Transcriptomic profiles of wild brown trout chronically exposed to metals using RNA-seq in a Illumina GAII platform
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ABSTRACT:
ORGANISM(S): Salmo trutta
SUBMITTER: Ronny van Aerle
PROVIDER: E-GEOD-45637 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:These studies aimed to investigate the hepatic transcriptional response of brown trout to the natural estrogen, E2, and the herbicide linuron. We exposed mature male brown trout to three concentrations of each chemical for 4 days and sequenced the hepatic transcriptome of 3 individuals per treatment group in order to determine the global mechanisms of toxicity of these environmental contaminants. We assembled the brown trout transcriptome using a de novo approach. Subsequent differential expression analysis identified a total of 2113 differentially-regulated transcripts in the group exposed to the highest E2 treatment concentration, and 822 differentially-regulated transcripts across all linuron treatments. For E2, differentially-expressed transcripts included those encoding known oestrogen-responsive genes, while regulated processes included those associated with vitellogenesis including lipid metabolism, cellular proliferation and ribosome biogenesis. For linuron, there was a striking down-regulation of transcripts encoding the majority of the enzymes involved in the cholesterol biosynthesis pathway, and also a considerable induction of transcripts involved in cellular stress response including Cyp1a. Fish were exposed to 3 concentrations of E2 (measured concentrations were 1.9, 18.1 and 34.4 ng/L), 3 concentrations of linuron (measured concentrations were 1.7, 15.3 and 225.9 µg/L) and water controls for 4 days. Liver mRNA from 3 replicate individuals per treatment was sequenced in an Illumina HiSeq 2500 platform. Two control groups (n=6 fish in total) were included. Using a de novo approach, we assembled the hepatic transcriptome for brown trout. Sequence reads were re-mapped to the assembled transcriptome using Bowtie2 and transcript expression profiling was conducted using EdgeR. ERCC spike controls were added to all individual samples, allowing for the assessment of the reproducibility and dynamic range for transcript expression quantification in our experiments.
2015-05-08 | E-GEOD-57490 | biostudies-arrayexpress
Project description:This study aimed to investigate the hepatic transcriptional response of brown trout to glyphosate, and its formulated product, Roundup. We exposed juvenile female brown trout to three concentrations of glyphosate (0.01, 0.5 and 10 mg/L) and Roundup (0.01, 0.5 and 10 mg/L glyphosate acid equivalent) for 14 days and sequenced the hepatic transcriptome of 6 individual females per treatment group in order to determine the global mechanisms of toxicity of this widely used herbicide. We assembled the brown trout transcriptome using an optimised de novo approach, and subsequent differential expression analysis identified a total of 1020 differentially-regulated transcripts across all treatments. Differentially-expressed transcripts included those encoding components of the antioxidant system, a number of stress-response proteins and pro-apoptotic signalling molecules. Functional analysis also revealed over-representation of pathways involved in regulation of cell-proliferation and turnover, and up-regulation of energy metabolism and other metabolic processes. Together, these transcriptional changes are consistent with generation of oxidative stress and the widespread induction of compensatory cellular stress response pathways. The mechanisms of toxicity identified were similar across both glyphosate and Roundup treatments, including for environmentally relevant concentrations. The significant alterations in transcript expression observed at the lowest concentrations tested raises concerns for the toxicity of this herbicide to fish populations inhabiting contaminated rivers. Fish were exposed to 3 concentrations of glyphosate (0.01, 0.1 and 10 mg/L), 3 concentrations of Roundup (0.01, 0.5 and 10 mg/L glyphosate acid equivalent) and water controls for 14 days. Liver mRNA from 6 replicate individuals per treatment was sequenced in an Illumina HiSeq 2500 platform. Two control groups (n=6 fish per group) were included. Using a de novo approach, we assembled the hepatic transcriptome for brown trout. Sequence reads were re-mapped to the assembled transcriptome using Bowtie2 and transcript expression profiling was conducted using EdgeR. ERCC spike controls were added to all individual samples, allowing for the assessment of the reproducibility and dynamic range for transcript expression quantification in our experiments. For the group exposed to 0.1 mg/L glyphosate, only 3 females were available to sequence and the variability between individuals was very high with 1 female identified as an outlier. For this reason, data from this treatment group was deemed unreliable and excluded from the analysis.
