Development of gene expression profile in different tissues of zebra mussel and larvae
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ABSTRACT:
ORGANISM(S): Dreissena polymorpha
SUBMITTER: Anna Navarro Cuenca
PROVIDER: E-GEOD-35352 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To analyze the different pattern of expression among tissues in D. polymorpha it was used acustom microarray designed in our laboratory using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using gills, digestive gland, gonad and half a body of adult zebra mussel and larvae 24 h pf. The samples analyzed in the microarray were not treated in order to detect the normal pattern of expression in each tissue. A total of 221 transcripts changed significantly their mRNA levels in the different tissues (ANOVA p<0.01, fc ±1.5). The results showed a clear separation on transcriptome profiles between samples with the main changes in gills, larvae and half a body.
2012-01-27 | GSE35352 | GEO
Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues.
2012-09-04 | GSE24101 | 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: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. Digestive Gland Samples: In this study, we analyzed six (6) samples, three (3) pools of digestive gland of Manila clam sampled in Marghera and three(3) pools of digestive gland of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 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. Feature Extraction (FE) 9.5 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. Gills Samples: In this study, we analyzed six (6) samples, three (3) pools of gills of Manila clam sampled in Marghera and three(3) pools of gills of Manila clam sampled in Alberoni. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 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. Feature Extraction (FE) 9.5 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.
2012-08-25 | E-GEOD-27194 | biostudies-arrayexpress
Project description:A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues. In this study, we analyzed six (6) samples, three (3) pools of digestive gland and three (3) pools of gills. Gene expression profiling was performed using the Agilent-019810 Ruditapes philippinarum Oligo Microarray platform (GPL10900) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 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. Feature Extraction (FE) 9.5 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.
2012-09-04 | E-GEOD-24101 | biostudies-arrayexpress
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
Project description:To analyze the impact of seasonal and environmental variations on the physiology and metabolism of zebramussel, we use a custom microarray developed in our laboratory, using 4057 publicly availabe DNA sequences from Dreissena and other realted genera. Transcriptome profiles were analyszed using half-body samples captured in Riba Roja (low Ebro River), a location considered relatively free of chemical pollution, at three different stages of the vital cycle. The results showed a clear separation on transcriptome profiles between samples collected in February and June (pre- and spawning, respectively) and samples collected during gonad resorption (September). A total of 753 transcripts changed significantly their mRNA levels during these three months (ANOVA p<0.01, fc ±1.5). These changes could be considered as response to variations of temperature, reproductive stages, as well as food availability. Genes involved in oxidative stress were overrepresented in September, whereas genes related to reproductive functions were overrrepresented in the spawning and pre-spawning period. For each season (February: pre-spawning; June: Spawning; September: gonad resorption) it was used 2 biological replicates using the half body as a target tissue to analyze .
2012-01-27 | E-GEOD-35353 | biostudies-arrayexpress
Project description:Direct comparison of the transcriptional patterns between male and female in the digestive gland of a natural population of the marine mussel Mytilus galloprovincialis sampled in the Bizerta Lagoon, Tunisia, across November 2007 -February March 2008 (four stages, winter peak). Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the Digestive gland (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses. Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes. Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression. Test/reference design (female/male). Direct comparison of RNA extracts obtained from the Digestive gland tissue of female and male animals. Two (male, female) x four conditions (gonad developmental stage 1, stage 2, stage 3, stage 4). Dual color competitive hybridizations with label swap. Single individuals. Four biological replicates. One replicate per array.
2011-06-06 | E-GEOD-23051 | biostudies-arrayexpress
Project description:Deep sequencing of samples from different development stages, different adult organs and different stress treatments of Pacific oyster Crassostrea gigas Samples of 38 developmental stages from egg to juvenile were analyzed using single-end 49 bp RNA-seq. Two libraries mixed by RNAs from different developmental stages were analyzed using paired-end 90 bp RNA-seq. A total of 11 samples mainly from 8 organs (mantle, gill,adductor muscle, digestive gland, hemocyte, labial palp, female gonad and male gonad) were analyzed using paired-end 90 bp RNA-seq. At the same time, single-end 49 bp RNA-seq was conducted on 61 samples collected from adult oysters subjected to 9 types of environmental stressors (exposure to air, salinity, temperature, and exposure to metals).
2012-09-13 | E-GEOD-31012 | biostudies-arrayexpress
Project description:This is a prepublication dataset that should change as updates are made to the underling genomes and annotations. Additional samples may be deposited and some samples may fail quality control. Please contact Haiwang Yang <haiwang.yang@nih.gov> for details. The RNA-seq data set contains the transcriptional profiling of eight sexed tissue types (head, thorax, carcass, abdomen w/o gonad, gonad, other reproductive tract, genitalia, and digestive system) and/or whole adult flies from five strains of Drosophila grimshawi, two strains of D. silvestris, and one strain each of D. hemipeza, D. heteroneura, and D. hawaiiensis. Samples were collected in duplicate to quadruplicate from sexually mature sexed adults (4-5 weeks post eclosion), which had been allowed to freely mate. Single-end stranded 76bp PolyA+ RNA-seq was performed on all samples. Libraries were multiplexed with indexed adaptors, and some were also prepared as mixed libraries with RNA from genetically distant species: Drosophila melanogaster (GSE81142) and Anopheles stephensi (GEO entry in preparation). All whole adult samples were prepared from single flies. Tissues were pooled from 3-5 individuals depending on the size of both the tissue and the species. For the G1 strain (reference assembly strain) of D. grimshawi, we profiled seven adult tissues for each sex in addition to whole flies. Samples were whole fly (one fly per sample), head (5 flies), thorax (5 flies), abdomen w/o gonad (5 flies), gonad (testes or ovaries) (5 flies), other reproductive tract (accessory gland and male reproductive duct or female spermatheca and oviduct; 10 flies per sample), genitalia (10 flies), and digestive system (proventriculus, crop, salivary gland, gut, and renal tubule; 5 flies). We prepared sexed single fly whole body samples in quadruplicate for ZA27Z2, ZA27Z3, and Mo010 strains of D. grimshawi. We also prepared sex-specific head, carcass, gonad, other reproductive tract with genitalia with duplicate for Wm1041 strain of D. grimshawi and other species - D. silvestris (Y11R6 and U26B9 strains), D. hemipeza (W40B14 strain), D. heteroneura (W48B6 strain), and D. hawaiiensis (Y17P5 strain). We used reduced number of flies for the non-grimshawi species (i.e., 3 heads, gonads or carcasses per sample, and 6 reproductive tracts plus genitalia per sample).
2016-06-01 | E-GEOD-80124 | biostudies-arrayexpress