frame in {system}_traj.trr for the a03ws run 1, a03ws run 2, and C36m simulations. Here, the weights of frames in which the peptide interacts with its periodic image have been set to zero. The cutoff was 0.95 nm for C36m, and 1.2 nm for the other force fields.</li> <li>top_frames_{system}.npy - numpy array of frames index for the a03ws run 1, a03ws run 2, a99sb, and C36m simulations. Frames were selected based on weights_corr.dat.</li> <li>top_frames_{system}.trr - trajectory of frames for the a03ws run 1, a03ws run 2, a99sb, and C36m simulations. Frames were selected based on weights_corr.dat</li> <li>top_frames_{system}_rw_cis.npy - numpy array of cis-P57 frames index for the a03ws run 1, a03ws run 2, and C36m simulations. Frames were selected based on _weights_saxs_bme.dat</li> <li>top_frames_{system}_rw_trans.npy - numpy array of trans-P57 frames index for the a03ws run 1, a03ws run 2, and C36m simulations. Frames were selected based on _weights_saxs_bme.dat</li> <li>top_frames_{system}_rw_cis.trr - trajectory of cis-P57 frames for the a03ws run 1, a03ws run 2, and C36m simulations. Frames were selected based on _weights_saxs_bme.dat</li> <li>top_frames_{system}_rw_trans.trr - trajectory of trans-P57 frames for the a03ws run 1, a03ws run 2, and C36m simulations. Frames were selected based on _weights_saxs_bme.dat</li> <li>CS_COLVAR_{system} - experimental and CamShift predicted chemical shifts for all four systems (a03ws run1, run2, a99sb, and C36m) as well as the cis and trans sub-ensembles for a03ws run1, a03ws run2, and C36m</li> </ul> <h1>Nuclear magnetic resonance spectroscopy (NMR) data</h1> <p>The <code>NMR_Zenodo.tar.xz</code> directory contains data for the backbone and sidechain assignment experiments, backbone 15N relaxation rates experiments, and 15N diffusion experiments (.ft2 and .ft3 files). Unless specified otherwise, NMR spectra were collected on uniformly 15N-labelled and 13C, 15N-labelled ORF6-CTR at concentrations of 300 micromolar and on unlabelled NAc-ORF6-CTR at concentations of 400 micromolar. All peptides were prepared in 25 mM HEPES buffer at pH 6.9, 150 mM NaCl, containing 5% D2O, 1 mM sodium azide, and 1 mM EDTA. NMR data were recorded at 288.15 K (15 degrees celsius). Spectra were measured at a static magnetic field strength of 14. T (600 MHz), unless specified otherwise.</p> <p>Once downloaded, this directory should be extracted using the following command:</p> <p><code>tar -xzvf NMR_Zenodo.tar.xz</code></p> <p>Note: this data is not required to run the NMR analysis on GitHub at <a href="https://github.com/hansenlab-ucl/orf6-ctr_cis_trans_conformers/tree/master/NMR"><code>https://github.com/hansenlab-ucl/orf6-ctr_cis_trans_conformers/tree/master/NMR</code></a> but it can be used for you to repeat your own analysis.</p> <p>NMR chemical shifts have been deposited in the Biological Magnetic Resonance Data Bank (BMRB; <a href="../records/13748215/preview/www.bmrb.wisc.edu"><code>www.bmrb.wisc.edu</code></a>) under the following accession codes: <strong>52459</strong> for the ORF6CTR cis-P57 and trans-P57 configurations, and <strong>52460</strong> for the unlabelled NAc-ORF6CTR.</p> <h2>This dataset contains:</h2> <ul> <li>1H-1H-tocsy-nac-orf6-ctr.ft2 - 2D 1H-1H tocsy on the NAc-ORF6-CTR. Standard dipsi2esgpph Bruker pulse sequence, with spectral widths of 14 ppm (direct dimension) and 12 ppm (indirect dimension), and 1,024 x 512 complex points, respectively. 