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PMC:1186732 / 51841-56370 JSONTXT 5 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T12761 0-10 NN denotes Microarray
T12762 11-19 NN denotes analysis
T12763 19-20 . denotes .
T12764 20-176 sentence denotes Total retinal RNA samples were isolated from P0, P6, P14, and P21 Nr2e3 mutant mice using the Trizol reagent (Gibco, San Diego, California. United States).
T12765 21-26 JJ denotes Total
T12767 27-34 JJ denotes retinal
T12768 35-38 NN denotes RNA
T12766 39-46 NNS denotes samples
T12770 47-51 VBD denotes were
T12769 52-60 VBN denotes isolated
T12771 61-65 IN denotes from
T12772 66-68 NN denotes P0
T12774 68-70 , denotes ,
T12775 70-72 NN denotes P6
T12776 72-74 , denotes ,
T12777 74-77 NN denotes P14
T12778 77-79 , denotes ,
T12779 79-82 CC denotes and
T12780 83-86 NN denotes P21
T12781 87-92 NN denotes Nr2e3
T12782 93-99 NN denotes mutant
T12773 100-104 NNS denotes mice
T12783 105-110 VBG denotes using
T12784 111-114 DT denotes the
T12786 115-121 NN denotes Trizol
T12785 122-129 NN denotes reagent
T12787 130-131 -LRB- denotes (
T12788 131-136 NNP denotes Gibco
T12789 136-138 , denotes ,
T12790 138-141 NNP denotes San
T12791 142-147 NNP denotes Diego
T12792 147-149 , denotes ,
T12793 149-159 NNP denotes California
T12794 159-160 , denotes .
T12795 161-167 NNP denotes United
T12796 168-174 NNP denotes States
T12797 174-175 -RRB- denotes )
T12798 175-176 . denotes .
T12799 176-265 sentence denotes Total retinal RNA samples from age-matched wild-type C57BL/6 mice were used as controls.
T12800 177-182 JJ denotes Total
T12802 183-190 JJ denotes retinal
T12803 191-194 NN denotes RNA
T12801 195-202 NNS denotes samples
T12805 203-207 IN denotes from
T12806 208-211 NN denotes age
T12808 211-212 HYPH denotes -
T12807 212-219 VBN denotes matched
T12810 220-224 JJ denotes wild
T12812 224-225 HYPH denotes -
T12811 225-229 NN denotes type
T12813 230-235 NN denotes C57BL
T12814 235-236 HYPH denotes /
T12815 236-237 CD denotes 6
T12809 238-242 NNS denotes mice
T12816 243-247 VBD denotes were
T12804 248-252 VBN denotes used
T12817 253-255 IN denotes as
T12818 256-264 NNS denotes controls
T12819 264-265 . denotes .
T11828 265-352 sentence denotes Individual total RNA samples were derived from four retinas (pooled from two animals).
T11829 266-276 JJ denotes Individual
T11831 277-282 JJ denotes total
T11832 283-286 NN denotes RNA
T11830 287-294 NNS denotes samples
T11834 295-299 VBD denotes were
T11833 300-307 VBN denotes derived
T11835 308-312 IN denotes from
T11836 313-317 CD denotes four
T11837 318-325 NNS denotes retinas
T11838 326-327 -LRB- denotes (
T11839 327-333 VBN denotes pooled
T11840 334-338 IN denotes from
T11841 339-342 CD denotes two
T11842 343-350 NNS denotes animals
T11843 350-351 -RRB- denotes )
T11844 351-352 . denotes .
T11845 352-454 sentence denotes All microarray experiments were performed in triplicate, in each case with separate RNA preparations.
T11846 353-356 DT denotes All
T11848 357-367 NN denotes microarray
T11847 368-379 NNS denotes experiments
T11850 380-384 VBD denotes were
T11849 385-394 VBN denotes performed
T11851 395-397 IN denotes in
T11852 398-408 NN denotes triplicate
T11853 408-410 , denotes ,
T11854 410-412 IN denotes in
T11856 413-417 DT denotes each
T11857 418-422 NN denotes case
T11855 423-427 IN denotes with
T11858 428-436 JJ denotes separate
T11860 437-440 NN denotes RNA
T11859 441-453 NNS denotes preparations
T11861 453-454 . denotes .
T11862 454-545 sentence denotes Microarray experiments with cDNAs were performed with the P0, P6, and P14 derived samples.
T11863 455-465 NN denotes Microarray
T11864 466-477 NNS denotes experiments
T11866 478-482 IN denotes with
T11867 483-488 NNS denotes cDNAs
T11868 489-493 VBD denotes were
T11865 494-503 VBN denotes performed
T11869 504-508 IN denotes with
T11870 509-512 DT denotes the
T11872 513-515 NN denotes P0
T11874 515-517 , denotes ,
T11875 517-519 NN denotes P6
T11876 519-521 , denotes ,
T11877 521-524 CC denotes and
T11878 525-528 NN denotes P14
T11873 529-536 VBN denotes derived
T11871 537-544 NNS denotes samples
T11879 544-545 . denotes .
T11880 545-746 sentence denotes Probes were labeled with either Cy3 or Cy5 using the Array 900 kit from Genisphere (Hatfield, Pennsylvania, United States) starting with 5 μg of total RNA according to the manufacturer's instructions.
