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Long Serial Analysis of Gene Expression (LongSAGE) of Chinook salmon (Oncorhynchus tshawytscha) brain tissue.

ABSTRACT: Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Populations return to freshwater for spawning at many different times of year, resulting in segregated populations that may use differing molecular pathways for these large behavioral and physiological differences. Using a population of Chinook from California’s Central Valley, we sought to generate novel expressed sequences using Long Serial Analysis of Gene Expression (LongSAGE). We constructed three LongSAGE libraries from brains of samples caught in the spring and fall in freshwater and from the ocean. Using cDNA libraries from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), we were able to assign 59% of putatively differentially expressed tags to genes. Additionally, we tested the expression levels of seven genes, indicated by LongSAGE to be putatively differentially expressed between the fall and spring, and found none significantly differentially expressed. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future research on gene expression differences between Chinook salmon of different populations, as well as underlying mechanisms of differing physiology and behavior. Keywords: seasonal difference Single individuals were used to construct each LongSAGE library. The fall, spring and ocean samples were then compared between each other and examined for differences in the number of tags observed.

ORGANISM(S): Oncorhynchus tshawytscha

SUBMITTER: Jeremiah Bernier

PROVIDER: E-GEOD-6009 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Long Serial Analysis of Gene Expression (LongSAGE) of Chinook salmon (Oncorhynchus tshawytscha) brain tissue.

Project description:Chinook salmon (Oncorhynchus tshawytscha) display the greatest variability of return times to freshwater of all Pacific salmon. Populations return to freshwater for spawning at many different times of year, resulting in segregated populations that may use differing molecular pathways for these large behavioral and physiological differences. Using a population of Chinook from California’s Central Valley, we sought to generate novel expressed sequences using Long Serial Analysis of Gene Expression (LongSAGE). We constructed three LongSAGE libraries from brains of samples caught in the spring and fall in freshwater and from the ocean. Using cDNA libraries from Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), we were able to assign 59% of putatively differentially expressed tags to genes. Additionally, we tested the expression levels of seven genes, indicated by LongSAGE to be putatively differentially expressed between the fall and spring, and found none significantly differentially expressed. This study is the first to apply LongSAGE to salmon and provides a framework for conducting future research on gene expression differences between Chinook salmon of different populations, as well as underlying mechanisms of differing physiology and behavior. Keywords: seasonal difference

2007-10-10 | GSE6009 | GEO

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [liver]

Project description:There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.

2019-12-03 | GSE123307 | GEO

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [gill]

2019-12-03 | GSE123305 | GEO

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [muscle]

2019-12-03 | GSE123306 | GEO

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments [brain]

2019-12-03 | GSE123304 | GEO

RL-SAGE analysis of Zea mays leaf transcriptome

Project description:Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-10 | E-GEOD-25994 | biostudies-arrayexpress

LongSAGE analysis significantly improves genome annotation

Project description:Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2098 LongSAGE tags fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline. CONCLUSIONS: LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse. Keywords: other Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries.

2005-07-20 | E-GEOD-2967 | biostudies-arrayexpress

SAGE: unfertilized eggs

Project description:LongSAGE library was constructed by standard methods with several modifications. Additional amplification step was not performed. Keywords: other

2005-12-11 | E-GEOD-2070 | biostudies-arrayexpress

Spore formation of Lentinula edodes (LongSAGE)

Project description:Gene expression profiles before and after spore formation of Lentinula edodes (L54) grown at sawdust. SAGE were used to generate tags from RNA of fruit bodies of L. edodes. RNA were extracted from the fruit bodies before and after spore observed. Gene expression profiles of both stages were compared to screen out genes may relate to spore formation. To facilitate comparison of LongSAGE and SAGE data in GEO, LongSAGE tags (15bp) were trimmed to become 10bp and uploaded in previous submission (GSM87320, GSM87321). The current submission are actual LongSAGE experimental data without any extrapolation from SAGE data.

2010-11-24 | E-GEOD-25463 | biostudies-arrayexpress

C. elegans SAGE

Project description:The SAGE libraries were built from total mRNA populations in specific tissues, cells, mutation-specific populations, and all developmental stages of C. elegans. Tissue- and cell-specific libraries were generated from FACS-sorted cells marked by expression of specific promoter::GFP fusions Keywords = SAGE Keywords = LongSAGE Keywords = Caenorhabditis elegans Keywords = development Keywords = dauer Keywords: other

2004-06-11 | E-GEOD-1447 | biostudies-arrayexpress

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