32 scans were recorded, with an inter-scan delay of 1.5 s.</li> <li>1H-1H-tocsy.ft2 - 2D 1H-1H total correlation spectroscopy (TOCSY) on the ORF6-CTR. Same details as above.</li> <li>1H-13C-hsqc-nac-orf6-ctr.ft2 - 2D 1H-13C heteronuclear single quantum coherence (HSQC) spectra on the NAc-ORF6-CTR. Standard hsqcgpph Bruker sequence was employed, with 192 scans, spectral widths of 14 ppm (1H) and 80 ppm for (13C), and 512 x 180 complex points, respectively. The recycle delay was set to 1.5 s, with carriers set to the position of the water peak (1H) and 35 ppm relative to TMS (13C).</li> <li>1H-15N.ft2 - 2D 1H-15N HSQC spectra on the 15N-labelled ORF6-CTR. Spectra were acquired using the hsqcetf3gpsi2 Bruker pulse sequence. Spectral widths were set to 16 ppm (1H) and 20.5 ppm (15N), with 1,536 x 128 complex points acquired, respectively. Carriers were set to the position of the water peak (1H) and 121.5 ppm (15N), with 4 scans and a recycle delay of 1 s.</li> <li>1H-15N-hsqc-310K.ft2 - 2D 1H-15N HSQC spectra on the 15N-labelled ORF6-CTR at 310.15 K (37 degrees celsius). Same details as above.</li> <li>15N-edited-dosy-950MHz.ft2 - Pseudo-3D diffusion pulsed field-gradient spin echo (PFGSE) 1H-15N-Diffusion Ordered Spectroscopy-HSQC (1H-15N-DOSY-HSQC) experiment with a bipolar gradient at a static magnetic field strength of 22.3 T (950 MHz) on the 15N-labelled ORF6-CTR. Six gradient experiments were acquired for each data set, with the gradient strengths augmented linearly through the acquisition from 0.9 to 39.5 G/cm and all other delays and pulses held constant. Gradient pulses (δ) were applied for 3 ms and a diffusion delay (Δ) of 200 ms. 80 scans were acquired per gradient experiment with 1,536 x 176 complex points (1H, 15N), using the same spectral widths and carriers as used before for the 2D 1H-15N HSQC experiment.</li> <li>15N-edited-noesy.ft3 - 15N-edited nuclear Overhauser effect spectroscopy HSQC (15N-NOESY-HSQC) on the ORF6-CTR. Spectra were acquired using the noesyhsqcfpf3gpsi3d Bruker pulse sequence. Spectra were recorded with 8 scans, 2,048 x 24 x 96 complex points (1H, 15N, 1H), and a spectral width of 16 x 20.5 x 16 ppm, respectively. Carriers were set to the water peak (1H) and 121.5 ppm (15N). A recycle delay of 1.5 s and a mixing time of 0.25 s were used</li> <li>15N-edited-tocsy.ft3 - 15N-TOCSY-HSQC on the ORF6-CTR. Spectra were acquired using a pulse sequence based on the original Bruker dipsihsqcf3gpsi3d with a flip-flop spectroscopy (FLOPSY)-16 scheme. Spectra were acquired with 16 scans, 1,024 x 32 x 96 complex points (1H, 15N, 1H), and a spectral width of 16 x 20.5 x 16 ppm, respectively. Carriers were set to the water peak (1H) and 121.5 ppm (15N), with a recycle delay of 1 s. A TOCSY mixing time of 0.1 s was used and an 8 kHz TOCSY spin lock was applied.</li> <li>ccconh.ft3 - CC(CO)NH spectra were acquired on the 13C, 15N-labelled ORF6-CTR. Spectra were acquired using a pulse sequence based on the original Bruker ccconhgp3d.2 with a FLOPSY-16 scheme. Spectra were recorded with 16 scans, 1,024 x 30 x 84 complex points (1H, 15N, 13C), and a spectral width of 14 x 20.5 x 71 ppm, respectively. Carriers were set to the water peak (1H), 121.5 ppm (15N) and 43 ppm (13C). A recycle delay of 1.5 s, along with a TOCSY mixing time of 18 ms were used.