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25,372 results for “Transcriptomics”
Hepatic transcriptomic analysis reveals differential regulation of metabolic and immune pathways in three strains of chickens with distinct growth rate exposed to mixed parasites infections
<p><span>This dataset was generated from the study investigating hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after either an experimental infection (n = 18) with both <em>A. galli</em> and <em>H. gallinarum or kept as uninfected control (n = 12)</em>. </span></p>
Decoding NY-ESO-1 TCR T Cells: Transcriptomic Insights Reveal Dual Mechanisms of Tumor Targeting in a Melanoma Murine Xenograft Model
<p><span>Single-cell RNA-seq data of NY-ESO-1-specific TCR T-cells generated with the BD Rhapsody™ system.</span></p> <p><span>Biogroup information: Control (<em>n</em><span> </span>= 4), PB (murine peripheral blood, <em>n</em><span> </span>= 4).</span></p> <p><span>Cell preparation: NY-ESO-1-specific TCR T-cells were obtained via a retroviral transduction of an anti-NY-ESO-1-TCR construct, murine peripheral blood T-cells were enriched using anti-CD3 magnetic separation via MojoSortTM Human CD3 Selection Kit.</span></p> <p><span>Single-cell analysis system: BD Rhapsody™</span></p> <p><span>Library strategy: 3' mRNA sequencing</span></p> <p><span>Library preparation protocol: BD Rhapsody™ Targeted mRNA and Sample Tag Library Preparation</span></p> <p><span>mRNA panel: BD Rhapsody™ Immune Response Panel HS</span></p> <p><span>BD Pipeline version: 1.11L</span></p>
Code and data of "Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA"
<p>Code and data to reproduce the analyses and figures presented in "Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA"</p>
Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins
<p><strong>Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins</strong><br> </p> <p>Rémi Allio<sup>1,2,§,</sup>*, Sophie Teullet<sup>1,§</sup>, Dave Lutgen<sup>1,3,4,§</sup>, Amandine Magdeleine<sup>1</sup>, Rachid Koual<sup>1</sup>, Marie-Ka Tilak<sup>1</sup>, Benoit de Thoisy<sup>5,6</sup>, Christopher A. Emerling<sup>1,7</sup>, Tristan Lefébure<sup>8</sup>, and Frédéric Delsuc<sup>1,</sup>*</p> <p><br><sup>1</sup>ISEM, Univ. Montpellier, CNRS, IRD, Montpellier, France</p> <p><sup>2</sup>CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France </p> <p><sup>3</sup>Institute of Ecology and Evolution, University of Bern, Bern, Switzerland</p> <p><sup>4</sup>Swiss ornithological Institute, Sempach, Switzerland</p> <p><sup>5</sup>Institut Pasteur de la Guyane, Cayenne, French Guiana, France</p> <p><sup>6</sup>Kwata NGO, Cayenne, French Guiana, France</p> <p><sup>7</sup>Biology Department, Reedley College, Reedley, CA, USA</p> <p><sup>8</sup>Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France</p> <p><sup>§</sup>Equal contribution</p> <p> </p> <p>*Correspondence</p> <p>Rémi Allio: remi.allio@inrae.fr</p> <p>Frédéric Delsuc: frederic.delsuc@umontpellier.fr</p> <p> </p> <p><strong>Abstract</strong></p> <p>Ant-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, hypertrophied salivary glands producing large amounts of saliva, and powerful claws for ripping open ant and termite nests. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas, and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution.</p> <p> </p> <p><strong><em>Figures & Tables</em></strong></p> <p><strong>Figure 1</strong>: Dated placental mammal phylogeny including representative species of the four major clades (Afrotheria, Xenarthra, Euarchontoglires, and Laurasiatheria) for which CHIA gene repertoires have been previously characterized. Numbers between brackets represent percentages of invertebrates included in the diet with myrmecophagous species indicated by an ant silhouette. Ψ symbols indicate CHIA pseudogenes as determined in previous studies (Emerling et al. 2018; Janiak et al. 2018; Wang et al. 2020<a href="https://www.zotero.org/google-docs/?IVkGtZ">)</a>. Ancestral CHIA gene repertoires for Placentalia and Ferae (Pholidota + Carnivora) as inferred by Emerling et al. (2018) are presented. The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 2</strong>: A. Mammalian chitinase-like gene family tree reconstructed using a maximum likelihood gene-tree/species-tree reconciliation approach on protein sequences. The nine chitinase paralogs are indicated on the outer circle. Scale bar represents the mean number of amino acid