Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1108452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28965438_1.fastq.gz | Fastqsanger.gz | |||
| SRR28965438_2.fastq.gz | Fastqsanger.gz | |||
| SRR28965439_1.fastq.gz | Fastqsanger.gz | |||
| SRR28965439_2.fastq.gz | Fastqsanger.gz | |||
| SRR28965440_1.fastq.gz | Fastqsanger.gz |
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Project description:The mantle is a thin tissue from which proteins are secreted dictating the mollusk shell construction. As a conserved organ involved in shell formation throughout mollusks, the mantle is an excellent foundation from which to study biomineralization. A P. maxima mantle tissue specific cDNA microarray, termed PmaxArray 1.0, has been developed comprising 5000 cDNA transcripts derived from the mantle tissue of P. maxima. This tool has been used to investigate the spatial functional dynamics of the mantle tissue identifying over 2000 PmaxArray 1.0 spots as differentially expressed spatially within this organ. Gene expression profiles observed for these transcripts indicated 5 major spatial functions for the mantle, 3 of which have been putatively attributed to shell formation roles associated with nacre microstructure, calcite prismatic microstructure and periostracum. These transcripts are further examined with in situ expression localization and comparative sequence analyses in reference to potential shell formation roles. This spatial investigation has expedited the elucidation of functions within the dynamic mantle organ, paying particular attention to of shell biomineralization. Keywords: Spatial expression profiling by array
2010-02-05 | GSE14303 | GEO
Project description:The mantle is a thin tissue from which proteins are secreted dictating the mollusk shell construction. As a conserved organ involved in shell formation throughout mollusks, the mantle is an excellent foundation from which to study biomineralization. A P. maxima mantle tissue specific cDNA microarray, termed PmaxArray 1.0, has been developed comprising 5000 cDNA transcripts derived from the mantle tissue of P. maxima. This tool has been used to investigate the spatial functional dynamics of the mantle tissue identifying over 2000 PmaxArray 1.0 spots as differentially expressed spatially within this organ. Gene expression profiles observed for these transcripts indicated 5 major spatial functions for the mantle, 3 of which have been putatively attributed to shell formation roles associated with nacre microstructure, calcite prismatic microstructure and periostracum. These transcripts are further examined with in situ expression localization and comparative sequence analyses in reference to potential shell formation roles. This spatial investigation has expedited the elucidation of functions within the dynamic mantle organ, paying particular attention to of shell biomineralization. Keywords: Spatial expression profiling by array The mantle tissue from 9 animals was dissected into 5 separate sections: outer fold (OF), middle fold (MF), inner fold (IF), ventral mantle tissue (VM) and dorsal mantle tissue (DM). Total RNA was extracted from these tissues and pooled across subjects in order to reduce the effect of biological variation; such that 3 individuals were pooled together totaling 3 pooled replicate samples for each tissue. All the biologically pooled tissue types were compared against a common reference in which total RNA from all tissues types and all nine animals was equally pooled. A total of 30 dual channel microarrays hybridizations were performed and analyzed.
2010-05-15 | E-GEOD-14303 | biostudies-arrayexpress
Project description:This project was conducted in collaboration with the Stachowicz and Dorrestein labs exploring the effects of eelgrass genotypic diversity on rhizosphere exometabolome production under marine heat wave versus ambient conditions. This data was collected from cultures of eelgrass genotypes grown in various levels of poly or monoculture under marine heat wave or ambient conditions in mesocosm. After simulating a 15 week marine heat wave regime, we sampled for each culture type-treatment combination’s rhizosphere metabolome and used non-targeted LC-MS/MS to examine how root exudates at the culture-level interact with genotypic diversity and temperature stress in a marine habitat forming species. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).
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2024-11-19 | MSV000096471 | GNPS
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Project description:Purpose:Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout Methods:miRNAs of rainbow trout were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries of the kidney tissues under control (18℃) and heat-treated (24℃) conditions Results:high-throughput sequencing was performed to identify miRNAs responsive to heat stress. We obtained 41,991,119 and 43,882,123 raw reads and 39,756,736 and 42,538,331 clean reads from under control (18℃) and heat-treated (24℃) .A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. In addition to, including 393 negative correlation miRNA-target gene pairs Conclusions:through high-throughput sequencing of the six libraries from head kidney tissue of rainbow trout, the expression level of miRNA has significant changes after heat stress.
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