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Fig. 3 in Successful transcription but not translation or assembly of Solenopsis invicta virus 3 in a baculovirus-driven expression system
Fig. 3. (A) Plaque assay results for recombinant SINV-3 (AcSINV-3) transfection of Sf21 cells indicating the dilution used for each plate. (B upper panel) Representa- tive plaque with Sf21 cells stained with neutral red 10 d afer transfection (magnified 100 times). (B lower panel) Corresponding mock-infected Sf21 cells (negative control) afer 10 d of exposure. Plaque areas identify infection of insect cells by virus with corresponding cell death.
Fig. 2 in Successful transcription but not translation or assembly of Solenopsis invicta virus 3 in a baculovirus-driven expression system
Fig. 2. (A) pFastBac1_SINV-3 hybrid construct map. Locations of the restriction sites (black hash marks), bacterial transposon Tn7 sites (grey triangles), polyhedrin promoter (angled arrow corresponding to the sequence below), SINV-3 open reading frames (dark closed arrows), and approximate location of the area detected by the polyclonal antibody preparation (pAb) are shown. (B) Verified sequence of the pFastBac1_SINV-3 hybrid construct illustrating the late gene polyhedrin promoter (angled arrow). SINV-3 sequence is in bold font,with pFastBac1 sequence in normal font, and restriction sites are superscripted and corresponding sequences italicized.Underlined sequence represents the inserted late gene polyhedrin core promoter.Analyzed sequences of the 5'and 3'termini and restriction sites were identical to the wild-type virus.
Fig. 1 in Successful transcription but not translation or assembly of Solenopsis invicta virus 3 in a baculovirus-driven expression system
Fig. 1. Schematic of the SINV-3 genome and sub-cloning strategy to assemble the pFastBac1 donor plasmid/SINV-3 construct. (A) Organization of the SINV-3 genome illustrating the 2 ORFs numbered 1 and 2 that encode for non-structural and structural proteins, respectively, and the genome sections sub-cloned. Oligonucleotide primers used to generate cDNA and amplify each section are indicated. Primers with introduced restriction sites are also indicated. (B) Unique restriction sites for each sub-clone and the assembly process employed to concatenate the entire SINV-3 genome in the pFastBac1 donor vector.
Рис. 8. ОтноситеΛьная преΑставΛенность транскриптов патогенраспознающих рецепторов в гемоцитах моΛΛюсков Planorbarius corneus, заражённых трематоΑами Bilharziella polonica (I) и незаражённых особей (N) Fig. 8. Relative number of transcripts of pattern recognition receptors from hemocytes of Planorbarius corneus molluscs infected with Bilharziella polonica trematodes (I) and uninfected individuals (N) in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 8. ОтноситеΛьная преΑставΛенность транскриптов патогенраспознающих рецепторов в гемоцитах моΛΛюсков Planorbarius corneus, заражённых трематоΑами Bilharziella polonica (I) и незаражённых особей (N) Fig. 8. Relative number of transcripts of pattern recognition receptors from hemocytes of Planorbarius corneus molluscs infected with Bilharziella polonica trematodes (I) and uninfected individuals (N)
Data for "A replicable and modular benchmark for long-read transcript quantification methods"
<p>This archive contains the input necessary to run the inital (TranSigner-protocol and IsoQuant-protocol) benchmarks associated with the <a href="https://github.com/COMBINE-lab/lr_quant_benchmarks" target="_blank" rel="noopener"><code>lr_quant_benchmarks repository</code></a>. The archive can be decompressed with <code>tar</code> and <code>zstd</code> using the command <code>tar --use-compress-program=zstd -xf input.tar.zstd</code>.</p>
Updated spiny mouse transcriptome assembly (now includes embryo-specific transcripts)
