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opencc-by-4.0Feb 2022View details →

Gene expression and splicing counts from 49 tissues from GTEx v8 genome build hg38 - non-strand specific

Dataset description: 49 folders, each corresponding to one tissue from GTEx v8 and containing the following files: <ol> <li> geneCounts: gene-level counts  </li> <li> k_j: split counts spanning from one exon to another. </li> <li> k_theta: non-split counts covering a splice site </li> <li> n_psi3: total split counts from a given acceptor site </li> <li> n_psi5: total split counts from a given donor site </li> <li> n_theta: total split and non-split counts for a given splice site </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> The gene counts were originated using the GTF file from <a href="https://www.gencodegenes.org/human/release_29.html">release 29 of GENCODE</a>, and the split and non-split counts contain only the annotated junctions from the same release. Statistics are reported only for GENCODE-annotated introns and splice sites, in compliance with the regulations of the GTEx consortium. For a description of the samples, methods, and protocols, see the GTEx publication specified below. Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the <a href="https://github.com/gagneurlab/drop">Detection of RNA outliers Pipeline (DROP) </a> can be used to compute gene expression and splicing outliers. Organism: Homo sapiens Genome assembly: hg38 Gene annotation: gencode29 Strand specific: FALSE Paired end: TRUE Protocol: poly(A) enrichment Contact: Vicente A. Yepez, yepez at in.tum.de; Christian Mertes, mertes at in.tum.de; Julien Gagneur, gagneur at in.tum.de Citation: Write the following in the "Data availability" section of the manuscript or similar replacing the three citations by the ones from the References section below: <blockquote> The count matrices for the GTEx samples <cite GTEx publication, see below> were downloaded from Zenodo (doi: 10.5281/zenodo.6078397) and were generated through DROP <cite DROP, see below> using the release 29 of the GENCODE annotation <cite GENCODE, see below>. </blockquote> Also, write the following in the Acknowledgements section:   <blockquote> The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The raw data used for the analyses described in this manuscript were obtained from the GTEx Portal on June 12, 2017, under accession number dbGaP  phs000424.v8.p2. </blockquote>

opencc-by-4.0Mar 2022View details →

Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in Sorghum bicolor

Supplementery materials of journal article "Integrating differential expression and weighted correlation network analysis for identifying genes controlling shoot development in Sorghum bicolor"

opencc-by-4.0Dec 2020View details →

Host and pathogen gene expression profiles in Necrotizing Soft Tissue Infections

Data underlying the article Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and poly-microbial necrotizing soft tissue infections Sanjeevan Jahagirdar1, Lorna Morris2, Nirupama Benis3, Oddvar Oppegaard4, Mattias Svenson5, Ole Hyldegaard6, Steinar Skrede4,7, Anna Norrby-Teglund5, INFECT Study group, Vitor A. P. Martins dos Santos1,2, Edoardo Saccenti1* Contains Data described in 4.3.2 Sample Selection and in Figure 6: INFECT_DualRNASeq_norm_counts_Human.txt  Normalised counts from Kallisto mapping to GRCh38 (release 91) for 81 NSTI patients INFECT_DualRNASeq_relative_abundance_Bacteria.txt Relative abundance for all species from HumanN2 mapping for 81 NSTI patients BStrep_filtered_D1 - INFECT_DualRNASeq_relative_abundance_Bacteria.txt filtered for samples classified as Streptococcal from Thänert et al (2019) taken on the day of admission (day 1). BPoly_filtered_D1 - INFECT_DualRNASeq_relative_abundance_Bacteria.txt filtered for samples classified as polymicrobial from Thänert et al (2019) taken on the day of admission (day 1). HStrep_filtered_D1 - INFECT_DualRNASeq_norm_counts_Human.txt filtered for samples classified as Streptococcal from Thänert et al (2019) taken on the day of admission (day 1). HPoly_filtered_D1 - INFECT_DualRNASeq_norm_counts_Human.txt filtered for samples classified as polymicrobial from Thänert et al (2019) taken on the day of admission (day 1).

opencc-zeroApr 2022View details →

Gene expression in male and female sticklebacks from populations with convergent and divergent throat coloration

Understanding of genetic mechanisms underlying variation in sexual dichromatism remains limited, especially for carotenoid-based colors. We addressed this knowledge gap in a gene expression study with threespine stickleback. We compared male and female throat tissues across five populations, including two in which female red coloration has evolved convergently. We found that the expression of individual genes, gene ontologies, and coexpression networks associated with red female color within a population differed between California and British Columbia populations, suggesting differences in underlying mechanisms. Comparing females from each of these populations to females from populations dominated by dull females, we again found extensive expression differences. For each population, genes and networks associated with female red color showed the same patterns for males only inconsistently. The functional roles of genes showing correlated expression with female color are unclear within populations, whereas genes highlighted through inter-population comparisons include some previously suggested to function in carotenoid pathways. Among these, the most consistent patterns involved TTC39B (Tetratricopeptide Repeat Domain 39B), which is within a known red coloration QTL in stickleback and implicated in red coloration in other taxa.

