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400 results for “zebrafish embryos”
Gene-level counts according to their poly(A) length and additional uridine modifications in several stages of zebrafish, Xenopus, and mouse embryos
<p>This HDF5 file contains the processed data of primary poly(A) tail length analyses for the TAIL-seq runs used for Chang and Yeo et al. (2018; doi:10.1016/j.molcel.2018.03.004). The read count tables are stored under the two-level group structure of the run identifier as the first level and the sample identifier as the second level. A dataset at a leaf node is an unsigned integer array of the read count numbers by the length of poly(A) in rows and the length of U tails following after poly(A) in columns.</p> <p>Please refer to the <a href="https://data.mendeley.com/datasets/tzc5wwczyg/1">supplementary data page</a> of the original paper for more information about the experimental design.</p> <p> </p>
Data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos
<p>This contains the data for the manuscript Feugere et al., "Heat induces multiomic and phenotypic stress propagation in zebrafish embryos" (2023). Zebrafish embryos were exposed to thermal stress ("TS") and stress metabolites ("SM") released by heat-stressed conspecifics in a two-way factorial design ("TSxSM"). The folder includes raw molecular data (cortisol levels, HSP70 protein levels, and gene expression acquired with LAMP and RNA-seq) and raw phenotypic data (morphology, hatching, survival, and behaviour) of zebrafish <em>Danio rerio </em>at 1 day and 4 days of development.</p> <p>The .csv files contain all quantitative data, whilst the .tab files contain the gene count data required for gene expression analysis. The data were analysed in R using the code shared in the "TSxSM2.stats.Rmd" file. The "Metadata" document provides the reader with an extensive description of each file.</p>
Transcriptomic profiling of clobetasol propionate-induced immunosuppression in challenged zebrafish embryos
<p>We have conducted an immune challenge experiment on 48h zebrafish embryos, which were previously treated with the immunosuppressive drug clobetasol propionate (CP). The embryos' immune system was challenged by injection of a mix of different pathogen associated molecular patterns (PAMPs). RNA sequencing was performed in order to detect altered molcular expression levels induced by CP, PAMPs and a combination of both. The data was published in <a href="https://doi.org/10.1016/j.ecoenv.2022.113346" target="_blank" rel="noopener">Essfeld <em>et al.</em> 2022</a>.</p> <p>The uploaded data archive (<a href="https://www.7-zip.org/">7-zip</a> compressed) consists of three major data types:<br>1. MultiQC reports from raw RNA-Seq read processing and QC (50bp SR)<br>2. Result tables from differential gene expression analysis (DGEA) with DESEq2<br>3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler</p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8) . Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log<sub>2</sub>-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118).</p> <p>The ArrayExpress accession number E-MTAB-11092, provides access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>
Zebrafish Embryos Imaging Data for Virtual Orientation Tools Article
<p>The zebrafish embryos were imaged in a 96-well plate using an Acquifer IM (Bruker, Heidelberg), an automated fluorescence widefield screening microscope, and a Nikon objective</p>
Figure 4 in Use of melatonin as an inhibitor of apoptotic process for cryopreservation of zebrafish (Danio rerio) embryos
Figure 4. Representative images of zebrafish (Danio rerio) embryos showing reactive oxygen species (ROS) formation (A-D) and DNA fragmentation (E-H) following vitrification for the control group and vitrified treatments with 0, 1 µM and 1 mM melatonin respectively. Arrows and arrow heads point to tissues affected in the body axis and those in close proximity to the yolk respectively.
Figure 3 in Use of melatonin as an inhibitor of apoptotic process for cryopreservation of zebrafish (Danio rerio) embryos
Figure 3. Percentage area of zebrafish (Danio rerio) embryos affected by reactive oxygen species (ROS) formation and DNA fragmentation after vitrification for the control group and vitrified treatments with 0, 1 µM and 1 mM melatonin respectively. Bars with different letter within the same assay were significantly different from one another (P <0.05).
Figure 2 in Use of melatonin as an inhibitor of apoptotic process for cryopreservation of zebrafish (Danio rerio) embryos
Figure 2. Bax, bcl-2 and caspase-3 mRNA expression levels in zebrafish (Danio rerio) embryos for the control group and vitrified treatments with 0, 1 µM and 1 mM melatonin respectively obtained by the 2-∆∆CT method. Boxes with same letter are not significantly different from one another (P> 0.05).
