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Supplementary Table S5 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S5. Repository data showing genes identified by MapMan in Giza 178 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose.  E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S4 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S4. Repository data showing genes identified by MapMan in Giza 177 in different pathways.  A, Cell wall modifications. B, Hemicellulose synthesis. C, Cellulose synthesis. D, Mannan-xylose-arabinose-fucose. E, cell wall peroxidase. F, TF MYB.  G, bZIP.   H, Histone.

Supplementary Table S2 - Article:Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S2. Repository data for the global analysis produced for cv Giza 177.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 177 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 177 up regulated genes.    D, GOEA results for Giza 177 down regulated genes.

Supplementary Table S3 - Article: Transcriptome Analysis Provides Novel Insights into Salinity Stress Response in two Egyptian Rice Varieties with Different Tolerance Levels

Table S3. Repository data for the global analysis produced for cv Giza 178.  A, Up regulated genes observed when comparing salt stressed plants vs unstressed controls.  B, Down regulated genes in Giza 178 observed when comparing salt stressed plants vs unstressed controls. C, Gene Ontology enrichment analysis (GOEA) results for Giza 178 up regulated genes.    D, GOEA results for Giza 178 down regulated genes.

Summary statistics from "Impact of medication on blood transcriptome reveals off-target regulations of beta-blockers"

The zipped csv-file is comma-delimited and contains the following columns: identifier: Probe number and associated active substance PROBE_ID.Adult: Probe number logFC.Adult: log fold change of specific probe in LIFE-Adult SE.Adult: Stand error for probe in LIFE-Adult P.Value.Adult: p-value for probe in LIFE-Adult qval.Adult: q-value for probe in LIFE-Adult medi.Adult: associated active substance in in LIFE-Adult P.Value.Heart: p-value for probe in LIFE-Heart logFC.Heart: p-value for probe in LIFE-Heart SE.Heart: Standard error for probe in LIFE-Heart qval.Heart: q-value for probe in LIFE-Heart medi.Heart: associated active substance in LIFE-Heart symbol_INGENUITY: Gene associated with probe according to Ingenuity description_INGENUITY: Description of gene associated with probe according to Ingenuity For LIFE-Adult the results were calculated for all probes associated with the relevant 83 active substances described. For LIFE-Heart results were only calculated for probes that were also available LIFE-Adult.

opencc-by-4.0May 2022View details →

Full-Length Spatial Transcriptomics Reveals the Unexplored Isoform Diversity of the Myocardium Post-MI

We introduce Single-cell Nanopore Spatial Transcriptomics (scNaST), a software suite to facilitate the analysis of spatial gene expression from second- and third-generation sequencing, allowing to generate a full-length near-single-cell transcriptional landscape of the tissue microenvironment. Taking advantage of the Visium Spatial platform, we adapted a strategy recently developed to assign barcodes to long-read single-cell sequencing data for spatial capture technology. Here, we demonstrate our workflow using four short axis sections of the mouse heart following myocardial infarction. We constructed a de novo transcriptome using long-read data, and successfully assigned 19,794 transcript isoforms in total, including clinically-relevant, but yet uncharacterized modes of transcription, such as intron retention or antisense overlapping transcription. We showed a higher transcriptome complexity in the healthy regions, and identified intron retention as a mode of transcription associated with the infarct area. Our data revealed a clear regional isoform switching among differentially used transcripts for genes involved in cardiac muscle contraction and tissue morphogenesis. Molecular signatures involved in cardiac remodeling integrated with morphological context may support the development of new therapeutics towards the treatment of heart failure and the reduction of cardiac complications.

opencc-zeroMay 2022View details →

Effects of acute exposure to polystyrene nanoplastics on the channel catfish larvae: Insights from energy metabolism and transcriptomic analysis

Microplastics (nanoplastics) pollution has been a major ecological issue threatening global aquatic ecosystems. However, knowledge of the adverse effects of nanoplastics and the effects on freshwater ecosystems is still limited. To understand the impacts of nanoplastics on freshwater ecosystems, it is essential to reveal the physiological changes caused by nanoplastics in freshwater organisms, especially at their early life-history stages. In the present study, the larval channel catfish Ietalurus punetaus were exposed to gradient concentrations (0, 5, 10, 25 and 50 mg/L) of 75-nm polystyrene nanoplastics (PS-NPs) for 24 h or 48 h, and changes in contents of energy metabolites, metabolic enzyme activities and transcriptome were assessed. The results showed glucose and triglyceride contents increased after 24 h of exposure to 10 or 25 mg/L of PS-NPs but decreased with increased concentrations or prolonged exposure duration. Activities of most metabolic enzymes analyzed decreased in the larvae after 48 h of exposure, especially in 25 or 50 mg/L of PS-NPs. These suggested that PS-NPs caused huge energy consumption and disturbed the energy metabolism in larval fish. Transcriptomic analysis showed that 48 h of exposure to 50 mg/L PS-NPs affected the expression of genes involved in protein digestion and induced response of proteasomes or heat shock proteins in the larval I. punetaus. The genes involved in peroxisome proliferator-activated receptors (PPAR) pathway and biosynthesis of amino acids were activated after the exposure. PS-NPs also depressed the expression of the genes involved in gonad development or muscle contraction in the larval I. punetaus. Overall, acute exposure to 75-nm PS-NPs disrupted the energy metabolism by consuming the energy reserves, and affected a series of molecular pathways which may further affect the development and survival of fish. This study provided the information about adverse effects of nanoplastics on the fish larvae and revealed the molecular pathways for the potential adverse outcomes.

