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SAGE analysis of normal human mammary epithelial cells, breast carcinoma (malignant effusion), and breast adenocarcinoma (malignant pleural effusion)

ABSTRACT: These libraries represent Cancer Genome Anatomy Project libraries, which are 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. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

ORGANISM(S): Homo sapiens

SUBMITTER: C Aldaz

PROVIDER: E-GEOD-25748 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SAGE analysis of normal human mammary epithelial cells, breast carcinoma (malignant effusion), and breast adenocarcinoma (malignant pleural effusion)

Project description:These libraries represent Cancer Genome Anatomy Project libraries, which are 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.

2010-12-01 | GSE25748 | GEO

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Isolation and transcriptional profiling of embryonic human neural crest cells

Project description:To identify new candidate genes for neurocristopathies, a Long-SAGE library has been made from human neural crest cells (hNCC) derived from a normal embryo at Carnegie stage 13. Data analysis indicates the expression of a number of genes in multiple GO functional classes that were anticipated based on animal studies and/or human disease. An average linkage hierarchical clustering was performed using SAGE data from hNCC and 14 other normal tissues and cell lines. This and other analyses indicate a high degree of molecular identity between hNCC and the two human embryonic stem cells (hES) lines included, compared to the other tissue or cell types included, including more tissue-restricted stem cells, such as mesenchymal stem cells, or hNCC derivatives such as Schwann cells. Keywords: Cell type comparison Total RNA was extracted from a confluent 10 cm dish of hNCC (line N5) from a female human embryo at 28-32 dpf (Carnegie stage 13). Half the RNA was used to construct a SAGE bank with long tags using NlaIII and MmeI. Data was then compared to currently publicly available SAGE data from fourteen banks made from normal human tissues for hierarchical clustering. Third-party GEO accession numbers for human SAGE data: GSM41360, hES3; GSM41362, hES4; GSM48250, sciatic nerve; GSM48251, Schwann cells (in vitro); GSM31931, brain substantia nigra; GSM824, muscle; GSM785, liver; GSM708, kidney; GSM676, brain white matter; GSM761, brain cerebellum; GSM762, lung. Other third-party data: Cancer Genome Anatomy Project http://cgap.nci.nih.gov/SAGE/SAGELibraryFinder: SAGE_Prostate_normal_B_2 (prostate) Umbilical cord- and bone marrow-derived mesenchymal stem cell data had been downloaded from currently broken links http://bit.fmrp.usp.br/uc-msc_tags/ and http://bit.fmrp.usp.br/msc_tags/ as referenced in Panepucci et al. (2004) Stem Cells 22:1263-1278; DOI: 10.1634/stemcells.2004-0024 (UC-MSC) and Silva et al. (2003) Stem Cells 21:661-669.

2008-08-07 | E-GEOD-8368 | biostudies-arrayexpress

SAGE analysis of cardiac fibroblasts isolated from adult mouse heart

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Human_SAGE_cervix_normal_B_1

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2010-12-01 | E-GEOD-25753 | biostudies-arrayexpress

Mouse_SAGE_P23_cerebellum

Project description:P23 C57BL6/J mouse cerebellum This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-01 | E-GEOD-25751 | biostudies-arrayexpress

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Project description:SAGE profile of rat hippocampus mRNA from Wistar rats This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-01 | E-GEOD-25750 | biostudies-arrayexpress

RL-SAGE analysis of Zea mays leaf transcriptome

Project description:Using the RL-SAGE method (Gowda et al. 2004), a maize leaf longSAGE library (cv. inbred line B73) was constructed. Leaf tissues were harvested from 4-week old B73 plants for RNA isolation. The conditions in the growth chamber were 12 h light (500 µmol photons m-2 sec-1), 20oC at night, 26oC in the day and 85% relative humidity. A total of 44,870 unique tags (17 bases +CATG) were identified from 232,948 individual tags in the maize leaf library. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-10 | E-GEOD-25994 | biostudies-arrayexpress

SAGE analysis of human glomerular endothelial cell

Project description:Tissue from macroscopically healthy parts of nephrectomized kidneys. Endothelial cells were purified from the cell outgrowth of glomeruli twice using CD31 magnetic beads and cultured on fibronectin coated surface. Cells were not passaged more than eight times and stained with vWf, CD31, and after stimulation with TNF alpha also with CD62E/P. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-01 | E-GEOD-25760 | biostudies-arrayexpress

SAGE analysis of A. thaliana leaf tissue

Project description:Arabidopsis thaliana (Col-4) aerial tissue collected from 14-day old plants. Grown under sterile conditions at 22 degrees Celsius and 125 uE light on 0.5xMS media. This GEO Series was created by the GEO staff as part of a cleanup effort to ensure that all GEO Samples are included within a Series entry.

2010-12-10 | E-GEOD-25993 | biostudies-arrayexpress

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