RNA-seq data from the blue mussel (Mytilus edulis) gill samples in response to salinity and temperature
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Mytilus edulis
SUBMITTER: Nick Barrett
PROVIDER: E-MTAB-11178 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The invasive marine mussel Mytilus galloprovincialis has displaced the native congener Mytilus trossulus from central and southern California, but the native species remains dominant at more northerly sites that have high levels of freshwater input. To determine the extent to which interspecific differences in physiological tolerance to low salinity might explain limits to the invasive species’ biogeography, we used an oligonucleotide microarray to compare the transcriptional responses of these two species to an acute decrease in salinity. Among 6,777 genes on the microarray, 117 genes showed significant changes that were similar between species, and 12 genes showed significant species-specific responses to salinity stress. Osmoregulation and cell cycle control were important aspects of the shared transcriptomic response to salinity stress, whereas the genes with species-specific expression patterns were involved in mRNA splicing, polyamine synthesis, exocytosis, translation, cell adhesion, and cell signaling. Forty-five genes that changed expression significantly during salinity stress also changed expression during heat stress, but the direction of change in expression was typically opposite for the two forms of stress. These results (i) provide insights into the role of changes in gene expression in establishing physiological tolerance to acute decreases in salinity, and (ii) indicate that transcriptomic differences between M. galloprovincialis and M. trossulus in response to salinity stress are subtle and involve only a minor fraction of the overall suite of gene regulatory responses. Two species (Mytilus galloprovincialis, Mytilus trossulus), hypo-osmotic shock for four hours (850 mOs/kg), one control group (1000 mOs/kg) sampled at the end of the treatment exposure (850 mOs/kg), one control group (1000 mOs/kg) sampled at the beginning. Biological replicates: 6 in each treatment group, 6 in each control group. Heterologous and homologous hybridization to a microarray constructed from Mytilus californianus and Mytilus galloprovincialis sequences. A reference design that used separate pools of reference RNA for each species was employed. Reference amplified RNA (aRNA) was created for each species by pooling RNA before and after amplification. The reference pool was made up of RNA from six different samples: two base-line control samples from the beginning of the experiment, two treatment samples from the end of the four-hour hypo-osmotic exposure, and two time-control samples from the end of the four-hour exposure time. To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.5 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. Only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses. In order to determine significant changes in expression, we conducted a two-way ANOVA, in which salinity and species were modeled as fixed effects, and focused on genes that were significant for the salinity effect or the species x temperature interaction. We ignored the species term from the ANOVA as this effect could have highlighted genes that differentially bound to probes on the microarray due to differences in sequence homology, thus not reflecting true differences in gene expression. In accordance with statistical convention, all genes with a significant species x temperature interaction were deemed not to have significant temperature effects, even if the temperature term from the ANOVA had a low P-value. All genes with FDR-corrected (Benjamini and Hochberg, 1995) P-values less than 0.05 were considered significant. Analyses were conducted in the R statistical programming environment (R Development Core Team, 2009).
2011-01-10 | E-GEOD-25111 | biostudies-arrayexpress
Project description:Drought, salinity and sub-optimal temperatures are stresses that cause adverse effects on the growth of plants and the productivity of crops. In this study, we have analyzed the expression profiles of rice genes under control and abiotic stress conditions using microarray technology to identify the genes differentially expressed during various abiotic stresses. Experiment Overall Design: Seven-day-old light-grown rice seedlings grown under controlled conditions and those subjected to various abiotic stress conditions were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. For salt treatment (SS), the rice seedlings were transferred to a beaker containing 200 mM NaCl solution for 3 h. For desiccation (DS), rice seedlings were dried for 3 h between folds of tissue paper at 28±1 degree C, in a culture room. For cold treatment (CS), the seedlings were kept at 4±1 degree C for 3 h. The seedlings kept in water for 3 h, at 28±1 degree C, served as control (Seedling).
2008-11-08 | E-GEOD-6901 | biostudies-arrayexpress
Project description:To identify biological function of HSFB transcriptional repressor, we subjected hsfb1 hsfb2b double mutant and wild-type Arabidopsis plant under heat condition (32 Celsius degree) and did microarray experiment. The microarray experiment under non-heated condition is described in GSE14702. We found expression of many heat-shock proteins (HSPs) is not fully enhanced in the double mutant when compared to wild-type plant. This data suggest that the inhibition of expression of HSPs in non-heated condition is important for fully heat-stress response in plant. hsfb1 hsfb2b double mutant vs. wild-type seedlings of Arabidopsis thaliana subjected under heat condition (32 Celsius degree). Biological replicates: 4 replicates.
