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Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS kidneys injected or not with heme
<p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of kidney (indicated rein) from HbSS mice injected or not with <span>heme</span> are presented here . </p> <p>The results of kidney (indicated rein) from HbAA mice injected or not with <span>heme</span> can be found at number 10.5281/zenodo.10963926.</p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin Institute INSERM U1016</span>. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA livers injected or not with heme
<p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.<span>Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.</span>All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of <span>livers (indicated foie)</span> from HbAA mice injected or not with <span>heme</span> are presented here . </p> <p>The results of <span>livers <span>(indicated foie)</span></span> from <span>HbSS</span> mice injected or not with <span>heme</span> can be found at number <a href="https://doi.org/10.5281/zenodo.10962971">10.5281/zenodo.10962971</a>. </p> <p>Thirty μm-thick frozen tissue sections of <span>livers</span> were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin</span> Institute INSERM U1016. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA kidneys injected or not with heme
<p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of kidney (indicated rein) from HbAA mice injected or not with <span>heme</span> are presented here . </p> <p>The results of kidney (indicated rein) from HbSS mice injected or not with <span>heme</span> can be found at number </p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin</span> Institute INSERM U1016. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p>
Data for the paper titled 'Dynamic Molecular Atlas for Cardiac Fibrosis at Single-Cell and Spatial Resolution: CD248 in Orchestrating Fibroblast-Immune Interaction'
<p>The deposited data were employed to generate the figures concerning single-cell RNA (scRNA) and spatial transcriptomic analyses in the paper titled 'Dynamic Molecular Atlas for Cardiac Fibrosis at Single-Cell and Spatial Resolution: CD248 in Orchestrating Fibroblast-Immune Interaction'.</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS lung injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of lung (indicated poumon) from HbSS mice injected or not with heme are presented here . </p> <p>The results of lung (indicated poumon) from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10965912</p> <p>Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA lung injected or not with heme
<div> <div> <p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease.Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease.All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of lung (indicated poumon) from HbAA mice injected or not with heme are presented here . </p> <p>The results of lung (indicated poumon) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10966094</p> <p>Thirty μm-thick frozen tissue sections of lungs were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p> </div> </div>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS heart injected or not with heme
<div> <p>The objective of this experiment was to explore the <span>transcriptome</span> of the <span>HbSS Townes</span> <span>mouse model</span> of <span>sickle cell disease</span>.Townes model mice carry several human hemoglobin <span>knock-in</span> genes replacing the endogenous mouse genes and may be useful in studying <span>sickle cell disease</span>.All mice were <span>genotyped</span>, age- and sex-matched littermates. All <span>HbAA</span> (control, normal human hemoglobin) vs HbSS (<span>sickle cell disease</span>, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group <span>heterogeneity</span>. <span>Hemin</span> (<span>Ferriprotoporphyrin IX</span>) was purchased from <span>Frontiers Scientific</span> and injected <span>intravenously</span> (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received <span>PBS</span> instead. Mice were anesthetized with <span>isoflurane</span> 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>The results of heart (indicated coeur) from HbSS mice injected or not with <span>heme</span> are presented here . </p> <p>The results of heart (indicated coeur) from <span>HbAA</span> mice injected or not with <span>heme</span> can be found at number 10.5281/zenodo.10964042</p> <p>Thirty μm-thick frozen tissue sections of kidneys were cut as above and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit <span>Promega</span> AS1280). The quality and quantity of mRNA were evaluated using a 2100 bioanalyzer with TNA 6000 NanoKits (all <span>Agilent Technologies</span>, <span>Palo Alto, CA</span>, <span>USA</span>). RNA Integrity Numbers superior to 7 were eligible for subsequent <span>reverse transcription</span> into <span>cDNA</span>. <span>RNAseq</span> was performed at the GenomIC plateform <span>Cochin</span> Institute INSERM U1016. After <span>RNA extraction</span>, RNA quality (<span>RNA integrity number</span>) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (<span>Illumina</span>) according to manufacturer instructions. Briefly, purified <span>poly-A</span> containing mRNA molecules were fragmented and <span>reverse-transcribed</span> using random <span>primers</span>. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the <span>cDNA</span> was followed by <span>ligation</span> of <span>Illumina</span> adapters.<br>Libraries were quantified by <span>qPCR</span> using <span>KAPA Library Quantification</span> Kits for <span>Illumina</span> Libraries (KapaBiosystems, <span>Wilmington</span>, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an <span>Agilent</span> Bioanalyzer. Libraries were sequenced on an <span>Illumina</span> Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a <span>paired-end</span> mode. After sequencing, primary analysis based on AOZAN software (ENS, <span>Paris</span>), was applied to <span>demultiplex</span> and control the quality of the <span>raw data</span> (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA <span>PBS</span>, HbAA <span>heme</span>, HbSS <span>PBS</span>, <span>HbSS</span> <span>heme</span>. </p> </div>
Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway
<p>This is Supplement Tables of Recombinant Klotho protein protects pulmonary alveolar epithelial cells against sepsis-induced apoptosis by inhibiting the Bcl-2/Bax/caspase-3 pathway.</p>
Lysosome training dataset for live cell anatomy segmentation
Open the record for dataset details and reuse information.