T11881 546-552 NNS denotes Probes
T11883 553-557 VBD denotes were
T11882 558-565 VBN denotes labeled
T11884 566-570 IN denotes with
T11885 571-577 CC denotes either
T11886 578-581 NN denotes Cy3
T11887 582-584 CC denotes or
T11888 585-588 NN denotes Cy5
T11889 589-594 VBG denotes using
T11890 595-598 DT denotes the
T11892 599-604 NN denotes Array
T11893 605-608 CD denotes 900
T11891 609-612 NN denotes kit
T11894 613-617 IN denotes from
T11895 618-628 NNP denotes Genisphere
T11896 629-630 -LRB- denotes (
T11897 630-638 NNP denotes Hatfield
T11898 638-640 , denotes ,
T11899 640-652 NNP denotes Pennsylvania
T11900 652-654 , denotes ,
T11901 654-660 NNP denotes United
T11902 661-667 NNP denotes States
T11903 667-668 -RRB- denotes )
T11904 669-677 VBG denotes starting
T11905 678-682 IN denotes with
T11906 683-684 CD denotes 5
T11907 685-687 NN denotes μg
T11908 688-690 IN denotes of
T11909 691-696 JJ denotes total
T11910 697-700 NN denotes RNA
T11911 701-710 VBG denotes according
T11912 711-713 IN denotes to
T11913 714-717 DT denotes the
T11914 718-730 NN denotes manufacturer
T11916 730-732 POS denotes 's
T11915 733-745 NNS denotes instructions
T11917 745-746 . denotes .
T11918 746-819 sentence denotes Wild-type control probes were compared to mutant on the same microarray.
T11919 747-751 JJ denotes Wild
T11921 751-752 HYPH denotes -
T11920 752-756 NN denotes type
T11923 757-764 NN denotes control
T11922 765-771 NNS denotes probes
T11925 772-776 VBD denotes were
T11924 777-785 VBN denotes compared
T11926 786-788 IN denotes to
T11927 789-795 NN denotes mutant
T11928 796-798 IN denotes on
T11929 799-802 DT denotes the
T11931 803-807 JJ denotes same
T11930 808-818 NN denotes microarray
T11932 818-819 . denotes .
T11933 819-967 sentence denotes In two of the three replicates, the mutant probe was labeled with Cy3 and the wild type with Cy5, and in the third replicate the dyes were swapped.
T11934 820-822 IN denotes In
T11936 823-826 CD denotes two
T11938 827-829 IN denotes of
T11939 830-833 DT denotes the
T11937 834-839 CD denotes three
T11940 840-850 NNS denotes replicates
T11941 850-852 , denotes ,
T11942 852-855 DT denotes the
T11944 856-862 NN denotes mutant
T11943 863-868 NN denotes probe
T11945 869-872 VBD denotes was
T11935 873-880 VBN denotes labeled
T11946 881-885 IN denotes with
T11947 886-889 NN denotes Cy3
T11948 890-893 CC denotes and
T11949 894-897 DT denotes the
T11951 898-902 JJ denotes wild
T11950 903-907 NN denotes type
T11952 908-912 IN denotes with
T11953 913-916 NN denotes Cy5
T11954 916-918 , denotes ,
T11955 918-921 CC denotes and
T11956 922-924 IN denotes in
T11958 925-928 DT denotes the
T11960 929-934 JJ denotes third
T11959 935-944 NN denotes replicate
T11961 945-948 DT denotes the
T11962 949-953 NNS denotes dyes
T11963 954-958 VBD denotes were
T11957 959-966 VBN denotes swapped
T11964 966-967 . denotes .
T11965 967-1255 sentence denotes Labeled probe was hybridized to microarray slides spotted with approximately 11,500 cDNA clones from the brain molecular anatomy project library (kind gift of B. Soares, University of Iowa; see http://trans.nih.gov/bmap/index.htm for details) and 500 cDNA clones from our lab collection.
T11966 968-975 VBN denotes Labeled
T11967 976-981 NN denotes probe
T11969 982-985 VBD denotes was
T11968 986-996 VBN denotes hybridized
T11970 997-999 IN denotes to
T11971 1000-1010 NN denotes microarray
T11972 1011-1017 NNS denotes slides
T11973 1018-1025 VBN denotes spotted
T11974 1026-1030 IN denotes with
T11975 1031-1044 RB denotes approximately
T11976 1045-1051 CD denotes 11,500
T11978 1052-1056 NN denotes cDNA
T11977 1057-1063 NNS denotes clones
T11979 1064-1068 IN denotes from
T11980 1069-1072 DT denotes the
T11982 1073-1078 NN denotes brain
T11984 1079-1088 JJ denotes molecular
T11983 1089-1096 NN denotes anatomy
T11985 1097-1104 NN denotes project
T11981 1105-1112 NN denotes library
T11986 1113-1114 -LRB- denotes (
T11988 1114-1118 NN denotes kind
T11987 1119-1123 NN denotes gift
T11989 1124-1126 IN denotes of
T11990 1127-1129 NNP denotes B.
