title: 3860


title: 3871

status: Public on Feb 20 2007

type: genomic

city: Toronto

first: Christian

middle: R.

last: Marshall

state: ON

address: 101 College St.

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay. 1. Prepare the Hybridization Cocktail Master Mix (for multiple samples make 5% excess). 2. Transfer each of the labeled sample from the plate to a 1.5 mL Eppendorf tube. Aliquot 190 uL of the Hybridization Cocktail Master Mix into the 70 uL of labeled DNA samples. 3. Heat the 260 uL of hybridization mix and labeled DNA at 95°C in a heat block for 10 minutes to denature. 4. Cool down on crushed ice for 10 seconds. 5. Spin briefly at 2,000 rpm for 1 minute in a microfuge to collect any condensate. 6. Place the tubes at 48°C for 2 minutes. 7. Inject 80 uL denatured hybridization mix into the array. 8. Hybridize at 48°C for 16 to 18 hours at 60 rpm.

scan_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual. Fluidics Station 450/250 was used to automate the washing and staining of GeneChip® Mapping probe arrays. Arrays were scanned with the GeneChip® Scanner 3000 using GeneChip Operating Software (GCOS)

data_processing: Genotype calls were made using Affymetrix GeneChip Operating Software (GCOS) and Affymetrix GeneChip DNA Analysis Software (GDAS). Copy number variation was inferred using DNA Chip Analyzer (dCHIP).

label: Biotin Streptavidin Phycoerythin (SAPE)

molecule: genomic DNA

organism: Homo sapiens

source_name: blood or lymphoblast

label_protocol: See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual, experiments were run in 96-well plate format 1. Prepare Labeling Mix as master mix ON ICE and vortex at medium speed for 2 seconds (for multiple samples, make 5% excess). 2. Aliquot 19.4 uL of Labeling Master Mix into the fragmentation plate containing 50.6 uL of fragmented DNA samples. 3. Seal the plate tightly with a plate cover. 4. Vortex the plate at medium speed for 2 seconds, and briefly spin the plate at 2,000 rpm for 1 minute. 5. Run the following program: 37ºC for 2 hours, 95ºC for 15 minutes, 4ºC Hold. 6. Briefly spin the plate at 2,000 rpm for 1 minute after the labeling reaction.

extract_protocol: standard phenol/chloroform method


title: 3861


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title: 3773


title: 3767

description: NAAR CP-E1-C6-8081-202


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title: 3314


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description: NAAR CP-C1-A7-8076-111


