LongSAGE analysis of wild-type mouse brain regions
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE7593 | GEO | 2008/02/05
SECONDARY ACCESSION(S): PRJNA100317
REPOSITORIES: GEO
Similar Datasets
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
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
2008-02-05 | GSE7594 | GEO
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
Project description:SAGE analysis of various brain regions from 8- to 12-week-old male C57BL/6 mice. Keywords: other
2003-07-10 | GSE348 | GEO
Project description:SAGE analysis of various brain regions from 8- to 12-week-old male C57BL/6 mice. Keywords: other
2003-07-10 | E-GEOD-348 | biostudies-arrayexpress
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
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
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
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2009-03-20 | GSE15312 | GEO
Project description:This series represents the Cancer Genome Anatomy Project SAGE library collection. Libraries contained herein were either produced through CGAP funding, or donated to CGAP. The Cancer Genome Anatomy Project (CGAP: http://cgap.nci.nih.gov) is an interdisciplinary program established and administered by the National Cancer Institute (NCI: http://www.nci.nih.gov) to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. SAGE libraries are named according to the following convention: * SAGE_Organ_histology_code_unique identifier, e.g., SAGE_Colon_adenocarcinoma_CL_Caco2 * Codes: B = bulk; CL = cell line; CS = short-term cell culture; MD = micro-dissected; AP = antibody purified.
2004-10-28 | GSE1902 | GEO