Find research datasets worth reusing

Zebrafish with lyz:EGFP expressing neutrophils: Mesh Well Inserts Z-stack 2

96-well plate z-stack of zebrafish with lyz:EGFP expressing neutrophils acquired with a multi-camera array microscope (MCAM)(Ramona Optics Inc., Durham, NC, USA). Mesh well inserts are used and half of the zebrafish on the plate were injected with csf3r morpholino. The overall z-stack is broken into four files.   HDF5 files can be opened using open source Python software: https://docs.xarray.dev/

Zebrafish with lyz:EGFP expressing neutrophils: csf3r_MO injected stack

96-well plate z-stack of zebrafish with lyz:EGFP expressing neutrophils acquired with a multi-camera array microscope (MCAM)(Ramona Optics Inc., Durham, NC, USA). Zebrafish larvae have been injected with csf3r morpholino.   HDF5 files can be opened using open source Python software: https://docs.xarray.dev/

opencc-by-4.0Jul 2023View details →

Zebrafish with lyz:EGFP expressing neutrophils: Dibutyl phthalate Stack

96-well plate z-stack of zebrafish with lyz:EGFP expressing neutrophils acquired with a multi-camera array microscope (MCAM)(Ramona Optics Inc., Durham, NC, USA). Fish were treated with Dibutyl pthalate or DMSO prior to imaging.   HDF5 files can be opened using open source Python software: https://docs.xarray.dev/

Zebrafish with lyz:EGFP expressing neutrophils: Mesh Well Inserts Z-stack 1

Zebrafish with lyz:EGFP expressing neutrophils: Non-injected stack

96-well plate z-stack of zebrafish with lyz:EGFP expressing neutrophils acquired with a multi-camera array microscope (MCAM)(Ramona Optics Inc., Durham, NC, USA).   HDF5 files can be opened using open source Python software: https://docs.xarray.dev/

opencc-zeroAug 2023View details →

Data for: Expression of trematode-induced zombie-ant behavior is strongly associated with temperature

Parasite-induced modification of host behavior increasing transmission to a next host is a common phenomenon. However, field-based studies are rare and the role of environmental factors in eliciting host behavioral modification is often not considered. We examined the effects of temperature, relative humidity (RH), time of day, date, and an irradiation-proxy on behavioral modification of the ant Formica polyctena (Förster, 1850) by the brain-encysting lancet liver fluke Dicrocoelium dendriticum (Rudolphi, 1819). This fluke induces ants to climb, and bite to vegetation by the mandibles in a state of temporary tetany. A total of 1,264 individual ants expressing the modified behavior were observed over 13 non-consecutive days during one year in the Bidstrup Forests, Denmark. A sub-set of those ants (N=172) was individually marked to track attachment and release of infected ants in relation to variation in temperature.

opencc-by-4.0Aug 2023View details →

Clinical expression of programmed maxillary buccal expansion and buccolingual crown inclination with Invisalign® EX30® and SmartTrack® aligners and investigating the effect of 1-week vs 2-week aligner change regimes: A retrospective study.

Objective: The objective of this retrospective cohort study is to assess and compare the accuracy of three different Invisalign® treatment regimens involving variations of aligner change frequency and type of aligner material in achieving maxillary dental buccal expansion.   Methods: 120 adult patients whose treatment involved maxillary dental expansion with Invisalign® were selected. Three groups, each of 40 patients were identified: SmartTrack® one-week changes (ST1), SmartTrack® two-week changes (ST2)  and EX30® two-week changes (EX2). The groups were assessed by comparing actual changes achieved with those prescribed by ClinCheck®. The rates of clinically significant inaccuracies (CSI) seen for buccal expansion (≥ 0.5mm) and buccolingual inclination (≥2°) during expansion were then ascertained.   Results: With respect to expansion, the ST1 group showed the highest rate of CSI at all tooth levels studied while the ST2 group showed the lowest rate of CSI as well as the lowest mean inaccuracy for each tooth level studied. In terms of buccolingual inclination, the ST1 group displayed the highest rate of CSI across all tooth levels studied, while the EX2 group displayed the lowest rate of CSI at all tooth levels except for the canine level where the ST2 group displayed the lowest rate of CSI. A tendency toward overexpression of buccal crown inclination, and underexpression of buccal expansion was seen at all tooth levels.   Conclusions: Two-week aligner change regimens offer improved accuracy compared with one-week aligner changes. SmartTrack® two-week changes were the most accurate for buccal expansion, while EX30® 2-week changes were the most accurate for buccolingual inclination.

