Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1327658 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To assess the diurnal gene expression in gills of oyster Crassotrea gigas, gills of 6 oysters were pooled and analyzed by RNa-seq every 4h for 52h (i.e. 13 sampling times). This procedure was executed simultaneously for control oysters fed with the non-harmful algae Heterocapsa triquetra (H.t condition), and for oysters fed with the harmful algae Alexandrium minutum (A.m condition) (L:D 9:15). Alexandrium minutum exposure led to a remodeling of the cycling transcriptome in gills of Crassostrea gigas.
2017-11-20 | E-MTAB-5345 | biostudies-arrayexpress
Project description:To study hepatic gene expression differences, liver samples from infected pigs (n = 10) were compared with liver samples from the non-infected control group (n = 5). Ten microarrays were performed, such that 5 randomly selected cDNA samples from the infected group were labeled with Oyster 550 (Genisphere Inc., Hatfield, PA, USA) and compared directly to 5 control animals labeled with Oyster 650 (Genisphere) analysing a pair of samples (one from an infected animal and one from a randomly chosen non-infected animal) on each microarray slide. The remaining five cDNA preparations from the infected group were labeled with Oyster 650 and compared in the same way to the five controls labeled with Oyster 550 on the remaining 5 microarray slides. This dye-swap design was applied to reduce variation due to dye effects and to provide as much biological replication as possible. Keywords: Disease state analysis
2009-09-08 | GSE11404 | GEO
Project description:Research using the oyster Crassostrea gigas as a model has experienced a rapid growth in recent years thanks to the development of high throughput molecular technologies. As many as 56,268 EST sequences have so far been sequenced, representing a genome-wide resource that can be used for microarray investigations. We have developed an oyster microarray containing cDNAs representing 31,918 unique transcribed sequences. The genes spotted on the array have been selected from the publicly accessible GigasDatabase established from cDNA libraries derived from a wide variety of tissues and different developmental stages. n this paper, we report the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps and digestive gland. Following validation of the microarray, statistical analyses were used to identify genes differentially expressed among tissues and define clusters of tissue-specific genes. These genes reflect well major tissue-specific functions at the molecular level. Analysis of hierarchical clustering data also predicted the involvement of un-annotated genes in selected functional pathways. In a second instance, microarray data were used to accurately select housekeeping genes common to all tissues. Their expression profiles was compared to common oyster standard genes used for quantitative RT-PCR calibration (actin, g3apdh and ef1α). The novel candidate housekeeping gene, adp-ribosylation factor 1 (arf1) and g3apdh gene seem to be more robust for normalizing gene expression data of tissues. This study provides a new source for annotating the oyster genome. It also identified new candidate housekeeping genes, a prerequisite for accurate quantitative RT-PCR expression profiling. Gene expression was measured in 9 tissues: Female gonad, male gonad, mantle, gills, posterior adductor muscle, visceral ganglion, hemocytes, labial palps, digestive gland.Three to four biological replicates were analysed per tissue. These were from distinct animals for female gonad, male gonad, mantle, gills, posterior adductor muscle, labial palps and digestive glands, or obtained from a pool of 6 individuals for hemocytes and visceral ganglion.
2011-10-15 | E-GEOD-26265 | biostudies-arrayexpress
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas
2012-09-13 | GSE31012 | GEO
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:Low salinity is one of the main factors limiting the distribution and survival of marine species. As a euryhaline species, the Pacific oyster Crassostrea gigas can be tolerant to relative low salinity. Through Illumina sequencing, we generated two transcriptomes with samples taken from gills of oysters exposed to the low salinity seawater versus the optimal seawater. By RNAseq technology, we found 1665 up-regulation genes and 1815 down-regulation genes that may regulate osmotic stress in C. gigas. As blasted by GO annotation and KEGG pathway mapping, functional annotation of the genes recovered diverse biological functions and processes. The genes regulated significantly were dominated in cellular process and regulation of biological process, intracellular and cell, binding and protein binding according to GO annotation. The results highlight genes related to osmoregulation and signaling and interactions of osmotic stress response, anti-apoptotic reactions as well as immune response, cell adhesion and communication, cytosqueleton and cell cycle. The study aimed to compare the expression data of the two transcriptomes to provide some useful insights into signal transduction pathways in oysters and offer a number of candidate genes as potential markers of tolerance to hypoosmotic stress for oysters. In addition, the characterization of C. gigas transcriptome will facilitate research into biological processes underlying physiological adaptations to hypoosmotic shock for marine invertebrates. Twelve Pacific oysters were exposed in low salinity (8‰) seawater and in optimal salinity (25‰) seawater, respectively. Gills from six oysters in each condition were balanced mixed respectively. The transcriptomes of two samples were generated by deep sequencing, using Illumina HiSeq2000.
2012-12-15 | E-GEOD-38022 | biostudies-arrayexpress
Project description:The N6-methyladenosine (m6A) has recently emerged as an important layer of the gene expression regulatory network with critical implications in vertebrate and insect development. However, despite an m6A-RNA pathway is present in the pacific oyster Crassostrea gigas, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. We performed RNA sequencing (RNA-seq) and m6A-RNA immunoprecipitation sequencing (MeRIP-seq) on 10 developmental stages, on two distinct developments, to covering the whole oyster developement. The m6A-RNA methylomes show the conservation of m6A consensus motif RRACH, a m6A peak around the stop codon and highlight specific m6A signatures according to RNA species between mRNAs, lncRNAs and transposable elements. The differentially methylated RNAs constitute developmental clusters that correspond to chronological steps of oyster development (cleavage, gastrulation, tissues differentiation and metamorphosis). They are marked with an overall drop of mRNA and lncRNA methylation at the morula stage followed by a global increase up to pre-metamorphosis. Messenger RNA m6A levels are correlated to transcript content and shifts in methyladenine profiles correspond to expression kinetics. The m6A of TE transcripts is also regulated and peaks during the gastrulation. Altogether our results indicate that m6A epitranscriptomes are an important regulator of oyster development. This first epitranscriptome profiling across the development of a lophotrochozoan model brings new insights into the epigenetic control of developmental processes and their evolution.
2021-07-20 | GSE180388 | GEO
Project description:Digestive Gland Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of digestive gland for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed. Gills Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of gills for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed.
2012-08-25 | GSE27194 | GEO