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25,372 results for “Transcriptomics”
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
<p>Spatial transcriptomics (ST) technologies enable high throughput gene expression characterization within thin tissue sections. However, comparing spatial observations across sections, samples, and technologies remains challenging. To address this challenge, we developed STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. We apply STalign to align ST datasets within and across technologies as well as to align ST datasets to a 3D common coordinate framework. We show that STalign achieves high gene expression and cell-type correspondence across matched spatial locations that is significantly improved over landmark-based affine alignments. Applying STalign to align ST datasets of the mouse brain to the 3D common coordinate framework from the Allen Brain Atlas, we highlight how STalign can be used to lift over brain region annotations and enable the interrogation of compositional heterogeneity across anatomical structures. STalign is available as an open-source Python toolkit at <a href="https://github.com/JEFworks-Lab/STalign">https://github.com/JEFworks-Lab/STalign</a> and as supplementary software with additional documentation and tutorials available at <a href="https://jef.works/STalign">https://jef.works/STalign</a>.</p> <p>Here we have included alignment results that were used in performance analysis of STalign:</p> <p>We aligned Slice 2 Replicate 3 to Slice 2 Replicate 2 of the MERFISH mouse coronal brain sections available from Vizgen Data Release V1.0. May 2021 (<a href="https://info.vizgen.com/mouse-brain-map">https://info.vizgen.com/mouse-brain-map</a>).</p> <ul> <li>STalign_S2R3_to_S2R2.csv.gz contains cell ids, original cell centroid positions of S2R3, cell positions of S2R3 after alignment to S2R2 with STalign, cell positions of S2R3 after supervised affine alignment to S2R2, and counts for genes and blanks.</li> <li>STalign_S2R2.csv.gz contains cell ids, cell centroid positions of S2R2 and counts for genes and blanks.</li> </ul> <p>Additionally, we aligned Slice 2 Replicate 3 to a Visium dataset of an FFPE preserved adult mouse brain were obtained from the 10X Datasets website for <em>Spatial Gene Expression Dataset by Space Ranger 1.3.0</em> (<a href="https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0">https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0</a>).</p> <ul> <li>STalign_S2R3_to_Visium.csv.gz contains cell ids, original cell centroid positions of S2R3, cell positions of S2R3 after alignment to Visium H&E staining with STalign, and counts for genes and blanks.</li> </ul> <p>Furthermore, we performed alignments with the 50um resolution 3D Allen Reference Atlas Nissl common coordinate framework, CCF (<a href="https://help.brain-map.org/display/mouseconnectivity/API">https://help.brain-map.org/display/mouseconnectivity/API</a>). We applied STalign to align the Allen CCF to each of the 9 MERFISH slices (3 slice locations with 3 biological replicates) provided by Vizgen. Because the Allen CCF has annotated brain regions, we were able to lift over those brain region annotations to label all cells in the MERFISH datasets.</p> <p>Also, since the STalign mappings from the Allen CCF to the MERFISH slices are invertible, for each slice we can apply the inverse of the mapping to get cell positions in the Allen CCF coordinates.</p> <ul> <li>STalign_SXRX_with_structure_id_name.csv.gz contains cell ids for Slice X Replicate X, original cell centroid positions, cell xyz-coordinates in Allen CCF, brain structure id per cell, brain structure acronym</li> </ul> <p>To evaluate the 3D CCF alignment, we performed unified transcriptional clustering analysis and cell-type annotation. All MERFISH datasets were combined. Transcriptional clustering analysis and cell type annotation was performed using the SCANPY package [version 1.9.1]. Data were normalized to counts per million (scanpy: normalize_total) and log transformed (scanpy: log1p). PCA (scanpy: pca) was computed on the cell by gene matrix. A neighborhood graph of cells using the top 10 PCs and 10 nearest neighbors was created (scanpy: neighbors), and Leiden clustering was performed on this graph (scanpy: leiden) to identify 29 clusters. Differentially expressed genes were extracted from each cluster (scanpy: rank_genes_groups), and cell-types were annotated based on marker genes in each cluster.</p> <ul> <li>STalign_celltypeannotations_merfishslices_v2.csv.gz contains for all nine slices cell ids and cell type annotations</li> </ul> <p>This updated (v2) cell-type annotation file contains a new column with simplified cell-types. Briefly, we fixed typos, standardized lower case/upper case formats, merged subclasses of each cell-types. For example, subclasses of astrocytes­­, which are originally labeled as “Astrocytes”, “Astrocytes(1)”, “Astrocytes(2)”, “Astrocytes(3)”, are all labeled as “Astrocytes” in the added column.</p> <p>Note: Cell ids may have been mutated from original string of numbers through reading and writing across programming languages that handle numbers with different precision. If using R to read the files shared here, one can find the cells in STalign_celltypeannotations_merfishslices_v2.csv.gz that correspond with STalign_SXRX_with_structure_id_name.csv.gz when cell ids are formatted as a double in scientific notation, which is how R will read the file automatically.</p>