<p><strong>Summary</strong></p> <p>Updated spiny mouse transcriptome. Embryo-specific contigs generated from BioProject PRJNA436818 were added to the Trinity_v2.3.2 spiny mouse <em>de novo </em>transcriptome assembly (https://doi.org/10.5281/zenodo.808870).</p> <p> </p> <p><strong>Methods</strong></p> <p>Embryos were collected from female spiny mice (n=12) in accordance with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes with approval from the Monash Medical Centre Animal Ethics Committee. Female dams were staged from delivery of their previous litter (spiny mice conceive their next litter approximately 12h postpartum) and culled at specific time-points for embryo retrieval at the required stage: 2-cell at 48h postpartum (n=4), 4-cell at 52h postpartum ('early' 4-cell; n=2) or at 68h postpartum ('late 4-cell'; n=2), and 8-cell at 72h postpartum (n=4). Embryos were snap frozen in cell lysis solution per the Nugen SoLo protocol (version M01406v3; available from NuGEN). After ligation of cDNA, qPCR was performed on all samples to determine the number of amplification cycles required to ensure that amplification was in the linear range. Based on these results, each sample was amplified using 24 cycles. Final libraries were quantitated by Qubit and size profile determined by the Agilent Bioanalyzer. All libraries were in the expected size range (~320-360 bp). Custom 'AnyDeplete' rRNA depletion probes were designed and produced by NuGEN Technologies, Inc (San Carlos, CA, USA) using rRNA sequences from our reference transcriptome (Mamrot et al., 2017; https://doi.org/10.5281/zenodo.808870). Prior to use, efficacy and off-target effects of the rRNA depletion probes were examined <em>in silico</em> by NuGEN. Samples were loaded using c-Bot (200pM per library pool) and run on 2 lanes of an Illumina HiSeq 3000 8-lane flow-cell. PhiX spike-in was not used directly due to incompatibility with the custom rRNA depletion probes, however it was incorporated into other lanes of the same HiSeq 3000 run. RNA-Seq data (100bp, paired-end reads) are available from the NCBI as Bioproject PRJNA436818.</p> <p>The quality of RNA-Seq reads was assessed using FastQC v0.11.6 (<a href="https://github.com/s-andrews/FastQC">https://github.com/s-andrews/FastQC</a>; 50f0c26), with MultiQC v1.4 (<a href="https://github.com/ewels/MultiQC">https://github.com/ewels/MultiQC</a>; baefc2e) reports available from Github (<a href="https://github.com/jpmam1">https://github.com/jpmam1</a>) (Ewels et al., 2016). Adapter sequences were trimmed from the reads using trim-galore v0.4.2 (<a href="https://github.com/FelixKrueger/TrimGalore">https://github.com/FelixKrueger/TrimGalore</a>; d6b586e), implementing cutadapt v1.12 (<a href="https://github.com/marcelm/cutadapt">https://github.com/marcelm/cutadapt</a>; 98f0e2f). Reads with a quality scores lower than 20 and read pairs in which either forward or reverse reads were trimmed to fewer than 35 nucleotides were discarded. Further trimming of poor quality reads was conducted using Trimmomatic v0.36 (<a href="http://www.usadellab.org/cms/index.php?page=trimmomatic">http://www.usadellab.org/cms/index.php?page=trimmomatic</a>) with settings "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 AVGQUAL:25 MINLEN:35" (Bolger et al., 2014). Nucleotides with quality scores lower than 3 were trimmed from the 3’ and 5’ read ends. Reads with an average quality score lower than 25 or with a length of fewer than 35 nucleotides after trimming were removed. Error correction of reads was performed using Rcorrector v1.0.2 (<a href="https://github.com/mourisl/Rcorrector">https://github.com/mourisl/Rcorrector</a>; 144602f) (Song et al., 2015). FastQC was used to assess the improvement in read quality after trimming adapter removal; MultiQC reports are available from Github (<a href="https://github.com/jpmam1">https://github.com/jpmam1</a>).</p> <p>Error corrected reads were assembled using Trinity v2.4.0 (<a href="https://github.com/trinityrnaseq/trinityrnaseq">https://github.com/trinityrnaseq/trinityrnaseq</a>; 1603d80) with settings "--max_memory 400G, --CPU 32 and --full_cleanup" (Haas et al., 2013). Assembly statistics were computed using the TrinityStats.pl from the Trinity package, and summary statistics are provided in Table S1. All reads were aligned to this transcriptome assembly using Bowtie2 v2.2.5 (<a href="https://github.com/BenLangmead/bowtie2">https://github.com/BenLangmead/bowtie2</a>; e718c6f) with settings: "--end-to-end, --score-min L,-0.1,-0.1, --no-mixed, --no-discordant, -k 100, -X 1000, --time, -p 24" (Langmead & Salzberg, 2012).