opencc-by-4.0Jun 2022View details →

Other supporting data for our manuscript "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"

Other supplementary data for our paper "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"

opencc-zeroMay 2022View details →

A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO2/HCO3-), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists' findings. Here, we propose a novel method for controlling pH levels by relying only on the physiological buffering system. pH was manipulated in a repurposed commercial bioreactor set-up, using a two-sided control loop of CO2 and N2 gas in NaHCO3--buffered medium. This method produces optimal and stable dO2 profiles and tightly maintains pH levels. With this procedure, we analyzed the effects of different pH levels (6.8, 7.0, 7.2, and 7.4) on the performance and transcriptome of the human GM12878 cell line over a 72-hours experiment. Our results showed that inflammation and negative cellular proliferation are among the signatures activated at low pH. This further highlights the importance of a thorough pH control during cell culture.

opencc-by-4.0Feb 2021View details →

Data from: Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs

Data from: Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs

opencc-zeroJun 2022View details →

Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - albeit significant - effect of strain × environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.

opencc-by-4.0Jun 2022View details →

Transcriptome Analysis of Retinoic Acid-Inducible Gene I Overexpression Reveals the Potential Genes for Autopha-gy-related Negative Regulation

Supplementary table 1: Primer pairs used for quantitative RT-PCR analysis. Supplementary file 2: All DEGs are listed in the excel file.

opencc-zeroJun 2022View details →

The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

The plant genus Oenothera has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section Oenothera exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to Oenothera diversification and rapid gene family evolution.

opencc-zeroJun 2022View details →

Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period

Aim: Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. Methods: Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. Results: Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (Htr1a, Rims1, Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (Gpld1, Sirt1, Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (Mmp2, Itpr1, Nrf1, etc.). Conclusion: The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.

opencc-by-4.0Jun 2022View details →

Hydractinia symbiolongicarpus genome and transcriptome assemblies

Scaffold-level genome assemblies for Hydractinia symbiolongicarpus histoincompatible siblings BC-3 and BC-15 from a back-cross population derived from wildtype individuals . Assemblies generated with ABySS short read assembler using Illumina 200-bp insert paired-end libaries and 3-Kbp insert mate pair 'long jumping distance' libraries. The trimmed read depths were ~36X and ~49X for BC-3 and BC-15, respectively. Transcriptome assemblies for Hydractinia symbiolongicarpus wildtype individuals HWB-103 and HWB-29. Assemblies generated with Trinity using Illumina mRNA libraries.

opencc-by-4.0Jul 2022View details →

Supplementary Files - Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns.

Supplementary Files for the paper intitled Transcriptomic analysis of CPM-positive hiPSCs-derived liver progenitor cells in a microfluidic device shows zonation-like patterns.

opencc-zeroJul 2022View details →

What can cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

Little is known about the evolution of cold tolerance in polar plant species and how they differ from temperate relatives. To gain insight into their biology and the evolution of cold tolerance, we compared the molecular basis of cold response in three Arctic Brassicaceae species. We conducted a comparative time series experiment to examine transcriptional responses to low temperature. RNA was sampled at 22 °C, and after 3h, 6h, and 24h at 2 °C. We then identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana. Most differentially expressed genes were species-specific, but a significant portion of the cold response was also shared among species. Among thousands of differentially expressed genes, ~200 were shared among the three Arctic species and A. thaliana, while ~100 were exclusively shared among the three Arctic species. Our results show that cold response differs markedly between Arctic Brassicaceae species, but likely builds on a conserved basis found across the family. They also confirm that highly polygenic traits such as cold tolerance may show little repeatability in their patterns of adaptation.

opencc-zeroAug 2022View details →

Genetic and transcriptomic datasets characterizing gene drive mosquitoes expressing antimicrobial peptides that retard Plasmodium sporogonic development

Gene drives hold promise for the genetic control of malaria vectors. The development of vector population modification strategies hinges on the availability of effector mechanisms impeding parasite development in transgenic mosquitoes. We augmented a midgut gene of the malaria mosquito Anopheles gambiae to secrete two exogenous antimicrobial peptides, Magainin 2 and Melittin. This small genetic modification, capable of efficient non-autonomous gene drive, hampers oocyst development in both Plasmodium falciparum and Plasmodium berghei. It delays the release of infectious sporozoites while it simultaneously reduces the lifespan of homozygous female transgenic mosquitoes. Modeling the spread of this modification using a large-scale agent-based model of malaria epidemiology reveals that it can break the cycle of disease transmission across a range of transmission intensities.

opencc-zeroSep 2022View details →

Simulated data from: Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. RNA-Bloom2 is available on GitHub at: <a href="https://github.com/bcgsc/RNA-Bloom">https://github.com/bcgsc/RNA-Bloom</a>. We benchmarked the assembly quality and the computational performance of RNA-Bloom2 on simulated data. We prepared two mouse simulated datasets with Trans-NanoSim for the cDNA and dRNA sequencing protocols model on experimental ONT data. The datasets were simulated based on the mouse ENSEMBL annotation for GRCm39. To investigate the effect of sequencing depth, we subsampled each dataset to 2, 10, and 18 million reads, resulting in a total of six sets of reads for our benchmarking experiments. Using the simulated data, we showed that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods.