SAGE analysis of wild-type mouse brain regions
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE7594 | GEO | 2008/02/05
SECONDARY ACCESSION(S): PRJNA100179
REPOSITORIES: GEO
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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: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
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 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:A plethora of research has focused on the human embryonic stem cells (hESC) ever since they were first reported mainly due to their distinct features of self renewal and pluripotency. Probing of the hESC transcriptome using global expression profiling tools such as DNA microarray, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) and Expressed Sequence Tag (EST) analysis have contributed significantly in our current understanding of hESCs. In fact, a large number of markers to assess the pluripotent and differentiation status of hESCs have been presented by such studies. However, till date clarity is lacking in identifying a robust set of markers to assess the true state of the hESCs. In this paper, we report the generation of long SAGE libraries for partially differentiated and differentiated HES3 along with a deeper profiling of our previously reported HES3 undifferentiated library. Clustering analysis of these libraries in concert with long and short SAGE libraries available in public databases using Hierarchical Cluster Analysis (HCA) as well as a poison-based approach helped in identification of expression patterns distinct from those reported for the well established pluriptency/differentiation markers. Almost all the previous studies reporting a robust set of markers have focused on a gene by gene comparison in listing out the upregulated and downregulated genes rather than look at the expression patterns in establishing a list of markers. In this analysis, however, we report a new set of markers as well as add confidence to some previously reported markers based on their novel expression patterns as identified by SAGE analysis and also confirm it by real-time PCR analysis. For the real-time PCR confirmation, instead of taking two extreme data sets such as undifferentiated and a late stage embryoid body, we profiled a time series of embryoid body stages so that we could identify those genes which show a dramatic increase or decrease upon differentiation and hence would serve as more reliable markers. The hESC lines HES3 from ES Cell International, Singapore (http://www.escellinternational.com) were cultured on mouse embryonic fibroblast feeders (MEFs) as described previously. Selection of cells for library construction was done by micro-dissection following our established protocols. Spontaneous differentiation was induced by prolonged culture without changing the feeder layer. Briefly the HES3 cell line was grown to 18 passages (P18) on MEFs, after which no sub-culturing was performed. The medium was changed daily for 25 days and the differentiated cell population was harvested at the end of the culture period by micro-dissection. Cell differentiation was confirmed by Immuno-cytochemistry for markers to the three germ layers, as well as RT-PCR for the differentiation markers. For construction of the partially differentiated library, colonies which had started differentiation, as suggested by the morphological changes towards the centre and periphery of the colonies were used. Entire HES3 colonies (24P) which had started differentiation were harvested by micro-dissection and used for library construction. MmeI was used as tagging enzyme and libraries were constructed using the LS-SAGE kit from Invitrogen (http://www.invitrogen.com). Cloning of concatemerized ditags and sequencing of tags were done as outlined earlier. The 10 bp SAGE tags were extracted using Microsoft Excel for direct comparisons between libraries.
2010-02-17 | E-GEOD-12611 | biostudies-arrayexpress
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 | GSE15309 | 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 | GSE15311 | 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. These libraries were downloaded from the CGAP Web site on March 17, 2009 This SuperSeries is composed of the SubSeries listed below.
2001-11-29 | GSE14 | GEO
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 | GSE10 | GEO