</p> <p>Read-supported contigs were identified within the embryo-specific Trinity <em>de novo </em>transcriptome assembly using samtools "idxstats" v1.5 (contigs with >=1 reads aligning were retained) (<a href="https://github.com/samtools/samtools">https://github.com/samtools/samtools</a>; f510fb1) (Li et al., 2009). The read-supported contigs from the embryo-specific assembly (n=54,660) were added to the reference spiny mouse transcriptome assembly previously described (Mamrot, J., Legaie, R., Ellery, S.J., Wilson, T., Seemann, T., Powell, D.R., Gardner, D.K., Walker, D.W., Temple-Smith, P., Papenfuss, A.T. and Dickinson, H., 2017. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Scientific Reports, 7(1), p.8996).</p> <p>The updated transcriptome is comprised of 2,274,638 transcripts in total.</p>
Extension of Partial Gene Transcripts by Iterative Mapping of RNA-Seq Raw Reads
<p>Trinity assembled transcriptome of <em>Drosophila melanogaster</em> and <em>Osmia </em><em>bicornis</em></p>
Transkripte von elf Video-Ansprachen der Schweizer Regierung vor Volksabstimmungen. Transcripts of Eleven TV Addresses Given by the Swiss Government before Popular Votes
<p>Der Datensatz enthält Transkripte (doc, html, pdf, txt) von elf TV-Ansprachen der Schweizer Regierung vor Volksabstimmungen. Die Ansprachen wurden nach GAT 2 transkribiert. / The dataset contains transcripts (doc, html, pdf, txt) of eleven TV addresses given by the Swiss government before popular votes. The addresses were transcribed according to GAT 2.</p> <p> </p> <p><strong>Quellenangabe der Transkripte / Reference to the Transcripts</strong></p> <p>Schröter, Juliane, Keller, Stefan, 2018. Transkripte von elf Video-Ansprachen der Schweizer Regierung vor Volksabstimmungen. Transcripts of Eleven TV Addresses Given by the Swiss Government before Popular Votes. doi: 10.5281/zenodo.1324476.</p> <p><em>Falls Sie sich nur auf eines oder einige der elf Transkripte beziehen, passen Sie die Quellenangabe bitte entsprechend an. / If you are only referring to one or some of the eleven transcripts, please adopt the reference accordingly. </em></p> <p><em>Disclaimer: Die Mitglieder des Bundesrates haben mündliche Ansprachen gehalten. </em><em>Für den Wortlaut der Transkripte sind sie nicht verantwortlich. / The members of the Federal Council have delivered oral addresses. They are not responsible for the wording of the transcripts.</em></p> <p> </p> <p><strong>Quellenangaben der Videos / References to the Videos</strong></p> <p>Bundesrat, 2017a. [TV-Ansprache zum] Bundesgesetz „Unternehmenssteuerreform III“. Produziert von SRG SSR. <a href="https://www.admin.ch/gov/de/start/dokumentation/abstimmungen/20170212/bundesgesetz-ueber-steuerliche-massnahmen-zur-staerkung-der-wett.html">https://www.admin.ch/gov/de/start/dokumentation/abstimmungen/20170212/bundesgesetz-ueber-steuerliche-massnahmen-zur-staerkung-der-wett.html</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2017b. [TV-Ansprache zum] Energiegesetz. Produziert von SRG SSR. <a href="https://www.admin.ch/gov/de/start/dokumentation/abstimmungen/20170521/Energiegesetz.html">https://www.admin.ch/gov/de/start/dokumentation/abstimmungen/20170521/Energiegesetz.html</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2016. [TV-Ansprache zur] Initiative „Für Ehe und Familie gegen die Heiratsstrafe“. Produziert von SRG SSR. <a href="https://www.srf.ch/play/tv/abstimmungen-teilw--in-gebaerdensprache/video/vorlage-heiratsstrafe-sendung-mit-gebaerdensprache?id=8e482ca4-52e3-4777-b956-529ce64f96d1">https://www.srf.ch/play/tv/abstimmungen-teilw--in-gebaerdensprache/video/vorlage-heiratsstrafe-sendung-mit-gebaerdensprache?id=8e482ca4-52e3-4777-b956-529ce64f96d1</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2015a. [TV-Ansprache zur] Änderung des Bundesgesetzes über Radio und Fernsehen. Produziert von SRG SSR. <a