ER training dataset for live cell anatomy segmentation
Open the record for dataset details and reuse information.
dataset figures - Assessing the Performance of Fuel Cell Electric Vehicles Using Synthetic Hydrogen Fuel - Article Energies
<p>Dataset for Table 1 - 2 and for Figure 4</p>
Gene expression data from clones of FAO cells with different glucose production capability
<div> <div> <div> <p>In response to energy and nutrient shortage, the liver triggers several catabolic processes to promote survival. Despite recent progresses, the precise molecular mechanisms regulating the hepatic adaptation to fasting remain incompletely characterized. Here, we report the identification of Hydroxysteroid dehydrogenase-like 2 (HSDL2) as a mitochondrial protein highly induced by fasting. We show that activation of PGC1a-PPARa and inhibition of the PI3K- mTORC1 axis stimulate HSDL2 expression in hepatocytes. We found that HSDL2 depletion decreases cholesterol conversion to bile acids (BAs) and impairs FXR activity. HSDL2 knockdown also reduces mitochondrial respiration, fatty acid oxidation, and TCA cycle activity. Bioinformatics analyses revealed that hepatic Hsdl2 expression positively associates with the postprandial excursion of various BA species in mice. Here, we show that liver-specific HSDL2 depletion impacts BA metabolism and decreases circulating cholesterol levels upon refeeding. Overall, our report identifies HSDL2 as a fasting-induced mitochondrial protein that links nutritional signals to BAs and cholesterol homeostasis.</p> </div> </div> </div>
Suppl. Table 2: Cell morphometrics in each embryo.
<p>Samuel Boscq Thesis Chapter 3 Supplementary data</p>
Data from: Evaluating single-cell variability in proteasomal decay
<p>Gene expression is a stochastic process that leads to variability in mRNA and protein abundances even within an isogenic population of cells grown in the same environment. <br>This variation, often called gene-expression noise, has typically been attributed to transcriptional and translational processes while ignoring the contributions of protein decay variability across cells. <br>Here we estimate the single-cell protein decay rates of two degron GFPs in \textit{Saccharomyces cerevisiae} using time-lapse microscopy. <br>We find substantial cell-to-cell variability in the decay rates of the degron GFPs.<br>We evaluate cellular features that explain the variability in the proteasomal decay and find that the amount of 20s catalytic beta subunit of the proteasome marginally explains the observed variability in the degron GFP half-lives. <br>We propose alternate hypotheses that might explain the observed variability in the decay of the two degron GFPs.<br>Overall, our study highlights the importance of studying the kinetics of the decay process at single-cell resolution and that decay rates vary at the single-cell level, and that the decay process is stochastic. <br>A complex model of decay dynamics must be included when modeling stochastic gene expression to estimate gene expression noise.</p>
BEHAV3D: A 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response
<p>The use of patient-derived material and immune cell co-cultures in modeling immune-oncology has gained significant interest for understanding and manipulating immune cell tumor targeting in a patient-specific context. However, current protocols have limitations in visualizing and analyzing the dynamic cellular features of these living culture systems. We recently developped a workflow names BEHAV3D, that combines multi-color live 3D imaging and computational tools to analyze cell death dynamics, classify T cell behavior, and generate data-informed 3D images and videos. Here we provide some example pre-processed dataset of videos of two co-culture set ups: breast cancer Patient Derived Organoids with αβ T cells engineered to express a γδ TCR (TEGs) and Acute Lymphoblastic Leukemia cells with CD19 CART cells.</p>
Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data
<p>This repository contains raw and processed data of the original datasets generated for Lee et al. "Segmentation aware probabilistic phenotyping of single-cell spatial protein expression data".</p> <p>The files Dilution_3_ROI02.ome.tiff, Dilution_3_ROI02_mask.ome.tiff, st_reclustered_expr_data.h5ad contain raw data (as ome tiff), a mesmer-generated segmentation mask, and single-cell quantification in anndata format of the cell pellet data generated for the study.</p> <p>The file tonsil-for-zenodo.tar.gz contains all raw and processed data of the IMC data of the 16 human tonsil ROIs:</p> <ul> <li>imc contains raw tiff stacks of the acquisition</li> <li>mask contains mesmer-generated masks</li> <li>channel.yml contains channel info</li> <li>exp_mat/dc/ contains single cell quantifications using mesmer segmentation</li> </ul>
PM_035422_B_Celles
<u>File Name</u>: PM_035422_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, Eglise Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Église paroissiale (Eglise Saint-Hadelin). Extérieur. Le site. <br><u>Description</u>: Parish church (Eglise Saint-Hadelin) Exterior The site <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Historic site, Houyet, Monuments, Namur, Romanesque, Styles, Thematic <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
PM_035425_B_Celles
<u>File Name</u>: PM_035425_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, L'Hermitage Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Abbaye (L'Hermitage Saint-Hadelin). Extérieur. Façade ouest et entrée. 19ème siècle ( ?). <br><u>Description</u>: Abbey (L'Hermitage Saint-Hadelin) Exterior West facade and entrance 19th century (?) <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Houyet, Monuments, Namur, Neo-Romanesque, Romanesque, Styles <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
PM_035415_B_Celles
<u>File Name</u>: PM_035415_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, Eglise Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Église paroissiale (Eglise Saint-Hadelin). Intérieur. La nef. 11ème siècle (1040 ?). <br><u>Description</u>: Parish church (Eglise Saint-Hadelin) Interior The nave 11th century (1040 ?) <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Houyet, Monuments, Namur, Romanesque, Styles <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells
<p>The raw data presented in this folder corresponds to the publication<br># Dynamic cortical behavior of plant protoplasts reveals unexpected similarities between plant and animal cells</p> <p>Johanna E. M. Dickmann 1,2, Marjolaine Martin 1,§, Claire Lionnet 1,§, Zoe Nemec-Venza 1, Olivier Hamant 1,2</p> <p>1 Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, INRAE, CNRS, UCBL1 <br>2 Correspondence: olivier.hamant@ens-lyon.fr, johanna.dickmann@ens-lyon.fr <br>§ Equal contribution </p> <p>ORCIDs:<br>* Johanna Dickmann: 0000-0002-0861-4440<br>* Zoe Nemec-Venza: 0000-0002-2346-2596<br>* Olivier Hamant: 0000-0001-6906-6620</p> <p>Submitted to bioRxiv in November 2024 </p> <p>This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 521501033 to J.D. and the European Research Council (ERC-2021-AdG-101019515 “Musix” to O.H.).</p> <p>## Data organization</p> <p>The data are organized according to the figure panels in the publication. For large experiments, the folders may contain subfolders for each experimental repeat and/or condition. For explanations on the data and the methods, please refer to the publication.</p> <p>All data presented here are the original raw data output of the microscopes in the CZI format, a proprietary format developed by Zeiss, encapsulating both 4D image data and metadata, i.e. acquisition settings. This format is supported by open-source software such as Fiji and Open Microscopy Environment.