Figure 1 in Use of melatonin as an inhibitor of apoptotic process for cryopreservation of zebrafish (Danio rerio) embryos
Figure 1. Representative scanning electron micrographs of vitrified and non-vitrified zebrafish (Danio rerio) embryos. (A) Control group; (B-D) Vitrified with 0, 1 µM and 1 mM melatonin respectively. Arrows, arrow head and asterisk point to invaginations and perforations, rupture of the vitelline membrane and wrinkling of the epidermis respectively.
Time-lapse (4D) volumetric fluorescence microscopy image sequence of a living zebrafish embryo
<p>The dataset contains a time-lapse (4D) volumetric fluorescence microscopy image sequence of a living zebrafish embryo (cxcr4aMO). The sequence has been captured with a confocal laser-scanning microscope during zebrafish gastrulation and shows endodermal cells that have been fluorescently labelled.</p> <p>The sequence is best viewed with Fiji (https://fiji.sc/) and can be loaded into Matlab with tiffread.m (http://www.cytosim.org/misc/index.html).</p> <p>For the treatment of the specimen see:</p> <p>S. Nair and T. F. Schilling. Chemokine signaling controls endodermal migration during zebrafish gastrulation. Science, 322(5898):89–92, October 2008.</p>
HRAS_GFP zebrafish Embryo z-stack and 3D reconstruction visualized through LSFM
<p>A 2dpf zebrafish larvae is imaged through a custom developed LSFM setup developed at ICFO, at the Super-resolution Light microscopy and Nanoscopy (SLN) facility, with a resolution of 1 um, and with a double illumnation scheme.</p> <p>Pixel size is 0.43 um. Voxel depth is 2 um.</p> <p>The transgenic line is expressing HRAS_GFP labeling.</p> <p>The z-stack and corresponding 3D reconstruction are showed.</p> <p> </p> <p> </p>
Fluorescent oil droplet in developing zebrafish embryo
<p>Multichannel image data of fluorescently-labelled oild droplet injected into developing Zebrafish embryo. The frame rate is 3min and the interfacial tension of the injected droplet equals 3.3 mN/m²</p>
Toxicogenomic profiles of neuronal targeting insecticides in zebrafish embryos as non-target aquatic vertebrate model
<p>We have conducted semi-static exposure studies with six neuronal targeting insecticides on fertilized zebrafish (Danio rerio) eggs, similar to the OECD 236 guideline for the 96h zebrafish embryo toxicity test. The aim of these transcriptomic profiling experiments was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of pesticides. Data published in <a href="https://doi.org/10.1016/j.chemosphere.2021.132746">Reinwald et al. 2021</a> (PMID:<strong>34748799</strong>).</p> <p>For experimental details please refer to the publicly accessible experiment description and treatment protocols deposited in the <a href="https://www.ebi.ac.uk/arrayexpress/">ArrayExpress database </a>at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under the following accession numbers: <a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9852/">E-MTAB-9852</a> (Abamectin), <a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9855/">E-MTAB-9855 </a>(Carbaryl),<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9853/"> E-MTAB-9853</a> (Chlorpyrifos), <a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9854/">E-MTAB-9854</a> (Fipronil), <a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9859/">E-MTAB-9859</a> (Imidacloprid), <a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9860/">E-MTAB-9860</a> (Methoxychlor).</p> <p>The uploaded data archives (<a href="https://www.7-zip.org/">7-zip</a> compressed) consists of three major data types:<br> 1. MultiQC reports from raw RNA-Seq read processing and QC (50bp SR) ( <a href="https://zenodo.org/api/files/5c06b1b3-0d96-4ab8-8925-a7419f0a379d/Neuotox_multiQCreports.7z">Neuotox_multiQCreports.7z </a>)<br> 2. Result tables of differential gene expression analysis (DGEA) with DESEq2 ( <a href="https://zenodo.org/api/files/5c06b1b3-0d96-4ab8-8925-a7419f0a379d/Neurotox_DESeq2_ResultTables.7z">Neurotox_DESeq2_ResultTables.7z </a>)<br> 3. Result tables of gene set enrichment analysis (GSEA) with clusterProfiler ( <a href="https://zenodo.org/api/files/5c06b1b3-0d96-4ab8-8925-a7419f0a379d/Neurotox_clusterProfiler_ResultTables.7z">Neurotox_clusterProfiler_ResultTables.7z </a>)<br> 4. Result tables of overrepresentation analysis (ORA) via <em>clusterProfiler::compareCluster() </em>( <a href="https://zenodo.org/api/files/c3fb14b4-6a90-4b12-a2be-ed5661d19683/Neurotox_clusterProfiler_ORA_on_core_DEGs.7z?versionId=2156d2be-b815-4157-b0f9-3eeed117b812">Neurotox_clusterProfiler_ORA_on_core_DEGs.7z </a>)</p> <p>Each data archive contains a README file describing the methods applied to generate the respective result tables / reports. For each tested substance and exposure condition a DGEA and GSEA result table is uploaded. The corresponding bash and R codes for each analysis step are available on github under:<br> <a href="https://github.com/hreinwal/zfeNeurotox">https://github.com/hreinwal/zfeNeurotox</a></p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8). Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log<sub>2</sub>-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895) before DGEA result tables were subjected to GSEA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118)<br> and reactomePA (<a href="https://pubs.rsc.org/en/content/articlehtml/2015/mb/c5mb00663e">Yu and He, 2016</a>, DOI 10.1039/C5MB00663E). The linked ArrayExpress accession numbers above, provide access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>
Zebrafish embryos time-course, 5'UTR nup43
<p>This Zenodo file contains data for the 5′ UTR-nup43-sfGFP mRNA reporter. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, 5'UTRs hnrnpl and egfl6
<p>This Zenodo file contains data for the 5′ UTR-hnrnpl-sfGFP and 5′ UTR-egfl6-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 2 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, M&Z 5'UTRs scarb2c
<p>This Zenodo file contains data for the maternal and zygotic 5′ UTR-scarb2c-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Zebrafish embryos time-course, M&Z 5'UTRs cfl1l
<p>This Zenodo file contains data for the maternal and zygotic 5′ UTR-cfl1l-sfGFP mRNA reporters. Data consists of raw microscopy images of embryos, as well as csv files with quantification of relative sfGFP expression data (normalized to a dextran dye control) and png files depicting ROIs used for quantification presented in Figure 7 of Reimão-Pinto et al., Dev Cell, 2024.</p> <p>Embryos were injected with 1 nL of an injection mix directly into the cell at the 1-cell stage with a microinjection needle (Sutter Instruments) and allowed to develop in standard conditions. For single-reporter injections, 40pg 5′ UTR-sfGFP test reporter were co-injected with 2 ng fluorescent red dextran dye (D1868, Invitrogen) as injection control per embryo. Embryos were collected at the desired developmental stage and placed on a custom-made agarose mold with squared indents for placing and aligning the embryos. For fluorescence intensity quantification, zebrafish embryo images were acquired using an upright ZEISS Axiozoom coupled to an Axiocam 503 color/mono digital camera (14-bit depth) in black & white color mode with fixed laser power (red laser power 85% and 300 ms exposure; green laser power 65% and 300 ms exposure), fixed zoom and fixed exposure time for red mRF12 (590/612) and green AF488 (493/517) channels. Two rounds of single-reporter injections (embryos from two different clutches) were performed for fluorescence intensity quantifications.</p> <p>Images were quantified using Fiji (Image J) using a macro for automated thresholding and channel fluorescence intensity measurement. For each image, the script automatically segments the image based on red channel intensity (control dextran dye) using FIJI’s auto thresholding tool (RenyiEntropy) and outputs csv files with mean fluorescence intensities of red and green channels for that region of interest (and a small invariant region for background correction). The mean fluorescence values outputted were then used for calculating normalized mean intensity ratios (sfGFP/dextran). A total of 25 embryos per injection round were quantified, for a total of 50 embryos per time-point, per reporter. This excel contains normalized fluorescence intensity values calculated. More embryos were quantified than the ones included in the analysis (due to unequal number of embryos imaged per experiment, we decided to consider a fixed number of 25 per reporter injection). Some embryos were not considered for normalized intensity calculations due to improper automatic segmentation (e.g. due to the presence of a background dirt spot that is recognized as "signal"), due to precipitation of the dextran dye in the embryo's chorion or due to improper embryo development resulting from injury from injection. All images acquired are available for inspection. The FIJI macro for automated segmentation and ROI intensity measurements are also provided in the Mendeley Repository associated to the study.</p>
Investigation the cytotoxicity of newly synthesized quinazo-line–sulfonamide derivatives in human leukemia cell lines and hematopoietic activity in zebrafish embryos.