href="https://www.srf.ch/play/tv/abstimmungen/video/br-ansprache-zum-rtvg?id=dd58817b-235b-472a-96a2-a67c721e6775&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7">https://www.srf.ch/play/tv/abstimmungen/video/br-ansprache-zum-rtvg?id=dd58817b-235b-472a-96a2-a67c721e6775&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2015b. [TV-Ansprache zur] Präimplantationsdiagnostik. Produziert von SRG SSR. <a href="https://www.srf.ch/play/tv/ansprachen-bundesrat-in-gebaerdensprache/video/br-ueli-maurer-zum-fortpflanzungsmedizingesetz-fmedg-geb-?id=cbbecc0d-c210-41a9-8190-4d282926c3a8&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7">https://www.srf.ch/play/tv/ansprachen-bundesrat-in-gebaerdensprache/video/br-ueli-maurer-zum-fortpflanzungsmedizingesetz-fmedg-geb-?id=cbbecc0d-c210-41a9-8190-4d282926c3a8&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2014a. [TV-Ansprache zur] Beschaffung des Kampfflugzeuges Gripen. Produziert von SRG SSR. <a href="https://www.srf.ch/play/tv/abstimmungen/video/bundesrat-ueli-maurer-zur-beschaffung-des-kampfflugzeuges-gripen?id=febd8e03-d4c3-42e7-b163-37e9e0d0176c&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7">https://www.srf.ch/play/tv/abstimmungen/video/bundesrat-ueli-maurer-zur-beschaffung-des-kampfflugzeuges-gripen?id=febd8e03-d4c3-42e7-b163-37e9e0d0176c&station=69e8ac16-4327-4af4-b873-fd5cd6e895a7</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2014b. [TV-Ansprache zur] Initiative „Für den Schutz fairer Löhne“. Produziert von SRG SSR. <a href="https://www.srf.ch/play/tv/abstimmungen-teilw--in-gebaerdensprache/video/ansprache-von-bundesrat-johann-schneider-ammann-vom-20-04-2014?id=3ea16bd4-401d-4d68-9d06-b07b83582405">https://www.srf.ch/play/tv/abstimmungen-teilw--in-gebaerdensprache/video/ansprache-von-bundesrat-johann-schneider-ammann-vom-20-04-2014?id=3ea16bd4-401d-4d68-9d06-b07b83582405</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2014c. [TV-Ansprache zur] Initiative „Gegen Masseneinwanderung“. Produziert von SRG SSR. <a href="https://www.youtube.com/watch?v=A91gPrFXFCs">https://www.youtube.com/watch?v=A91gPrFXFCs</a> (Abfrage: 23.05.2018).<br> <br> Bundesrat, 2014d. [TV-Ansprache zur] Initiative „Pädophile sollen nicht mehr mit Kindern arbeiten dürfen“. Produziert von SRG SSR. <a href="https://www.bk.admin.ch/bk/de/home/dokumentation/volksabstimmungen/volksabstimmung-20140518.html">https://www.bk.admin.ch/bk/de/home/dokumentation/volksabstimmungen/volksabstimmung-20140518.html</a> (Abfrage: 18.04.2018).<br> <br> Bundesrat, 2013. [TV-Ansprache zum] Bundesbeschluss über die Familienpolitik. Produziert von SRG SSR. Video bereitgestellt von SRG SSR.<br> <br> Bundesrat, 2010. [TV-Ansprache] Zur Ausschaffungsinitiative und zum Gegenentwurf des Bundesrates. Produziert von SRG SSR. Video bereitgestellt von SRG SSR.</p> <p> </p> <p><strong>Quellenangabe des Transkriptionssystems / Reference to the Conventions of Transcription</strong></p> <p>Selting, Margret, Auer, Peter, Barth-Weingarten, Dagmar et al., 2009. Gesprächsanalytisches Transkriptionssystem 2 (GAT 2). Gesprächsforschung 10, 353-402.</p>
Building Public Confidence in Constructed Wetlands for Wastewater Treatment and Reuse: Survey Data and Focus Group Transcripts
<p>Constructed wetlands have been proposed as a cost-effective wastewater treatment, storage, and reuse solution for communities that are considering alternative water supply options to meet essential demands. In 2016, we began exploring the idea of wastewater reuse and the construction of an experimental wetland in Sewanee, located in the southern U.S. state of Tennessee. As a major barrier to water reuse is often public resistance, we conducted a survey and focus groups to determine strategies to develop and initiate a community engagement campaign, aiming to empower residents to form reasoned opinions about local water supply options.</p> <p>This data set includes the survey that was distributed to Sewanee community members between November 2015 and February 2016, as well as protocols for three focus groups that were conducted with K12 teachers and community leaders on February 11 and 12, 2016. The survey results are summarized in a Microsoft Excel file. The three focus groups were transcribed, these transcripts are included here as PDF documents.</p>