IST-editing: Infinite spatial transcriptomic editing in a generated gigapixel mouse pup
<p>Mouse pup data (Xenium, main results):</p> <ol> <li>Mouse.zip: Training data</li> <li>dapi_raw.tif: The raw dapi WSI</li> <li>dapi_gen.tif: The generated dapi WSI by IST-editing</li> <li>he_raw.tif: The raw H&E WSI</li> <li>he_gen.tif: The generated H&E WSI by IST-editing</li> </ol> <p>Mouse brain data (Vizgen, supplementary results):</p> <ol> <li>brain_60988.zip: Training data from two brain sections </li> <li>609882_raw.tif: The raw dapi WSI for mouse with ID 609882</li> <li>609882_trn.tif: The generated WSI on the training brain section</li> <li>609882_tst.tif: The generated WSI on the test brain section</li> <li>609889_raw.tif: The raw dapi WSI for mouse with ID 609889</li> <li>609889_trn.tif: The generated WSI on the training brain section</li> <li>609889_tst.tif: The generated WSI on the test brain section</li> </ol> <p> </p> <p> </p> <p> </p>
Visium Spatially Resolved Transcriptomics of Glioblastoma Samples
<p>This repository contains samples (Visium Spatially resolved Transcriptomics) of the project entitled: <strong>Epigenetic neural glioblastoma integrates into neuron-to-glioma-networks and predicts therapeutic vulnerability</strong></p>
Transcriptomic Analysis of CIC and CTC from Tumor Bearing Mice
<p>CIC and CTC isolated from tumor bearing mice were subjected to transcriptomic analysis using Smart-seq3 library preparation method. n = 3 for each group. </p>
Transcriptomes of six Streptanthoid Complex species
<p>To increase the number of genomic resources available for species of Streptanthoid Complex, we created transcriptomes for six jewelflower species. Focal species from six branches were selected to cover a majority of the phylogenetic tree. The goal is for these transcriptome sequences to aide future studies which look to explore the evolution and adaptation of the Streptanthoid Complex as it radiated throughout the California Floristic Province.</p>
Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
<p>Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (<em>Fragum sueziense</em>) and a closely related non-symbiotic species (<em>Trigoniocardia granifera</em>) under different light conditions to detect potential molecular pathways involved in mollusk photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared to those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologs in <em>T. granifera</em> transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as mollusks and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in driving host-symbiont adaptations in diverse organisms.</p>
Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment
<p><strong>When using any of this data, please cite the corresponding manuscript</strong></p> <div> <div> <p><a title="Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment.Sci. Adv.10,eadl1710(2024).DOI:10.1126/sciadv.adl1710" href="https://doi.org/10.1126/sciadv.adl1710">Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. Sci. Adv. 10, eadl1710 (2024). DOI:10.1126/sciadv.adl1710</a></p> </div> </div> <p><strong>Original Data</strong></p> <p>The following files contain all count data for the original data of this manuscript:</p> <p>sepsis1_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis1 sequencing<br>sepsis1_velocyto.loom -> velocyto matrices for sepsis1<br>sepsis2_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis2 sequencing<br>sepsis2_velocyto.loom -> velocyto matrices for sepsis2</p> <p>sepsis_seurat.rds -> processed Seurat object containing original data cells. (Upd.: the meta.data-column "cellnames" contains the cell type annotation given in Figure 1B)</p> <p><strong>Original Data Scripts</strong></p> <p>process.R -> main analysis script<br>functions.R -> helper functions for main analysis script<br>enrichmentAnalysis.R -> script running the enrichment analysis<br>process_wgcna.R -> script performing the wgcna analysis<br>velocities_step1.R -> script performing velocity analysis (from seurat to data matrices)<br>velocities_step2.py -> actual velocity analysis<br><br><strong>GSE137539 Re-Analysis</strong></p> <p>gse137539_processed.Rds -> processed seurat object<br>gse137539_process.R -> analysis script</p> <p><strong>Bulk Analysis</strong></p> <p>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-> Raw UMI counts (intronic+exonic from zUMIs) and DE genes<br>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -> Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process</p>
Transcriptomic profiles of resected 50 pancreatic adenocarcinoma samples
<p><span><span>An aggregated retrospective database with standardized clinicopathological variables was created for patients resected </span><span>in Erasme and Pitié Salpêtrière hospitals. </span>RNA was extracted from the scrapped sections with the ALLPrep FFPE tissue kit<sup>©</sup> following the manufacturer’s instructions for semi-automated RNA extraction via Qiacube instrument (Qiagen, Venlo, The Netherlands). RNA samples were run on an Agilent 2100 bioanalyzer using the RNA 6000 Pico LabChip kit (Agilent, Diegem, Belgium). The bioanalyzer electropherograms were analyzed by Agilent 2100 Expert Software to determine the RNA quantity and quality. RNA samples with DV200 >30% were selected and 100 ng of RNA was used for the library preparation. NGS libraries were prepared using the QuantSeq Library Prep Kit for Illumina (Lexogen) as per manufacturer recommendations’. The libraries were sequenced on NovaSeq using NovaSeq 6000 S2 Reagent Kit with 100 bp single reads.</span></p>
