Clavularia sp.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA498001 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8102780_1.fastq.gz | Fastqsanger.gz | |||
| SRR8102780_2.fastq.gz | Fastqsanger.gz | |||
| SRR8102779_1.fastq.gz | Fastqsanger.gz | |||
| SRR8102779_2.fastq.gz | Fastqsanger.gz |
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Project description:Using Affymetrix GeneChips, we analyzed expression profiles of SP cells from EOM and TA. 348 differentially expressed transcripts defined the EOM-SP transcriptome: 229 upregulated in EOM-SP and 119 in TA-SP. Keywords: Expression Profiling
2008-10-09 | GSE9294 | GEO
Project description:In rainbow trout, type A spermatogonia can be split into SP cells and non-SP cells by the ability to exclude Hoechst 33342 dye (H33342). The H33342 fluorescence of SP cells are lower than that of non-SP cells, after H33342 staining. To investigate whether SP cells were transcriptomically distinct from non-SP cells, we compared the transcriptome of these cells. We used fluorescence-activated cell sorting (FACS) to isolate SP cells and non-SP cells from the type A spermatogonia in rainbow trout.
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Project description:Transcriptome studies of dinoflagellate sp. (DinoRsour)
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Project description:Animal and plant genomes produce numerous small RNAs (smRNAs) regulating gene expression affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 53 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.
2013-12-31 | GSE47373 | GEO
Project description:Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (‘Aiptasia’). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and B. minutum induced increased accumulation of symbiont proteins associated with acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of the host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding this analyses of the symbiont proteins to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners, native versus non-native symbionts, may impact the fitness of the cnidarian-dinoflagellate symbiosis in response to thermal stress. This PRIDE entry contains the Breviolum minutum data; Durusdinium trenchii data are uploaded in a separate entry with identical parameters.
2024-01-18 | PXD045585 | Pride
Project description:Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (‘Aiptasia’). We also compared the proteome of this native symbiont in the established symbiotic state with that of a non-native symbiont, Durusdinium trenchii. The onset of symbiosis between Aiptasia and B. minutum induced increased accumulation of symbiont proteins associated with acquisition of inorganic carbon and photosynthesis, nitrogen metabolism, micro- and macronutrient starvation, suppression of the host immune responses, tolerance to low pH, and management of oxidative stress. Such responses are consistent with a functional, persistent symbiosis. In contrast, D. trenchii predominantly showed elevated levels of immunosuppressive proteins, consistent with the view that this symbiont is an opportunist that forms a less beneficial, less well-integrated symbiosis with this model anemone. By adding this analyses of the symbiont proteins to the already known responses of the host proteome, our results provide a more holistic view of cellular processes that determine host-symbiont specificity and how differences in symbiont partners, native versus non-native symbionts, may impact the fitness of the cnidarian-dinoflagellate symbiosis in response to thermal stress. This PRIDE entry contains the Durusdinium trenchii data; Breviolum minutum data are uploaded in a separate entry with identical parameters.
2024-01-18 | PXD045587 | Pride
Project description:In rainbow trout, type A spermatogonia can be split into SP cells and non-SP cells by the ability to exclude Hoechst 33342 dye (H33342). The H33342 fluorescence of SP cells are lower than that of non-SP cells, after H33342 staining. To investigate whether SP cells were transcriptomically distinct from non-SP cells, we compared the transcriptome of these cells. We used fluorescence-activated cell sorting (FACS) to isolate SP cells and non-SP cells from the type A spermatogonia in rainbow trout. To compensate unavailability of genetically uniform rainbow trout in independent sampling, SP cells and non-SP cells were collected at 3 times from 3 different parental fish groups. This experimental design allowed us to estimate effects specific to each parental fish genotype on mRNA expression in SP cells by a statistical modeling and to exclude the effects in subsequent analysis.
2013-08-06 | E-GEOD-49565 | biostudies-arrayexpress
Project description:In humans there are two surfactant protein A (SP-A) functional genes SFTPA1 and SFTPA2 encoding innate immune molecules, SP-A1 and SP-A2, respectively, with numerous genetic variants each. SP-A interacts and regulates many of the functions of alveolar macrophages (AM). It is shown that SP-A variants differ in their ability to regulate the AM miRNome in response to oxidative stress (OxS). Because humans have both SP-A gene products, we were interested to determine the combined effect of co-expressed SP-A1/SP-A2 (co-ex) in response to ozone (O3) induced OxS on AM miRNome. Human transgenic (hTG) mice, carrying both SP-A1/SP-A2 (6A2/1A0, co-ex) and SP-A- KO were utilized. The hTG and KO mice were exposed to filtered air (FA) or O3 and miRNA levels were measured after AM isolation with or without normalization to KO. We found: (i) The AM miRNome of co-ex males and females in response to OxS to be largely downregulated after normalization to KO, but after Bonferroni multiple comparison analysis only in females the AM miRNome remained significantly different compared to control (FA); (ii) The targets of the significantly changed miRNAs were downregulated in females and upregulated in males; (iii) Several of the validated mRNA targets were involved in pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation; (iv) The AM of SP-A2 male, shown, previously to have major effect on the male AM miRNome in response to OxS, shared similarities with the co-ex, namely in pathways involved in the pro-inflammatory response and anti-apoptosis but also exhibited differences with the cell-cycle, growth, and proliferation pathway being involved in co-ex and ROS homeostasis in SP-A2 male. We speculate that the presence of both gene products versus single gene products differentially impact the AM responses in males and females in response to OxS.
2019-08-02 | GSE135233 | GEO
Project description:BACKGROUND: Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome. We investigated whether miRNome differences previously observed between AM from SP-A2 and SP-A1/SP-A2 mice are due to continued qualitative differences or a delayed response of mice carrying a single gene. METHODS: Human transgenic (hTG) mice, carrying SP-A2 or both SP-A genes and SP-A-KO mice were exposed to filtered air (FA) or O3. AM miRNA levels, target gene expression and pathways determined 18 h after O3 exposure. RESULTS: We found: (a) Differences in miRNome due to sex, SP-A genotype, and exposure; (b) miRNome of both sexes was largely downregulated by O3 ; co-ex had fewer changed (≥2X) miRNAs than either group. (c) the number and direction of expression of genes with significant changes in males and females in co-ex is almost the opposite of those in SP-A2; (iv) The same pathways were found in the studied groups; (e) O3 exposure attenuated sex differences; a higher number of genotype-dependent and genotype-independent miRNAs was common in both sexes after O3 exposure. CONCLUSION: Qualitative differences between SP-A2 and co-ex persist 18 h post-O3, and O3 attenuates sex differences.
2021-01-06 | GSE158401 | GEO