</li> <li>con.ft2 - 2D CON spectra were acquired on the 13C, 15N-labelled ORF6-CTR. Spectra were acquired using the c_con_iasq Bruker pulse sequence. Spectral widths were set to 40 ppm in both dimensions, with carriers set to 173 ppm relative to TMS (13C) and 121.5 ppm (15N), and 512 x 128 complex points, respectively. 32 scans and a recycle delay of 2 s were applied.</li> <li>hncacb.ft3 - The 3D HNCACB spectra were acquired on the 13C, 15N-labelled ORF6-CTR using the hncacbgp3d Bruker pulse sequence. Spectra were recorded with 16 scans, 1,024 x 30 x 72 complex points (1H, 15N, 13C), and a spectral width of 14 x 20.5 x 60.2 ppm, respectively. Carriers were set to the water peak (1H), 121.5 ppm (15N), and 43 ppm (13C), with a recycle delay of 1 s.</li> <li>hncaco.ft3 - The 3D HN(CA)CO spectra were acquired using the hncacogpwg3d Bruker pulse sequence on the 13C,15N-labelled ORF6-CTR. Spectra were recorded with 16 scans, 1,024 x 29 x 80 complex points (1H, 15N, 13C), and a spectral width of 14 x 20.5 x 7 ppm, respectively. Carriers were set to the position of the water peak (1H), 121.5 ppm (15N) and 173 ppm relative to TMS (13C), with a recycle delay of 1 s.</li> <li>hnco.ft3 - The 3D HNCO spectra were acquired using the hncogp3d Bruker pulse sequence on the 13C, 15N-labelled ORF6-CTR. The same details were used as for the hncaco.ft3.</li> <li>noe.ft2 - The {1H}-15N hetNOEs were recorded using a pseudo-3D experiment, with and without proton saturation on the 15N-labelled ORF6-CTR. Amide proton magnetisation saturation was accomplished by using a 5 s train of high-power 120° pulses applied at 5 ms intervals. The reference and saturated spectra were alternately recorded. To ensure complete recovery of the initial magnetisation at the start of each increment of the reference experiment, a long recycle delay of 15 s was applied. The spectral widths were 16 ppm (1H) and 20.5 ppm (15N), and 2,048 x 160 (1H, 15N) complex points were recorded at a static magnetic field strength of 14.1 T.</li> <li>noe-800MHz.ft2 - The same details as for noe.ft2, except it was measured at a static magnetic field strength of 18.8 T (800 MHz).</li> <li>r1.ft2 - Rates were measured using established proton-detected pulse sequences based on a gradient-selected, sensitivity-enhanced, refocused 15N sequences on the 15N-labelled ORF6-CTR. Spectra were recorded with 2,048 x 160 complex points and spectral widths as used before in the 2D 1H-15N HSQC experiment. Gradient pulses were used to suppress the water signal and a long recycle delay of 3 s was employed. N-H cross-correlated relaxation pathways were suppressed by hard 180˚ pulses every 20 ms during the relaxation delay. The R1 N-H planes were recorded with 8 relaxation delays ranging from 20 ms to 700 ms.</li> <li>r1-800MHz.ft2 - Same details as for r1.ft2, except the rates were measured at a static magnnetic field strength of 18.8 T (800 MHz).</li> <li>r1rho.ft2 - Similar details to r1.ft2, except cross-correlated relaxation was suppressed by hard 180˚ pulses during the 15N spin-lock. Magnetisation was explicitly aligned with the spin-lock field. N-H planes were recorded using 8 relaxation delays ranging from 2 ms to 140 ms, with a 15N spin-lock field strength of 2 kHz.</li> <li>r1rho_800MHz.ft2 - Same as r1rho.ft2, except the rates were measured at a static magenetic field strength of 18.8 T (800 MHz).