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LongSAGE analysis of wild-type mouse brain regions

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Jean-Marc Elalouf

PROVIDER: E-GEOD-7593 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models.

Brochier Camille C Gaillard Marie-Claude MC Diguet Elsa E Caudy Nicolas N Dossat Carole C Ségurens Béatrice B Wincker Patrick P Roze Emmanuel E Caboche Jocelyne J Hantraye Philippe P Brouillet Emmanuel E Elalouf Jean-Marc JM de Chaldée Michel M

Physiological genomics 20080205 2

Using serial analysis of gene expression, we collected quantitative transcriptome data in 11 regions of the adult wild-type mouse brain: the orbital, prelimbic, cingulate, motor, somatosensory, and entorhinal cortices, the caudate-putamen, the nucleus accumbens, the thalamus, the substantia nigra, and the ventral tegmental area. With >1.2 million cDNA tags sequenced, this database is a powerful resource to explore brain functions and disorders. As an illustration, we performed interregional comp ...[more]

PMID: 18252803

Similar Datasets

SAGE analysis of wild-type mouse brain regions

Project description:SAGE 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 Bsmf I as the tagging enzyme. Data are provided after linker removal.

2008-02-05 | E-GEOD-7594 | 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 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

2005-07-20 | GSE2967 | GEO

LongSAGE analysis significantly improves genome annotation

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

Babesia Infected/Control LongSAGE libraries for Boophilus microplus ovary tissue

Project description:Babesia infected (and control) ovary tissue was used to construct LongSAGE libraries. The intent was to find differential gene expression in both libraries. Details: The extraction was done using Ambion's ToTALLY RNA kit, and the concatemers where constructed using Invitrogen's I-SAGE Long kit. The concatmer files (multiple fasta sequence files) were processed using in-house perl scripts to extract the 17bp LongSAGE tags. **Note: contact person: Felix D. Guerrero. email: felix.guerrero@ars.usda.gov Keywords: LongSAGE

2009-03-01 | GSE9880 | GEO

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

Oryza Sativa and Magnaporthe Grisea LongSAGE

Project description:LongSAGE library in this series are from 'Whole Genome Analysis of Pathogen-Host Recognition and Subsequent Responses in the Rice Blast Patho-System' project. This work is supported by NSF-PGRP #0115642. Keywords: other

2004-11-08 | GSE1924 | GEO

Oryza Sativa and Magnaporthe Grisea LongSAGE

Project description:Oryza Sativa and Magnaporthe Grisea LongSAGE

| PRJNA90951 | ENA

Oryza Sativa and Magnaporthe Grisea LongSAGE

2004-11-07 | E-GEOD-1924 | 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

2007-10-10 | GSE6009 | GEO

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