T11991 1130-1136 NNP denotes Soares
T11992 1136-1138 , denotes ,
T11993 1138-1148 NNP denotes University
T11994 1149-1151 IN denotes of
T11995 1152-1156 NNP denotes Iowa
T11996 1156-1157 : denotes ;
T11997 1158-1161 VB denotes see
T11998 1162-1197 NN denotes http://trans.nih.gov/bmap/index.htm
T11999 1198-1201 IN denotes for
T12000 1202-1209 NNS denotes details
T12001 1209-1210 -RRB- denotes )
T12002 1211-1214 CC denotes and
T12003 1215-1218 CD denotes 500
T12005 1219-1223 NN denotes cDNA
T12004 1224-1230 NNS denotes clones
T12006 1231-1235 IN denotes from
T12007 1236-1239 PRP$ denotes our
T12009 1240-1243 NN denotes lab
T12008 1244-1254 NN denotes collection
T12010 1254-1255 . denotes .
T12011 1255-1312 sentence denotes Slides were printed and hybridized as described [59,60].
T12012 1256-1262 NNS denotes Slides
T12014 1263-1267 VBD denotes were
T12013 1268-1275 VBN denotes printed
T12015 1276-1279 CC denotes and
T12016 1280-1290 VBN denotes hybridized
T12017 1291-1293 IN denotes as
T12018 1294-1303 VBN denotes described
T12019 1304-1305 -LRB- denotes [
T12021 1305-1307 CD denotes 59
T12022 1307-1308 , denotes ,
T12020 1308-1310 CD denotes 60
T12023 1310-1311 -RRB- denotes ]
T12024 1311-1312 . denotes .
T12025 1312-1599 sentence denotes After hybridization and washing of slides according to the manufacturer's instructions (Genisphere), the slides were scanned on an Axon Instruments (Union City, California, United States) GenePix 4000 scanner and images were analyzed using the accompanying GenePix Pro software package.
T12026 1313-1318 IN denotes After
T12028 1319-1332 NN denotes hybridization
T12029 1333-1336 CC denotes and
T12030 1337-1344 NN denotes washing
T12031 1345-1347 IN denotes of
T12032 1348-1354 NNS denotes slides
T12033 1355-1364 VBG denotes according
T12034 1365-1367 IN denotes to
T12035 1368-1371 DT denotes the
T12036 1372-1384 NN denotes manufacturer
T12038 1384-1386 POS denotes 's
T12037 1387-1399 NNS denotes instructions
T12039 1400-1401 -LRB- denotes (
T12040 1401-1411 NNP denotes Genisphere
T12041 1411-1412 -RRB- denotes )
T12042 1412-1414 , denotes ,
T12043 1414-1417 DT denotes the
T12044 1418-1424 NNS denotes slides
T12045 1425-1429 VBD denotes were
T12027 1430-1437 VBN denotes scanned
T12046 1438-1440 IN denotes on
T12047 1441-1443 DT denotes an
T12049 1444-1448 NNP denotes Axon
T12050 1449-1460 NNPS denotes Instruments
T12051 1461-1462 -LRB- denotes (
T12053 1462-1467 NNP denotes Union
T12052 1468-1472 NNP denotes City
T12054 1472-1474 , denotes ,
T12055 1474-1484 NNP denotes California
T12056 1484-1486 , denotes ,
T12057 1486-1492 NNP denotes United
T12058 1493-1499 NNP denotes States
T12059 1499-1500 -RRB- denotes )
T12060 1501-1508 NNP denotes GenePix
T12061 1509-1513 CD denotes 4000
T12048 1514-1521 NN denotes scanner
T12062 1522-1525 CC denotes and
T12063 1526-1532 NNS denotes images
T12065 1533-1537 VBD denotes were
T12064 1538-1546 VBN denotes analyzed
T12066 1547-1552 VBG denotes using
T12067 1553-1556 DT denotes the
T12069 1557-1569 VBG denotes accompanying
T12070 1570-1577 NNP denotes GenePix
T12071 1578-1581 NNP denotes Pro
T12072 1582-1590 NN denotes software
T12068 1591-1598 NN denotes package
T12073 1598-1599 . denotes .
T12074 1599-1673 sentence denotes The complete raw cDNA microarray data set are available in Tables S6–S14.
T12075 1600-1603 DT denotes The
T12077 1604-1612 JJ denotes complete
T12078 1613-1616 JJ denotes raw
T12079 1617-1621 NN denotes cDNA
T12080 1622-1632 NN denotes microarray
T12081 1633-1637 NNS denotes data
T12076 1638-1641 NN denotes set
T12082 1642-1645 VBP denotes are
T12083 1646-1655 JJ denotes available
T12084 1656-1658 IN denotes in
T12085 1659-1665 NNS denotes Tables
T12086 1666-1668 NN denotes S6
T12087 1668-1669 SYM denotes –
T12088 1669-1672 NN denotes S14
T12089 1672-1673 . denotes .
T12090 1673-1782 sentence denotes Two types of normalization were performed on the raw intensity scores derived from the GenePix Pro analysis.
