De novo transcriptome assembly and functional annotation for Y-organs of the blue crab (Callinectes sapidus), and analysis of differentially expressed genes during pre-molt
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ABSTRACT:
ORGANISM(S): Callinectes sapidus
PROVIDER: GSE154560 | GEO | 2020/07/17
REPOSITORIES: GEO
Similar Datasets
Project description:De novo transcriptome assembly and functional annotation for Y-organs of the blue crab (Callinectes sapidus), and analysis of differentially expressed genes during pre-molt
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Project description:The decrease of pH level in the water affects animals living in aquatic habitat, such as crustaceans. The molecular mechanisms enabling these animals to survive this environmental stress remain unknown. To understand the modulatory function of neuropeptides in crustaceans when encountering drops in pH level, we developed and implemented a multifaceted mass spectrometric platform to investigate the global neuropeptide changes in response to water acidification in the Atlantic blue crab, Callinectes sapidus. Neural tissues were collected at different incubation periods to monitor dynamic changes of neuropeptides under different stress conditions occurring in the animal. Neuropeptide families were found to exhibit distinct expression patterns in different tissues and even each isoform had its specific response to the stress. Circulating fluid in the crabs (hemolymph) was also analyzed after 2-hour exposure to acidification condition, and together with results from tissue analysis, enabled the discovery of neuropeptides participating in the stress accommodation process as putative hormones. Two novel peptide sequences were detected in the hemolymph that appeared to be involved in the stress-related regulation in the crabs.
2021-09-08 | PXD013536 | Pride
Project description:Purpose: The goal of this stufy is to elucidate the transcriptional regulatory network in response to light in S. fimicola. We analyzed blue-light-induced genome-wide transcriptional responses by high-throughput RNA-seq to determine the transcriptional profiles between the wild type and Sfwc-1(∆lov) mutant. Untreated mycelia (constant darkness sample) and mycelia treated with blue light for 15 and 45 min were used to explore. Method: the S. fimiocla wild type and Sfwc-1(∆lov) mutant were grown on malt extract agar I in constant dark for 2 days. The drak grown samples were exposed to blue light for 15 and 45 min. The cDNA was synthesized from mRNA by using the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)and then sequencing involved using Illumina NextSeq 500. The clean RNA-seq reads were then de novo assembled into a transcript sequence by using the Trinity platform and the jaccard_clip option. The quantified gene and isoform abundances (transcript abundance estimation) were obtained by using RNA-seq by expectation-maximization (RSEM) software with the default setting of Bowtie. Then differentially expressed genes (DEGs) were identified by using the EdgeR Bioconductor package in Trinity platform. The normalized RSEM-estimated abundances weighted by Trimmed Mean of M values (TMM) method counted by EdgeR was used for pairwise comparison of each of the sample pairs. Conclusion: Our study represents the transcription regulatory nextwork existing in S. fmicola, generated by RNA-seq technology. The data analysis has been providing a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and contribute the understanding of biologic functions in S. fimicola.
2019-05-06 | GSE123811 | GEO
Project description:Analysis of MOLT-4 cells at various time points up to 6 hours following treatment with mouse anti-CD47 antibody (MABL) and goat anti-mouse IgG (GAM) as the crosslinker of MABL. MABL induces apoptosis in CD47-positive MOLT-4 cells. Cell death signals via CD47 ligation were analyzed by using Affymetrix Human Genome U133A microarray.
2011-04-01 | GSE16494 | GEO
Project description: Not available
| S-EPMC4388526 | biostudies-literature
Project description:As representatives of n-6 and n-3 fatty acids, many studies have analyzed the use of soybean oil and linseed oil rich in linoleic acid (18:2n-6, LA) and α-linolenic acid (18:3n-3, LNA) as better substitutes for fish oil. In aquatic animals, different dietary ratios of LA and LNA could have significant effects on growth, lipid metabolism, immune response, and reproduction. To assess the nutritive value of these two fatty acids for the Chinese mitten crab (Eriocheir sinensis), we performed transcriptome analysis and proteomic analysis using label-free quantification of the hepatopancreas of mitten crabs fed with LA or LNA diet. Our results provide new insights for further investigation into the replacement of fish oil from mitten crabs with vegetable oils and enable us to better understand the different roles and nutrition value of LA and LNA in mitten crabs.
2019-08-14 | PXD009864 | Pride
Project description:Analysis of MOLT-4 cells at various time points up to 6 hours following treatment with mouse anti-CD47 antibody (MABL) and goat anti-mouse IgG (GAM) as the crosslinker of MABL. MABL induces apoptosis in CD47-positive MOLT-4 cells. Cell death signals via CD47 ligation were analyzed by using Affymetrix Human Genome U133A microarray. MOLT-4 cell line was obtained from the American Type Culture Collection (ATCC) and grown in RPMI1640 medium (SIGMA) with 10% FBS(JBS). It was maintained at 37 degree C and 5% CO2. Cells were washed with PBS(-) followed by treatment with 10 ug/mL MABL (anti-CD47 antibody) for 0, 0.5, 1, 3 and 6 h. Total RNA was isolated and converted to cDNA using a Superscript Double Stranded cDNA synthesis kit (Invitrogen). Fragmented cDNA was hybridized to Affymetrix Human Genome U133A array and gene expression signals were analyzed. Probes showing >2 or <0.5 fold-change for both replicates compared with the control (geometric mean of 0h replicate signals) were selected at any time.
2011-04-01 | E-GEOD-16494 | biostudies-arrayexpress
Project description:Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 hours at 8˚C enhanced crab tolerance during a 1h exposure to -2°C relative to crabs acclimated to 18˚C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm and cold acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12h of thermal acclimation. Genes strongly upregulated in warm acclimated crabs represented immune response and extracellular / intercellular processes, suggesting that warm acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold acclimated crabs included many that are involved in glucose production suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene expression-related changes in homeostasis begin within 12 hours – the length of a tidal cycle. all array data and raw images archived at the Porcelain Crab Array Database (http://array.sfsu.edu) n=264 specimens were divided into warm (18°C, n=96), cold (8°C, n=96), and control (13°C, n=72) acclimation groups. Crabs were sampled from the 13°C group at 0 h (the start of the experiment) and 24 h, the termination of the experiment. Crabs were sampled from the warm and cold acclimation groups at 6, 12, 18, and 24 hours following the start of thermal acclimation. At each time point, heart tissue from n=16 crabs from each group was dissected, flash frozen and stored at −80°C. A pooled total aRNA sample was prepared for each group by mixing equal quantities of total RNA from n=5 individuals in each group in order to have the same amount of biological diversity within each pooled RNA sample. For microarray hybridizations we used n=25 slides in an incomplete loop design where each sample was hybridized n=5 times, 2-3 times labelled with each Cy dye
2012-03-01 | E-GEOD-35307 | biostudies-arrayexpress
Project description:Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 hours at 8˚C enhanced crab tolerance during a 1h exposure to -2°C relative to crabs acclimated to 18˚C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm and cold acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12h of thermal acclimation. Genes strongly upregulated in warm acclimated crabs represented immune response and extracellular / intercellular processes, suggesting that warm acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold acclimated crabs included many that are involved in glucose production suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene expression-related changes in homeostasis begin within 12 hours – the length of a tidal cycle. all array data and raw images archived at the Porcelain Crab Array Database (http://array.sfsu.edu)
2012-03-01 | GSE35307 | GEO