title: 3300


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title: 3186


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title: 3185


title: 3175

description: NAAR CP-G3-G10-8120-101


title: 3174


title: 3187


title: 3180


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title: 3173


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title: 3004


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title: 3003


title: 3665


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title: 3616


title: 3624


title: 3618


title: 3623


title: 3611


title: 3621


title: 3607

description: NAAR CP-G1-D8-8086-203


title: 3620


title: 3606


title: 3613


title: 3604


title: 3612


title: 3617


title: 3627


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title: 3581


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title: 3583


title: 3580


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title: 3542


title: 3553


title: 3539


title: 3543


title: 3541


title: 3538


title: 3540


title: 3534


title: 3533


title: 3536

description: NAAR CP-G5-G12-8120-201


title: 3537


title: 3529


title: 3527


title: 3523


title: 3535


title: 3526


title: 3518


title: 3517


title: 3530


title: 3525


title: 3522


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title: 3519


title: 3520


title: 3521


title: 3532


title: 3515


title: 3511


title: 3514


title: 3509


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title: 3502


title: 3489


title: 3506


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title: 3500


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title: 3505


title: 3508


title: 3498


title: 3503


title: 3516


title: 3531


title: 3487


title: 3486


title: 3493


title: 3492


title: 3488


title: 3497


title: 3475


title: 3482


title: 3480

description: NAAR CP-G2-A11-8252-202


title: 3484


title: 3478


title: 3483


title: 3490


title: 3473


title: 3481


title: 3472


title: 3471


title: 3476


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title: 3465


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title: 3440


title: 3434


title: 3442


title: 3438


title: 3433


title: 3432


title: 3427


title: 3429


title: 3431


title: 3524

description: NAAR CP-H2-B11-8256-201


title: 3430


title: 3423


title: 3424


title: 3425


title: 3422


title: 3417


title: 3420


title: 3421


title: 3428


title: 3419


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title: 2947


title: 2966


title: 2954


title: 2949


title: 2950


title: 2943


title: 2956


title: 2945


title: 2951


title: 2946

description: NAAR CP-G6-G6-8149-101_2


title: 2944


title: 2942


title: 2948


title: 2939


title: 2959


title: 2940


title: 2941


title: 2935


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title: 2889


title: 2887


title: 2898


title: 2888


title: 2894


title: 2892


title: 2896


title: 2890


title: 2882


title: 2893

description: NAAR CP-B1-D12-8059-111


title: 2886


title: 2884


title: 2891


title: 2881


title: 2879


title: 2880


title: 2877


title: 2958


title: 2876


title: 3354


title: 2871


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title: 2868


title: 2866


title: 2897


title: 2885


title: 2865


title: 2872


title: 2862


title: 2857


title: 2861


title: 2852

description: NAAR CP-D7-F11-8123-202


title: 2856


title: 2851


title: 2860


title: 2864


title: 2855


title: 2850


title: 2859


title: 2873


title: 2863


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title: 2854


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title: 2883


title: 2757


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title: 2740


title: 2750


title: 2735


title: 2737


title: 2736


title: 2734


title: 2739


title: 2738


title: 2730


title: 2727

description: NAAR CP-G8-A10-8289-111


title: 2729


title: 2741


title: 2731


title: 2728


title: 2726


title: 2724


title: 2733


title: 2720


title: 2721


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title: 2680


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title: 2732


title: 2641


title: 2744


title: 2654


title: 2639


title: 2638


title: 2623


title: 2634


title: 2637


title: 2629


title: 2622


title: 2636


title: 2631


title: 2630


title: 2640


title: 2633


title: 2632


title: 2635


title: 2627


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title: 2628


title: 2621


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title: 2616


title: 2613


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title: 2615


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title: 2604


title: 2599


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title: 2602


title: 2598


title: 2601


title: 2590


title: 2596


title: 2589


title: 2605


title: 2595


title: 2591


title: 2608


title: 2603


title: 2586


title: 2592


title: 2600


title: 2587


title: 2594


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title: 2585


title: 2597


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title: 2584


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title: 2582


title: 2618


title: 2581


title: 2562


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title: 2577


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title: 2572


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title: 2566


title: 2571


title: 2579


title: 2567


title: 2569


title: 2578


title: 2557


title: 2559


title: 2564


title: 2575


title: 2568


title: 2570


title: 2678


title: 2565


title: 2560


title: 2555


title: 2573


title: 2558


title: 2580


title: 2561


title: 2556


title: 2552


title: 2550


title: 2551


title: 2546


title: 2545


title: 2549


title: 2548


title: 2547


title: 2544


title: 2553


title: 2540


title: 2542


title: 2531


title: 2529


title: 2539


title: 2543


title: 2541


title: 2526


title: 2532


title: 2538


title: 2534


title: 2527


title: 2533


title: 2525


title: 2535


title: 2536


title: 2528


title: 2537


title: 2523


title: 2520


title: 2522


title: 2518


title: 2519


title: 2524


title: 2521


title: 2517


title: 2514


title: 2516


title: 2510


title: 2505


title: 2500


title: 2504


title: 2499


title: 2506


title: 2501


title: 2512


title: 2507


title: 2509


title: 2503


title: 2513


title: 2498


title: 2508


title: 2511


title: 2554


title: 2495


title: 2496


title: 2497


title: 2502


title: 2494


title: 2493


title: 2515


title: 2492


title: 2489


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title: 2488


title: 2484


title: 2530


title: 2479


title: 2487


title: 2472


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title: 2480


title: 2469


title: 2483


title: 2470


title: 2473


title: 2475


title: 2468


title: 2482


title: 2463


title: 2477


title: 2464


title: 2481


title: 2465


title: 2486


title: 2476


title: 2467


title: 2462


title: 2471


title: 2460


title: 2466


title: 2461


title: 2459


title: 2457


title: 2456


title: 2454


title: 2452


title: 2458


title: 2449


title: 2450


title: 2455


title: 2451


title: 2453


title: 2445


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title: 2434


title: 2446


title: 2440


title: 2447


title: 2435


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title: 2433


title: 2438


title: 2442


title: 2443


title: 2430


title: 2432


title: 2437


title: 2431


title: 2441


title: 2424


title: 2426


title: 2428


title: 2425


title: 2427


title: 2429


title: 2423


title: 2421


title: 2422


title: 2419


title: 2420


title: 2411


title: 2415


title: 2410


title: 2413


title: 2418


title: 2416


title: 2409


title: 2414


title: 2404


title: 2406


title: 2403


title: 2439


title: 2405


title: 2401


title: 2412


title: 2407


title: 2400


title: 2402


title: 2398


title: 2478


title: 2399


title: 2417


title: 2491


title: 2397


title: 2391


title: 2396


title: 2392


title: 2394


title: 2390


title: 2393


title: 2386


title: 2395


title: 2389


title: 2385


title: 2382


title: 2383


title: 2384


title: 2379


title: 2381


title: 2387


title: 2380


title: 2374


title: 2375


title: 2377


title: 2372


title: 2376


title: 2373


title: 2371


title: 2367


title: 2368


title: 2369


title: 2366


title: 2364


title: 2365


title: 2370


title: 2357


title: 2362


title: 2378


title: 2358


title: 2361


title: 2363


title: 2354


title: 2353


title: 2356


title: 2351


title: 2350


title: 2345


title: 2355


title: 2342


title: 2348


title: 2359


title: 2349


title: 2346


title: 2344


title: 2347


title: 2338


title: 2340


title: 2335


title: 2339


title: 2341


title: 2337


title: 2336


title: 2332


title: 2343


title: 2334


title: 2333


title: 2330


title: 2331


title: 2448


title: 2328


title: 2327


title: 2329


title: 2326


title: 2325


title: 2324


title: 2321


title: 2323


title: 2319


title: 2320


title: 2408


title: 2317


title: 2312


title: 2318


title: 2303


title: 2306


title: 2315


title: 2307


title: 2313


title: 2310


title: 2311


title: 2309


title: 2316


title: 2360


title: 2305


title: 2301


title: 2314


title: 2352


title: 2304


title: 2300


title: 2299


title: 2298


title: 2302


title: 2297


title: 2296


title: 2295


title: 2294


title: 2291


title: 2293


title: 2290


title: 2388


title: 2289


title: 2284


title: 2287


title: 2279


title: 2283


title: 2282


title: 2277


title: 2281


title: 2275


title: 2285


title: 2276


title: 2286


title: 2274


title: 2280


title: 2270


title: 2271


title: 2288


title: 2272


title: 2273


title: 2269


title: 2266


title: 2268


title: 2265


title: 2263


title: 2267


title: 2308

description: NAAR CP-A9-B2-8290-111


title: 2262


title: 2259


title: 2258


title: 2261


title: 2257


title: 2252


title: 2256


title: 2247


title: 2254


title: 2249


title: 2244


title: 2243


title: 2253


title: 2251


title: 2250


title: 2248


title: 2241


title: 2255


title: 2245


title: 2240


title: 2292


title: 2237


title: 2239


title: 2238


title: 2235


title: 2233


title: 2232


title: 2231


title: 2246


title: 2236


title: 2234


title: 2230


title: 2225


title: 2220


title: 2227


title: 2228


title: 2223


title: 2218


title: 2224


title: 2229


title: 2217


title: 2219


title: 2222


title: 2221


title: 2214


title: 2213


title: 2210


title: 2212


title: 2207


title: 2208


title: 2278


title: 2226


title: 2215


title: 2205


title: 2216


title: 2206


title: 2211


title: 2202


title: 2204


title: 2203


title: 2201


title: 2198


title: 2200


title: 2199


title: 2196


title: 2260


