Find research datasets worth reusing

opencc-by-4.0Oct 2015View details →

Mouse and Human Co-expression maps and supplementary material for: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels"

Co-expression maps of the human and mouse species derived from microarray data for the first release of the GeneFriend tool. The two co-expression maps  have been compared in order to discern similarities and differences between the two species. The results have been described in the manuscript titled: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels". The supplementary material of the manuscript have also been included in this repository.

opencc-by-sa-4.0Sep 2016View details →

R data set: The Cancer Genome Atlas Gene Expression data

This compound data set comprises the following information from the The Cancer Genome Atlas: <ul> <li>RNA-Seq counts for 60483 genes across 11093 samples</li> <li>HuEx 1.0 ST gene expression data for 18632 genes across 1211 samples</li> <li>clinical indicators for 11160 patients</li> </ul> All gene expression data is annotated across ENSEMBL, ENTREZ and symbols. Samples are annotated by TCGA barcodes. To read the data set into R (requires 6 GB of RAM) use: tcga <- readRDS("tcga.rds")

opencc-by-4.0Feb 2017View details →

Analysis of gene expression in autoimmune and autoinflammatory diseases using GSEA

This dataset contains the results of gene set enrichment analysis (GSEA) of gene expression in the studied diseases. The archive is organized in folders according the GEO accessions for the raw data (see table 1 of the main article). If multiple diseases were studied within one GEO data series, GSEA was performed for each disease separately. Healthy subject data included in each data series were used as reference. For example "GSE3365.IBD" folder contains GSEA for Crohn's disease (CD) and ulcerative colitis (US). The "results" folder in "GSE3365.IBD" contains two subfolders "GSE3365CDvcHC" and "GSE3365UCvcHC", respectively. The results can be browsed with "index.html" files located in each subfolder.

opencc-by-4.0May 2022View details →

Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels

<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>

Joint profiling of cell morphology and gene expression during in vitro neurodevelopment

Cell Painting processed data for "Joint profiling of cell morphology and gene expression during in vitro neurodevelopment".

Coupled gene expression on single DNA molecules (raw single-molecule movies + description)

Raw single-molecule movies and corresponding experimental details in description file

Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."

Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."

Analysis of heme and iron influence on Porphyromonas gingivalis A7436 and ATCC 33277 strains genes expression (microarray results)

The aim of this study was to analyze phenotypic differences between P. gingivalis more virulent A7436 and less virulent ATCC 33277 (33277) strains. The analysis comprised the influence of heme and iron on P. gingivalis gene expression. P. gingivalis A7436 and 33277 strains were cultured in basal medium (3% trypticase soy broth and 0.5% yeast extract), supplemented with 3.6 mM L-cysteine hydrochloride, and 0.5 mg/l menadione, in anaerobic conditions (80% N2, 10% H2 and 10% CO2). To generate heme and iron-limited conditions, the medium was supplemented with 0.16 mM of the iron chelator 2,2-dipyridyl (DIP conditions). To generate heme and iron-rich conditions, the medium was supplemented with 0.0077mM hemin chloride (Hm conditions). Three sample replicates of A7436 and 33277 strains were grown in Hm or DIP conditions for 20 hours. RNA isolation and microarray analysis were performed in IMGM laboratories (Martinsried, Germany), as described by Śmiga et al. (2023).The online tool eArray (http://earray.chem.agilent.com/; Agilent Technologies, Santa Clara, CA, USA) was used to design an Agilent Custom Porphyromonas gingivalis A7436 Gene Expression Microarray (8×15K format). Probes were prepared based on P. gingivalis transcriptome information derived from the NCBI reference sequence NZ_CP011995.1. Total RNA isolation, RNA quantity, and quality were determined as described by Curaszkiewicz et al. 2014. For internal labeling control, the total RNA was spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix; Agilent Technologies). Subsequently, samples were reverse transcribed into cDNA and then converted into cyanine-3-labeled complementary RNA (cRNA) with Low Input Quick-Amp Labeling Kit One-Color (Agilent Technologies). For microarray hybridization, a Gene Expression Hybridization Kit (Agilent Technologies) was used. Labeled cRNA was hybridized for 17 hours at 65℃ on Agilent Custom GE 8×15K Microarrays, washed according to the manufacturer's protocol, and dried with acetonitrile (Sigma-Aldrich). The fluorescence of samples was detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner (Agilent Technologies) and extracted from the images using Feature Extraction 10.7.3.1 software (Agilent Technologies). For data analysis, Feature Extraction 10.7.3.1 (Agilent Technologies), GeneSpring GX 13.1.1 (Agilent Technologies), and Excel 2010 (Microsoft, Redmond, WA, USA) were used. For statistical analysis, Welch's approximate t-test was used. Differences in gene expression are shown as fold change values (FC). The average was calculated from the normalized signal values and they were transformed from the log2 to the linear scale. Increases and decreases in gene expression are shown as positive and negative numbers, respectively. The fold change in gene expression was considered significant for FC ≥ 2 or FC ≤ -2 and P-value ≤ 0.05<ul><li>Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. 2014. Fur homolog regulates Porphyromonas gingivalis virulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 29:333-353. doi: 10.1111/omi.12077.</li><li>Śmiga M, Ślęzak P, Olczak T. 2023. Comparative analysis of Porphyromonas gingivalis A7436 and ATCC 33277 strains reveals differences in the expression of heme acquisition systems. Microbiol Spectr (revised manuscript under revision).</li></ul>

