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49 results for “DNA-binding Proteins”
Predictive modeling of moonlighting DNA-binding proteins
<p>This repository contains the codes used for the prediction of moonlighting proteins in the paper "Predictive modeling of moonlighting DNA binding proteins".</p> <p>The repository is organized as the following:</p> <p>1. The DNA binding protein identifiers and their features that were used to train the models for the prediction of DNA binding Moonlighting proteins.</p> <p>2. Five feature sets were used to create Catboost models that make predictions. The source code for generating predictions based on all the features and predictions based on particular features is supplied. In addition, the source code for generating maximum and average ensemble predictions has been made available. A detailed explanation is given in README file.</p>
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (1/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>Cneg</td> <td>RNASEQ-AVF1</td> <td>RNASEQ-AVF1_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF1_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF2</td> <td>RNASEQ-AVF2_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF2_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF3</td> <td>RNASEQ-AVF3_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF3_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF4</td> <td>RNASEQ-AVF4_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF4_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF5</td> <td>RNASEQ-AVF5_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF5_S5_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA A</td> <td>RNASEQ-AVF6</td> <td>RNASEQ-AVF6_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF6_S6_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA B</td> <td>RNASEQ-AVF7</td> <td>RNASEQ-AVF7_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF7_S7_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA C</td> <td>RNASEQ-AVF8</td> <td>RNASEQ-AVF8_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF8_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (2/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>TDP-43 siRNA D</td> <td>RNASEQ-AVF9</td> <td>RNASEQ-AVF9_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF9_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF10</td> <td>RNASEQ-AVF10_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF10_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF11</td> <td>RNASEQ-AVF11_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF11_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF12</td> <td>RNASEQ-AVF12_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF12_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF13</td> <td>RNASEQ-AVF13_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF13_S5_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF14</td> <td>RNASEQ-AVF14_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF14_S6_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos B+C</td> <td>RNASEQ-AVF15</td> <td>RNASEQ-AVF15_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF15_S7_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos A+B+C</td> <td>RNASEQ-AVF16</td> <td>RNASEQ-AVF16_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF16_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
Data Sets and Results for "Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins"
<p>Data sets and results for "Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins"<br> <br> The file "dna_binding_protein_sequences.zip" has the training and testing sets from the paper:<br> <br> RLL - "random_<train/test>_full_1000.csv"<br> RSL - "random_<train/test>_40.csv"<br> RS&LL - "random_<train/test>_40_1000.csv"<br> RLL where included positive examples have verified DNA binding activity - "random_<train/test>_hq_1000.csv"<br> The 10 RS&LL data sets - "random_<train/test>_40_1000.csv" + "random_<train/test>_40_1000_cv_<0-8>.csv"</p> <p>The results files are named similarly. See "see_results.ipynb" in the <a href="https://doi.org/10.5281/zenodo.5153683">codebase</a> that supplement these data sets<br> The species data sets are derived from "uniprot_data_bac.tab" and "uniprot_data_not_bac.tab." See <a href="https://doi.org/10.5281/zenodo.5153683">code</a>. <br> <br> The ESM embeddings used by the XGBoost model are in "dna_binding_protein_esm.zip"</p>
X-ray scattering datasets and simulations associated with the publication "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine"
<p>This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (<a href="https://doi.org/10.1039/D2CP05053F">https://doi.org/10.1039/D2CP05053F</a>)</p> <p>Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included.[1]</p> <p>TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from <a href="https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry">https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry</a> which is further described in <a href="https://doi.org/10.26272/opus4-55751">https://doi.org/10.26272/opus4-55751</a>.</p> <p>This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission.</p> <p>[1] S. Su, Y.-G. Gao, H. Zhang, T. C. Terwilliger and A. H.-J. Wang, Protein Science, 1997, 6, 771–780.</p> <p> </p> <p><br> </p>
TIRF Microscopy Data Files. "Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides: Implications for target site search"
<p>TIRF-microscopy images and analysis data from single-molecule experiments assessing the direct transfer phenomenon in the TREX1 exonuclease. </p>
Structural adaptation of the single-stranded DNA-binding protein C-terminal to DNA metabolizing partners guides in-hibitor design
<p> </p> <ul> <li>Fluorescence anisotropy metadata and polarization values </li> <li>Isotermal titration calorimetry raw files (protein-ligand and background titrations)</li> <li>Input files for PRALINE calculation in FASTA format</li> <li>CSV file containing the SSB sequences in SMILES format and binding data</li> <li>The input files for the ExoI-bound wtSSB-Ct, E1-sSSB-Ct, and E2-sSSB-Ct and RecO-bound wtSSB-Ct, R1-sSSB-Ct, and R2-sSSB-Ct together with the corresponding trajectory files </li> </ul>
Dataset associated with the study titled "Systematic discovery of regulatory motifs associated with human insulator sites" It includes data used for predicting insulator-associated DNA-binding proteins.
<p><strong>This dataset was used in the study on the prediction of insulator-associated DNA-binding proteins.</strong></p> <p>The three files included here are intended for use with the code available in the following GitHub repository:<br><a href="https://github.com/reposit2/insulator" target="_new" rel="noopener">https://github.com/reposit2/insulator</a></p> <p>To use the data, extract all three files and place them in the same directory as the code files.</p>
Locus-specific paramutation in Zea mays is maintained by a chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function
GEO Series GSE158990. Zea mays. 5 samples. Type: Non-coding RNA profiling by high throughput sequencing.
A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments
GEO Series GSE212751. Bacillus subtilis PY79. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins
GEO Series GSE171735. Homo sapiens; synthetic construct. 5 samples. Type: Other.
Ibf1 and Ibf2 are DNA-binding proteins required for insulator function in Drosophila [ChIP-seq]
GEO Series GSE46614. Drosophila melanogaster. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Elucidating DNA-binding protein dynamics in Salmonella Typhimurium within macrophages using a breakthrough low-input ChIP-exo workflow [RNA-seq]
GEO Series GSE270061. Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S. 4 samples. Type: Expression profiling by high throughput sequencing.
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
GEO Series GSE47753. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Intrinsically Disordered Regions in Chromodomain Helicase DNA-binding (CHD) Proteins Shape Distinct Protein Interaction Networks
GEO Series GSE275475. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Multiplexed identification of the genomic targets of DNA-binding proteins
GEO Series GSE27381. Saccharomyces cerevisiae. 22 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (ChIP-Seq I)
GEO Series GSE190497. Plasmodium falciparum. 11 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (ChIP-Seq II)
GEO Series GSE230206. Plasmodium falciparum. 32 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins
GEO Series GSE134258. Arabidopsis thaliana. 72 samples. Type: Expression profiling by high throughput sequencing.
High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins (ETS1 only)
GEO Series GSE171732. synthetic construct; Homo sapiens. 1 samples. Type: Other.
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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)
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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.