Find research datasets worth reusing

opencc-by-4.0Jan 2023View details →

Supplemental materials for Altered expression of several molecular mediators of cerebral spinal fluid production in Hyp mice

X-Linked Hypophosphatemia (XLH) is a genetic disease causing life-long hypophosphatemia due to overproduction of FGF23. XLH is associated with Chiari malformations, cranial synostosis, and syringomyelia. FGF23 signals through FGFR1c and requires a co-receptor, a-Klotho, which is expressed in the renal distal convoluted tubules and the choroid plexus (ChP). In the ChP, a-Klotho participates in regulating cerebral spinal fluid (CSF) production by shuttling the sodium/potassium adenosine triphosphatase (Na+/K+-ATPase) to the luminal membrane. The sodium/potassium/chloride cotransporter 1 (NKCC1) also makes a substantial contribution to CSF production. Real-time PCR (RT-PCR) demonstrated significant upregulation of Klotho transcripts in the fourth ventricle but a trend toward reduced expression in the lateral ventricles of Hyp mice compared to controls. Transcript levels for Fgfr1c were unchanged in Hyp mice. Na+/K+-ATPase alpha-1 subunit transcripts were downregulated in all three ventricles, reaching significance in the third and lateral ventricles. Expression levels of the Slc12a2 transcript (which encodes NKCC1) were unchanged in Hyp mice compared to controls. In situ hybridization (ISH) was used to obtain anatomical corelates to the changes observed by RT-PCR. ISH confirmed the presence of all four transcripts in the lateral ventricle ChP of both WT and Hyp mice. This is the first study to document a significant change in the level of expression of the molecular machinery required for CSF production in Hyp mice. Whether similar changes occur in patients with XLH, potentially contributing to the cranial and spinal cord abnormalities frequently seen in XLH remains to be determined.

opencc-by-4.0Jan 2023View details →

[DATA] Amplicon-based gene expression profiling of blood from mice stimulated with R848 and treated with TLR7/8 inhibitor MHV370

129/Sv mice (5 per group) were treated with daily R848 i.p. (2.5 mg/kg) for 14 days. From day 7 onward, one group received oral doses of 15 mg/kg MHV370 b.i.d., one group vehicle. At day 14, both groups were compared to naive 129/Sv mice. Gene expression profiling of blood was performed via amplicon sequencing (Ion AmpliSeq Transcriptome Mouse Gene Expression Kit, Thermo Fisher Scientific). Raw amplicon counts, sample metadata and gene information are provided in tab-separated value (TSV) files counts.tsv, samples.tsv and genes.tsv, respectively. The entire dataset is also provided as a DGEList object saved as an RDS file (dge_unfiltered.rds) that can be explored using R (package edgeR). The respective code for analysis can be found under DOI: 10.5281/zenodo.7575672

opencc-zeroJan 2023View details →

Influence of RNA-Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation

RNA sequencing (RNA-Seq) is popular for measuring gene expression in non-model organisms, including wild populations. While RNA-Seq can detect gene expression variation among wild-caught individuals and yield important insights into biological function, sampling methods may influence gene expression estimates. We examined the influence of multiple technical variables on estimated gene expression in a non-model fish, the westslope cutthroat trout (Oncorhynchus clarkii lewisi), using two RNA-Seq library types: 3' RNA-Seq (QuantSeq) and whole mRNA-Seq (NEB). We evaluated effects of dip netting versus electrofishing, and of harvesting tissue immediately versus 5 minutes after euthanasia on estimated gene expression in blood, gill, and muscle. We found no significant differences in gene expression between sampling methods or tissue collection times with either library type. When library types were compared using the same blood samples, 58% of genes detected by both NEB and QuantSeq showed significantly different expression between library types, and NEB detected 31% more genes than QuantSeq. Although QuantSeq and NEB recovered different numbers of genes and expression levels, there were no differences in gene expression between sampling methods and tissue harvesting time for either library type. Our study suggests that researchers can safely rely on different fish sampling strategies in the field. In addition, while QuantSeq is more cost-effective, NEB detects more expressed genes. Therefore, when it is crucial to detect as many genes as possible (especially low expressed genes), when alternative splicing is of interest, or when working with an organism lacking good genomic resources, whole mRNA-Seq is more powerful.

opencc-by-4.0Jan 2023View details →

The Role of Biological Motion in Face Perception: Social Judgements of Morphed Expressions Differ from Videos and Photographs.