Long-term changes in pituitary gene expression following developmental exposure to environmental contaminants (BPS, BDE-47, or TBBPA) in male mice.

Experimental DesignIn this study we evaluate the long-term gene expression changes in pituitary in male mice exposed developmentally to one of three known endocrine disrupting chemicals: bisphenol-S (BPS), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), and 3,3',5,5'-tetrabromobisphenol A (TBBPA).  Male mice were exposed to chemical treatment through their mothers' during pregnancy (umbilical blood flow) and nursing, from pregnancy day 8 through weaning at postnatal day 21 (PND21). Each chemical exposure was calculated to equal 0.2mg/kg bw/day. The details of exposure protocol are described elsewhere (Kim et al, 2015). The male pups were allowed to grow untreated until adulthood at PND140. At PND140, male mice were euthanized, then their pituitaries removed, snap frozen in liquid nitrogen, and then stored at -80°C. The data-files described below represent major steps of our analysis:1. FASTQ files for mouse pituitary RNA-seq data.Male mouse pituitary RNA was isolated using a Trizol protocol, checked for purity and concentration and then processed for mRNA sequencing using the Illumina TruSeq kit and protocol (TruSeq Stranded mRNA LP, Cat # 20020594 and TruSeq RNA Sg Idx SetB, Cat # 20020493, Illumina, San Diego, CA) following the manufacturer's recommended procedures. High throughput sequencing was conducted using the NextSeq500 sequencing system. cDNA libraries were single-end sequenced in 76 cycles using a NSQ 500/550 Hi Output KT v2.5 (Cat #20024906 Illumina, San-Diego, CA) in one multiplex run (N=3/exposure group).  Read filtering, trimming, and de-multiplexing were performed using the BaseSpace cloud service by Illumina (<a href="https://basespace.illumina.com/home/index">https://basespace.illumina.com/home/index</a>, RRID:SCR_011881). Processed reads were mapped to the mouse reference genome (MM10) using the RNA-Seq Alignment v. 1.1.1. software with Bowtie 2. Each FASTQ file is a compressed file representing data from one sequencing flow cell lane for each sample (4 files per sample). Sample identifiers are coded for treatment: X = Vehicle control, R = TBBPA, C = BDE-47, E = BPS. 2. Differential expression data.Aligned reads were used to assemble transcripts and analyze differential expression using Cufflinks Assembly & DE v. 2.1.0. package. Reads aligned to known annotated regions for both control and exposed groups were used to calculate log2 FPKM ratios.  Differentially expressed genes were identified as genes altered with false discovery rate significance ≤ 0.05 (FDR, q ≤ 0.05).  Data on all exposure groups are shown in different sheets of the same file - Differential_expression.xlsx.3. Enrichment of biological categories associated with DEGs induced by chemical exposures. All differentially expressed genes were uploaded to Metascape for the analysis of enriched biological categories using default settings. Results of Metascape analysis are shown in two MS Excel files per exposure group, one showing negatively enriched categories and one positively enriched categories. The title of each file consists of three parts connected via underscore sign: the name of the chemical, the direction of enrichment, and the name of analysis - metascape (e.g., BDE-47_negative_metascape.xlsx).4. Pathway analysis for chemical exposures.All differentially expressed genes were uploaded to Ingenuity Pathway Analysis and enriched canonical pathways were identified  using default settings . Altered molecular or disease pathways, their p-values, and associated differentially expressed genes are provided for each exposure. Data for all exposure groups are shown in different sheets of the same file - IPA_pathway_analysis.xlsx.References:Kim B, Colon E, Chawla S, Vandenberg LN, Suvorov A. Endocrine disruptors alter social behaviors and indirectly influence social hierarchies via changes in body weight. Environ Health. 2015 Aug 5;14:64. doi: 10.1186/s12940-015-0051-6. PMID: 26242739; PMCID: PMC4524022.