title: 2195


title: 2194


title: 2193


title: 2186


title: 2184


title: 2192


title: 2189


title: 2182


title: 2190


title: 2185


title: 2177


title: 2197


title: 2187


title: 2188


title: 2179


title: 2191


title: 2172


title: 2176


title: 2183


title: 2180


title: 2174


title: 2173


title: 2175


title: 2169


title: 2168


title: 2170


title: 2166


title: 2165


title: 2164


title: 2167


title: 2242


title: 2159


title: 2154


title: 2162


title: 2157


title: 2158


title: 2160


title: 2163


title: 2209


title: 2155


title: 2152


title: 2156


title: 2153


title: 2150


title: 2145


title: 2151


title: 2161


title: 2146


title: 2144


title: 2143


title: 2149


title: 2141


title: 2142


title: 2147


title: 2148


title: 2140


title: 2137


title: 2139


title: 2138


title: 2171


title: 2126


title: 2131


title: 2127


title: 2134


title: 2129


title: 2132


title: 2128


title: 2123


title: 2120


title: 2121


title: 2115


title: 2135


title: 2130


title: 2136


title: 2122


title: 2112


title: 2117


title: 2111


title: 2118


title: 2116


title: 2110


title: 2119


title: 2114


title: 2124


title: 2125


title: 2108


title: 2105


title: 2106


title: 2103


title: 2101


title: 2104


title: 2102


title: 2095


title: 2097


title: 2099


title: 2096


title: 2094


title: 2098


title: 2133


title: 2089


title: 2092


title: 2093


title: 2090


title: 2087


title: 2088


title: 2091


title: 2086


title: 2085


title: 2084


title: 2080


title: 2081


title: 2082


title: 2083


title: 2079


title: 2077


title: 2075


title: 2078


title: 2074


title: 2073


title: 2072


title: 2070


title: 2071


title: 2076


title: 2069


title: 2068


title: 2067


title: 2058


title: 2062


title: 2063


title: 2057


title: 2065


title: 2054


title: 2049


title: 2066


title: 2053


title: 2064


title: 2052


title: 2047


title: 2050

description: NAAR CP-A8-C8-8228-203


title: 2061


title: 2059


title: 2060


title: 2055

description: NAAR CP-H7-B8-8225-101


title: 2056


title: 2045


title: 2051


title: 2046


title: 2048


title: 2043


title: 2100


title: 2044


title: 2042


title: 2041


title: 2038


title: 2037


title: 2036


title: 2033


title: 2040


title: 2028


title: 2032


title: 2023


title: 2035


title: 2039


title: 2030


title: 2018


title: 2107


title: 2034


title: 2027


title: 2019


title: 2025


title: 2022


title: 2020


title: 2017


title: 2109


title: 2031


title: 2026


title: 2015


title: 2013


title: 2021


title: 2010


title: 2011


title: 2016


title: 2006


title: 2002


title: 2012


title: 2005


title: 2009


title: 2008


title: 1998


title: 1994


title: 2000


title: 1996


title: 1993


title: 2014


title: 1997


title: 1999


title: 1995


title: 2007


title: 2001


title: 1987

description: NAAR CP-A6-B8-8130-101


title: 1988


title: 1986


title: 1992


title: 1989


title: 2029


title: 1984


title: 1991


title: 1983


title: 1985

description: NAAR CP-A2-F7-8092-101_2


title: 1981

description: NAAR CP-H4-A7-8126-111


title: 1978


title: 1977


title: 1982


title: 2024


title: 1980


title: 1976


title: 1979


title: 1975


title: 2004


title: 1973


title: 1972


title: 1970


title: 1971


title: 1969


title: 1968


title: 1965


title: 1966


title: 1964


title: 1962


title: 1967


title: 1963


title: 1959


title: 1974


title: 1951


title: 1960


title: 1958


title: 1955


title: 1952


title: 1953


title: 1954


title: 1949


title: 1947


title: 1956


title: 1950


title: 1961


title: 1944


title: 1945


title: 1948


title: 1943


title: 1940


title: 1942


title: 1941


title: 1946


title: 1939


title: 1936


title: 1938


title: 1934


title: 1929


title: 1933


title: 1928


title: 1931


title: 1937


title: 1930


title: 1924


title: 1935


title: 1932


title: 1957

description: NAAR CP-H5-B7-8128-203


title: 1925


title: 1917


title: 1916


title: 1921


title: 1915


title: 1923


title: 1926


title: 1922


title: 1927


title: 1920


title: 1919


title: 1990


title: 1918


title: 1914


title: 1910


title: 1911


title: 1909


title: 1913


title: 1908


title: 1907


title: 1912


title: 1902


title: 1903


title: 1904


title: 1906


title: 1905


title: 1900


title: 1899


title: 1891


title: 1901


title: 1898


title: 1896


title: 1886


title: 1897


title: 1893


title: 1895


title: 1888


title: 1890


title: 1892


title: 1887


title: 1894


title: 1889


title: 1883


title: 1881


title: 1882


title: 1879


title: 1878


title: 1885


title: 1884


title: 1880


title: 1877


title: 1870


title: 1867


title: 1871


title: 1862


title: 1865


title: 1875


title: 1858


title: 1873


title: 1863


title: 1872


title: 1876


title: 1869


title: 1874


title: 1868


title: 1866


title: 1861


title: 1859


title: 1860


title: 1864


title: 1857


title: 1855


title: 1852


title: 1853


title: 1849


title: 1851


title: 1850


title: 1856


title: 1848


title: 1843


title: 1842


title: 1837


title: 1839


title: 1845


title: 1833


title: 1838


title: 1834


title: 1846


title: 1835


title: 1844


title: 1840


title: 1832


title: 1841


title: 1836


title: 1831


title: 1829


title: 1823


title: 1825


title: 1820


title: 1822


title: 1854


title: 1826


title: 1830


title: 1824


title: 1847


title: 1821


title: 1827


title: 1819


title: 1818


title: 1816


title: 1817


title: 1815


title: 1804


title: 1814


title: 1794

description: NAAR CP-D3-D10-8109-202


title: 1812


title: 1809


title: 1811


title: 1802


title: 1801


title: 1805


title: 1810


title: 1800


title: 1792

description: NAAR CP-G7-A10-8162-201


title: 1803


title: 1807


title: 1795


title: 1797


title: 1796


title: 1806


title: 1799


title: 1793


title: 1808


title: 1798


title: 1813


title: 1789


title: 1790


title: 1788


title: 1791


title: 1786


title: 1785


title: 1783


title: 1828


title: 1784


title: 1787


title: 1781


title: 1764


title: 1776


title: 1771


title: 1767


title: 1779


title: 1770


title: 1775


title: 1777


title: 1768


title: 1782


title: 1773


title: 1774


title: 1772


title: 1769


title: 1780


title: 1765


title: 1778


title: 1759


title: 1761


title: 1763


title: 1762


title: 1760


title: 1757


title: 1756


title: 1753


title: 1755


title: 1736


title: 1742


title: 1754


title: 1744


title: 1737


title: 1739


title: 1747


title: 1748


title: 1752


title: 1749


title: 1758


title: 1741


title: 1738


title: 1745


title: 1740


title: 1750


title: 1743


title: 1735


title: 1751


title: 1731


title: 1733


title: 1730


title: 1766


title: 1728


title: 1734


title: 1729


title: 1726


title: 1727


title: 1722


title: 1723


title: 1716


title: 1715


title: 1720


title: 1721


title: 1717


title: 1718


title: 1713


title: 1725


title: 1710


title: 1732


title: 1711


title: 1719


title: 1708


title: 1712


title: 1724


title: 1714


title: 1707


title: 1706


title: 1701


title: 1699


title: 1702


title: 1700


title: 1697


title: 1709


title: 1705


title: 1704


title: 1698


title: 1693


title: 1688

description: NAAR CP-G4-G11-8120-111


title: 1689


title: 1703


title: 1694


title: 1692


title: 1682


title: 1695


title: 1677


title: 1679


title: 1672


title: 1691


title: 1680


title: 1696


title: 1684


title: 1687


title: 1690


title: 1674


title: 1685


title: 1678


title: 1670


title: 1683


title: 1676


title: 1675


title: 1686


title: 1681


title: 1671


title: 1669


title: 1330


title: 1668


title: 1667


title: 1673


title: 1332


title: 1331


title: 1666

description: NAAR CP-B7-F9-8213-101


title: 1325


title: 1329


title: 1324


title: 1320


title: 1326


title: 1322


title: 1321


title: 1328


title: 1323


title: 1318


title: 1317


title: 1315


title: 1316


title: 1306


title: 1310


title: 1311


title: 1327


title: 1313


title: 1308


title: 1303


title: 1304


title: 1309


title: 1314


title: 1300


title: 1307


title: 1319


title: 1302


title: 1312


title: 1301


title: 1298

description: NAAR CP-D4-D11-8110-101


title: 1305


title: 1295


title: 1297


title: 1296


title: 1293


title: 1294


title: 1299


title: 1291


title: 1292


title: 1289


title: 1287


title: 1288


title: 1284


title: 1281


title: 1286


title: 1290


title: 1283


title: 1280


title: 1279


title: 1285


title: 1276


title: 1282


title: 1272


title: 1278


title: 1265


title: 1260


title: 1270


title: 1271


title: 1258


title: 1268


title: 1261


title: 1273


title: 1264


title: 1274


title: 1267


title: 1277


title: 1266


title: 1259


title: 1269


title: 1257


title: 1262


title: 1254


title: 1253


title: 1275


title: 1263


title: 1256


title: 1255


title: 1252


title: 1246


title: 1251


title: 1247


title: 1243


title: 1248


title: 1241


title: 1242


title: 1238


title: 1249


title: 1245


title: 1244


title: 1250


title: 1237


title: 1234


title: 1232


title: 1235


title: 1236


title: 1240


title: 1230


title: 1227


title: 1231


title: 1226


title: 1225


title: 1224


title: 1229


title: 1228


title: 1239


title: 1233


title: 1218


title: 1223


title: 1221


title: 1222


title: 1214


title: 1211


title: 1217


title: 1215


title: 1208


title: 1219


title: 1213


title: 1209

description: NAAR CP-H3-H10-8123-203


title: 1216


title: 1220


title: 1203


title: 1210


title: 1207


title: 1212


title: 1205


title: 1202


title: 1200


title: 1199


title: 1204


title: 1206


title: 1195


title: 1201


title: 1196


title: 1197


title: 1189


title: 1186


title: 1194


title: 1190


title: 1181


title: 1191


title: 1184


title: 1185


title: 1198


title: 1174


title: 1193


title: 1173

description: NAAR CP-C2-B4-8102-111_2


title: 1187


title: 1180


title: 1176


title: 1175


title: 1178


title: 1179


title: 1192


title: 1177


title: 1182


title: 1183


title: 1188


title: 1172


title: 1170


title: 1171


title: 1167


title: 1168


title: 1169


title: 1164


title: 1165


title: 1163


title: 1166


title: 1150


title: 1157


title: 1151


title: 1153


title: 1143


title: 1141


title: 1147


title: 1162


title: 1154


title: 1161


title: 1142


title: 1156


title: 1152


title: 1140


title: 1155


title: 1146


title: 1159


title: 1145


title: 1149


title: 1158


title: 1148


title: 1138


title: 1128


title: 1144


title: 1123


title: 1139


title: 1125


title: 1133


title: 1121


title: 1134


title: 1136


title: 1135


title: 1131


title: 1160


title: 1129

description: NAAR CP-D6-C7-8132-201


title: 1126


title: 1130


title: 1137


title: 1119


title: 1124


title: 1127


title: 1132


title: 1114


title: 1122


title: 1117


title: 1115


title: 1112


title: 1116


title: 1118


title: 1111


title: 1109


title: 1105


title: 1104


title: 1108


title: 1093


title: 1110


title: 1102


title: 1103


title: 1098


title: 1107


title: 1097


title: 1096


title: 1094


title: 1091


title: 1106


title: 1090


title: 1120


title: 1088


title: 1095


title: 1100


title: 1084


title: 1099


title: 1087


title: 1089


title: 1101


title: 1086


title: 1080


title: 1081


title: 1083


title: 1077


title: 1076


title: 1078


title: 1071


title: 1070


title: 1074


title: 1082


title: 1075


title: 1072


title: 1069


title: 1066


title: 1113


title: 1065


title: 1073


title: 1061


title: 1062


title: 1060


title: 1064


title: 1059


title: 1058


title: 1057


title: 1063


title: 1085


title: 1079


title: 1055


title: 1056


title: 1051


title: 1053


title: 1050


title: 1046


title: 1054


title: 1048


title: 1043


title: 1049


title: 1047


title: 1052


title: 1040


title: 1045


title: 1031


title: 1037


title: 1032


title: 1044


title: 1042


title: 1035


title: 1039


title: 1067


title: 1033


title: 1038


title: 1041


title: 1034


title: 1030


title: 1025


title: 1026


title: 1028


title: 1027


title: 1029


title: 1021


title: 1022


title: 1023


title: 1017


title: 1016


title: 1019


title: 1012


title: 1014


title: 1007


title: 1013


title: 1010


title: 1018


title: 1004


title: 1006


title: 1011


title: 1015


title: 1003


title: 1002


title: 1024


title: 1008


title: 1001


title: 1005


title: 1020


title: 1000


title: 1009


title: 999


title: 1664


title: 1661


title: 1663


title: 1659


title: 1660


title: 1658


title: 1665


title: 1655


title: 1653


title: 1650


title: 1654


title: 1651


title: 1652


title: 1648


title: 1645


title: 1662


title: 1641


title: 1643


title: 1656


title: 1657


title: 1649


title: 1640


title: 1639


title: 1644


title: 1036


title: 1647


title: 1646


title: 1638


title: 1642


title: 1637


title: 1636


title: 1635


title: 1632


title: 1634


title: 1633


title: 1629


title: 1631


title: 1630


title: 1628


title: 1623


title: 1627


title: 1625


title: 1618


title: 1611


title: 1615


title: 1626


title: 1613


title: 1619


title: 1624


title: 1614


title: 1622


title: 1612


title: 1620


title: 1617


title: 1609


title: 1608


title: 1616


title: 1621

description: NAAR CP-E3-E10-8112-201


title: 1602


title: 1607


title: 1603


title: 1598


title: 1606


title: 1605


title: 1599


title: 1596


title: 1601


title: 1610


title: 1597


title: 1595


title: 1600


title: 1604


title: 1593


title: 1591


title: 1584


title: 1590


title: 5743


title: 1588


title: 1589


title: 1594


title: 1585


title: 1586


title: 1583


title: 1592


title: 1579


title: 1578


title: 1580


title: 1581


title: 1582


title: 1574


title: 1569


title: 1566


title: 1571


title: 1570


title: 1575


title: 1568


title: 1573


title: 1587


title: 1572


title: 1561


title: 1557


title: 1567


title: 1562


title: 1558


title: 1576


title: 1559


title: 1563


title: 1564


title: 1556


title: 1552


title: 1551


title: 1555


title: 1560


title: 1577


title: 1546


title: 1548


title: 1542


title: 1554


title: 1538


title: 1549


title: 1541


title: 1544


title: 1553


title: 1547


title: 1537


title: 1539


title: 1545


title: 1550


title: 1540


title: 1535


title: 1533


title: 1536


title: 1534


title: 1531


title: 1526


title: 1532


title: 1530


title: 1522


title: 1527


title: 1543


title: 1525


title: 1517


title: 1520


title: 1529


title: 1515


title: 1519


title: 1528


title: 1523


title: 1524


title: 1518


title: 1521


title: 1516


title: 1513


title: 1512


title: 1514


title: 1509


title: 1511


title: 1565


title: 1507


title: 1506


title: 1510


title: 1500


title: 1501


title: 1508


title: 1505


title: 1503


title: 1502


title: 1498


title: 1487


title: 1497


title: 1495


title: 1496


title: 1499


title: 1504


title: 1481


title: 1492


title: 1493


title: 1494


title: 1489


title: 1488


title: 1491


title: 1486


title: 1482


title: 1490


title: 1485


title: 1477


title: 1480


title: 1484


title: 1479


title: 1483


title: 1475


title: 1478


title: 1474


title: 1473


title: 1463


title: 1470


title: 1476


title: 1460


title: 1466


title: 1468


title: 1472


title: 1469


title: 1461


title: 1457


title: 1462


title: 1465


title: 1464


title: 1471


title: 1456


title: 1455


title: 1450


title: 1467


title: 1458


title: 1459


title: 1448


title: 1449


title: 1454


title: 1451


title: 1443


title: 1453


title: 1445


title: 1452


title: 1444


title: 1447


title: 1436


title: 1446


title: 1431


title: 1439


title: 1442


title: 1441


title: 1433


title: 1434


title: 1432


title: 1438


title: 1428


title: 1435


title: 1430


title: 1419


title: 1424


title: 1421


title: 1426


title: 1429


title: 1423


title: 1418


title: 1425


title: 1416


title: 1420


title: 1414


title: 1415


title: 1427


title: 1422


title: 1437


title: 1417


title: 1412


title: 1406


title: 1405


title: 1411


title: 1410


title: 1407


title: 1409


title: 1396

description: NAAR CP-E5-E12-8113-101


title: 1402


title: 1408


title: 1399


title: 1404


title: 1397


title: 1403


title: 1401


title: 1413


title: 1391


title: 1393


title: 1392


title: 1400


title: 1390


title: 1398


title: 1387


title: 1395


title: 1382


title: 1385


title: 1394


title: 1383


title: 1388


title: 1389


title: 1386


title: 1384


title: 1378


title: 1376


title: 1380


title: 1381


title: 1373


title: 1366


title: 1365


title: 1379


title: 1377


title: 1372


title: 1368


title: 1375


title: 1360


title: 1362


title: 1371


title: 1356


title: 1367


title: 1361


title: 1354


title: 1357


title: 1364


title: 1374


title: 1370


title: 1358


title: 1369


title: 1355


title: 1359


title: 1363


title: 1353


title: 1352


title: 1349


title: 1350


title: 1351


title: 1348


title: 1347


title: 1344


title: 665


title: 1339


title: 1341


title: 1333


title: 664


title: 662


title: 1346


title: 1342


title: 1334


title: 1337


title: 1343


title: 1336


title: 658


title: 1345


title: 1340


title: 1335


title: 653


title: 1338


title: 661


title: 663


title: 659


title: 654


title: 657


title: 660


title: 655


title: 656


title: 651


title: 648


title: 642


title: 637


title: 638


title: 649


title: 644


title: 630


title: 632


title: 652


title: 650


title: 647


title: 1440


title: 645


title: 643


title: 646


title: 641


title: 640


title: 636


title: 625


title: 621


title: 639


title: 626


title: 622


title: 624


title: 631


title: 633


title: 618


title: 619


title: 620


title: 617


title: 634


title: 629


title: 635


title: 627


title: 615


title: 628


title: 623


title: 609


title: 616


title: 610


title: 605


title: 614


title: 600


title: 611


title: 607


title: 613


title: 602


title: 608


title: 612


title: 604


title: 595


title: 603


title: 598


title: 589


title: 593


title: 601


title: 596


title: 597


title: 587


title: 592


title: 590


title: 594


title: 588


title: 599


title: 591


title: 576


title: 580


title: 585


title: 584


title: 581


title: 583


title: 582


title: 571


title: 574


title: 578


title: 569


title: 572


title: 577


title: 562


title: 557


title: 566


title: 559


title: 561


title: 556


title: 567


title: 573


title: 555


title: 586


title: 564


title: 570


title: 568


title: 563


title: 575


title: 549


title: 554


title: 560


title: 553


title: 558


title: 552


title: 565


title: 551


title: 548


title: 550


title: 546


title: 538


title: 534


title: 544


title: 547


title: 542


title: 545


title: 539


title: 540


title: 541


title: 535


title: 532


title: 537


title: 543


title: 536


title: 531


title: 533


title: 526


title: 529


title: 522


title: 520


title: 525


title: 523


title: 530


title: 528


title: 519


title: 524


title: 527


title: 521


title: 517


title: 518


title: 516


title: 515


title: 512


title: 510


title: 514


title: 505


title: 507


title: 511


title: 506


title: 513


title: 508


title: 509


title: 502


title: 496


title: 500


title: 501


title: 503


title: 495


title: 499


title: 494


title: 489


title: 498


title: 491


title: 493


title: 487


title: 497


title: 484


title: 492


title: 478


title: 477

description: NAAR CP-E4-E11-8112-202


title: 485


title: 490


title: 480


title: 488


title: 470


title: 462


title: 461


title: 474


title: 486


title: 465


title: 483


title: 459


title: 482


title: 468


title: 481


title: 471


title: 476


title: 472


title: 475


title: 455


title: 469


title: 451


title: 473


title: 479


title: 450


title: 452


title: 466


title: 467


title: 464


title: 463


title: 448


title: 457


title: 453


title: 460


title: 436


title: 438


title: 458


title: 446


title: 443


title: 456


title: 454


title: 433


title: 440


title: 428


title: 430


title: 437


title: 432


title: 441


title: 442


title: 445


title: 447


title: 449


title: 444


title: 426


title: 435


title: 434


title: 439


title: 431


title: 429


title: 421


title: 418


title: 424


title: 414


title: 417


title: 427


title: 425


title: 416


title: 423


title: 420


title: 419


title: 422


title: 415


title: 413


title: 408


title: 410


title: 403


title: 406


title: 409


title: 401


title: 404


title: 407


title: 411


title: 396


title: 405


title: 402


title: 399


title: 394


title: 400


title: 395


title: 412


title: 391


title: 390


title: 389


title: 398


title: 393


title: 392


title: 384


title: 388


title: 385


title: 397


title: 386


title: 387


title: 382


title: 378


title: 373


title: 383


title: 381


title: 376


title: 372


title: 375


title: 371


title: 377


title: 379


title: 370


title: 368


title: 374


title: 380


title: 362


title: 369


title: 366


title: 363


title: 364


title: 361


title: 358


title: 365


title: 359


title: 357


title: 353


title: 360


title: 355


title: 354


title: 352


title: 367


title: 349


title: 351


title: 356


title: 350


title: 344


title: 347


title: 342


title: 345


title: 341


title: 346


title: 340


title: 339


title: 343


title: 348


title: 338


title: 998


title: 336


title: 335


title: 996


title: 333


title: 997


title: 995


title: 334


title: 993


title: 989


title: 986


title: 991


title: 981


title: 990


title: 987


title: 982