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Project description:In order to provide a global insight on the transcripts expressed in the venom gland of the Brazilian ant species Tetramorium bicarinatum and to unveil the potential of its products, high-throughput expressed sequence tags were generated using Illumina paired-end sequencing technology. A total of 212,371,758 pairs of quality-filtered, 100-base-pair Illumina reads were obtained. The de novo assemblies yielded 36,042 contigs for which 27,873 have at least one predicted ORF among which 59.77% produce significant hits in the available databases. The investigation of the reads mapping toxin class revealed a high diversification with the major part consistent with the classical hymenopteran venom protein signature represented by venom allergen (33.3%) followed by a diverse toxin-expression profile including several distinct isoforms of phospholipase A1 and A2, venom serine protease, hyaluronidase, protease inhibitor and secapin. Moreover, our results revealed for the first time the presence of toxin-like peptides that have been previously identified from unrelated venomous animals such as waprin-like (snakes) and agatoxins (spiders and conus). 300 ant specimens from the species Tetramorium bicarinatum were dissected in order to extract the RNA from their venom gland, The whole ant body was used as a reference,
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Project description:In order to facilitate understanding of pigment cell biology, we developed a method to concomitantly purify melanocytes, iridophores, and retinal pigmented epithelium from zebrafish, and analyzed their transcriptomes. Comparing expression data from these cell types and whole embryos allowed us to reveal gene expression co-enrichment in melanocytes and retinal pigmented epithelium, as well as in melanocytes and iridophores. We found 214 genes co-enriched in melanocytes and retinal pigmented epithelium, indicating the shared functions of melanin-producing cells. We found 62 genes significantly co-enriched in melanocytes and iridophores, illustrative of their shared developmental origins from the neural crest. This is also the first analysis of the iridophore transcriptome. Gene expression analysis for iridophores revealed extensive enrichment of specific enzymes to coordinate production of their guanine-based reflective pigment. We speculate the coordinated upregulation of specific enzymes from several metabolic pathways recycles the rate-limiting substrate for purine synthesis, phosphoribosyl pyrophosphate, thus constituting a guanine cycle. The purification procedure and expression analysis described here, along with the accompanying transcriptome-wide expression data, provide the first mRNA sequencing data for multiple purified zebrafish pigment cell types, and will be a useful resource for further studies of pigment cell biology. mRNA profiles of zebrafish pigment cells were generated using Illumina GAIIX sequencing
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Project description:Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative condition characterized by loss of motor neurons in the brain and spinal cord. Expansions of a hexanucleotide repeat (GGGGCC) in the noncoding region of the C9ORF72 gene are the most common cause of the familial form of ALS (C9-ALS), as well as frontotemporal lobar degeneration and other neurological diseases. How the repeat expansion causes disease remains unclear, with both loss of function (haploinsufficiency) and gain of function (either toxic RNA or protein products) proposed. We report a cellular model of C9-ALS with motor neurons differentiated from induced pluripotent stem cells (iPSCs) derived from ALS patients carrying the C9ORF72 repeat expansion. No significant loss of C9ORF72 expression was observed, and knockdown of the transcript was not toxic to cultured human motor neurons. Transcription of the repeat was increased, leading to accumulation of GGGGCC repeat–containing RNA foci selectively in C9-ALS iPSC-derived motor neurons. Repeat-containing RNA foci colocalized with hnRNPA1 and Pur-?, suggesting that they may be able to alter RNA metabolism. C9-ALS motor neurons showed altered expression of genes involved in membrane excitability including DPP6, and demonstrated a diminished capacity to fire continuous spikes upon depolarization compared to control motor neurons. Antisense oligonucleotides targeting the C9ORF72 transcript suppressed RNA foci formation and reversed gene expression alterations in C9-ALS motor neurons. These data show that patient-derived motor neurons can be used to delineate pathogenic events in ALS. Transcriptome profiling from iPSC derived motor neurons compared to controls
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