Aggregated frequencies of transcription initiations observed in FANTOM5 CAGE data on GRCh38, including alignments with low mapping qualities
<p><strong>Overview</strong></p> <p>Aligned reads of the FANTOM5 CAGE data have been used after filtering (ones with mapping quality less than 20 or percent identity less than 85% were discarded) for general purpose, resulting in the data set consisting of only the reads aligned with confidence. The filtering process made possible to interpret the data without ambiguity, however it also limited interpretation of paralogous or duplicated regions within the genome. Here all of the 5'-ends of the CAGE read alignments, including the ones with low mapping quality, were counted. The counts in the individual profiles were aggregated and summed up. </p> <p> </p> <p><strong>Special usage note</strong></p> <p>As noted above, this data derived from the alignments with low mapping qualities, as well as the ones with high mapping qualities. The result has to be examined very carefully: observations on the genome does not support transcription initiation with confidence, and even absence of such observation does not support silence of transcription with confidence. For example, file size on the forward strand is substantially larger than the one on the reverse strand, which is likely caused by an arbitrary preference of the alignment process. It does not mean transcription happens more frequently on the forward strand. Interpretation has to be made always in comparison with the standard data (BED files under http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v4/basic/ or bigWig files under http://fantom.gsc.riken.jp/5/datahub/hg38/reads/).</p> <p> </p> <p><strong>Data files</strong></p> <p>The resulting data files are formatted as bigWig (https://genome.ucsc.edu/FAQ/FAQformat.html#format6.1). '*.fwd.bw' and '*.rev.bw' represent forward and reverse strand on the genome, respectively. </p> <p> </p> <p><strong>Methods</strong></p> <p>The BAM files under http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v4/basic/ were subjected to 5'-end counting by bedtools v2.27.1 (https://github.com/arq5x/bedtools2), followed by conversion into bigWig with jksrc v357 (http://hgdownload.cse.ucsc.edu/admin/).</p> <p> </p>
Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1
<p>This repository contains the modeling files and the analysis related to the article <a href="https://www.ncbi.nlm.nih.gov/pubmed/30190596">"Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1"</a> by Jishage et al. in Nat Struct Mol Biol 2018.</p> <p><strong>For more information</strong> about how to reproduce this modeling, see the <a href="https://salilab.org/pol_ii_g/">Sali lab website</a> or the README file.</p>
Summary statistics - Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits
<p>Summary statistics for all trans-acting/target gene pairs tested in our manuscript.</p> <p>Preprint available: <a href="https://doi.org/10.1101/471748">https://doi.org/10.1101/471748</a></p>
Negev Walking Focusing Interviews: Original Transcripts (Anonymous)
<p>The attached files are 30 interview transcripts for the article: "In Search for the Authentic Nature Experience: Walking-Focusing Interviews as a Tool for Evaluating Cultural Ecosystem Services", written for People and Nature. </p> <p>The material is available for download as individual files (one for each interview) or as a ZIP file (.rar) if you wish to download all.</p> <p>The interviews took place in the Negev Desert, Israel, on a trail named "Bor Hemet", which is part of an official protected area, in October-December 2018 by the authors. Their analysis intends to provide an indication to whether this form of interviews - Walking-Focusing interviews - can provide meaningful qualitative and holistic information pertaining to Cultural Ecosystem Services that other methodologies have difficulties providing. </p> <p> </p> <p>For more details on the study, see the following poster: </p> <p>https://www.researchgate.net/publication/325924203_Walking_Focusing_and_Evaluating_the_Cultural_Ecosystem_Services_of_Drylands</p> <p> </p> <p>And the People and Nature website (open access journal):</p> <p> </p> <p>https://www.britishecologicalsociety.org/publications/journals/people-and-nature/</p> <p> </p> <p> </p> <p> </p> <p> </p>