opencc-zeroNov 2023View details →

Data from: Repeated divergence in opsin genes expression mirrors photic habitat changes in rapidly evolving crater lake cichlid fishes

<div> <div> <div class="msocomtxt"> Selection pressures differ along environmental gradients and organisms' phenotypes. Traits tightly linked to fitness (e.g., the visual system) are expected to closely track environmental variation along gradients. Within such gradients, adaptation to local conditions might be due to heritable and non-heritable, environmentally induced variation. Disentangling these sources of phenotypic variation requires studying, in nature and the laboratory, closely related populations experiencing different environments. The Nicaraguan great and crater lakes show an environmental gradient in photic conditions extending from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (Amphilophus cf. citrinellus) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated the variation in visual sensitivities along this photic gradient by measuring differential cone opsin gene expression among populations from different lakes. The visual sensitivities observed in all seven derived crater lake populations have not changed randomly but shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Intrapopulation phenotypic variation decreases as environments become spectrally narrower suggesting different selective landscapes within the gradient. Comparing wild-caught and lab-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Our results demonstrate deterministic, rapid phenotypic evolution that fine-tunes visual sensitivity to fine-scale environmental variation. </div> </div> </div>

opencc-zeroNov 2023View details →

A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size

The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). Most prior studies of host genetic predictors of HIV control have focused on "elite controllers," rare individuals able to control virus in the absence of ART. However, there have been few genetic studies among ART-suppressed non-controllers, who make up the majority of people living with HIV (PLWH). We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q=0.006), IL-1/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-a protein associations achieving statistical significance (p<0.05). Of note, plasma IL-10 was also significantly inversely associated with HIV DNA (p=0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. Further data are needed to validate these findings, including functional genomic studies, larger cohorts including underrepresented PLWH in research, and those including dedicated assays to measure the replication-competent HIV reservoir.

opencc-by-4.0Dec 2022View details →

Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected to virus-induced gene silencing using Tobacco rattle virus (TRV) vector.

Figure S1. Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected  to virus-induced gene silencing using Tobacco rattle virus (TRV) vector. (A) Relative expression levels of Sgt1 analyzed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) in tomato plants infected with TRV vector alone (TRV2), TRV carrying Sgt1 silencing constructs (TRV-Sgt1), and mock-inoculated (Mock). Transcript levels were normalized using tomato genes encoding elongation factor 1-α and SAND as internal references, with Mock as the calibrator. (B) Relative expression levels of Hsp90 analyzed by RT-qPCR in tomato plants infected with TRV2, TRV-Hsp90, and Mock. Gene expression levels were normalized using the same reference genes as in (A). (C) Quantification of the relative accumulation of TRV RNA in plants infected with TRV2 and in silenced plants (TRV-Sgt1 and TRV-Hsp90). The expression levels were normalized using tomato genes for elongation factor 1-α and SAND, with TRV2 as the calibrator. All samples were collected at 19 dpi to anticipate the observed decline. Error bars represent standard errors of five biological replicates, and an asterisk indicates a significant difference, as determined by one-way ANOVA with P < 0.05

opencc-by-4.0Dec 2023View details →

Differentially expressed genes in berries and rachis of berry shrivel grape clusters used to prepare figures for a review

Grapevine berry shrivel is a ripening disorder leading to significant economic losses in the worldwide wine and table grape industries. Sugar accumulation stops early after ripening onset accompanied with cell death in berreis and subtending pecicels and rachis finally resulting in berry shrinkage. To date, the triggers of BS remain unknown. The dataset supports figures prepared for an review which aims to summarize and critically discuss the current knowledge. Data are expressed as differentially expressed genes obtained from grape berries samples collected at six developmental stages (pre- until post-veraison) analysed with RNASeq and two pooled samples (pre- and BS symptomatic) from the rachis analyzed with a microarray study. Extracted information focus on primary metabolic processes including sugar transport and metabolism, organic acid metabolism, stress signaling and cell as well as cell wall organisation. Data are mean values of three biological represent and presented as log2 fold changes including statistical information. A meta-data sheet provides the most relevant information and references.