</li> <li>rdd.ft2 - Exchange-free 15N transverse relaxation (Rdd) rates were measured using pulse schemes for the four 1H-15N relaxation rates R1ρ(2HzN’z), R1ρ(2H’zNz), R1ρ2(2H’zN’z), and R1(2HzNz) on the 15N-labelled ORF6-CTR. A total of 8 relaxation delays between 2 ms and 26 ms were used for all experiments (same delays used for each rate measurement). A 10 kHz 1H spin lock and a 2 kHz 15N spin lock were applied. Spectral widths were the same as those used before in {1H}-15N hetNOE experiments, with 1,536 x 640 (1H, 15N) complex points.</li> </ul> <h1>Small-angle X-ray scattering (SAXS) data</h1> <p>Experimental and predicted SAXS data for the NAc-ORF6-CTR. Once downloaded, this directory should be extracted using the following command:</p> <p><code>tar -xzvf SAXS_calculations_Zenodo.tar.xz</code></p> <h2>This dataset contains:</h2> <ul> <li>saxs_exp_nac_orf6_ctr.dat - experimental SAXS data collected on Instrument B21 at Diamond Light Source (Didcot, UK). Measurements were recorded on 800 micromolar unlabelled ORF6-CTR at 310.15 K (37 degrees celsius). Data sets of 26 frames with a frame exposure time of 1 s each were acquired.</li> <li>{system}_saxs_calc_nac_orf6_ctr.dat - calculated SAXS data using PEPSI-SAXS for the a03ws run 1, a03ws run 2, and C36m metadynamics simulations. There is one column per experimental average (total = 2570) and a row for each frame in the trajectory, which depends on the number of frames in the a03ws run 1, a03ws run 2, and C36m simulations.</li> </ul> <h2>Jupyter notebooks</h2> <p>All Jupyter notebooks can be accessed from GitHub. Open Jupyter notebooks using <code>jupyter lab</code> in the analysis environment.</p>
Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius
<p></p><p>In Heliconius butterflies, wing pattern diversity is controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knock-outs in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.</p><p></p>
Text-fig. 1. Geographical position of the localities studied. in A New Species Of The Genus Tumidopteris Naugolnykh From The Permian Of The Pechora Cis-Urals, Russia
Text-fig. 1. Geographical position of the localities studied.
Fig. 20 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 20. Hemibrycon polyodon, KU 20004, female, 52.5 mm SL. Scale bar = 1 mm.
Fig. 5. Hemibrycon helleri, ANSP 180775 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 5. Hemibrycon helleri, ANSP 180775, female, 81.1 mm SL, upper río Ucayali basin, Peru.
Fig. 1. Hemibrycon beni, CAS 44333 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 1. Hemibrycon beni, CAS 44333, syntype, male, 56.0 mm SL, upper río Beni basin, Bolivia.
Fig. 16. Hemibrycon mikrostiktos, MUSM 35490 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 16. Hemibrycon mikrostiktos, MUSM 35490, holotype, 44.4 mm SL, upper río Ucayali basin, Peru.
Fig. 12. Hemibrycon jelskii, MUSM 19562 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 12. Hemibrycon jelskii, MUSM 19562, male, 69.0 mm SL, upper río Ucayali basin, Peru.
Fig. 19 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 19. Hemibrycon polyodon, KU 20004, male, 71.2 mm SL, río Pastaza basin, Ecuador.
Fig. 8. Hemibrycon huambonicus, ROM 55406 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 8. Hemibrycon huambonicus, ROM 55406, male, 73.3 mm SL, upper río Ucayali basin, Peru.
Fig. 18. Hemibrycon polyodon, BMNH 1858.7.25.41 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 18. Hemibrycon polyodon, BMNH 1858.7.25.41, holotype, female, 70.4 mm SL, Guayaquil, Ecuador.