<p>These videos contain the time lapse imaging of the wild type zebrafish embryos showing the circulation, control (mock 0.5% V/V DMSO) and compound 4a treated embryos at 72 hours post fertilization. The compound 4a specifically blocked the formation of blood and no circulation was seen in these embryos. </p>
Raw Sanger sequences of the tyr fragment from crispant and control zebrafish embryos
<p><span>Thanks to the amenability to genetic modifications, the minimal or non-invasive phenotyping possibilities in early embryos and larvae and the presence of a high percentage of genes orthologous to humans, zebrafish is a successful alternative vertebrate to validate new disease genes and variants and to study mechanisms underlying human diseases. We developed an optimized method allowing early and gentle genotype detection to reduce further possible suffering associated with the generation of genetically modified zebrafish and valid to strategize the employment of "surplus" animals (e.g., those needed solely for line generation or without the desired genotype). The method is based on minimally-invasive tissue (fin) scratching (FS) to obtain genomic DNA material and perform genotyping in early zebrafish embryos. We showcase the method's usefulness for various genotyping needs, including screening both F0 and stable CRISPR/Cas9 lines and obtaining genomic material compatible with Sanger sequencing. Here we provide the raw sequences obtained from FS-derived genomic DNA of single mutant F0 embryos carrying mutations in the <em>tyr</em> gene generated with Base editor (BE) CRISPR/Cas9 technology. We compared the sequencing outcome of FS- vs whole embryos (WE)-based genomic DNA preparation (the WE sequencing results are also provided here). Sequences show the successful C>T (G>A) conversion generating crispant <em>tyr</em> mutants that FS-derived genomic DNA can capture. The resulting dataset demonstrates the compatibility of the method developed with sequencing-based genotyping of early crispant embryos. </span></p>
Annotated and processed 3D confocal microscopy images of dorsal aorta in wild-type and Endoglin-deficient zebrafish embryos at 48 hpf and 72 hpf
<p>This repository contains the original 3D confocal microscopy images that were used for the analysis of vessel geometry and endothelial cell morphology in the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos at 48 hours post fertilization (hpf) and 72 hpf in the article <a href="https://www.biorxiv.org/content/10.1101/2024.02.19.580931">Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos</a>. In this article, we developed a novel mathematical approach that allows to consistently estimate 3D vessel geometry and endothelial cell surface morphology using only information from endothelial cell contours. For the article's analysis, endothelial cell contours were manually annotated on Pecam1-EGFP-labeled cell junctions. Furthermore, dorsal aorta cross-sections were outlined on Dextran Texas Red-perfused vessel lumens. Further details are provided in the article's Materials and methods section.</p> <p>This repository contains 14 images of 7 wild-type embryos, each imaged at 48hpf and 72hpf. Furthermore, 12 images of 6 Endoglin-deficient embryos, each imaged at 48hpf and 72hpf are included. These combined files (called "analysis data" in the article) are stored in "eng_wt_data.zip". Secondly, images of 2 wild-types at 72hpf with repeated cell contour annotation and outlined vessel lumens (called "validation data" in the article) are located in "wt_angiogram_data.zip". The provided files are stored in Imaris format and can be inspected using the free <a href="https://imaris.oxinst.com/imaris-viewer">Imaris Viewer software</a>.</p> <p>To allow inspection of the endothelial cell contours that we manually annotated for the article's analysis and compare them against the intermediate results of our novel mathematical approach, i.e., contour enrichments by neighboring cells, contour smoothing splines and their projections onto the estimated vessel surfaces, we imported these contours into the Imaris files. Note that the contours' coordinates in these files are slightly less precise than in our article's analysis and thus are intended for visual inspection. To exactly reproduce the results in our article, refer to the files in <a href="https://doi.org/10.5281/zenodo.10549101">our other Zenodo repository</a>.</p>
Gene biomarkers for the assessment of thyroid-disrupting activity in zebrafish embryos
<p>We have conducted an exposure study on zebrafish embryos using thyroidal active compounds. Based on OECD guideline 236, freshly fertilized zebrafish embryos were exposed to two sublethal concentrations of triiodothyronine (T3), 6-Propyl-2-thiouracil (6-PTU), methimazole (MMI) and iopanoic acid (IOP) until 96 hours post fertilization. RNA was extracted and sequenced to identify thyroid-related gene expression patterns. .</p> <p>The uploaded data archive consists of three major data types:<br>1. MultiQC reports from raw RNA-Seq read processing and QC<br>2. Result tables from differential gene expression analysis (DGEA) with DESeq2 (apeglm shrunk results indicated by "reslfs")<br>3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler</p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8). Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log<sub>2</sub>-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118).</p> <p>The ArrayExpress accession numbers E-MTAB-14185 (IOP), E-MTAB-14184 (MMI), E-MTAB-14183 (T3) and E-MTAB-9054 (6-PTU), provide access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>
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.