What makes research software sustainable? Anonymized interview transcripts
<p>Anonymized transcripts of a series of interviews with the developers of research software.</p> <p>We also include the Participant Information Sheet provided to all participants before the interview commences.</p>
Data set for Sicoli et al. - Conformational tuning of a DNA-bound transcription factor
<p>The data set contains NMR, EPR and MD data. The NMR folder contains 1H-15N correlation NMR data of DNA-bound MAX with a paramagnetic MTSL spin label at position 5, with a chemically reduced, diamagnetic spin label, respectively. The EPR folder contains DEER data of MAX for three difference labeling positions R5C, G35C and R55C, with and without bound DNA. The MD folder contains MD trajecrories at three different temperatures, 310 K, 320 K and 330 K. Further details can be found in the readme.txt files in the respective folders.</p>
Feature count data for Love et al. 2019 analysis for "Using equivalence class counts for fast and accurate testing of differential transcript usage" paper
<p>Feature count data for Love et al. 2019 analysis used in the "Using equivalence class counts for fast and accurate testing of differential transcript usage" paper. For reproducing the analyses and figures using the <a href="https://github.com/Oshlack/ec-dtu-paper/">ec-dtu-paper</a> code.</p> <p>Contains:</p> <ul> <li>Equivalence class count matrix for all 24 samples (using counts from Salmon)</li> <li>Salmon quantification results for all 24 samples</li> <li>Exon counts for all 24 samples using DEXSeq-count</li> </ul>
Transcripts of interviews conducted with female agricultural entrepreneurs in the West of Ireland in 2018
<p>The file contains transcripts of recorded interviews with 10 women in the West of Ireland, who in the past had started a diversification business on or with farm resources. The objective of the research was to identify barriers for starting and growing a business for women in the agricultural domain. Furthermore resources used by these women for starting a business were explored. The method employed was that of narrative enquiries. The interviewer in all instances was the researcher.</p>
Transcripts of interviews conducted with female agricultural entrepreneurs in Bavaria conducted in 2018
<p>The file contains transcripts of recorded interviews with 19 women in Bavaria, who in the past had started a diversification business on or with farm resources. The objective of the research was to identify barriers for starting and growing a business for women in the agricultural domain. Furthermore resources used by these women for starting a business were explored. The method employed was that of narrative enquiries. The interviewer in all instances was the researcher.</p>
Processed data from "Chromatin information content landscapes inform transcription factor and DNA interactions"
<p><strong>Chromatin information content landscapes inform transcription factor and DNA interactions</strong></p> <p>Authors: Ricardo D’Oliveira Albanus, Yasuhiro Kyono, John Hensley, Arushi Varshney, Peter Orchard, Jacob O. Kitzman, Stephen C. J. Parker</p> <p><a href="https://doi.org/10.1101/777532">https://doi.org/10.1101/777532</a></p> <p> </p> <p>This record contains the processed data used in our manuscript. For instructions on how to use or regenerate this data, please refer to <a href="https://github.com/ParkerLab/chromatin_information">https://github.com/ParkerLab/chromatin_information</a>.</p>
Fig 2 in Docosahexaenoic Acid (DHA) Reduces LPSInduced Inflammatory Response Via ATF3 Transcription Factor and Stimulates Src/ Syk Signaling-Dependent Phagocytosis in Microglia
<p>Proteome profiler arrays (A and B) and expression of ATF3 gene (C) in microglia. Representative array membranes (A) and the relative levels of cytokines and chemokines (B) in microglia preincubated with 20 μM DHA and next treated with 10 ng/ml LPS.</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.