T12091 1674-1677 CD denotes Two
T12092 1678-1683 NNS denotes types
T12094 1684-1686 IN denotes of
T12095 1687-1700 NN denotes normalization
T12096 1701-1705 VBD denotes were
T12093 1706-1715 VBN denotes performed
T12097 1716-1718 IN denotes on
T12098 1719-1722 DT denotes the
T12100 1723-1726 JJ denotes raw
T12101 1727-1736 NN denotes intensity
T12099 1737-1743 NNS denotes scores
T12102 1744-1751 VBN denotes derived
T12103 1752-1756 IN denotes from
T12104 1757-1760 DT denotes the
T12106 1761-1768 NNP denotes GenePix
T12107 1769-1772 NNP denotes Pro
T12105 1773-1781 NN denotes analysis
T12108 1781-1782 . denotes .
T12109 1782-1948 sentence denotes First, for a given experiment, the average intensity of all the spots in the weaker of the two channels (Cy3 or Cy5) was normalized to those in the stronger channel.
T12110 1783-1788 RB denotes First
T12112 1788-1790 , denotes ,
T12113 1790-1793 IN denotes for
T12114 1794-1795 DT denotes a
T12116 1796-1801 VBN denotes given
T12115 1802-1812 NN denotes experiment
T12117 1812-1814 , denotes ,
T12118 1814-1817 DT denotes the
T12120 1818-1825 JJ denotes average
T12119 1826-1835 NN denotes intensity
T12121 1836-1838 IN denotes of
T12122 1839-1842 PDT denotes all
T12124 1843-1846 DT denotes the
T12123 1847-1852 NNS denotes spots
T12125 1853-1855 IN denotes in
T12126 1856-1859 DT denotes the
T12127 1860-1866 JJR denotes weaker
T12128 1867-1869 IN denotes of
T12129 1870-1873 DT denotes the
T12131 1874-1877 CD denotes two
T12130 1878-1886 NNS denotes channels
T12132 1887-1888 -LRB- denotes (
T12133 1888-1891 NN denotes Cy3
T12134 1892-1894 CC denotes or
T12135 1895-1898 NN denotes Cy5
T12136 1898-1899 -RRB- denotes )
T12137 1900-1903 VBD denotes was
T12111 1904-1914 VBN denotes normalized
T12138 1915-1917 IN denotes to
T12139 1918-1923 DT denotes those
T12140 1924-1926 IN denotes in
T12141 1927-1930 DT denotes the
T12143 1931-1939 JJR denotes stronger
T12142 1940-1947 NN denotes channel
T12144 1947-1948 . denotes .
T12145 1948-2203 sentence denotes Second, in a given set of experiments done in triplicate at a particular time point, the two experiments with the weaker average signal intensity over all spots were normalized to those in the third microarray with the strongest average signal intensity.
T12146 1949-1955 RB denotes Second
T12148 1955-1957 , denotes ,
T12149 1957-1959 IN denotes in
T12150 1960-1961 DT denotes a
T12152 1962-1967 VBN denotes given
T12151 1968-1971 NN denotes set
T12153 1972-1974 IN denotes of
T12154 1975-1986 NNS denotes experiments
T12155 1987-1991 VBN denotes done
T12156 1992-1994 IN denotes in
T12157 1995-2005 NN denotes triplicate
T12158 2006-2008 IN denotes at
T12159 2009-2010 DT denotes a
T12161 2011-2021 JJ denotes particular
T12162 2022-2026 NN denotes time
T12160 2027-2032 NN denotes point
T12163 2032-2034 , denotes ,
T12164 2034-2037 DT denotes the
T12166 2038-2041 CD denotes two
T12165 2042-2053 NNS denotes experiments
T12167 2054-2058 IN denotes with
T12168 2059-2062 DT denotes the
T12170 2063-2069 JJR denotes weaker
T12171 2070-2077 JJ denotes average
T12172 2078-2084 NN denotes signal
T12169 2085-2094 NN denotes intensity
T12173 2095-2099 IN denotes over
T12174 2100-2103 DT denotes all
T12175 2104-2109 NNS denotes spots
T12176 2110-2114 VBD denotes were
T12147 2115-2125 VBN denotes normalized
T12177 2126-2128 IN denotes to
T12178 2129-2134 DT denotes those
T12179 2135-2137 IN denotes in
T12180 2138-2141 DT denotes the
T12182 2142-2147 JJ denotes third
T12181 2148-2158 NN denotes microarray
T12183 2159-2163 IN denotes with
T12184 2164-2167 DT denotes the
T12186 2168-2177 JJS denotes strongest
T12187 2178-2185 JJ denotes average
T12188 2186-2192 NN denotes signal
T12185 2193-2202 NN denotes intensity
T12189 2202-2203 . denotes .
T12190 2203-2293 sentence denotes All spots with signal levels equal to or below background were removed from the analysis.
T12191 2204-2207 DT denotes All
T12192 2208-2213 NNS denotes spots
T12194 2214-2218 IN denotes with
T12195 2219-2225 NN denotes signal
T12196 2226-2232 NNS denotes levels
T12197 2233-2238 JJ denotes equal
T12198 2239-2241 IN denotes to
T12199 2242-2244 CC denotes or
T12200 2245-2250 IN denotes below
T12201 2251-2261 NN denotes background
T12202 2262-2266 VBD denotes were
T12193 2267-2274 VBN denotes removed
T12203 2275-2279 IN denotes from
T12204 2280-2283 DT denotes the
T12205 2284-2292 NN denotes analysis
T12206 2292-2293 . denotes .