opencc-zeroAug 2023View details →

Cytoplasmic male sterility and abortive seed traits generated through mitochondrial genome editing coupled with allotopic expression of atp1 in tobacco

Genome editing tools have recently been developed that are capable of generating deletions and/or rearrangements in plant mitochondrial genomes. We utilized custom-designed meganuclease constructs targeting the essential mitochondrial gene atp1 in tobacco plants carrying a version of atp1 that had been repurposed to function as a nuclear gene. Leaf extracts enriched in mitochondria from three independent genome editing events were evaluated by PacBio sequencing and analysis. Contigs that display sequence homology to the reference mitochondrial genome BA000042 are deposited here. Some of the contigs correspond to the tobacco mitochondrial genome as expected, while others corresponded to sequences from the nucleus where the ancient transfer of portions of the mitochondrial genome became incorporated into the nuclear genome. Still other contigs correspond to the chloroplast genome, or pieces of the chloroplast genome anciently transferred to the nucleus, as small fragments of the chloroplast genome are interspersed in plant mitochondrial genomes. Analysis of contigs of genuine mitochondrial origin demonstrated that the double-strand breaks imposed by the genome editing enzymes resulted in the deletion of atp1 and neighboring sequences, along with rearrangements in overall genome structure.

opencc-by-4.0Aug 2023View details →

Processed RNA expression count data and metadata from Gupta et al.:Systems genomics of salinity stress response in rice

We assessed gene expression variation in a population of 130 accessions of rice (Oryza sativa) belonging to the major varietal group indica. The field experiment was conducted in the dry season of 2017 at IRRI in Los Banos, Laguna, Philippines. Seeds from each accession were sown on December 16, 2016, and seedlings were then transplanted into the experimental fields at 17 days after sowing (DAS), on January 5, 2017. The field experiments was conducted across two locations close-by: one non-salinized normal field and the other salinized field. Both field environments used a randomized complete block experimental design with each accession planted in three replicates. Each experimental plot included the accessions NSICRC 222 and NSICRC 182 serving as border rows. The application of salt in Block L5 started on January 19, 2017 when the plants were 31 days old. The salinity level was monitored by recording electrical conductivity (EC), using EC meters installed in each of the parcels at a depth of 30 cm. The salinity levels were then maintained at 6 dS/m (considered mild to moderate salinity stress) until maturity. Management and maintenance of the fields included the application of basal fertilizer, spraying of insecticides against thrips and removal of plants potentially infected with the rice tungro virus disease. Tissue collection for transcriptome. Briefly, leaf collection was done at 38 DAS (8 days after the beginning of the salt treatment) in the non-saline and saline field. Transcript levels were measured using a liquid automation-based 3 prime mRNA-seq quantification approach. Samples were multiplexed in batches of 96 per library. Raw sequencing data are available at the SRA in BioProject accession number PRJNA1010833. A key to the raw sequencing data in this BioProject can be found in the metadata of the processed RNA expression count data here

opencc-zeroAug 2023View details →

Data for: A predominant role of genotypic variation in both expression of sperm competition genes and paternity success in Drosophila melanogaster

The study focuses on investigating the impact of both environmental and genotypic variations on the expression of sperm competition genes and relative paternity success (i.e. second male paternity; P2) in Drosophila melanogaster. To address this, the research leverages the Drosophila Genetic Reference Panel (DGRP) inbred lines and introduces manipulation of developmental population density, specifically larval density. This experimental design allows for the examination of the effects of genotype, environment, and potential genotype-environment interactions (GEI) on the expression of seminal fluid genes, namely Sex Peptide, Acp36DE, and CG9997 and sperm competitiveness. In light of the observed genotypic influence on genes' expression, a genome-wide association study (GWAS) was also conducted for Sex Peptide and Acp36DE.

Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture

Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.

Video clips related to the paper "Humanoid facial expressions as a tool to study human behavior

During the experiment, participants observed video-clips of the iCub robot performing a gentle or rude arm movement (giving request) with a happy or angry facial expressions.

opencc-by-nc-nd-4.0Sep 2023View details →

Models and Data associated with: Single-cell gene expression prediction from DNA sequence at large contexts

This archive holds trained models and associated data for the <a href="https://www.biorxiv.org/content/10.1101/2023.07.26.550634v1">manuscript</a>: "Single-cell gene expression prediction from DNA sequence at large contexts" Structure: <ul> <li>configs - example configs for the workflows to produce publication data </li> <li>data_* - pre-processed single cell data used for publication</li> <li>models_* - model checkpoints, hyperparameters and training progress in tensorboard logs</li> <li>preprocessing - additional data required to reproduce the pre-processing workflow</li> </ul>   "Copyright 2023 GlaxoSmithKline Research & Development Limited. All rights reserved."