This study aimed to explore the impact of realistic and artifical facial dynamism on social percpetion. We compared ratings of emotion intensity and genuineness on video recordings, dynamic morphs, and static photographs of happy, sad, fearful, and angry expressions. The experiment was created using the online behavioural experiment builder Gorilla (AnwylIrvine et al., 2020). Each participant completed 144 trials, including 48 trials for each display type (video recording, morph, static), with 12 trials for each emotion (happy, disgust, fear, sadness).

opencc-by-4.0Feb 2023View details →

Unified bursting strategies in ectopic and endogenous even-skipped expression patterns - Supplemental Data

This dataset contains the supplemental data of the article "Unified bursting strategies in ectopic and endogenous even-skipped expression patterns".

opencc-by-4.0Mar 2022View details →

The EGFR signaling modulates in mesenchymal stem cells the expression of miRNAs involved in the interaction with breast cancer cells

We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.We previously demonstrated that the epidermal growth factor receptor (EGFR) modulates in mesenchymal stem cells (MSCs) the expression of a number of genes coding for secreted proteins that promote breast cancer progression. However, the role of the EGFR in modulating in MSCs the expression of miRNAs potentially involved in the progression of breast cancer remains largely unexplored. Following small RNA-sequencing, we identified 36 miRNAs differentially expressed between MSCs untreated or treated with the EGFR ligand transforming growth factor α (TGFα), with a fold change (FC) <0.56 or FC ≥1.90 (CI, 95%). KEGG analysis revealed a significant enrichment in signaling pathways involved in cancer development and progression. EGFR activation in MSCs downregulated the expression of different miRNAs, including miR-23c. EGFR signaling also reduced the secretion of miR-23c in conditioned medium from MSCs. Functional assays demonstrated that miR-23c acts as tumor suppressor in basal/claudin-low MDA-MB-231 and MDA-MB-468 cells, through the repression of IL-6R. MiR-23c downregulation promoted cell proliferation, migration and invasion of these breast cancer cell lines. Collectively, our data suggested that the EGFR signaling regulates in MSCs the expression of miRNAs that might be involved in breast cancer progression, providing novel information on the mechanisms that regulate the MSC-tumor cell cross-talk.

opencc-by-4.0Mar 2023View details →

Recombinant Expression and Purification of ABHD2 from E. coli

α/β Hydrolase domain-containing protein 2 (ABHD2), is a member of the metabolic serine hydrolases superfamily & a progesterone membrane receptor. In sperm, it supports the activation of CatSper which leads to sperm hypermotility. ABHD2 is 425 aa and has a N-terminal transmembrane domain followed by an extracellular facing domain. Here we report the recombinant expression and purification of ABHD2 amino acids 33-435 from E. coli. To the best of our knowledge, we are the first to have recombinantly purified active ABHD2.

Data for: Breeding honey bees (Apis mellifera L.) for low and high Varroa destructor population growth: gene expression of bees performing grooming behavior

Background Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restraining the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry. We conducted a bidirectional breeding program to select honey bee colonies with low and high varroa population growth (LVG and HVG, respectively). Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Results Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified, including four odorant-binding proteins and a gustatory receptor. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the HVG line showed higher levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1), and Deformed wing virus-A (DWV-A) compared to bees of the LVG line. Conclusions The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways. Therefore, our results provide new insights into the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic-assisted selection to improve breeding programs.

opencc-by-4.0Mar 2023View details →

Single-cell RNA-seq count data used in differential expression benchmark study

Count matrices and meta data tables from simulated and real world immune cell single-cell RNA-seq experiments. All files are in Rds format and can be read by R using "readRDS()".  <ul> <li>10k_*: These files contain a filtered version of the 10k Human PBMCs, 3' v3.1 data <a href="https://www.10xgenomics.com/resources/datasets/10k-human-pbmcs-3-v3-1-chromium-controller-3-1-high">published</a> by 10x Genomics</li> <li>blueprint_data.Rds: This file contains the bulk RNA-seq data downloaded from <a href="http://dcc.blueprint-epigenome.eu">BLUEPRINT</a></li> <li>blueprint_immune_comparisons.Rds: Results from running three bulk RNA-seq differential expression methods</li> <li>sim_data*: These files contain the count matrices and meta data tables for the simulated data. Every file contains a list of 13 replicates.</li> </ul>