title: 988


title: 978


title: 985


title: 973


title: 977


title: 994


title: 992


title: 983


title: 337


title: 970


title: 968


title: 976


title: 963

description: NAAR CP-B9-C5-8293-202


title: 975


title: 984


title: 980


title: 974


title: 954


title: 972


title: 979


title: 953


title: 959


title: 956


title: 955


title: 952


title: 965


title: 946


title: 960


title: 947


title: 958


title: 971


title: 948


title: 950


title: 966


title: 961


title: 945


title: 969


title: 949


title: 964


title: 951


title: 957


title: 967


title: 962


title: 944


title: 940


title: 941


title: 943


title: 935


title: 939


title: 937


title: 938


title: 942


title: 934


title: 936


title: 932


title: 925


title: 930


title: 923


title: 920


title: 926


title: 928


title: 927


title: 929


title: 921


title: 918


title: 919


title: 915


title: 916


title: 931


title: 933


title: 914


title: 922


title: 924


title: 917


title: 911


title: 913


title: 910


title: 908


title: 912


title: 909


title: 907


title: 906


title: 903


title: 904


title: 902


title: 901


title: 905


title: 895


title: 899


title: 894


title: 888


title: 897


title: 889


title: 892


title: 896


title: 893


title: 891


title: 900


title: 878


title: 886


title: 882


title: 887


title: 883


title: 885


title: 880


title: 877


title: 884


title: 879


title: 881


title: 890


title: 898


title: 876


title: 875


title: 873


title: 870


title: 872


title: 867


title: 869


title: 864


title: 862


title: 865


title: 866


title: 871


title: 859


title: 860


title: 861


title: 863


title: 850


title: 857


title: 856


title: 868


title: 854


title: 874


title: 852


title: 851


title: 847


title: 849


title: 858


title: 845


title: 855


title: 853


title: 848


title: 846


title: 843


title: 842


title: 844


title: 841


title: 840


title: 839


title: 838


title: 836


title: 835


title: 832


title: 833


title: 834


title: 823


title: 827


title: 831


title: 818


title: 826


title: 828


title: 816


title: 817


title: 821


title: 822


title: 829


title: 824


title: 813


title: 820


title: 819


title: 830


title: 825


title: 814


title: 811


title: 815


title: 812


title: 808


title: 805


title: 810


title: 806


title: 809


title: 803


title: 804


title: 807


title: 837


title: 799


title: 802


title: 793


title: 794


title: 797


title: 800


title: 792


title: 801


title: 785


title: 777


title: 782


title: 779


title: 784


title: 795


title: 783


title: 789


title: 796


title: 790


title: 791


title: 786


title: 780


title: 798


title: 787


title: 781


title: 778


title: 767


title: 776


title: 775


title: 773


title: 774


title: 768


title: 765


title: 762


title: 766


title: 771


title: 769


title: 772


title: 770


title: 764


title: 752


title: 749


title: 755


title: 757


title: 750


title: 759


title: 753


title: 747


title: 763


title: 761


title: 760


title: 751


title: 756


title: 739


title: 754


title: 748


title: 746


title: 738


title: 744


title: 743


title: 742


title: 737


title: 740


title: 745


title: 741


title: 736


title: 735


title: 758


title: 734


title: 731


title: 729


title: 730


title: 733


title: 727


title: 732


title: 728


title: 713


title: 723


title: 718


title: 720


title: 705


title: 711


title: 724


title: 709


title: 725


title: 722


title: 721


title: 715


title: 712


title: 707


title: 717


title: 714


title: 708


title: 719


title: 726


title: 710


title: 703


title: 716


title: 704


title: 699


title: 702


title: 700


title: 701


title: 696


title: 697


title: 698


title: 695


title: 692


title: 684


title: 679


title: 687


title: 683


title: 682


title: 691


title: 681


title: 678


title: 677


title: 690


title: 676


title: 680


title: 688


title: 694


title: 675


title: 693


title: 689


title: 685


title: 686


title: 669


title: 668


title: 670


title: 671


title: 674


title: 666


title: 673


title: 672


title: 667


title: 331


title: 332


title: 326


title: 330


title: 329


title: 325


title: 314


title: 328


title: 318


title: 312


title: 327


title: 320


title: 323


title: 317


title: 313


title: 324

description: NAAR CP-F6-D12-8140-201


title: 322


title: 316


title: 315


title: 319


title: 321


title: 311


title: 307


title: 308


title: 310


title: 303


title: 302


title: 304


title: 305


title: 306


title: 301


title: 309


title: 299


title: 300


title: 295


title: 297


title: 288


title: 293


title: 283


title: 291


title: 290


title: 298


title: 296


title: 289


title: 279


title: 294


title: 271


title: 273


title: 274


title: 292


title: 285


title: 278


title: 287


title: 280


title: 286


title: 276


title: 284


title: 277


title: 272


title: 275


title: 281


title: 282


title: 270


title: 269


title: 267


title: 265


title: 268


title: 258


title: 264


title: 266


title: 263


title: 261


title: 255


title: 249


title: 257


title: 250


title: 244


title: 254


title: 247


title: 262


title: 253


title: 248


title: 251


title: 243


title: 259


title: 256


title: 246


title: 241


title: 242


title: 240


title: 260


title: 234


title: 235


title: 239


title: 236


title: 225


title: 237


title: 232


title: 230


title: 227


title: 219


title: 222


title: 228


title: 233


title: 226


title: 245


title: 220


title: 223


title: 229


title: 218


title: 252


title: 212


title: 231


title: 213


title: 217


title: 215


title: 216


title: 221


title: 209


title: 208


title: 224


title: 214


title: 211


title: 210


title: 206


title: 238


title: 200


title: 195


title: 207


title: 204


title: 201


title: 194


title: 202


title: 203


title: 205


title: 199


title: 185


title: 188


title: 196


title: 193


title: 198


title: 190


title: 189


title: 184


title: 187


title: 191


title: 192


title: 197


title: 186


title: 183


title: 181


title: 178


title: 177


title: 182


title: 174


title: 179


title: 172


title: 180


title: 176


title: 171


title: 166


title: 173


title: 169


title: 168


title: 161


title: 167


title: 163


title: 175


title: 160


title: 170


title: 165


title: 164


title: 159

description: NAAR CP-D8-F1-8240-101


title: 158


title: 156


title: 153


title: 154


title: 162


title: 157


title: 152


title: 155


title: 150


title: 148


title: 149


title: 145


title: 146


title: 151


title: 142


title: 131


title: 135


title: 141


title: 130


title: 147


title: 138


title: 143


title: 133


title: 134


title: 136


title: 137

description: NAAR CP-C9-D7-8300-202


title: 144


title: 139


title: 126


title: 129


title: 125


title: 124


title: 122


title: 123


title: 116


title: 118


title: 120


title: 121


title: 132


title: 128


title: 127


title: 119


title: 117


title: 140


title: 990375T

city: Singapore

first: wei

last: chen

address: 11 Hospital Drive

country: Singapore

institute: Agenica Research Pte Ltd

description: SNP profiling for breast tumors

hyb_protocol: Following Manufactruer's protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000

data_processing: The data were analyzed Dchip software for normalization and expression estimation

label: biotinylated dideoxy ATP

source_name: Breast Tumor

label_protocol: biotinylated dideoxy ATP is terminal deoxynucleotidyl transferased

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions.

tag: Tissue

value: Breast


title: 114


title: 990113T

description: SNP profiling for breast tumors


title: 990082T

description: SNP profiling for breast tumors


title: 112


title: 980383T

description: SNP profiling for breast tumors


title: 115


title: 109


title: 110


title: 107


title: 113


title: 980338T

description: SNP profiling for breast tumors


title: 111


title: 990075T

description: SNP profiling for breast tumors


title: 980216T

description: SNP profiling for breast tumors


title: 980214T

description: SNP profiling for breast tumors


title: 104


title: 980346T

description: SNP profiling for breast tumors


title: 103


title: 980197T

description: SNP profiling for breast tumors


title: 980404T

description: SNP profiling for breast tumors


title: 105


title: 106


title: 20020158T

description: SNP profiling for breast tumors


title: 20020160T

description: SNP profiling for breast tumors


title: 108


title: 980247T

description: SNP profiling for breast tumors


title: 980217T

description: SNP profiling for breast tumors


title: 100


title: 99


title: 101


title: 20020071T

description: SNP profiling for breast tumors


title: 94


title: 2000804T

description: SNP profiling for breast tumors


title: 98


title: 20020041T

description: SNP profiling for breast tumors


title: 96


title: 20020051T

description: SNP profiling for breast tumors


title: 2000787T

description: SNP profiling for breast tumors


title: 97


title: 91


title: 2000779T

description: SNP profiling for breast tumors


title: 89


title: 95


title: 20020056T

description: SNP profiling for breast tumors


title: 102


title: 2000215T

description: SNP profiling for breast tumors


title: 88


title: 92


title: 90


title: 2000237T

description: SNP profiling for breast tumors


title: 2000376T

description: SNP profiling for breast tumors


title: 2000420T

description: SNP profiling for breast tumors


title: 87


title: 2000155T

description: SNP profiling for breast tumors

value: lymphocytes


title: 2000209T

description: SNP profiling for breast tumors


title: 93


title: 2000731T

description: SNP profiling for breast tumors


title: 86


title: 81


title: 82


title: Male normal lymphocytes 3

description: SNP profiling for normal lymphocytes

source_name: Male donator


title: Male normal lymphocytes 1

description: SNP profiling for normal lymphocytes


title: Male normal lymphocytes 2

description: SNP profiling for normal lymphocytes


title: 84


title: Male normal lymphocytes 4

description: SNP profiling for normal lymphocytes


title: 79


title: Prostate tumor metastases in para tracheal lymph node EB667LNPT4_Uniset20K

type: RNA

city: Houston

first: Federico

middle: Alberto

last: Monzon

state: TX

address: 6565 Fannin St, MS205

department: Pathology

country: USA

institute: The Methodist Hospital

description: CodeLink gene expression data from metastatic prostate tumor samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr at 37C on Human Uniset 20K arrays (GE Healthcare, Piscataway, NJ). Arrays were washed and stained according to the standard CodeLink manual.

scan_protocol: CodeLink arrays were scanned with the GenePix 4000B scanner using GenePix Pro 4.1 software.

data_processing: For CodeLink arrays, image files were analyzed with the CodeLink Expression Analysis Software version 4.1 (GE HealthCare) with use of the normalized intensity values in downstream analysis.

label: biotin

molecule: total RNA

source_name: EB667LNPT4, metastatic prostate tumor samples in para tracheal lymph node from patient EB667

label_protocol: Biotinylated cRNA were prepared according to the standard CodeLink protocol from 1 ug total RNA.

extract_protocol: Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Specimens were received directly from the operating room. Samples (>500 mg) were excised and snap frozen in liquid nitrogen within 30 min of excision and stored at -80°C until extraction of RNA. Metastatic tumor samples were obtained from a warm autopsy program and processed similarly to primary tumors. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Dissection of the frozen tissue block was performed with the guidance of a marked H & E slide to minimize the presence of host tissue in the metastatic samples. All samples used in the study contained >80% tumor. Metastatic tumor samples were minced and divided into two equal portions to be extracted with the sample protocol used for each set of primary tumors.

value: prostate tumor metastases in para tracheal lymph node


title: Prostate tumor metastases in retroperitoneal lymph node FB561LNRP2_Uniset20K

source_name: FB561LNRP2, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561

value: prostate tumor metastases in retroperitoneal lymph node


title: 83


title: Female normal lymphocytes 1

description: SNP profiling for normal lymphocytes

source_name: Female donator


title: Female normal lymphocytes 4

description: SNP profiling for normal lymphocytes


title: 78


title: Breast normal sample 4

description: SNP profiling for normal breast tissue

source_name: Cosmetic Surgery for breast


title: 76


title: Breast normal sample 1

description: SNP profiling for normal breast tissue


title: Breast normal sample 3

description: SNP profiling for normal breast tissue


title: Breast normal sample 2

description: SNP profiling for normal breast tissue


title: Prostate tumor metastases in para tracheal lymph node EB667LNPT3_Uniset20K

source_name: EB667LNPT3, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: 74


title: 77


title: Female normal lymphocytes 2

description: SNP profiling for normal lymphocytes


title: Female normal lymphocytes 3

description: SNP profiling for normal lymphocytes


title: 80


title: 85


title: 73


title: 75


title: Prostate tumor metastases in liver FB561LI2_Uniset20K

source_name: FB561LI2, metastatic prostate tumor samples in liver from patient FB561

value: prostate tumor metastases in liver


title: Prostate tumor metastases in para tracheal lymph node EB561LNPT2_Uniset20K

source_name: FB561LNPT2, metastatic prostate tumor samples in para tracheal lymph node from patient FB561


title: 72


title: 71


title: 69


title: Prostate tumor metastases in para tracheal lymph node EB667LNPT_Uniset20K

source_name: EB667LNPT, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: Prostate tumor metastases in para aortic lymph node FB561LNPA_Uniset20K

source_name: FB561LNPA, metastatic prostate tumor samples in para aortic lymph node from patient FB561

value: prostate tumor metastases in para aortic lymph node


title: Prostate tumor metastases in lung FB561LU_Uniset20K

source_name: FB561LU, metastatic prostate tumor samples in lung from patient FB561

value: prostate tumor metastases in lung


title: Prostate tumor metastases in para tracheal lymph node EB667LNPT5_Uniset20K

source_name: EB667LNPT5, metastatic prostate tumor samples in para tracheal lymph node from patient EB667


title: 66


title: 68


title: Prostate tumor metastases in left inguinal lymph node EB667LNIN_Uniset20K

source_name: EB667LNIN, metastatic prostate tumor samples in left inguinal lymph node from patient EB667

value: prostate tumor metastases in left inguinal lymph node


title: 70

description: NAAR CP-F1-D11-8087-201


title: Prostate tumor metastases in liver FB561LI_Uniset20K

source_name: FB561LI, metastatic prostate tumor samples in liver from patient FB561


title: 65


title: 64


title: Prostate tumor metastases in retroperitoneal lymph node EB667LNRP_Uniset20K

source_name: EB667LNRP, metastatic prostate tumor samples in retroperitoneal lymph node from patient EB667


title: Prostate tumor metastases in para aortic lymph node EB669LNPA_Uniset20K

source_name: EB669LNPA, metastatic prostate tumor samples in para aortic lymph node from patient EB669


title: 67

source_name: blood or lymphoblast


title: 62


title: Prostate tumor metastases in liver EB669LI2_Uniset20K

source_name: EB669LI2, metastatic prostate tumor samples in liver from patient EB669 2


title: Prostate tumor metastases in retroperitoneal lymph node FB561LNRP_Uniset20K

source_name: FB561LNRP, metastatic prostate tumor samples in retroperitoneal lymph node from patient FB561


title: Prostate tumor metastases in adrenal gland EB667AD2_Uniset20K

source_name: EB667AD2, metastatic prostate tumor samples in adrenal gland from patient EB667

value: prostate tumor metastases in adrenal gland


title: 59


title: Prostate tumor metastases in adrenal gland EB667AD_Uniset20K

source_name: EB667AD, metastatic prostate tumor samples in adrenal gland from patient EB667


title: 61


title: 60


title: 54


title: 58


title: Primary prostate tumor 04_0082_Uniset20K

description: CodeLink gene expression data from normal prostate tissues free of any pathological alteration

treatment_protocol: Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.

tag: Tissue:primary prostate tumor


title: Prostate tumor metastases in para tracheal lymph node FB561LNPT_Uniset20K

source_name: FB561LNPT, metastatic prostate tumor samples in para tracheal lymph node from patient FB561


title: Metastases recurrent in prostate FB561PR_Uniset20K

source_name: FB561PR, metastatic prostate tumor samples recurrent in prostate from patient FB561

value: metastases recurrent in prostate


title: 55


title: 56


title: Prostate tumor metastases in liver EB666LI_Uniset20K

source_name: EB666LI, metastatic prostate tumor samples in liver from patient EB666


title: 63


title: Prostate tumor metastases in liver EB669LI_Uniset20K

source_name: EB669LI, metastatic prostate tumor samples in liver from patient EB669


title: 51


title: 53


title: Primary prostate tumor 04_0087_Uniset20K


title: Primary prostate tumor 04_0083_Uniset20K


title: 57


title: Primary prostate tumor 04_0007_Uniset20K


title: Primary prostate tumor 04_0013_Uniset20K


title: 52


title: 49


title: 50


title: Primary prostate tumor 04_0008_Uniset20K


title: Primary prostate tumor 04_0006_Uniset20K

value: primary prostate tumor


title: Primary prostate tumor 04_0014_Uniset20K


title: Primary prostate tumor 04_0011_Uniset20K


title: 48


title: 45


title: 47


title: 44


title: 46


title: Primary prostate tumor 04_0012_Uniset20K


title: 41


title: 35


title: 40


title: 36


title: 43


title: 34


title: 24


title: 42


title: 30


title: 33


title: 39


title: 31


title: 22


title: 38


title: 26


title: 27


title: 19


title: 21


title: 28


title: 32


title: 20


title: 23


title: 29


title: 17


title: 16


title: 25


title: 13


title: 18


title: 37


title: 11


title: 14


title: 6


title: 7


title: 15


title: 12


title: 8


title: 3


title: 10


title: 4


title: 9


title: 5


title: 2


title: White adipose B6 wildtype Control Pool (n=19) vs. White adipose from Rosiglitazone treated mouse 3

status: Public on Feb 17 2007

city: Seattle

first: eric

middle: e

last: schadt

state: WA

address: 401 Terry Ave N

department: Genetics

institute: Merck

description: white adipose

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Mus musculus

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose ZFP90 transgenic female animal 1