Summary statistics for "Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin"

Publication: Deecke et al., Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin, manuscript under revision Brief summary: Solar lentigines (SL) are a characteristic of the aging skin. Their occurrence is likely determined by a combination of genetic variants and environmental factors such as chronic sun exposure. However, the genetic factors underlying SL formation remain largely unknown. A recently performed genome-wide association study (GWAS) of SL in two Chinese cohorts reported TERT and OCA2 as novel genome-wide significant genetic loci for SL, while only the TERT locus could be validated in a cohort of European descent (Peng et al, 2023). The telomerase reverse transcriptase TERT is known to be involved in the process of maintenance of telomere lengths, but interestingly no causal relationship between telomere length and the SL GWAS results was observed by the investigators. In this study, we quantified the heritability of SL located on the back of the hands and performed a de novo GWAS in 1,137 elderly participants (aged 60 and more) of European descent from the Berlin Aging Study II. We confirmed TERT as the only genome-wide significant locus for SL (top SNP: rs2735940, p= 1.35E-16). In line with the previous Mendelian Randomization (MR) results by Peng et al., our updated MR using substantially larger datasets did not show a causal relationship between the occurrence of SL and telomere lengths measured in blood leukocytes. Importantly, rs2735940 modifies TERT expression in skin tissue (based on GTEx data), but not in any of the other GTEx tissues including blood. Furthermore, colocalization analyses suggested a shared causal effect of rs2735940 on SL occurrence and on TERT expression in skin but not in blood. Thus, we could show that variants in the TERT gene increase the occurrence of SL by modifying TERT expression exclusively in the skin, based on currently available GTEx data. This skin-specific effect was not reported previously and may provide the hitherto missing functional link for the occurrence of SLs via TERT expression and telomere length alterations.

Data From: Effects of measurement methods and growing conditions on phenotypic expression of photosynthesis in seven diverse rice genotypes

Introduction: Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (nonsequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the specific light level. Methods: Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to field conditions 2-3 days before measurements), and field environments. We selected seven diverse rice genotypes (five genotypes from the USDA rice minicore collection: 310588, 310723, 311644, 311677, 311795; and 2 additional genotypes: Nagina 22 and Zhe 733) to understand (1) the limitations of different methods, and (2) phenotypic plasticity of photosynthesis in rice grown under different environments. Results: Our results show that the non-sequential method was time-efficient and captured more variability of field conditions than the sequential method, but the model parameters were generally similar between the two methods except for the maximum photosynthesis rate (Amax). Amax was significantly lower across all genotypes under greenhouse conditions compared to the growth chamber and field conditions consistent with prior work, but surprisingly the apparent quantum yield (α) and the mitochondrial respiration (Rd) were generally not different among growing environments or measurement methods. Discussion: Our results suggest that field conditions are best suited to quantify phenotypic differences across different genotypes, and the nonsequential method was better at capturing the variability in photosynthesis.

Small Toy Adipose TPM Expression Dataset

Small TPM expression of genes in the adipose (subcutaneous). Original data is from GTEX V8 on TPM counts of genes in the adipose.

Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells

Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH, and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites in vitro using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easily targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.

Dim artificial light at night alters immediate early gene expression throughout the avian brain

Artificial light at night (ALAN) is a pervasive pollutant that alters physiology and behavior. However, the underlying mechanisms triggering these alterations are unknown, as previous work shows that dim levels of ALAN may have a masking effect, bypassing the central clock. Light stimulates neuronal activity in numerous brain regions which could in turn activate downstream effectors regulating physiological response. In the present study, taking advantage of immediate early gene (IEG) expression as a proxy for neuronal activity, we determined the brain regions activated in response to ALAN. We exposed zebra finches to dim ALAN (1.5 lux) and analyzed 24 regions throughout the brain. We found that the overall expression of two different IEGs, cFos and ZENK, in birds exposed to ALAN were significantly different from birds inactive at night. Additionally, we found that ALAN-exposed birds had significantly different IEG expression from birds inactive at night and active during the day in several brain areas associated with vision, movement, learning and memory, pain processing, and hormone regulation. These results give insight into the mechanistic pathways responding to ALAN that underlie downstream, well-documented behavioral and physiological changes.

Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes

Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following: <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - de novo assembled transcriptomes for non-model species</li> </ul>