Data from: House mouse Slx and Sly CNV and expression data

A remarkable gene copy number (CN) arms race system has recently been described in laboratory mice, where Slx;Slxl1 and Sly genes compete over transmission by altering fertilisation success of X and Y chromosome-bearing sperm, respectively. Here, we focus on this system in nature, where natural selection can counter CN/gene product escalation. Our model is house mouse subspecies hybridising in Europe. In some regions, Y chromosomes of the Eastern subspecies have introgressed onto Western genomic backgrounds, accompanied by sex ratio distortion in favour of males, consistent with the inbred-lines suggested mechanism: overabundance of SLY protein expressed by invading Y chromosomes. We take Slx as representative of the X side of this arms race and measure Slx|Sly CN and expression across an 'Invasion' transect where Ys introgress and a 'Control' transect with negligible introgression. Since we found similar Slx|Sly ratios in both transects, SLY overabundance is unlikely to explain the introgression. However, Slx CN is relatively low in the introgression area, suggesting Slx is less able to combat Sly effects here. Further, deterministic changes in Slx;Sly expression proportions versus CN proportions suggest standing variation for trans regulation of Slx|Sly is being co-opted in nature where their arms race reduces population fitness.

Data from: Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids

Mitochondrial functions are intimately reliant on proteins and RNAs encoded in both the nuclear and mitochondrial genomes, leading to inter-genomic coevolution within taxa. Hybridization can break apart coevolved mitonuclear genotypes, resulting in decreased mitochondrial performance and reduced fitness. This hybrid breakdown is an important component of outbreeding depression and early-stage reproductive isolation. However, the mechanisms contributing to mitonuclear interactions remain poorly resolved. Here we scored variation in developmental rate (a proxy for fitness) among reciprocal F2 inter-population hybrids of the intertidal copepod Tigriopus californicus, and used RNA sequencing to assess differences in gene expression between fast- and slow-developing hybrids. In total, differences in expression associated with developmental rate were detected for 2,925 genes, whereas only 135 genes were differentially expressed as a result of differences in mitochondrial genotype. Up-regulated expression in fast developers was enriched for genes involved in chitin-based cuticle development, oxidation-reduction processes, hydrogen peroxide catabolic processes, and mitochondrial respiratory chain complex I. In contrast, up-regulation in slow developers was enriched for DNA replication, cell division, DNA damage, and DNA repair. Eighty-four nuclear-encoded mitochondrial genes were differentially expressed between fast- and slow-developing copepods, including twelve subunits of the electron transport system (ETS) which all had higher expression in fast developers than in slow developers. Nine of these genes were subunits of ETS complex I. Our results emphasize the major roles that mitonuclear interactions within the ETS, particularly in complex I, play in hybrid breakdown, and resolve strong candidate genes for involvement in mitonuclear interactions.

Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion

Structural, functional, and molecular reorganization of denervated neural networks is often observed in neurological conditions. The loss of input is accompanied by homeostatic synaptic adaptations, which can affect the reorganization process. A major challenge of denervation-induced homeostatic plasticity operating in complex neural networks is the specialization of neuronal inputs. It remains unclear whether neurons respond similarly to the loss of distinct inputs. Here, we used in vitro entorhinal cortex lesion (ECL) and Schaffer collateral lesion (SCL) in mouse organotypic entorhino-hippocampal tissue cultures to study denervation-induced plasticity of CA1 pyramidal neurons. We observed microglia accumulation, presynaptic bouton degeneration, and a reduction in dendritic spine numbers in the denervated layers three days after SCL and ECL. Transcriptome analysis of the CA1 region revealed complex changes in differential gene expression following SCL and ECL compared to non-lesioned controls with a specific enrichment of differentially expressed synapse-related genes observed after ECL. Consistent with this finding, denervation-induced homeostatic plasticity of excitatory synapses was observed three days after ECL but not after SCL. Chemogenetic silencing of the EC but not CA3 confirmed the pathway-specific induction of homeostatic synaptic plasticity in CA1. Additionally, increased RNA oxidation was observed after SCL and ECL. These results reveal important commonalities and differences between distinct pathway lesions and demonstrate a pathway-specific induction of denervation-induced homeostatic synaptic plasticity.

opencc-zeroApr 2023View details →

RNA-seq and RT-qPCR data showing MDF role in RNA splicing and gene expression control in Arabidopsis

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways.

opencc-by-4.0Apr 2023View details →

Xenon's sedative effect is at least partly mediated by interaction with the cyclic nucleotide-binding domain (CNBD) of HCN2 channels expressed by thalamocortical neurons of the ventrobasal nucleus in mice

Xenon (70%xenon, 30%O2) application in the last 10 min of the open field test manage to sedate wild-type mice but not HCN2EA. Wild-type mice in the xenon_wild-type video can be seen moving freely in the early minutes but the general activity starts to decrease sharply in the last 2 minutes and is absent between min 9 and 10 while HCN2EA mice in the xenon_HCN2EA can be seen moving throughout the entire time of the xenon gas mixture application.