</p> <p>Refer to the README files in the subfolders for information on which exact file was used to display in the figure.</p> <p>## Explanation of the file names</p> <p>### Arabidopsis experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g.”PLA001”, “PRO077”)</p> <p>* the line of the imaged plant material (e.g. “pUBQ10-LTi6B-TdTomato”)</p> <p>* sometimes information on the ecotype of the line (e.g. “Col-0”)</p> <p>* the age of the plants (e.g. “7d” = 7 day old plants)</p> <p>* sometimes information on a stain added (e.g. “FM4-64_0_5ugPml” = FM4-64 dye at a final concentration of 5 ug/ml)</p> <p>* sometimes information on a treatment (e.g. “beforeFDA” = image taken before FDA was added; “FDA2.5ugPml” = after adding FDA at a final concentration of 2.5 ug/ml, sometimes with additional information on the time between adding the FDA and imaging, e.g. “25min”)</p> <p>* sometimes information on the centrifugation speed (e.g. “100g”)</p> <p>* sometimes information on the imaging support (e.g. “bucket” = NOA73 container, “wells” = NOA73 microwells, “coverslip”)</p> <p>* sometimes information on the imaging mode (“z-stack”, “t-series” = time series/timelapse, “6x” = zoom of 6 in Zen software)</p> <p>* the solution the sample was imaged in (“Solution A” or “A” = hyperosmotic buffer with D-mannitol, “AS” = hyperosmotic buffer with D-sorbitol)</p> <p>* sometimes information on experimental setup (“ON” = overnight timelapse imaging)</p> <p>* increasing numbers at the end of the file name indicate subsequent fields of view or positions imaged with the same settings</p> <p>* for Fig. 1A: information about the length of the plasmolysis (“50 min”)</p> <p>* for Fig. 4c,d: information on which solution the protoplasts are and have been imaged in: “A” = hyperosmotic buffer solution with 600 mM D-mannitol. “B” = hyperosmotic buffer solution with 280 mM D-mannitol. Times indicate time between addition of new buffer and onset of imaging of the position list.</p> <p>* for Fig. 4e-f: the concentration of the hyperosmotic buffer solution is indicated. For the control, the number of additions of hyperosmotic buffer solution with 600 mM D-mannitol is indicated.</p> <p>### Physcomitrium patens experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g. "PyP001") </p> <p>* “Physco_wt” referring to Physcomitrium patens wild type</p> <p>* the age of the moss tissue used for protoplasting (e.g. “6d” = 6 days)</p> <p>* information on the stain added (e.g. “ Fm4-64_2ugPml” = FM4-64 dye at a final concentration of 2 ug/ml)</p> <p>* information on the imaging support (e.g. “bucket” = NOA73 container, “coverslip”)</p> <p>### Maize experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* the date on which the experiment was performed (yyyymmdd)</p> <p>* the plant species (“Maize”)</p> <p>* sometimes information in the solution used for digestion ("A+E" = hyperosmotic buffer solution with D-mannitol)</p> <p>### Bead experiments</p> <p>The filenames contain the following information, separated by underscores:<br>* an experiment identifier (e.g. “beads008”)</p> <p>* a description of the beads (“fluoresbrite1micron” = Fluoresbrite beads of a diameter of 1 um)</p> <p>* sometimes a short description of the protocol (e.g. “SolAwashed-2-3mLsolA” = NOA73 microwells were washed in hyperosmotic buffer with 600 mM D-mannitol 2x prior to imaging, beads were imaged in 3 ml hyperosmotic buffer solution with 600 mM D-mannitol.)</p> <p>* an information on the size of the field of view (e.g. “small FOV” = small field of view, i.e. one microwell with beads)</p> <p>* information at which approx. height of the microwell the image was taken (“TopOfWells” = close to the opening of the wells on the top)</p> <p>* sometimes information on the zoom of the Zen software (e.g. “7x”)</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.