opencc-zeroApr 2022View details →

Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles

Ocean warming challenges marine organisms' resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures. Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, Pinctada margaritifera. We benefit from two ecotypes for which local environmental conditions are characterized by either large diurnal variations in the tide-pools (Marquesas archipelago) or lower mean temperature with stable to moderate seasonal variations (Gambier archipelago). We explored the physiological basis of individual responses to elevated temperature, genetic divergence as well as plasticity and acclimation by combining lipidomic and transcriptomic approaches. We show that P. margaritifera has certain capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Genetic variation across populations overlaps with gene expression and involves the mitochondrial respiration machinery, a central physiological process that contributes to species thermal sensitivity and their distribution ranges. Our results present evidence for acclimation potential in P. margaritifera and urge for longer term studies to assess populations resilience in face of climate change.

opencc-by-4.0Dec 2021View details →

SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure

This repository contains the source code and data used in the paper: SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure.1.

opencc-zeroMay 2022View details →

Pea aphid winged and wingless males exhibit reproductive, gene expression, and lipid metabolism differences

Alternative, intraspecific phenotypes offer an opportunity to identify the mechanistic basis of differences associated with distinctive life-history strategies. Wing dimorphic insects, in which both flight-capable and flight-incapable individuals occur in the same population, are particularly well-studied in terms of why and how the morphs trade-off flight for reproduction. Yet despite a wealth of studies examining the differences between female morphs, little is known about male differences, which could arise from different causes than those acting on females. Here we examined reproductive, gene expression, and biochemical differences between pea aphid (Acyrthosiphon pisum) winged and wingless males. We find that winged males are competitively superior in one-on-one mating circumstances, but wingless males reach reproductive maturity faster and have larger testes. We suggest that males tradeoff increased local matings with concurrent possible inbreeding for outbreeding and increased ability to find mates. At the mechanistic level, differential gene expression between the morphs revealed a possible role for activin and insulin signaling in morph differences; it also highlighted genes not previously identified as being functionally important in wing polymorphism, such as genes likely involved in sperm production. Further, we find that winged males have higher lipid levels, consistent with their use as flight fuel, but we find no consistent patterns of different levels of activity among five enzymes associated with lipid biosynthesis. Overall, our analyses provide evidence that winged versus wingless males exhibit differences at the reproductive, biochemical, and gene expression levels, expanding the field's understanding of the functional aspects of morph differences.

opencc-by-4.0Jan 2022View details →

Supplementary information for 'Distinct gene expression dynamics in developing and regenerating crustacean limbs', by Sinigaglia et al.

Supplementary data and code for the manuscript 'Distinct gene expression dynamics in developing and regenerating crustacean limbs', by Sinigaglia et al.

opencc-zeroJul 2022View details →

Data and script files: Gene expression in response to estrone sulfate in Trachemys scripta

Variation in developmental conditions can affect a variety of embryonic processes and shape a number of phenotypic characteristics that can affect offspring throughout their lives. This is particularly true of oviparous species where development typically occurs outside of the female, and studies have shown that traits such as survival and behavior can be altered by both temperature and exposure to steroid hormones during development. In species with temperature-dependent sex determination (TSD), the fate of gonadal development can be affected by temperature and by maternal estrogens present in the egg at oviposition and there is evidence that these factors can affect gene expression patterns. Here, we explore how thermal fluctuations and exposure to an estrogen metabolite, estrone sulfate, affect the expression of several genes known to be involved in sexual differentiation; Kdm6b, Dmrt1, Sox9, FoxL2, and Cyp19A1. We found that most of the genes responded to both temperature and estrone sulfate exposure, but that the responses to these factors was not identical in that estrone sulfate effects occur downstream of temperature effects. Our findings demonstrate that conjugated hormones such as estrone sulfate are capable of influencing temperature dependent pathways to potentially alter how embryos respond to temperature and highlight the importance of studying the interaction of maternal hormone and temperature effects.

opencc-zeroAug 2022View details →

Seasonal but not sex-biased gene expression of the carotenoid ketolase, CYP2J19, in the sexually dichromatic southern red bishop (Euplectes orix)

Intense red colors in birds are often due to ketocarotenoids (KCs). In many land birds, KCs are oxidized from dietary yellow precursors, presumably by the avian carotenoid ketolase CYP2J19, the regulation and constraints of which have important implications for condition-dependence and honest signaling of carotenoid color displays. Here we investigate hepatic CYP2J19 gene expression in the seasonally and sexually dichromatic southern red bishop (Euplectes orix) in relation to season, sex, progression of the prenuptial moult, testis size, body condition, reflectance-based redness (hue), and circulating sex steroids. A coloration function of CYP2J19 is supported by seasonal upregulation prior to and during the carotenoid-depositing stage of the male prenuptial moult. However, upregulation was similar in females (which do not moult prenuptially), and remained high in males after moult, suggesting additional or alternative functions of hepatic CYP2J19 or its products, such as detoxification or antioxidants, respectively. In males, the CYP2J19 upregulation preceded and was unrelated to the rise in plasma testosterone, but was correlated with androstenedione, likely of adrenal origin and compatible with luteinizing hormone-induced and (in females) estrogen-suppressed moult. Finally, contrary to ideas that carotenoid ketolation rate mediates honest signaling, CYP2J19 expression was not related to male body condition or plumage redness.

