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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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North American Beaver (Castor canadensis) RNAseq 16 pooled tissue samples.

ABSTRACT: RNAseq from Illumina MiSeq 75bp paired end for transcriptome assembly. The following tissue samples were pooled: skeletal muscle; kidney; spleen; ovaries; placenta; castor gland; tail; toe webbing; whole blood; brain; lung; liver; heart; stomach; tongue; intestine

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Castor canadensis

SUBMITTER: Brent Kronmiller

PROVIDER: E-MTAB-6258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNAseq of 16 North American Beaver (Castor canadensis) tissues

Project description:RNAseq from the following tissue samples: skeletal muscle; kidney; spleen; ovaries; placenta; castor gland; tail; toe webbing; whole blood; brain; lung; liver; heart; stomach; tongue; intestine

2019-07-02 | E-MTAB-8038 | biostudies-arrayexpress

Transcriptome analysis of alveolar macrophages in asthma

Project description:Purpose: The goal of this study is to investigate the alteration of gene expression pattern of alveolar macrophages by allergen challenge in human asthmatics. Method: By using subsegmental bronchial provocation with allergen (SBP-AG) protocol, we obtained BAL fluids, before and 48 hours after allergen challenge in the subjects enrolled in the protocol. Alveolar macrophages were purified from the BAL fluids and total RNA was isolated. Next-generation sequencing data were generated by using the Illumina system. Results: Using an optimized data analysis workflow, we mapped about 75 million sequence reads per sample to the human genome and identified 29,691 transcripts in the macrophage mRNAs. Among them, the change in the expression profiles of 37 transcripts were statistically significant. Conclusions: It has been well accepted that Th2 cytokine enriched environment transforms the phenotype of macrophages into alternatively activated form. However, the details of a genome-wide gene expression profiles of macrophages were not well investigated. Using RNA-seq technology, we provided comprehensive data of macrophage gene expression profiles in allergic lung inflammation. Our data could offer a framework to study biologic functions of alternatively activated macrophage in chronic inflammatory diseases. mRNA profiles of alveolar macrophages obtained from asthmatics, before and after allergen challenge.

2015-04-01 | E-GEOD-65039 | biostudies-arrayexpress

Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth

Project description:The aim of the project was to elucidate the inter-organellar interplay of plastids, mitochondria, and peroxisomes during storage reserve mobilization in the endosperm to supply the growing seedling with nutrients upon germination. Organelles from endosperm of etiolated castor bean seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry. The data were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes.

2024-01-09 | PXD040932 | Pride

A transcriptional map following the developmental trajectory of the Arabidopsis stomatal lineage

Project description:Developmental transitions can be described in terms of morphology and individual genes expression patterns, but also in terms of global transcriptional and epigenetic changes. Most of the large-scale studies of such transitions, however, have only been possible in synchronized cell culture systems. Here we generate a cell type specific transcriptome of an adult stem-cell lineage in the Arabidopsis leaf using RNA sequencing and microarrays. RNA profiles of stomatal entry, commitment, and differentiating cells, as well as of mature stomata and the entire aerial epidermis give a comprehensive view of the developmental progression. To obtain pure cell populations corresponding to different stomatal lineage cell types we used Fluorescent Activated Cell Sorting (FACS) in combination with markers of early (SPCHp::SPCH-YFP, SSY), middle (MUTEp::nucGFP, MG), and late (FAMAp::GFP-FAMA, FGF) precursor stages, as well of mature stomata (enhancer trap E1728::GFP, E1728G) and a marker of the entire epidermis (ML1p::YFP-RCI2A, ML1Y). To minimize transcriptional differences due to age, all cell types were sorted from 10-day old aerial rosettes, and the specificity of expression pattern at this common time point confirmed via confocal microscopy. Total RNA was extracted from purified protoplasts (4,000 to 20,000 cells/replicate; 2 replicates/marker line; 3 replicates/SSY marker line) and transcript abundance measured using RNA sequencing.