description: 1002413_C_1 adipose


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose b6 wildtype male animal 1

description: 1002413_C_1 adipose

source_name: white adipose b6 wildtype male animal 1

tag: white adipose b6 wildtype male animal 1


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose b6 wildtype male animal 2

description: 1002413_C_1 adipose

source_name: white adipose b6 wildtype male animal 2

tag: white adipose b6 wildtype male animal 2


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose ZFP90 transgenic male animal 2

description: 1002413_C_1 adipose


title: White adipose B6 wildtype Control Pool (n=19) vs. White adipose from Rosiglitazone treated mouse 2

description: white adipose


title: 1


title: pool of liver from wildtype b6 mice on chow diet (n=5) vs. liver from diet induced obesity wildtype b6 animal 2

description: liver


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose b6 wildtype female animal 2

description: project 1 adipose

source_name: white adipose tissue


title: pool of liver from wildtype b6 mice on chow diet (n=5) vs. liver from diet induced obesity wildtype b6 animal 1

description: liver


title: pool of liver from wildtype b6 mice on chow diet (n=5) vs. liver from diet induced obesity wildtype b6 animal 5

description: liver


title: pool of liver from wildtype b6 mice on chow diet (n=5) vs. liver from diet induced obesity wildtype b6 animal 4

description: liver


title: White adipose B6 wildtype Control Pool (n=19) vs. White adipose from Rosiglitazone treated mouse 1

description: white adipose


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose ZFP90 transgenic male animal 1

description: 1002413_C_1 adipose


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose b6 wildtype female animal 3

description: project 1 adipose


title: Murray_2-10_T19-APH_Rep1_ATH1

status: Public on Feb 16 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description:
DNA replication inhibitor: aphidicolin
growth media type: liquid culture media
light regime: continuous darkness
nutrients: 100 ml MS salts, 3% sucrose, 0.5 mg/l NAA, 0.05 mg/l kinetin
average daily temperature: 27oC

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

organism: Arabidopsis thaliana

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T19 sample was taken at 19 hours after washing to release the block (exp. variable; time course).

tag: Developmental stage

value: early stationary phase

value: cell suspension


title: White adipose wildtype Control Pool males and females (n=5) vs. white adipose b6 wildtype female animal 1

description: project 1 adipose


title: HF001_AG_HF5

institute: Nottingham Arabidopsis Stock Centre (NASC)

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 92.64
Background Stdev (float) = 5.57
Background Max (float) = 106.6
Background Min (float) = 82.5
Noise Avg (float) = 3.22
Noise Stdev (float) = 0.38
Noise Max (float) = 4.1
Noise Min (float) = 2.5
RawQ (float) = 2.34
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 31
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: HF001_AG_HF5.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 1 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 236 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4497 (type integer); Parameter Upper right corner y coordinate = 218 (type integer); Parameter Lower right corner x coordinate = 4514 (type integer); Parameter Lower right corner y coordinate = 4483 (type integer); Parameter Lower left corner x coordinate = 252 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.718632 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

label_protocol: Preparation of biotin-labeled cRNA; RNA samples were quality controlled using the Agilent 2100 Bioanalyzer. 100 pmol T7-(dT)24 primer (5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3')  was hybridized with the Total RNA ( 8 - 12ug) at 70°C for 10 minutes. First strand cDNA was synthesized by reverse transcription using 400 units SuperScript II Reverse Transcriptase in a reaction containing 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiothreitol (DTT) and 0.5 mM dNTPs at 42C for 1 hour.  The reaction was then put on ice for 2 mins, followed by second strand cDNA synthesis.  130ul of the second strand reaction mix was added to the 20ul  first strand synthesis reaction. The second strand reaction mix  contained 40 units E. coli DNA polymerase I, 10 units E. coli DNA ligase, 2 units  E. coli RNase H and 0.2 mM dNTPs in a buffer containing 20 mMTris-HCl (pH 6.9), 90 mM KCl, 4.6 mM MgCl2, 10mM (NH4)SO4 and 0.15 mM ß-NAD+. The reaction was incubated at 16 C for 2 hours.  10 units T4 DNA Polymerase was added and the reaction incubated for a further 5 minutes at 16 C, then the reaction was terminated using EDTA.  The double-stranded cDNA was cleaned up using the cDNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The double-stranded cDNA was used as a template for in Vitro transcription of biotin-labeled cRNA using the ENZO BioArray RNA Transcript Labeling Kit supplied by Affymetrix.  The Transcript Labeling kit produces large amounts of hybridizable biotin-labeled RNA targets by in Vitro transcription from bacteriophage T7 RNA polymerase promoters.  The reaction mixture containing Biotin-Labeled ribonucleotides (ATP, GTP, CTP, UTP with Bio-UTP and Bio-CTP), DTT, RNase inhibitor mix and T7 RNA polymerase was incubated at 37 C for 5 hrs, gently mixing every 30 minutes during the incubation. This produced an average of 40ug biotin-labeled cRNA . The biotin-labeled cRNA  was cleaned up using the cRNA Cleanup Spin Column supplied in the Affymetrix GeneChip Sample Cleanup Module.  The quantity and quality of the cRNA was measured using the Agilent 2100 Bioanalyzer. The total amount of cRNA was calculated, the starting quantity of RNA subtracted to give the quantity of adjusted cRNA.  The cRNA was fragmented by metal-induced hydrolysis to break down full-length cRNA to 35-200 base fragments.  15ug of adjusted cRNA was used to prepare 300ul of hybridization cocktail of which 200ul was hybridized with the GeneChip.   ; Protocol Type = labeling; Performers: John,Y,Okyere, Janet,,Higgins

growth_protocol: unknown; Parameter location = Growth Room; Parameter Humidity = 65; Parameter Temperature = 18oC; Parameter Lighting = 16h light/8 hours dark; Parameter Medium = Gamborg's B-5 basal medium with minimal organics; Parameter Water = every other day.; Performer: Hillel,,Fromm

extract_protocol: TriZOL; Protocol:   ; Protocol Type = nucleic_acid_extraction; Performer: Hillel,,Fromm

tag: OrganismPart

value: whole plant

tag: Ecotype

value: WS

tag: NASC:Growth Stage


title: HF001_AG_HF3

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 64.86
Background Stdev (float) = 3.35
Background Max (float) = 75.3
Background Min (float) = 58.3
Noise Avg (float) = 1.98
Noise Stdev (float) = 0.24
Noise Max (float) = 2.8
Noise Min (float) = 1.6
RawQ (float) = 1.83
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 11
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: HF001_AG_HF3.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 3 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 235 (type integer); Parameter Upper left corner y coordinate = 232 (type integer); Parameter Upper right corner x coordinate = 4496 (type integer); Parameter Upper right corner y coordinate = 216 (type integer); Parameter Lower right corner x coordinate = 4514 (type integer); Parameter Lower right corner y coordinate = 4481 (type integer); Parameter Lower left corner x coordinate = 253 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.903987 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

tag: StrainOrLine


title: HF001_AG_HF4

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 74.44
Background Stdev (float) = 4.06
Background Max (float) = 86.2
Background Min (float) = 65.3
Noise Avg (float) = 2.24
Noise Stdev (float) = 0.25
Noise Max (float) = 3.2
Noise Min (float) = 1.8
RawQ (float) = 1.99
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 21
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: HF001_AG_HF4.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 4 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 233 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4494 (type integer); Parameter Upper right corner y coordinate = 244 (type integer); Parameter Lower right corner x coordinate = 4485 (type integer); Parameter Lower right corner y coordinate = 4509 (type integer); Parameter Lower left corner x coordinate = 224 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.846794 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

tag: GeneticModification

value: Single, segregating flank-tagged T3-generation T-DNA lines generated by vacuum infiltration of Columbia (Col) plants with Agrobacterium tumefaciens vector pROK2


title: Adipose 5LO Knockout Animal 3 versus Wildtype Pool

description: 1000439 adipose

tag: White Adipose Wildtype BL6 pool (n=4)

tag: Adipose 5LO Knockout Animal 3


title: Adipose 5LO Knockout Animal 2 versus Wildtype Pool

description: 1000439 adipose

tag: Adipose 5LO Knockout Animal 2


title: HF001_AG_HF2

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 75.57
Background Stdev (float) = 2.35
Background Max (float) = 85.4
Background Min (float) = 68.8
Noise Avg (float) = 2.47
Noise Stdev (float) = 0.27
Noise Max (float) = 3.3
Noise Min (float) = 1.9
RawQ (float) = 2.08
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 58
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: HF001_AG_HF2.DAT