opencc-zeroJan 2024View details →

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce

The naturally occurring bisexual cone of gymnosperms is considered to have been a potential intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in a conifer species Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of genes crucial for cone development, including PcDAL12, PcDAL10, PcNEEDLY and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the development of bisexuality.

opencc-zeroJan 2024View details →

Data for: Neuroendocrine gene expression coupling of interoceptive bacterial food cues to foraging behavior of C. elegans

Animal internal state is modulated by nutrient intake, resulting in behavioral responses to changing food conditions. The neural mechanisms by which internal states are generated and maintained are not well understood. Here, we show that in the nematode Caenorhabditis elegans, distinct cues from bacterial food – interoceptive signals from the ingestion of bacteria and gustatory molecules sensed from nearby bacteria – act antagonistically on the expression of the neuroendocrine TGF-beta ligand DAF-7 from the ASJ pair of sensory neurons to modulate foraging behavior. A positive-feedback loop dependent on the expression of daf-7 from the ASJ neurons acts to promote transitions between roaming and dwelling foraging states and influence the persistence of roaming states. SCD-2, the C. elegans ortholog of mammalian Anaplastic Lymphoma Kinase (ALK), which has been implicated in the central control of metabolism of mammals, functions in the AIA interneurons to regulate foraging behavior and cell-non-autonomously control the expression of DAF-7 from the ASJ neurons. Our data establish how a dynamic neuroendocrine daf-7 expression feedback loop regulated by SCD-2 functions to couple sensing and ingestion of bacterial food to foraging behavior. We further suggest that this neuroendocrine feedback loop underlies previously characterized exploratory behaviors in C. elegans. Our data suggest that the expression of daf-7 from the ASJ neurons contributes to and is correlated with an internal state of "unmet need" that regulates exploratory foraging behavior in response to bacterial cues in diverse physiological contexts.

opencc-zeroJan 2024View details →

Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression

Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the Major Histocompatibility Complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi-locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ datasets of three-spined stickleback gDNA, cDNA, and "artificial" plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, gDNA-optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template-specific pipeline optimization for reliable genotyping of multi-locus gene families. Through accurate paired gDNA-cDNA typing and MHC-II haplotype inference, we show that MHC-II allele-specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship-assisted cDNA-typing of MHC-I revealed novel variants linked in haplotype blocks and a higher-than-previously-reported individual MHC-I allelic diversity. In conclusion, we provide novel genotyping protocols for the three-spined stickleback MHC-I and -II genes and evaluate the performance of popular NGS-genotyping pipelines. We also show that fine-tuned genotyping of paired gDNA-cDNA samples facilitates amplification bias-corrected MHC allele expression analysis.

opencc-zeroFeb 2024View details →

Diet-induced plasticity of life-history traits and gene expression in outbred Drosophila melanogaster population

Food is fundamental for the survival of organisms, governing growth, maintenance, and reproduction through the provision of essential macronutrients. However, access to food with optimum macronutrient composition, which will maximize the evolutionary fitness of an organism, is not always guaranteed. This leads to dietary mismatches with potential impacts on organismal performance. To understand the consequences of such dietary mismatches, we examined the effects of isocaloric diets varying in macronutrient composition on eight key organismal traits spanning across the lifespan of a large outbred Drosophila melanogaster population (n ~ 2500). Our findings reveal that carbohydrate-reduced isocaloric diets correlates to accelerated pre-adult development and boosts reproductive output without impacting pre-adult viability and body size. Conversely, an elevated dietary carbohydrate content correlated to reduced lifespan in flies, evidenced by accelerated functional senescence including compromised locomotor activity and deteriorating gut integrity. Furthermore, transcriptomic analysis indicated a substantial difference in gene regulatory landscapes between flies subject to high carbohydrate vs high protein diet, with elevated protein levels indicating transcriptomes primed for reduced synthesis of fatty acids. Taken together, our study helps advance our understanding of the effect of macronutrient composition on life history traits and their interrelations, offering critical insights into potential adaptive strategies that organisms might adopt against the continual dietary imbalances prevalent in the rapidly evolving environment.

opencc-by-4.0Mar 2024View details →

Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry: Source and Supplementary Data

Source and Supplementary data for AANRI manuscript

opencc-by-4.0Dec 2023View details →

Gene expression landscape of cutaneous squamous cell carcinoma progression

Data files associated with "Gene expression landscape of cutaneous squamous cell carcinoma progression" by Bencomo and Lee. The README.md file has descriptions for each file.Funding support: This work was supported by a Scholar-Innovator Award from the Harrington Discovery Institute and a Discovery Boost grant from the American Cancer Society (CSL).