T12207 2293-2353 sentence denotes The resulting files contained on average about 6,000 spots.
T12208 2294-2297 DT denotes The
T12210 2298-2307 VBG denotes resulting
T12209 2308-2313 NNS denotes files
T12211 2314-2323 VBD denotes contained
T12212 2324-2326 IN denotes on
T12213 2327-2334 JJ denotes average
T12214 2335-2340 IN denotes about
T12215 2341-2346 CD denotes 6,000
T12216 2347-2352 NNS denotes spots
T12217 2352-2353 . denotes .
T12218 2353-2653 sentence denotes These files were then sorted according to Cy3/Cy5 signal intensity, and those spots with the 10% highest and 10% lowest intensity ratios (approximately 600 spots/experiment) were compared across the three experiments at a given time point using custom Perl scripts (available upon request from JCC).
T12219 2354-2359 DT denotes These
T12220 2360-2365 NNS denotes files
T12222 2366-2370 VBD denotes were
T12223 2371-2375 RB denotes then
T12221 2376-2382 VBN denotes sorted
T12224 2383-2392 VBG denotes according
T12225 2393-2395 IN denotes to
T12226 2396-2399 NN denotes Cy3
T12228 2399-2400 HYPH denotes /
T12227 2400-2403 NN denotes Cy5
T12230 2404-2410 NN denotes signal
T12229 2411-2420 NN denotes intensity
T12231 2420-2422 , denotes ,
T12232 2422-2425 CC denotes and
T12233 2426-2431 DT denotes those
T12234 2432-2437 NNS denotes spots
T12236 2438-2442 IN denotes with
T12237 2443-2446 DT denotes the
T12239 2447-2449 CD denotes 10
T12240 2449-2450 NN denotes %
T12241 2451-2458 JJS denotes highest
T12242 2459-2462 CC denotes and
T12243 2463-2465 CD denotes 10
T12244 2465-2466 NN denotes %
T12245 2467-2473 JJS denotes lowest
T12246 2474-2483 NN denotes intensity
T12238 2484-2490 NNS denotes ratios
T12247 2491-2492 -LRB- denotes (
T12249 2492-2505 RB denotes approximately
T12250 2506-2509 CD denotes 600
T12248 2510-2515 NNS denotes spots
T12251 2515-2516 SYM denotes /
T12252 2516-2526 NN denotes experiment
T12253 2526-2527 -RRB- denotes )
T12254 2528-2532 VBD denotes were
T12235 2533-2541 VBN denotes compared
T12255 2542-2548 IN denotes across
T12256 2549-2552 DT denotes the
T12258 2553-2558 CD denotes three
T12257 2559-2570 NNS denotes experiments
T12259 2571-2573 IN denotes at
T12260 2574-2575 DT denotes a
T12262 2576-2581 VBN denotes given
T12263 2582-2586 NN denotes time
T12261 2587-2592 NN denotes point
T12264 2593-2598 VBG denotes using
T12265 2599-2605 NN denotes custom
T12267 2606-2610 NN denotes Perl
T12266 2611-2618 NNS denotes scripts
T12268 2619-2620 -LRB- denotes (
T12269 2620-2629 JJ denotes available
T12270 2630-2634 IN denotes upon
T12271 2635-2642 NN denotes request
T12272 2643-2647 IN denotes from
T12273 2648-2651 NNP denotes JCC
T12274 2651-2652 -RRB- denotes )
T12275 2652-2653 . denotes .
T12276 2653-2835 sentence denotes All spots which were present in the top 10% most up- or down-regulated genes in two out of three or three out of three experiments were recorded (the latter are listed in Table S3).
T12277 2654-2657 DT denotes All
T12278 2658-2663 NNS denotes spots
T12280 2664-2669 WDT denotes which
T12281 2670-2674 VBD denotes were
T12282 2675-2682 JJ denotes present
T12283 2683-2685 IN denotes in
T12284 2686-2689 DT denotes the
T12286 2690-2693 JJ denotes top
T12287 2694-2696 CD denotes 10
T12285 2696-2697 NN denotes %
T12289 2698-2702 RBS denotes most
T12291 2703-2705 RB denotes up
T12292 2705-2706 HYPH denotes -
T12293 2707-2709 CC denotes or
T12294 2710-2714 RB denotes down
T12295 2714-2715 HYPH denotes -
T12290 2715-2724 VBN denotes regulated
T12288 2725-2730 NNS denotes genes
T12296 2731-2733 IN denotes in
T12297 2734-2737 CD denotes two
T12299 2738-2741 IN denotes out
T12300 2742-2744 IN denotes of
T12298 2745-2750 CD denotes three
T12302 2751-2753 CC denotes or
T12303 2754-2759 CD denotes three
T12305 2760-2763 IN denotes out
T12306 2764-2766 IN denotes of
T12304 2767-2772 CD denotes three
T12301 2773-2784 NNS denotes experiments
T12307 2785-2789 VBD denotes were
T12279 2790-2798 VBN denotes recorded
T12308 2799-2800 -LRB- denotes (
T12310 2800-2803 DT denotes the
T12311 2804-2810 JJ denotes latter
T12312 2811-2814 VBP denotes are
T12309 2815-2821 VBN denotes listed
T12313 2822-2824 IN denotes in
T12314 2825-2830 NN denotes Table
T12315 2831-2833 NN denotes S3
T12316 2833-2834 -RRB- denotes )
T12317 2834-2835 . denotes .