Bilateria Phyla CANTATA Transcriptomes
<p>CANTATA is a Community bAsed Non-bilaTeriAn Transcriptome Archive aiming to provide an archive of non-bilaterian transcriptomic resources assembled and annotated in a standardized manner.</p> <p> </p> <p>In this repository, we provide the transcriptomes assemblies corresponding to different bilaterian animal Phyla.</p> <p> </p> <p>Currently the following species are available:</p> <ul> <li><em>Branchiostoma floridae</em></li> <li><em>Danio rerio</em></li> <li><em>Daphnia pulex</em></li> <li><em>Eucidaris tribuloides</em></li> <li><em>Oligometra serripinna</em></li> <li><em>Platynereis dumerilii</em></li> <li><em>Priapulus caudatus</em></li> <li><em>Ptychodera flava</em></li> <li><em>Strongylocentrotus purpuratus</em></li> <li><em>Symsagittifera roscoffensis</em></li> <li><em>Tubulanus polymorphus</em></li> <li><em>Xenoturbella bocki</em></li> </ul> <p> </p> <p>The details about the read files used to assemble each transcriptome can be found at the CANTATA repository (https://gitlab.lrz.de/palmuc/cantata)</p>
Outgroup Phyla CANTATA Transcriptomes
<p>CANTATA is a Community bAsed Non-bilaTeriAn Transcriptome Archive aiming to provide an archive of non-bilaterian transcriptomic resources assembled and annotated in a standardized manner.</p> <p> </p> <p>In this repository, we provide the transcriptomes assemblies corresponding to different animal outgroup Phyla.</p> <p> </p> <p>Currently the following species are available:</p> <ul> <li><em>Abeoforma whisleri</em></li> <li><em>Acanthoeca spectabilis</em></li> <li><em>Amoebidium parasiticum</em></li> <li><em>Capsaspora owczarzaki</em></li> <li><em>Helgoeca nana</em></li> <li><em>Salpingoeca infusionum</em></li> </ul> <p>The details about the read files used to assemble each transcriptome can be found at the CANTATA repository (https://gitlab.lrz.de/palmuc/cantata)</p> <p> </p>
Phylum Cnidaria (Anthozoa: Octocorallia) CANTATA Transcriptomes
<p>CANTATA is a Community bAsed Non-bilaTeriAn Transcriptome Archive aiming to provide an archive of non-bilaterian transcriptomic resources assembled and annotated in a standardized manner.</p> <p> </p> <p>In this repository, we provide the transcriptomes assemblies corresponding to the Phylum Cnidaria (Class Anthozoa, Subclass Octocorallia).</p> <p> </p> <p>Currently, the following species are available:</p> <ul> <li><em>Alcyonium palmatum</em></li> <li><em>Corallium rubrum</em></li> <li><em>Dendronephthya gigantea</em></li> <li><em>Eunicea calyculata</em></li> <li><em>Eunicella cavolini </em></li> <li><em>Gorgonia ventalina</em></li> <li><em>Heliopora coerulea</em></li> <li><em>Muricea laxa</em></li> <li><em>Sarcothelia edmonsoni</em></li> <li><em>Sinularia cruciata</em></li> <li><em>Tubipora musica</em></li> </ul> <p>The details about the read files used to assemble each transcriptome can be found at the CANTATA repository (https://gitlab.lrz.de/palmuc/cantata)</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbSS livers 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 livers <span>(indicated foie)</span> from HbSS mice injected or not with heme are presented here. </p> <p>The results of livers <span>(indicated foie)</span> from HbAA mice injected or not with heme can be found at number 10.5281/zenodo.10963640. </p> <p>Thirty μm-thick frozen tissue sections of livers 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> <p> </p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice. Dataset for HbAA heart 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 heart (indicated coeur) from HbAA mice injected or not with heme are presented here . </p> <p>The results of heart (indicated coeur) from HbSS mice injected or not with heme can be found at number 10.5281/zenodo.10964159</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 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 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>
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>
Brain Transcriptome Single-cell (BTS) Atlas: Anndata, Seurat Object, CellTypist model, and Disorder Risk Geneplot
<p>Brain Transcriptome Single-cell Atlas (BTS) Anndata, Seurat object, and Celltypist model for further use of the atlas. The Celltypist model can be utilized to accurately annotate cell types in new datasets based on the atlas. Plots illustrating the expression profile for 3,380 neurological disorder risk genes across the atlas are also uploaded. Further availability for the data can be requested by the corresponding author.<br><br>This dataset is published in Kim, S., Lee, J., Koh, I.G. <em>et al.</em> An integrative single-cell atlas for exploring the cellular and temporal specificity of genes related to neurological disorders during human brain development. <em>Exp Mol Med</em> <strong>56</strong>, 2271–2282 (2024). https://doi.org/10.1038/s12276-024-01328-6</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.