2011-09-06 | E-GEOD-31883 | biostudies-arrayexpress
Project description:Pharmaceutical compounds are emerging contaminants in aquatic environment due to their massive use (human and veterinary medicines, agriculture and aquaculture) and a limited removal by waste water treatment plants (WWTPs). In this work, a representative determination of ecotoxicological potential of two different NSAIDs compounds was studied in the sensitive bioindicator marine organism M. Galloprovincialis. Mussels were exposed, under regulated laboratory conditions, to Ketoprofen (KET) and Nimesulide (NIM), dosed alone at the realistic environmental concentration of 0.5µg/L for 14 days. Gene expression analyses of Mytilus galloprovincialis exposed to KET and NIM have been performed through a DNA microarray platform. Mussels Mytilus galloprovincialis (5 ± 1 cm shell length) were obtained from a local farm (Numana, Ancona) and acclimatized for 10 days to laboratory conditions with aerated seawater, at 18 ± 1 °C, 37 � salinity, pH 7.5 ± 0.5 and oxygen saturation >94%. Mussels were distributed into three 17 L aquarium and exposed at 0.5µg/L to ketoprofen (KET) and nimesulide (NIM) dosed alone for 14 days. All treatments were compared to control (CTRL) containing 0.00001% of methanol. Water was changed every other day and concentration of molecules were restored. Gene transcription analyses of 12 digestive glands pools (four pools for each treatment composed by 3 digestive glands; CNTR, NIM and KET) were performed using a 8X60K Agilent oligo-DNA microarray platform GPL18667. Microarrays were synthesized in situ using the Agilent non-contact ink-jet technology including default positive and negative controls. Total RNA was isolated using Extract-all (Eurobio) procedure. RNA quality and integrity was controlled on the Agilent bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use. Gene expression profiling was performed using an Mytilus galloprovincialis oligo-DNA microarray of 59,971 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA at a resolution of 2 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. FeatureExtraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2016-02-22 | E-GEOD-66990 | biostudies-arrayexpress
Project description:Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition. RNA was isolated from CLIB214 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Isolates from normoxic condition were labeled with Cy3 and isolates from hypoxic condition were labeled with Cy5.
2011-11-30 | E-GEOD-32712 | biostudies-arrayexpress
Project description:Background: With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. Results: As shown in this study, suboptimal conditions can have considerable impact on biologically relevant observations. For example, deviation from the optimal temperature by one degree Celsius lead to a loss of 44% of differentially expressed genes identified. While genes from thousands of Gene Ontology categories were affected, transcription factors and other low-copy-number regulators were disproportionately lost. Calibrated protocols are thus required in order to take full advantage of the large dynamic range of microarrays. For an objective optimization of protocols we introduce an approach that maximizes the amount of information obtained per experiment. A comparison of two typical samples is sufficient for this calibration. We ensure, however, that optimization results are independent of the samples and the specific measures used for calibration. Both simulations and spike-in experiments confirm an unbiased determination of generally optimal experimental conditions. Conclusions: Well calibrated hybridization conditions are thus easily achieved and necessary for the efficient detection of differential expression. They are essential for the sensitive profiling of low-copy-number molecules. This is particularly critical for studies of transcription factor expression, or the inference and study of regulatory networks. Supporting material, including source code and data, is available at http://bioinf.boku.ac.at/pub/optMA2010/. Optimization of hybridization temperature via an assessment of differential expression between two samples (male vs female Drosophila melanogaster) in 6 technical replicates (3 regular + 3 dye-swaps) for hybridizations at different temperatures (in two batches of 50, 52, 54, and 56; and 47, 49, 50, and 51 degree Celsius, with the repeated hybridization at 50 degree Celsius serving to demonstrate batch-to-batch stability).
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2010-11-15 | E-GEOD-24074 | biostudies-arrayexpress
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2010-11-15 | E-GEOD-24073 | biostudies-arrayexpress
Project description:RNA-seq experiment comparing the transcriptomes of Bacillus cereus G9241 WT to B. cereus G9241 ∆pBCXO1 when cultured both 37 and 25 degree celsius. B. cereus G9241 is a B. cereus sensu stricto strain that was isolated from a welder with and anthrax-like illness. B. cereus G9241 carries the plasmids pBCXO1 and pBC210. pBCX01 has 99.6% sequence identity to pXO1 carried by Bacillus anthracis and encodes the tripartite anthrax toxin genes and atxA, a mammalian virulence transcriptional regulator. B. cereus G9241 WT and B. cereus G9241 ∆pBCXO1 were cultured to exponential phase at either 37 or 25 degree celsius before samples were taken for RNA extraction, library prep and sequencing.
2023-05-13 | E-MTAB-12883 | biostudies-arrayexpress