T12318 2835-2992 sentence denotes Microarray analysis of the P21 retinas was performed on Affymetrix mouse genome 430 2.0 GeneChip array (Affymetrix, Santa Clara, California, United States).
T12319 2836-2846 NN denotes Microarray
T12320 2847-2855 NN denotes analysis
T12322 2856-2858 IN denotes of
T12323 2859-2862 DT denotes the
T12325 2863-2866 NN denotes P21
T12324 2867-2874 NNS denotes retinas
T12326 2875-2878 VBD denotes was
T12321 2879-2888 VBN denotes performed
T12327 2889-2891 IN denotes on
T12328 2892-2902 NNP denotes Affymetrix
T12330 2903-2908 NN denotes mouse
T12331 2909-2915 NN denotes genome
T12332 2916-2919 CD denotes 430
T12333 2920-2923 CD denotes 2.0
T12334 2924-2932 NNP denotes GeneChip
T12329 2933-2938 NN denotes array
T12335 2939-2940 -LRB- denotes (
T12336 2940-2950 NNP denotes Affymetrix
T12337 2950-2952 , denotes ,
T12338 2952-2957 NNP denotes Santa
T12339 2958-2963 NNP denotes Clara
T12340 2963-2965 , denotes ,
T12341 2965-2975 NNP denotes California
T12342 2975-2977 , denotes ,
T12343 2977-2983 NNP denotes United
T12344 2984-2990 NNP denotes States
T12345 2990-2991 -RRB- denotes )
T12346 2991-2992 . denotes .
T12347 2992-3117 sentence denotes A total of six microarray hybridizations were performed: three with probes derived from mutant RNA and three from wild-type.
T12348 2993-2994 DT denotes A
T12350 2995-3000 NN denotes total
T12351 3001-3003 IN denotes of
T12349 3004-3007 CD denotes six
T12353 3008-3018 NN denotes microarray
T12352 3019-3033 NNS denotes hybridizations
T12355 3034-3038 VBD denotes were
T12354 3039-3048 VBN denotes performed
T12356 3048-3050 : denotes :
T12357 3050-3055 CD denotes three
T12358 3056-3060 IN denotes with
T12359 3061-3067 NNS denotes probes
T12360 3068-3075 VBN denotes derived
T12361 3076-3080 IN denotes from
T12362 3081-3087 NN denotes mutant
T12363 3088-3091 NN denotes RNA
T12364 3092-3095 CC denotes and
T12365 3096-3101 CD denotes three
T12366 3102-3106 IN denotes from
T12367 3107-3111 JJ denotes wild
T12369 3111-3112 HYPH denotes -
T12368 3112-3116 NN denotes type
T12370 3116-3117 . denotes .
T12371 3117-3245 sentence denotes Probes were synthesized starting with 10 μg of total RNA for each sample according to manufacturer's instructions (Affymetrix).
T12372 3118-3124 NNS denotes Probes
T12374 3125-3129 VBD denotes were
T12373 3130-3141 VBN denotes synthesized
T12375 3142-3150 VBG denotes starting
T12376 3151-3155 IN denotes with
T12377 3156-3158 CD denotes 10
T12378 3159-3161 NN denotes μg
T12379 3162-3164 IN denotes of
T12380 3165-3170 JJ denotes total
T12381 3171-3174 NN denotes RNA
T12382 3175-3178 IN denotes for
T12383 3179-3183 DT denotes each
T12384 3184-3190 NN denotes sample
T12385 3191-3200 VBG denotes according
T12386 3201-3203 IN denotes to
T12387 3204-3216 NN denotes manufacturer
T12389 3216-3218 POS denotes 's
T12388 3219-3231 NNS denotes instructions
T12390 3232-3233 -LRB- denotes (
T12391 3233-3243 NNP denotes Affymetrix
T12392 3243-3244 -RRB- denotes )
T12393 3244-3245 . denotes .
T12394 3245-3439 sentence denotes Hybridization, washing, and scanning of the microarrays were all performed at the Bauer Center for Genomics Research at Harvard University according to manufacturer's instructions (Affymetrix).
T12395 3246-3259 NN denotes Hybridization
T12397 3259-3261 , denotes ,
T12398 3261-3268 NN denotes washing
T12399 3268-3270 , denotes ,
T12400 3270-3273 CC denotes and
T12401 3274-3282 NN denotes scanning
T12402 3283-3285 IN denotes of
T12403 3286-3289 DT denotes the
T12404 3290-3301 NNS denotes microarrays
T12405 3302-3306 VBD denotes were
T12406 3307-3310 DT denotes all
T12396 3311-3320 VBN denotes performed
T12407 3321-3323 IN denotes at
T12408 3324-3327 DT denotes the
T12410 3328-3333 NNP denotes Bauer
T12409 3334-3340 NNP denotes Center
T12411 3341-3344 IN denotes for
T12412 3345-3353 NNP denotes Genomics
T12413 3354-3362 NNP denotes Research
T12414 3363-3365 IN denotes at
T12415 3366-3373 NNP denotes Harvard
T12416 3374-3384 NNP denotes University
T12417 3385-3394 VBG denotes according
T12418 3395-3397 IN denotes to
T12419 3398-3410 NN denotes manufacturer
T12421 3410-3412 POS denotes 's
T12420 3413-3425 NNS denotes instructions
T12422 3426-3427 -LRB- denotes (
T12423 3427-3437 NNP denotes Affymetrix
T12424 3437-3438 -RRB- denotes )
T12425 3438-3439 . denotes .