opencc-by-4.0Aug 2022View details →

Gene expression counts from induced Pluripotent Stem Cells

File description: <ol> <li> Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a> </li> <li> Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites </li> <li> Non-split counts covering exon-intron boundaries </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the workflow DROP can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Maintainer: Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a> URL: <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a>   Title: induced Pluripotent Stem Cells Number of samples: 330 Tissue: iPSCs Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease: None Strand specific: True Paired end: True Dataset contact: Marc Bonder, marcj89 at gmail.com Citation: Cite both the resource using Zenodo's citation and the publication under References

opencc-by-4.0Sep 2022View details →

Data from: Differential gene expression during recall of behaviorally conditioned immune enhancement in rats: a pilot study

Background: Behaviorally conditioned immune functions are suggested to be regulated by bidirectional interactions between CNS and peripheral immune system via the hypothalamic-pituitary-adrenal (HPA) axis, sympathetic nervous system (SNS), and the parasympathetic nervous system (PNS). Since the current knowledge about biochemical pathways triggering conditioned immune enhancement is limited, the aim of this pilot study was gaining more insights into that. Methods: Rats were conditioned with camphor smell and poly I:C injection, mimicking a viral infection. Following stimulus re-exposure, animals were sacrificed at different time points, and neural tissues along the HPA axis was analyzed with a rat genome array together with plasma protein using Luminex analysis. Results: In the hypothalamus, we observed a strong upregulation of genes related to Wnt/β-catenin signaling (Otx2, Spp1, Fzd6, Zic1), monoaminergic transporter Slc18a2 and opioid-inhibitory G-protein Gpr88 as well as downregulation of dopaminergic receptors, vasoactive intestinal peptide Vip, and pro-melanin-concentrating hormone Pmch. In the pituitary, we recognized mostly upregulation of steroid synthesis in combination with GABAergic, cholinergic and opioid related neurotransmission, in adrenal glands, altered genes showed a pattern of activated metabolism plus upregulation of adrenoceptors Adrb3 and Adra1a. Data obtained from spleen showed a strong upregulation of immunomodulatory genes, chemo-/cytokines and glutamatergic/cholinergic neurotransmission related genes, as also confirmed by increased chemokine and ACTH levels in plasma. Conclusions: Our data indicate that in addition to the classic HPA axis, there could be additional pathways as e.g. the cholinergic anti-inflammatory pathway (CAIP), connecting brain and immune system, modulating and finetuning communication between brain and immune system.

opencc-by-4.0Sep 2022View details →

Expression of immunoglobulin constant domain genes in neurons of the mouse central nervous system

Data related to the publication "Expression of immunoglobulin constant domain genes in neurons of the mouse central nervous system".  The fasta file (.fa) contains the sequence of neuronal FC-Ighm The .pdb files contain the model of the two different protein versions of Ighm The excel file contains the data of the quantification of co-expression and the ATG prediction results.

opencc-by-4.0Mar 2021View details →

Gene expression and splicing counts from the Yepez, Gusic et al study - non strand-specific

File description: <ol> <li> geneCounts: gene-level counts  </li> <li> k_j: split counts spanning from one exon to another. </li> <li> k_theta: non-split counts covering a splice site </li> <li> n_psi3: total split counts from a given acceptor site </li> <li> n_psi5: total split counts from a given donor site </li> <li> n_theta: total split and non-split counts for a given splice site </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol>   The gene counts were originated using the GTF file from release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a>, and the split and non-split counts contain only the annotated junctions from the same release. Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the DROP can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Number of samples: 154 Tissue: Fibroblast Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): E75: 1, E79: 13, E88: 118, G31: 9, K72: 3, NONE: 10 Strand specific: FALSE Paired end: TRUE Protocol: poly(A) enrichment Dataset contact: Vicente Yepez, yepez@in.tum.de; Julien Gagneur, gagneur@in.tum.de; Holger Prokisch, prokisch@helmholtz-muenchen.de Citation: Cite both the resource using Zenodo's citation and the publication under References

Figure 4 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)

Figure 4. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus

Figure 3 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)

Figure 3. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus

Figure 2 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)

Figure 2. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus

Figure 1 in Gene expression changes in response to combination stresses in Phaseolus vulgaris L. (Fabaceae)

Figure 1. Relative gene expression of some genes (OS, PR3, LOX, PR4 and PAL) by real-time PCR in Tetranychus

opencc-by-4.0Oct 2022View details →

Dataset for "Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR"

This dataset constitutes the pre-processed data contained in the publication 'Applicability of Control Materials To Support Gene Promoter Characterization and Expression in Engineered Cells Using Digital PCR' Analytical Chemistry (2022) 94(14):5566-5574 (DOI: 10.1021/acs.analchem.1c05134).