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SAGE

Human SAGE Genie Tools

Mouse SAGE Genie Tools

Digital Karyotyping

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mSAGE Experimental Viewer (mSEV)

The mSAGE Experimental Viewer (mSEV) automatically sets up the Digital Gene Expression Displayer (DGED) comparison for sets of mouse libraries that have been prepared as stand alone experiments. On the DGED set up page, the user decides which libraries to include in Pool A and Pool B and can change the default statistical parameters.

The experiments are organized by tissue, with a brief description of the libraries, and with the laboratoy name in the DGED link:

Tisssue Description DGED Setup
Bone marrow Bone marrow cells, first stimulated with GM-CSF and then with combinations of IL10, LPS and Vit D3. Cobbold_bone_marrow_DGED
Cerebellum Cerebellar granule cell precursor cells treated with and without SHH. Riggins_GCP_DGED
EC cells EC cells before and after differentiation into cardiomyocytes by DMSO. (1) Boheler_EC_cells_DGED
EC cells EC cells before and after differentiation into cartilage by BMP4. (2) Imai_EC_cells_DGED
ES cells ES cells differentiated with GM-CSF and IL3, with and without LPS. Cobbold_ES_cells_DGED
Hippocampus Hippocampus from short- and long-attack-latency mice. (3) Vreugdenhil_hippocampus_DGED
Mammary gland Normal mammary gland compared to adenocarcinoma, p53 wildtype and null. (4, 5)
Mammary gland from C3(1)SV40Tag mice, with and without LGD1069.* 		Aldaz_mammary_gland_DGED
Retina Retina at various stages of development, and Crx null tissue. (6, 7) Blackshaw_retina_DGED
Skin Normal skin compared to squamous cell carcinoma. (8) Aldaz_skin_DGED
Whole embryo Female embryos at TS26, Carm1 wildtype or null, treated with DES. Aldaz_whole_embryo_DGED
T-cells Naive T-cells, memory T-cells, T-cells expressing TCR α/β, and T-cell expressing TCR γ/δ. (9, 10) Shires_T_cells_DGED

* Targretin, a retinoid X-receptor selective ligand.

References

  1. Anisimov SV, Tarasov KV, Riordon D, Wobus AM, Boheler KR. SAGE identification of differentiation responsive genes in P19 embryonic cells induced to form cardiomyocytes in vitro. Mech Dev. (2002) 117:25-74.
  2. Wahl M, Shukunami C, Heinzmann U, Hamajima K, Hiraki Y, Imai K. Transcriptome analysis of early chondrogenesis in ATDC5 cells induced by bone morphogenetic protein 4. Genomics (2004)83:45-58.
  3. Feldker DE, Datson NA, Veenema AH, Meulmeester E, de Kloet ER, Vreugdenhil E. Serial analysis of gene expression predicts structural differences in hippocampus of long attack latency and short attack latency mice. Eur J Neurosci. (2003) 17:379-87.
  4. Hu Y, Sun H, Drake J, Kittrell F, Abba MC, Deng L, Gaddis S, Sahin A, Baggerly K, Medina D, Aldaz CM. From mice to humans: identification of commonly deregulated genes in mammary cancer via comparative SAGE studies. Cancer Res. (2004) 64:7748-55
  5. Aldaz CM, Hu Y, Daniel R, Gaddis S, Kittrell F, Medina D. Serial analysis of gene expression in normal p53 null mammary epithelium. Oncogene. (2002) 21:6366-76.
  6. Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell (2001) 30:579-89.
  7. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL. Genomic analysis of mouse retinal development. PLoS Biol. (2004) 2:E247.
  8. Rundhaug JE, Hawkins KA, Pavone A, Gaddis S, Kil H, Klein RD, Berton TR, McCauley E, Johnson DG, Lubet RA, Fischer SM, Aldaz CM. SAGE profiling of UV-induced mouse skin squamous cell carcinomas, comparison with acute UV irradiation effects. Mol Carcinog. (2004 Nov 16; [Epub ahead of print]
  9. Pennington DJ, Silva-Santos B, Shires J, Theodoridis E, Pollitt C, Wise EL, Tigelaar RE, Owen MJ, Hayday AC. The inter-relatedness and interdependence of mouse T cell receptor gammadelta+ and alphabeta+ cells. Nat Immunol. (2003) 4:991-8.
  10. Shires J, Theodoridis E, Hayday AC. Biological insights into TCRgammadelta+ and TCRalphabeta+ intraepithelial lymphocytes provided by serial analysis of gene expression (SAGE). Immunity (2001) 15:419-34.

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