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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Spore formation of Lentinula edodes (LongSAGE)

ABSTRACT: 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.

ORGANISM(S): Lentinula edodes

SUBMITTER: Hoi Shan Kwan

PROVIDER: E-GEOD-25463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Spore formation of Lentinula edodes

Project description:Gene expression profiles before and after spore formation of Lentinula edodes (L54)grown at sawdust. Keywords: time-course 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.

2006-02-08 | E-GEOD-4202 | biostudies-arrayexpress

Babesia Infected/Control LongSAGE libraries for Boophilus microplus ovary tissue

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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

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Spore formation of Lentinula edodes (LongSAGE)

Project description:Gene expression profiles before and after spore formation of Lentinula edodes (L54) grown at sawdust.

2010-11-24 | GSE25463 | GEO

LongSAGE analysis significantly improves genome annotation

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

LongSAGE transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

Project description:The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism. Keywords: Emiliania, gene expression, nutrients, SAGE, phosphate, nitrogen

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

LongSAGE transcriptome comparison on Botrytis cinerea conidia germination with and without resveratrol treatment

Project description:Two long serial analysis of gene expression (LongSAGE) libraries of germinating conidia of Botrytis cinerea were generated with and without resveratrol treatments for unraveling the antifungal mechanisms of this phytoalexin by global transcriptome analysis – 82,786 total tags and a minimum of 15,665 unitags were obtained respectively. By tag-to-gene mapping, about 55% of the total unitags were matched to known genes. There were 109 unitags that showed significant differences in the two LongSAGE libraries, corresponding to 43 up- and 44 down-regulated genes, and 22 unmatched unitags as new gene candidates. These results showed that resveratrol inhibited expression of genes related to the glycolysis-Krebs cycle and mitochondrial electron transport chains at multiple sites in conidia germination, with induction of modified Entner–Doudoroff pathway as metabolic compensation. The chaperone-mediated protein folding and ubiquitin proteolysis systems were inhibited, while detoxification of resveratrol via ABC transporters was activated in this fungal pathogen. Keywords: Botrytis cinerea; LongSAGE; metabolic pathway; resveratrol; transcriptome

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

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2007-10-10 | GSE6009 | GEO

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