substitutions per site. B. Synteny analysis of the nine chitinase paralogs in humans (Homo sapiens), tarsier (Carlito syrichta), nine-banded armadillo (Dasypus novemcinctus) and the two main focal convergent ant-eating species: the southern tamandua (Tamandua tetradactyla) and the Malayan pangolin (Manis javanica). Assembly names and accession numbers are indicated below species names. Boxes represent different contigs with their most upstream and downstream BLAST hit positions to chitinase genes (colored arrows). Genes PIFO and DENND2D (grey arrows) are not chitinase paralogs but were used in the synteny analysis. Arrow direction indicates gene transcription direction as inferred in Genomicus v100.01 <a href="https://www.zotero.org/google-docs/?qjXWzo">(Nguyen et al. 2022)</a> for genes located on short contigs. Ψ symbols indicate pseudogenes as determined in <a href="https://www.zotero.org/google-docs/?IVkGtZ">Emerling et al. (2018)</a>. Genes with non significant BLAST hits were not represented and are probably not functional or absent. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 3</strong>: Comparison of predicted ancestral protein sequences of the nine mammalian chitinase paralogs. A. Conserved amino acid residues of the canonical chitinolytic domain active site (DXXDXDXE). Arrows indicate paralogs in which changes occurred in the active site. B. Summary of the evolution of chitinase paralogs functionality. C. Conserved cysteine residues of the chitin-binding domain. The arrow indicates OVGP1 in which the last four cysteines have been replaced.</p> <p><strong>Figure 4</strong>: Expression of the nine chitinase paralogs in 40 mammalian salivary gland transcriptomes. The 33 species are presented in their phylogenetic context covering the four major placental clades: Afrotheria (AFR), Xenarthra (XEN), Euarchontoglires (EUA), and Laurasiatheria (LAU). The chronogram was extracted from <a href="http://www.timetree.org">www.timetree.org</a> <a href="https://www.zotero.org/google-docs/?Vr0bO1">(Kumar et al. 2022)</a>. Non-functional pseudogenes are only indicated for the three focal species (in bold) using a Ψ symbol: nine-banded armadillo (Dasypus novemcinctus), southern tamandua (Tamandua tetradactyla) and Malayan pangolin (Manis javanica). Expression level is represented as log10 (Normalized Counts + 1). Asterisks indicate the 16 new transcriptomes produced in this study. Myrmecophagous and insectivorous species are indicated by ant and beetle silhouettes, respectively. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 5</strong>: Expression of the nine chitinase paralogs in 72 transcriptomes from different organs of the three focal species: the nine-banded armadillo (Dasypus novemcinctus), the Malayan pangolin (Manis javanica), and the southern tamandua (Tamandua tetradactyla). Non-functional pseudogenes are represented by a Ψ symbol and hatched background. Boxes indicate organs of the digestive tract. Expression level is represented as log10 (Normalized Counts + 1). Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a>.</p> <p><strong>Figure 6</strong>: Summary figure presenting the evolution and expression of chitinase acidic (CHIA) paralogous genes in the convergently evolved Malayan pangolin (Manis javanica) and southern tamandua (Tamandua tetradactyla) in their phylogenetic context. Reconstructed CHIA gene repertoires are indicated for the two myrmecophagous species and for the most recent common ancestor (MRCA) of placentals, pangolins+carnivores (Ferae) and anteaters+sloths (Pilosa). Non-functional pseudogenes are represented by the Ψ symbol and dashed line contour. Organ icons indicate expression of the corresponding gene in different digestive organs. SG: Salivary glands; S: Stomach; T: Tongue; P: Pancreas; L: Liver; I: Intestine. Silhouettes were obtained from <a href="http://www.phylopic.org">www.phylopic.org</a> and <a href="https://www.vecteezy.com/">www.vecteezy.com</a>.</p> <p> </p> <p><em><strong>Supplementary Materials</strong></em></p> <p><strong>Table S1: </strong>Detailed information on the tissues sequenced or retrieved from public databases for the project.