hyb_protocol: EukGE-WS2v4; Protocol Type = Hybridization; Parameter Wash A1 Recovery Mixes = 0 (type integer); Parameter Wash A1 Temperature (C) = 25 (type integer); Parameter Number of Wash A1 Cycles = 10 (type integer); Parameter Mixes per Wash A1 Cycle = 2 (type integer); Parameter Wash B Recovery Mixes = 0 (type integer); Parameter Wash B Temperature (C) = 50 (type integer); Parameter Number of Wash B Cycles = 4 (type integer); Parameter Mixes per Wash B Cycle = 15 (type integer); Parameter Stain Temperature (C) = 25 (type integer); Parameter First Stain Time (seconds) = 600 (type integer); Parameter Wash A2 Recovery Mixes = 0 (type integer); Parameter Wash A2 Temperature (C) = 25 (type integer); Parameter Number of Wash A2 Cycles = 10 (type integer); Parameter Mixes per Wash A2 Cycle = 4 (type integer); Parameter Second Stain Time (seconds) = 600 (type integer); Parameter Third Stain Time (seconds) = 600 (type integer); Parameter Wash A3 Recovery Mixes = 0 (type integer); Parameter Wash A3 Temperature (C) = 30 (type integer); Parameter Number of Wash A3 Cycles = 15 (type integer); Parameter Mixes per Wash A3 Cycle = 4 (type integer); Parameter Holding Temperature (C) = 25 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Fluidics Station, Parameter: Parameter Station Number = 1 (type integer), Parameter: Parameter Position = 2 (type integer); Performers: John,Y,Okyere, , Janet,,Higgins

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 233 (type integer); Parameter Upper right corner x coordinate = 4495 (type integer); Parameter Upper right corner y coordinate = 221 (type integer); Parameter Lower right corner x coordinate = 4508 (type integer); Parameter Lower right corner y coordinate = 4486 (type integer); Parameter Lower left corner x coordinate = 248 (type integer); Parameter Lower left corner y coordinate = 4497 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.855256 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;

value: T3-generation T-DNA lines generated by vacuum infiltration of Columbia (Col) plants with Agrobacterium tumefaciens vector pROK2


title: HF001_AG_HF1

description:
Rows (integer) = 534
Cols (integer) = 534
Number of Probe Sets (integer) = 8297
Background Avg (float) = 60.73
Background Stdev (float) = 1.26
Background Max (float) = 65.6
Background Min (float) = 58.8
Noise Avg (float) = 1.94
Noise Stdev (float) = 0.18
Noise Max (float) = 2.4
Noise Min (float) = 1.6
RawQ (float) = 1.83
Number Cells Masked (integer) = 0
Number Outlier Cells (integer) = 20
Number Cells Modified (integer) = 0
Rows (integer) = 534
Cols (integer) = 534
Number of Cells (integer) = 285156
Image: HF001_AG_HF1.DAT

scan_protocol: Protocol Type = CEL Analysis; Parameter Algorithm name = Percentile (type string); Parameter Upper left corner x coordinate = 234 (type integer); Parameter Upper left corner y coordinate = 234 (type integer); Parameter Upper right corner x coordinate = 4494 (type integer); Parameter Upper right corner y coordinate = 245 (type integer); Parameter Lower right corner x coordinate = 4484 (type integer); Parameter Lower right corner y coordinate = 4511 (type integer); Parameter Lower left corner x coordinate = 224 (type integer); Parameter Lower left corner y coordinate = 4499 (type integer); Parameter Percentile = 75 (type integer); Parameter Cell margin = 2 (type integer); Parameter Outlier high = 1.500 (type float); Parameter Outlier low = 1.004 (type float); Software: type: Acquisition and analysis software; Protocol Type = Scan; Parameter Pixel Size = 3 (type integer); Parameter Number of Scans = 2 (type integer); Software: type: Acquisition and analysis software; Hardware: type: Scanner, Parameter: Parameter Scanner ID = not specified (type string), Parameter: Parameter Scanner Type = HP (type string); Performers: John,Y,Okyere, , Janet,,Higgins

data_processing: Protocol Type = CHP Analysis; Parameter Algorithm name = ExpressionStat (type string); Parameter Algorithm version = 5.0 (type string); Parameter Baseline file = not specified (type string); Parameter Alpha1 = 0.04 (type float); Parameter Alpha2 = 0.06 (type float); Parameter Tau = 0.015 (type float); Parameter Gamma1H = 0.0025 (type float); Parameter Gamma1L = 0.0025 (type float); Parameter Gamma2H = 0.003 (type float); Parameter Gamma2L = 0.003 (type float); Parameter Perturbation = 1.1 (type float); Parameter Normalization factor = 1.000000 (type float); Parameter Scale factor = 0.914310 (type float); Parameter Mask file = not specified (type string); Software: type: Acquisition and analysis software;


title: Adipose 5LO Knockout Animal 5 versus Wildtype Pool

description: 1000439 adipose

tag: Adipose 5LO Knockout Animal 5


title: Adipose 5LO Knockout Animal 4 versus Wildtype Pool

description: 1000439 adipose

tag: Adipose 5LO Knockout Animal 4


title: pool of liver from wildtype b6 mice on chow diet (n=5) vs. liver from diet induced obesity wildtype b6 animal 3

description: liver


title: Murray_2-2_T2-APH_Rep1_ATH1

treatment_protocol: 20 ml of an early stationary phase MM2d cell suspension (7 days after previous subculture) was transferred into 100 ml fresh MSS-medium (MS-salt, 3% sucrose, 0.5mg/l NAA, 0.05mg/l kinetin) and incubated in the presence of 4.16 ug/ml aphidicolin (not exp.variable) for 24 hours under continuous darkness by rotating at 130 rpm at a temperature of 27C. Cells were gently washed with 1 l MSS-medium through a nylon net (47um mesh size), followed by centrifugation (387 x g for 1 min, no brake applied) to remove the drug. Cells were resuspended in a total volume of 120 ml fresh MSS-medium, incubated as above and samples were taken 2-3 hourly for analysis. The T2 sample was taken at 2 hours after washing to release the block (exp. variable; time course).


title: Leaf_control_replicate 2

status: Public on Feb 15 2007

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

description: Publication: Naoya Hirose, Nobue Makita, Mikiko Kojima, Tomoe Kamada-Nobusada and Hitoshi Sakakibara (2007) Over-expression of a Type-A Response Regulator Alters Rice Morphology and Cytokinin Metabolism. Plant Cell Physiology, 48: in press.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

organism: Oryza sativa

source_name: Oryza sativa leaf, empty vector control

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Transgenic plants of the T0 generation from callus grown on regeneration agar plates for 6 weeks were transferred to agar plates containing 1 X Murashige and Skoog salts, 3 % (w/v) sucrose, and 50 µg mL-1 hygromycin-B (MS-agar plate) for 7 d, and then hydroponically grown until heading in an environment-controlled greenhouse with a photoperiod of 12 h light (30°C)/12 h dark (25°C).

extract_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

tag: Strain

value: Oryza sativa L. cv Nipponbare transformed with pActnos/Hmz, T0 line, Tissue:leaf, Age:75 days after germination


title: Adipose 5LO Knockout Animal 1 versus Wildtype Pool

description: 1000439 adipose

tag: Adipose 5LO Knockout Animal 1


title: Leaf_OsRR6-overexpressor_replicate 1

source_name: Oryza sativa leaf, OsRR6 overexpression

value: Oryza sativa L. cv Nipponbare transformed with pActnos/Hmz-OsRR6, T0 line, Tissue:leaf, Age:75 days after germination


title: Leaf_control_replicate 1


title: Leaf_tZ-treatment_120min_replicate 2

source_name: Oryza sativa leaf, tZ-treated, 120 min

growth_protocol: Rice (Oryza sativa L. cv Nipponbare) seeds were sterilized with 70 % ethanol for 1 min and then with 2 % (w/v) sodium hypochlorite for 15 min, soaked in distilled water at 30°C for 1 d and 30 germinated seeds were transferred to a nylon net floating on tap water that had been adjusted to pH 5.5. Seedlings were grown for 2-weeks in an environment-controlled greenhouse with a photoperiod of 12 h light (30°C)/12 h dark (25°C).

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 5 µM trans-zeatin (tZ) and 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.

value: Oryza sativa L. cv Nipponbare, Tissue:root, Age:two weeks after germination


title: Leaf_DMSO-treatment_120min_replicate 3

source_name: Oryza sativa leaf, DMSO-control, 120 min

treatment_protocol: Third leaves, which were cut at the lamina joint with a razor blade in water, were excised from the two-week-old seedlings and immediately dipped in distilled water containing 0.1% dimethylsulfoxide (DMSO). The excised organ was incubated at 30°C for 120 min, harvested and stored at -80°C until the RNA was extracted.

tag: Oryza sativa L. cv Nipponbare, Tissue

value: root, Age:two weeks after germination


title: Leaf_tZ-treatment_120min_replicate 3


title: Leaf_DMSO-treatment_120min_replicate 1