Fig. 14. Hemibrycon metae, INHS 61270 in A review of the Cis-Andean species of Hemibrycon Günther (Teleostei: Characiformes: Characidae: Stevardiinae), with description of two new species
Fig. 14. Hemibrycon metae, INHS 61270, female, 61.4 mm SL, río Apure basin, Venezuela.
Allele‐specific cis‐regulatory methylation of the gene for vasoactive intestinal peptide in white‐throated sparrows
<p>White-throated sparrows (<em>Zonotrichia albicollis</em>) offer a unique opportunity to connect genotype with behavioral phenotype. In this species, a rearrangement of the second chromosome is linked with territorial aggression; birds with a copy of this "supergene" rearrangement are more aggressive than those without it. The supergene has captured the gene <em>VIP</em>, which encodes vasoactive intestinal peptide, a neuromodulator that causes aggression in other songbirds. In white-throated sparrows, <em>VIP</em> expression is higher in the anterior hypothalamus of birds with the supergene than those without it, and expression of <em>VIP</em> in this region predicts the level of territorial aggression regardless of genotype. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of <em>VIP</em> both in breeding adults, which exhibit morph differences in territorial aggression, and in nestlings, before territorial behavior develops. We extracted and bisulfite-converted DNA from samples of the hypothalamus in wild-caught adults and nestlings and used high-throughput sequencing to measure DNA methylation of a region upstream of the <em>VIP</em> start site. We found that the allele inside the supergene was less methylated than the alternative allele in both adults and nestlings. The differential methylation was attributed primarily to CpG sites that were shared between the alleles, not to polymorphic sites, which suggests that epigenetic regulation is occurring independently of the genetic differentiation within the supergene. This work represents an initial step toward understanding how epigenetic differentiation inside chromosomal inversions leads to the development of alternative behavioral phenotypes.</p>
Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
<p>A library of 50 enhancers, each tested in three different lengths and with two different promoters (300 combinations), was packaged into AAV9 and delivered to newborn mice. Enhancers were selected from the VISTA Enhancer Browser of transgenic reporter data, and included 25 candidates active in the embryonic myocardium and 25 negative control candidates active in embryonic endothelium but not in myocardium. In the heart, AAV9 selectively transduces cardiomyocytes. After collecting ventricles at P28, the reporter transcripts were sequenced, and the frequency of each barcode was compared to its frequency in the viral pool DNA.</p> <p>Here we provide fastq files for each sample, an Excel spreadsheet (MPRA-Metadata.xls) containing annotation, and an Excel spreadsheet (MPRA-counts.xlsx) containing extracted barcode counts for each enhancer, as well as additional annotation and calculated enhancer activity.</p>
3F8/GM-CSF Immunotherapy Plus 13-Cis-Retinoic Acid for Primary Refractory Neuroblastoma in Bone Marrow
ClinicalTrials.gov study NCT01183897. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cyclosporine Inhalation Solution (CIS) in Lung Transplant and Hematopoietic Stem Cell Transplant Recipients for the Treatment of Bronchiolitis Obliterans Syndrome
ClinicalTrials.gov study NCT01287078. IPD Sharing: Not stated. Countries: 1. Publications: 3.
A Study of Heterologous Vaccine Regimen of Adenovirus Serotype 26 Mosaic4 Human Immunodeficiency Virus(Ad26.Mos4.HIV), Adjuvanted Clade C gp140 and Mosaic gp140 to Prevent HIV-1 Infection Among Cis-ge
ClinicalTrials.gov study NCT03964415. IPD Sharing: YES. Countries: 9. Publications: 1.
A Clinical Study to Evaluate the Effect of the Connected Inhaler System (CIS) on Adherence to Maintenance Therapy in Poorly Controlled Asthmatic Subjects
ClinicalTrials.gov study NCT03380429. IPD Sharing: YES. Countries: 7. Publications: 1.
ScienceDex guides
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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.