</p> <p><strong>Table S2</strong>: BUSCO v5 scores of all transcriptomes based on a dataset of 9,226 single-copy orthologs conserved in over 90% of mammalian species <a href="https://www.zotero.org/google-docs/?lrFE5h">(Manni et al. 2021)</a>. </p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>CHIAs_OG_tree-RAxML_EPA</strong><strong>.zip </strong>contains CHIA sequences (obtained from the OrthoFinder orthogroups and the sequences used to infer the chitinase genes evolution) and the corresponding ML tree. </p> <p><strong>Chitinases_ancestral_sequences.zip </strong>contains the ancestral chitinase sequence reconstructions, the associated posterior probabilities, and the alignment of the ancestral sequences inferred by RAxML-NG. </p> <p><strong>Chitinases_gene_tree.zip</strong> contains input and output files corresponding to the chitinase gene tree presented in Figure 2: </p> <p>- mammalina_species_tree_input_Generax.newick = species tree used for the reconciliation with Generax</p> <p>- chitinase_gene_alignment_renamed_input_Generax.fasta = chitinase gene alignment with the sequence names renamed for Generax</p> <p>- chitinase_gene_alignment_not_renamed.fasta = chitinase gene alignment with the original sequence names (for information)</p> <p>- chitinases_gene_tree_sequences_renamed_input_Generax.newick = chitinase gene tree inferred with RAxML-NG and reconciled using the TreeRecs algorithm to find the optimal rooting scheme; this tree was used for Generax</p> <p>- reconciled_chitinase_genes_tree_output_Generax.newick = reconciled chitinase gene tree inferred by Generax and presented in Figure 2</p> <p><strong>Chitinases_expression.zip </strong>contains all orthogroup gene expressions plus chitinase gene expressions.</p> <p><strong>Kallisto_abundances.zip</strong> contains the abundances estimated with kallisto for each organ of each species<em>.</em></p> <p><strong>Supplementary table figure 2B - BLAST</strong> <strong>results.xlsx</strong> contains BLAST results supporting sequence inferences. </p> <p><strong>Transcriptome_assemblies.tar.gz</strong> contains the transcriptome assemblies obtained for each organ and species with Trinity.</p>
Single-Cell Transcriptomics Reveals a Heterogeneous Cellular Response to BK Virus Infection
<p>The files are the Indrops count matrices for BKV and Mock samples corresponding to the 8 experiments and samples described in the Bioproject https://www.ncbi.nlm.nih.gov/bioproject/PRJNA715178</p> <p> </p>
Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas
<p>Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, including upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. Altogether, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.</p>
ATACSeq fastq files associated with the manuscript entitled 'Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion'
<p>This next-generation sequencing dataset is associated with the research manuscript entitled ‘<em>Interspecies transcriptome analyses identify genes that control the development and evolution of limb skeletal proportion</em>’ (https://www.biorxiv.org/content/10.1101/754002v2).</p> <p>The zipped folder ‘<strong>Zenodo_Saxena_etal_2021_ATACSeq_FastqFiles</strong>’ contains raw/unprocessed ATACSeq Fatsq read files for postnatal day 5 (P5) mouse (Mus) and jerboa (Jac) cartilage samples (Metatarsal = MT; Radius/Ulna = RU).</p> <p>> The <strong>Jac_P5</strong> subfolder contains paired-end reads (R1 and R2) for three jerboa metatarsals (MT1-3) and radius/ulna (RU1-3) biological replicates.</p> <p>> The <strong>Mus_P5</strong> subfolder contains paired-end reads (R1 and R2) for two mouse metatarsals (MT1-2) and radius/ulna (RU1-2) biological replicates.</p>
Raw data to: "Persistent RNA virus infection is short-lived at the single cell level but leaves transcriptomic footprints"
<p>Raw data underlying the publication by Reuther and Martin et al. entitled "Persistent RNA virus infection is short-lived at the single cell level but leaves transcriptomic footprints"</p>
Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris) – De novo reference transcriptome: Assemblerd contigs and gene annotations
<p>Assembled contigs (Trinity) and gene annotations (Trinotate) of a reference transcriptome for the Upland Chorus Frog, <em>Pseudacris feriarum</em>. Data to assemble the contigs were obtained by sequencing four tissue types: Brain, eyes, testis, and somatic (liver/heart/lung/skin/muscle). Raw reads are stored in the NCBI-SRA database (BioProject PRJNA723357).</p>
Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control
<p>The genus <i>Spodoptera</i> (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including <i>Spodoptera frugiperda</i>, <i>Spodoptera litura</i> and <i>Spodoptera exigua</i>. To effectively develop targeted pest control strategies for diverse <i>Spodoptera</i> species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of <i>S. exigua</i>, the beet armyworm. <i>Spodoptera exigua</i> is a polyphagous herbivore that can feed from > 130 host plants including several economically important crops.</p> <p>The 419 Mb beet armyworm genome was sequenced from a female <i>S. exigua</i> pupa. Using a hybrid genome sequencing approach (Nanopore long read data and Illumina short read), a high-quality genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS, 18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq data sets of 18 <i>S. exigua</i> samples as supporting evidence. In-depth analyses of developmental stage-specific expression in combination with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them <i>Spodoptera</i>-specific) upregulated during 1<sup>st</sup> and 3<sup>rd</sup> instar larval stages for targeted pest-outbreak management.</p> <p>The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provides critical insights into the biology of this devastating polyphagous insect pest species with a worldwide distribution. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive <i>Spodoptera</i> species and reveals potential lineage-specific target genes for pest control strategies.</p>
QTL mapping and transcriptome analysis of Sclerotinia-resistance in the wild cabbage species Brassica oleracea var. villosa [Main code]
<p>This is the main code supplement for my computational analysis for the manuscript: "QTL mapping and transcriptome analysis of Sclerotinia-resistance in the wild cabbage species <em>Brassica oleracea </em>var<em>. villosa".</em> The main code is availabe in separate html-files. DOI will be added if available.</p>
RNA-seq data of "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting Coffea arabica cultivars"
<p>This dataset represent FASTQ gziped files from the study "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting <em>Coffea arabica</em> cultivars" (<a href="https://doi.org/10.3389/fsufs.2021.735893">https://doi.org/10.3389/fsufs.2021.735893</a>). Sequencing was done using an Illumina Novaseq 6000 instrument, paired-sequencing (2 X150 bp). Sample details are also available at https://www.ebi.ac.uk/ena/browser/view/ERA6282544.</p> <p> </p> <p>All filenames have the following naming scheme:</p> <p>LCS7609_DS_AAA_leafBBB_(R1 or R2).fq.gz</p> <p>AAA stands for the abbreviations:</p> <p>- CC (Coffea arabica cv Catuai control)</p> <p>- CHx (Coffea arabica cv Catuai exposed to Hexanoic acid)</p> <p>- OC (Coffea arabica cv Obatã control)</p> <p>- OHx (Coffea arabica cv Obatã exposed to Hexanoic acid)</p> <p>BBB stands for the number of biological replicate (1, 2 or 3).</p> <p> </p> <p> </p> <p> </p>
Supplementary Data for AGouTI - flexible Annotation of Genomic and Transcriptomic Intervals
<p>The data allows to replicate the use-case scenario described in the manuscript "AGouTI - flexible Annotation of Genomic and Transcriptomic Intervals" by Jan G. Kosiński and Marek Żywicki.</p>
Piper longum transcriptomes generated using transXpress
<p>Piper longum transcriptome assemblies created and annotated using transXpress with rnaSPAdes and Trinity assemblers.</p>
Data for accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
<p>Simulated and experimental data used in the ReSort manuscript. It is necessary and sufficient to reproduce the results in the paper.</p>
On the correspondence between the transcriptomic response of a compound and its effects on its targets
<p>Dataset used in the manuscript "On the correspondence between the transcriptomic response of a compound and its effects on its targets".</p> <p>More info at https://github.com/enveda/transcriptomic-target-correlation</p>
Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases
<p>Spatial transcriptomic data (counts.csv) derived using the Nanostring GeoMx digital spatial profiler platform to analyse matched colonic primary and liver metastases from 4 patients with metastatic colorectal cancer. 48 AOIs of cancer transcriptome atlas data. Normalised using Q3 normalisation. In addition, normalised data (Counts - ncounter.csv) from ncounter bulk experiment comparing matched colonic primary and liver metastases</p>
Spatial transcriptomics stratifies health and psoriatic disease severity by emergent cellular ecosystems