T12426 3439-3546 sentence denotes Initial data analysis was carried out using the GeneChip Operating System (GCOS) software from Affymetrix.
T12427 3440-3447 JJ denotes Initial
T12429 3448-3452 NNS denotes data
T12428 3453-3461 NN denotes analysis
T12431 3462-3465 VBD denotes was
T12430 3466-3473 VBN denotes carried
T12432 3474-3477 RP denotes out
T12433 3478-3483 VBG denotes using
T12434 3484-3487 DT denotes the
T12436 3488-3496 NNP denotes GeneChip
T12438 3497-3506 NN denotes Operating
T12437 3507-3513 NN denotes System
T12439 3514-3515 -LRB- denotes (
T12440 3515-3519 NN denotes GCOS
T12441 3519-3520 -RRB- denotes )
T12435 3521-3529 NN denotes software
T12442 3530-3534 IN denotes from
T12443 3535-3545 NNP denotes Affymetrix
T12444 3545-3546 . denotes .
T12445 3546-3636 sentence denotes Pairwise comparisons were made between individual mutant microarray results and controls.
T12446 3547-3555 JJ denotes Pairwise
T12447 3556-3567 NNS denotes comparisons
T12449 3568-3572 VBD denotes were
T12448 3573-3577 VBN denotes made
T12450 3578-3585 IN denotes between
T12451 3586-3596 JJ denotes individual
T12453 3597-3603 NN denotes mutant
T12454 3604-3614 NN denotes microarray
T12452 3615-3622 NNS denotes results
T12455 3623-3626 CC denotes and
T12456 3627-3635 NNS denotes controls
T12457 3635-3636 . denotes .
T12458 3636-3786 sentence denotes All genes were removed from the analysis for which “absent” calls were made by the software for both the wild-type and mutant samples being compared.
T12459 3637-3640 DT denotes All
T12460 3641-3646 NNS denotes genes
T12462 3647-3651 VBD denotes were
T12461 3652-3659 VBN denotes removed
T12463 3660-3664 IN denotes from
T12464 3665-3668 DT denotes the
T12465 3669-3677 NN denotes analysis
T12466 3678-3681 IN denotes for
T12468 3682-3687 WDT denotes which
T12469 3688-3689 `` denotes “
T12471 3689-3695 JJ denotes absent
T12472 3695-3696 '' denotes ”
T12470 3697-3702 NNS denotes calls
T12473 3703-3707 VBD denotes were
T12467 3708-3712 VBN denotes made
T12474 3713-3715 IN denotes by
T12475 3716-3719 DT denotes the
T12476 3720-3728 NN denotes software
T12477 3729-3732 IN denotes for
T12478 3733-3737 CC denotes both
T12480 3738-3741 DT denotes the
T12481 3742-3746 JJ denotes wild
T12483 3746-3747 HYPH denotes -
T12482 3747-3751 NN denotes type
T12484 3752-3755 CC denotes and
T12485 3756-3762 NN denotes mutant
T12479 3763-3770 NNS denotes samples
T12486 3771-3776 VBG denotes being
T12487 3777-3785 VBN denotes compared
T12488 3785-3786 . denotes .
T12489 3786-3855 sentence denotes The remaining gene lists contained approximately 26,000 transcripts.
T12490 3787-3790 DT denotes The
T12492 3791-3800 VBG denotes remaining
T12493 3801-3805 NN denotes gene
T12491 3806-3811 NNS denotes lists
T12494 3812-3821 VBD denotes contained
T12495 3822-3835 RB denotes approximately
T12496 3836-3842 CD denotes 26,000
T12497 3843-3854 NNS denotes transcripts
T12498 3854-3855 . denotes .
T12499 3855-4009 sentence denotes These lists were then sorted according to the mutant-to-wild-type “signal log ratio” in order to identify the most markedly up- and down-regulated genes.
T12500 3856-3861 DT denotes These
T12501 3862-3867 NNS denotes lists
T12503 3868-3872 VBD denotes were
T12504 3873-3877 RB denotes then
T12502 3878-3884 VBN denotes sorted
T12505 3885-3894 VBG denotes according
T12506 3895-3897 IN denotes to
T12507 3898-3901 DT denotes the
T12509 3902-3908 NN denotes mutant
T12510 3908-3909 HYPH denotes -
T12511 3909-3911 IN denotes to
T12512 3911-3912 HYPH denotes -
T12513 3912-3916 JJ denotes wild
T12515 3916-3917 HYPH denotes -
T12514 3917-3921 NN denotes type
T12516 3922-3923 `` denotes “
T12517 3923-3929 JJ denotes signal
T12518 3930-3933 NN denotes log
T12508 3934-3939 NN denotes ratio
T12519 3939-3940 '' denotes ”
T12520 3941-3943 IN denotes in
T12521 3944-3949 NN denotes order
T12522 3950-3952 TO denotes to
T12523 3953-3961 VB denotes identify
T12524 3962-3965 DT denotes the
T12526 3966-3970 RBS denotes most
T12527 3971-3979 RB denotes markedly
T12529 3980-3982 RB denotes up
T12530 3982-3983 HYPH denotes -
T12531 3984-3987 CC denotes and
T12532 3988-3992 RB denotes down
T12533 3992-3993 HYPH denotes -
T12528 3993-4002 VBN denotes regulated
T12525 4003-4008 NNS denotes genes
T12534 4008-4009 . denotes .