2015-04-06 | E-GEOD-58856 | biostudies-arrayexpress

Ricin-Like Proteins from the Castor Plant Do Not Influence Liquid Chromatography-Mass Spectrometry Detection of Ricin in Forensically Relevant Samples

Project description:The toxic protein ricin (also known as RCA60), found in the seed of the castor plant (Ricinus communis) is frequently encountered in law enforcement investigations. The ability to detect ricin by analyzing its proteolytic (tryptic) peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is well established. However, ricin is just one member of a family of proteins in R. communis with closely related amino acid sequences, including R. communis agglutinin I (RCA120) and other ricin-like proteins (RLPs). Inferring the presence of ricin from its constituent peptides requires an understanding of the specificity, or uniqueness to ricin, of each peptide. Here we describe the set of ricin-derived tryptic peptides that can serve to uniquely identify ricin in distinction to closely-related RLPs and to proteins from other species. Other ricin-derived peptide sequences occur only in the castor plant, and still others are shared with unrelated species. We also characterized the occurrence and relative abundance of ricin and related proteins in an assortment of forensically relevant crude castor seed preparations. We find that whereas ricin and RCA120 are abundant in castor seed extracts, other RLPs are not represented by abundant unique peptides. Therefore, the detection of peptides shared between ricin and RLPs (other than RCA120) in crude castor seed extracts most likely reflects the presence of ricin in the sample.

2017-10-17 | PXD007933 | Pride

The genome of North American beaver provides insights into the mechanisms of its longevity and cancer resistance

Project description:Comparative proteome analysis of beaver (Castor canadensis) and mouse (Mus musculus) liver tissues

2022-02-16 | PXD028546 | Pride

Gene expression signatures in uteri from nuclear and membrane effects of Estradiol on Estrogen receptor ERÎ±

Project description:To further study gene expression regulated by 17b-estradiol in uteri, we have employed whole gene microarray profiling to identify genes specifically regulated by the Estrogen receptor ERÎ± localized either at the plasma membrane or in the nucleus. Two mice models have been used, the mice named ERa-AF2Â° (named AF2_KO and on C57BL6/J background) in which 7 aminoacids have been deleted in the AF2 domain and the mice C451A-ERa (named MISS_KO and on C57BL6/N background) mutated for the C451 into Ala on ERa. Control littermates were used for each mutant mice respectively name AF2_WT or MISS_WT. 17b-estradiol induced gene expression in uteri from ovariectomized mice was measured after 6 hours exposure to 0 (PLB) and 8Âµg/kg of 17b-estradiol (E2) injected subcutaneously in castor oil.

2014-07-01 | E-GEOD-53237 | biostudies-arrayexpress

A circular RNA Edis-Relish-castor axis regulates neuronal development in Drosophila

Project description:Circular RNAs (circRNAs) are a new group of noncoding and regulatory RNAs that are particularly abundant in the nervous system, although their physiological functions are underexplored. Here we report that the brain-enriched circular RNA Edis (Ect4-derived immune suppressor) plays an essential role in neuronal development in Drosophila, as its depletion causes defective axonal projection of mushroom body (MB) neurons in the brain, as well as impaired locomotor activity and shortened lifespan of adult flies. In addition, we show that the castor gene, which encodes a transcription factor involved in neurodevelopment, is upregulated in Edis knockdown neurons. Notably, castor overexpression phenocopies Edis knockdown, and reducing castor levels suppresses the neuronal developmental phenotypes in Edis-depleted neurons. Furthermore, chromatin immunoprecipitation analysis reveals that the immune transcription factor Relish occupies two sites at the castor promoter, and that both sites are required for optimal castor gene activation induced by either immune challenge or Edis depletion. Lastly, Relish mutation rescues both the castor hyperactivation phenotype and neuronal defects in Edis knockdown animals. We conclude that the circular RNA Edis acts through Relish and castor to regulate neuronal development.

2022-10-04 | GSE196213 | GEO

RNAseq of 16 North American Beaver (Castor canadensis) tissues

Project description:RNAseq of 16 North American Beaver (Castor canadensis) tissues

| PRJEB32966 | ENA

Uniformly 15N-Labeled Recombinant Ricin A-chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatog-raphy-Tandem Mass Spectrometry

Project description:Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well-suited because of their high speci-ficity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times rela-tive to a standard, namely uniformly 15N–labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable isotope labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.

2020-07-16 | PXD015698 | Pride

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