<p>While human inflammatory skin diseases' cellular and molecular features are well-characterized, their tissue context and systemic impact remain poorly understood. We thus profiled human psoriasis (PsO) as a prototypic immune-mediated condition with a high preference for extra-cutaneous involvement. Spatial transcriptomics (ST) analyses of 25 healthy, active, and clinically uninvolved skin biopsies, and integration with public single-cell transcriptomics data revealed striking differences in immune microniches between healthy and inflamed skin. Tissue scale-cartography further identified core disease features across all active lesions, including the emergence of an inflamed suprabasal epidermal state and the presence of B lymphocytes in lesional skin. Notably, both lesional and distal non-lesional samples were stratified by skin disease severity, and not by the presence of systemic disease. This segregation was driven by macrophage-, fibroblast- and lymphatic-enriched spatial regions with gene signatures associated with metabolic dysfunction. Taken together, these findings suggest that mild and severe forms of PsO have distinct molecular features and that severe PsO may profoundly alter the cellular and metabolic make up of distal unaffected skin sites. Additionally, our study provides an unprecedented resource for the research community to study spatial gene organization of healthy and inflamed human skin. </p>
Supplementary data for: Transcriptomics of mosaic brain differentiation underlying complex division of labor in a social insect
<p>Concerted developmental programming may constrain changes in component structures of the brain, thus limiting the ability of selection acting on individual brain compartments to form an adaptive mosaic independent of total brain size or body size. Measuring patterns of gene expression underpinning brain scaling in conjunction with anatomical brain atlases can aid in identifying influences of concerted and/or mosaic evolution. Species exhibiting exceptional size and behavioral polyphenisms provide excellent systems to test predictions of brain evolution models by quantifying brain gene expression. We examined patterns of brain gene expression in a remarkably polymorphic and behaviorally complex social insect, the leafcutter ant <em>Atta</em> <em>cephalotes</em>. Approximately ~50% of differential gene expression observed among three morphologically, behaviorally, and neuroanatomically differentiated worker size groups was attributable to body size, but we also found strong evidence of differential brain gene expression unexplained by worker morphological variation. Transcriptomic analysis identified patterns of gene expression not linearly correlated with worker size but rather, in some cases, mirroring neuropil scaling. Additionally, we observed enriched gene ontology terms associated with nucleic acid regulation, metabolism, neurotransmission, and sensory perception, further supporting a relationship between brain gene expression and worker social role. These findings demonstrate that differential brain gene expression among polymorphic workers is linked to behavioral and neuroanatomical differentiation underpinning complex agrarian division of labor in <em>A</em>. <em>cephalotes</em>.</p>
Data for: Heterosigma akashiwo transcriptome gene annotations
<p>Heterosigma akashiwo is a eukaryotic, cosmopolitan, and unicellular alga (class: Raphidophyceae), and produces fish-killing blooms. There is a substantial scientific and practical interest in its ecophysiological characteristics that determine bloom dynamics and its adaptation to broad climate zones. A well-annotated genomic/genetic sequence information enables researchers to characterize organisms using modern molecular technology. In the present study, we conducted H. akashiwo RNA sequencing, a de novo transcriptome assembly of 84,693,530 high-quality deduplicated short-read sequences. The obtained RNA reads were assembled by Trinity assembler and 144,777 contigs were identified with N50 values of 1085. The raw data were deposited in the NCBI SRA database (BioProject PRJDB6241 and PRJDB15108), and the assemblies are available in NCBI TSA database (ICRV01). Total 60,877 open reading frames with the length of 150 bp or greater were predicted. Here, the top Gene Ontology terms, the pfam hits, and the BLAST hits were annotated for all the predicted genes, and shared as text files.</p>
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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.