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C. elegans SAGE

ABSTRACT: 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

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Kim Wong

PROVIDER: E-GEOD-1447 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans.

Jones S J SJ Riddle D L DL Pouzyrev A T AT Velculescu V E VE Hillier L L Eddy S R SR Stricklin S L SL Baillie D L DL Waterston R R Marra M A MA

Genome research 20010801 8

Gene expression in a developmentally arrested, long-lived dauer population of Caenorhabditis elegans was compared with a nondauer (mixed-stage) population by using serial analysis of gene expression (SAGE). Dauer (152,314) and nondauer (148,324) SAGE tags identified 11,130 of the predicted 19,100 C. elegans genes. Genes implicated previously in longevity were expressed abundantly in the dauer library, and new genes potentially important in dauer biology were discovered. Two thousand six hundred ...[more]

PMID: 11483575

Similar Datasets

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 | GSE1447 | GEO

LongSAGE analysis of wild-type mouse brain regions

Project description:LongSAGE libraries generated from various brain regions of 8- to 12-week-old male C57BL/6 mice. Keywords: Micro-dissection, Brain regions, SAGE Sau3A I was used as the anchoring enzyme and Mme I as the tagging enzyme. Data are provided after linker removal.

2008-02-05 | E-GEOD-7593 | biostudies-arrayexpress

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 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.

2007-10-09 | E-GEOD-6009 | 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

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

Adult mouse testis

Project description:SAGE libraries generated from total testes of adult mouse males. Keywords = testis Keywords: other

2005-03-14 | E-GEOD-1939 | biostudies-arrayexpress

Large scale gene expression of Vero cell correlated to infection of infectious bursal disease virus

Project description:Infectious bursal disease virus (IBDV) is the pathogenic agent of infectious bursal disease (IBD). Scine it was observed in 1957, IBD spread worldwidely in the chicken flocks, is a important immunosuppressive disease and an threat to poultry industry. Although many studies have be done about IBDV, interaction of IBDV infection and IBDV-encoding genes to host cell gene expression are little known. In this study, the LongSAGE library of Vero-cell, IBDV- infected vero cell, Vero-cell transfected with IBDV-VP5 gene, Vero-cell transfected with IBDV A frament and Vero-cell transfected with IBDV VP243 frament were obtained. We got 96,213 gene tags (17 nucleotides), which represented 24,475 transcripts. Keywords: Transcripts of different state vero-cell 1.Cloning of the full-length genomic A-segment, VP5 ORF cDNA, VP243 ORF cDNA of IBDV 2.Establishing cloned Vero cell lines expressing VP5, VP243 and A fragment of IBDV 3.Construction of Long-SAGE libraries 4. Sequencing

2007-11-04 | E-GEOD-6243 | biostudies-arrayexpress

LongSAGE analysis of wild-type mouse brain regions

Project description:LongSAGE libraries generated from various brain regions of 8- to 12-week-old male C57BL/6 mice. Keywords: Micro-dissection, Brain regions, SAGE

2008-02-05 | GSE7593 | GEO

Luteinisation genes

Project description:Two SAGE libraries generated before (PMSG) or after (PMSG/hCG) the onset of granulosa cell luteinisation induced by hCG Keywords = granulosa Keywords = PMSG Keywords = hCG Keywords = luteinisation Keywords: other

2004-09-17 | E-GEOD-1771 | biostudies-arrayexpress

eye-SAGE

Project description:Human retinal and RPE SAGE libraries. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Keywords: other

2001-10-03 | E-GEOD-10 | biostudies-arrayexpress

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