opencc-by-4.0Feb 2023View details →

Pento-DIARef: A Diagnostic Dataset for Learning the Incremental Algorithm for Referring Expression Generation from Examples

We present a Diagnostic dataset of IA References in a Pentomino domain (Pento-DIARef) that ties extensional and intensional definitions more closely together, insofar as the latter is the generative process creating the former. We create a novel synthetic dataset of examples that pairs visual scenes with generated referring expressions; examine two variants of the dataset, representing two different ways to exemplify the underlying task; and evaluate an LSTM-based baseline, a transformer and a modified version with region embeddings on them. See https://github.com/clp-research/pento-diaref for more information.

opencc-by-4.0Dec 2023View details →

Multi-omic integration of DNA methylation and gene expression data reveals molecular vulnerabilities in glioblastoma (processed data)

Glioblastoma multiforme (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of GBM patients has led to an improved categorisation into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome-wide multi-omic approaches to identify potential molecular vulnerabilities existing in GBM patients. Integration of gene expression and DNA methylation data from both bulk GBM and patient-derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype-specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP1, SMAD3 and RUNX1 / RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype-specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal-like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.

opencc-zeroMay 2023View details →

Data from: Docosahexaenoic acid intake suppresses acute silica-induced inflammation, autoantibody production, and autoimmune-related gene expression in lupus-prone mice

Short-term repeated intranasal exposure crystalline silica (cSiO2), a known human autoimmune trigger, induces uncontrolled inflammation, upregulated IFN-stimulated gene expression, diverse autoantibody production, and glomerulonephritis in lupus-prone female NZBWF1 mice. Dietary supplementation with the omega-3 fatty acid docosahexaenoic acid (DHA) prevents subchronic cSiO2 triggering of these lupus hallmarks. To understand how this intervention impacts acute effects of cSiO2, we fed NZBWF1 mice control (CON) or DHA-containing diet, subjected them to a single acute intranasal instillation of 2.5 mg cSiO2, then compared pulmonary inflammatory/autoimmune responses and autoimmune-related gene expression in experimental cohorts terminated at 7 and 28 d post-instillation (PI). Acute cSiO2 exposure of CON-fed mice elicited decreased macrophage and increased neutrophil numbers at 7 d PI, whereas at 28 d PI, CON-fed mice treated with particle displayed elevated total cell, macrophage, neutrophil, and lymphocyte counts. In contrast, DHA-fed mice treated with cSiO2 exhibited less macrophage loss at 7 d PI and reduced total cell, macrophage, and lymphocyte accumulation at 28 d PI. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) of lung sections suggested that cSiO2 induced more robust cell death at 7 d PI in CON-fed than DHA-fed mice. Targeted multiplex ELISA of lung extracts showed that at 28 d PI, cSiO2 induced higher concentrations of inflammation-associated cytokines (IL-1α, IL-6, and GM-CSF) and IFN-stimulated chemokines (CCL2, CCL3, CXCL10) in the CON-fed cohort than in the DHA-fed cohort. Autoantigen protein microarray of BALF collected at 28 d PI indicated that cSiO2 induced higher autoantibody responses for representative nuclear, ribosomal, mitochondrial, and complement proteins in CON-fed mice than DHA-fed mice. Gene expression analyses with NanoString Autoimmune Gene Expression assay revealed greater cSiO2-triggered upregulation of genes associated with TLR activation, DNA signaling, proinflammatory cytokines, chemokines, type 1 and 2 IFN response signatures, lymphocyte trafficking, MHC class 1 antigen presentation, B and T cell activation at 7 and 28 d PI in CON-fed mice than those fed DHA. Ingenuity Pathway Analysis (IPA) further demonstrated that DHA supplementation quelled cSiO2-induced responses top upstream regulators of proinflammatory and IFN-regulated gene networks to observed in CON-fed mice. Altogether, this short-term model illustrated that DHA suppression of aberrant acute cSiO2-induced inflammation is linked to altered regulation of autoimmune-related gene expression in lupus-prone mice.

opencc-zeroMay 2023View details →

Lipid analysis of S.c. cells expressing ProtA-ScNdc1 (261-655), ProtA-AHNdc1-ProtA, or ProtA-ScHmg1

Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, and few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.

opencc-by-4.0Mar 2023View details →

Positive p53 expression is significantly found higher in luminal B HER-2 negative cases with primary endocrine therapy resistance: A multicenter retrospective cross-sectional study in Indonesia

Positive p53 expression is significantly found higher in luminal B HER-2 negative cases with primary endocrine therapy resistance: A multicenter retrospective cross-sectional study in Indonesia