T12535 4009-4331 sentence denotes The top 500 most up- and down-regulated transcripts (approximately 2% of all genes in each case) from each of the three pairwise comparisons between mutant and wild-type were compared using custom Perl scripts (available upon request from JCC) to identify those genes that were present in two or three out of three lists.
T12536 4010-4013 DT denotes The
T12538 4014-4017 JJ denotes top
T12539 4018-4021 CD denotes 500
T12540 4022-4026 RBS denotes most
T12542 4027-4029 RB denotes up
T12543 4029-4030 HYPH denotes -
T12544 4031-4034 CC denotes and
T12545 4035-4039 RB denotes down
T12546 4039-4040 HYPH denotes -
T12541 4040-4049 VBN denotes regulated
T12537 4050-4061 NNS denotes transcripts
T12548 4062-4063 -LRB- denotes (
T12550 4063-4076 RB denotes approximately
T12551 4077-4078 CD denotes 2
T12549 4078-4079 NN denotes %
T12552 4080-4082 IN denotes of
T12553 4083-4086 DT denotes all
T12554 4087-4092 NNS denotes genes
T12555 4093-4095 IN denotes in
T12556 4096-4100 DT denotes each
T12557 4101-4105 NN denotes case
T12558 4105-4106 -RRB- denotes )
T12559 4107-4111 IN denotes from
T12560 4112-4116 DT denotes each
T12561 4117-4119 IN denotes of
T12562 4120-4123 DT denotes the
T12564 4124-4129 CD denotes three
T12565 4130-4138 JJ denotes pairwise
T12563 4139-4150 NNS denotes comparisons
T12566 4151-4158 IN denotes between
T12567 4159-4165 NN denotes mutant
T12568 4166-4169 CC denotes and
T12569 4170-4174 JJ denotes wild
T12571 4174-4175 HYPH denotes -
T12570 4175-4179 NN denotes type
T12572 4180-4184 VBD denotes were
T12547 4185-4193 VBN denotes compared
T12573 4194-4199 VBG denotes using
T12574 4200-4206 NN denotes custom
T12576 4207-4211 NN denotes Perl
T12575 4212-4219 NNS denotes scripts
T12577 4220-4221 -LRB- denotes (
T12578 4221-4230 JJ denotes available
T12579 4231-4235 IN denotes upon
T12580 4236-4243 NN denotes request
T12581 4244-4248 IN denotes from
T12582 4249-4252 NNP denotes JCC
T12583 4252-4253 -RRB- denotes )
T12584 4254-4256 TO denotes to
T12585 4257-4265 VB denotes identify
T12586 4266-4271 DT denotes those
T12587 4272-4277 NNS denotes genes
T12588 4278-4282 WDT denotes that
T12589 4283-4287 VBD denotes were
T12590 4288-4295 JJ denotes present
T12591 4296-4298 IN denotes in
T12592 4299-4302 CD denotes two
T12594 4303-4305 CC denotes or
T12595 4306-4311 CD denotes three
T12596 4312-4315 IN denotes out
T12597 4316-4318 IN denotes of
T12593 4319-4324 CD denotes three
T12598 4325-4330 NNS denotes lists
T12599 4330-4331 . denotes .
T12600 4331-4443 sentence denotes Those genes that were up- or down-regulated in three out of three experiments were recorded (Tables S4 and S5).
T12601 4332-4337 DT denotes Those
T12602 4338-4343 NNS denotes genes
T12604 4344-4348 WDT denotes that
T12606 4349-4353 VBD denotes were
T12607 4354-4356 RB denotes up
T12608 4356-4357 HYPH denotes -
T12609 4358-4360 CC denotes or
T12610 4361-4365 RB denotes down
T12611 4365-4366 HYPH denotes -
T12605 4366-4375 VBN denotes regulated
T12612 4376-4378 IN denotes in
T12613 4379-4384 CD denotes three
T12615 4385-4388 IN denotes out
T12616 4389-4391 IN denotes of
T12614 4392-4397 CD denotes three
T12617 4398-4409 NNS denotes experiments
T12618 4410-4414 VBD denotes were
T12603 4415-4423 VBN denotes recorded
T12619 4424-4425 -LRB- denotes (
T12621 4425-4431 NNS denotes Tables
T12620 4432-4434 NN denotes S4
T12622 4435-4438 CC denotes and
T12623 4439-4441 NN denotes S5
T12624 4441-4442 -RRB- denotes )
T12625 4442-4443 . denotes .
T12626 4443-4529 sentence denotes The complete pairwise Affymetrix microarray datasets are available in Tables S15–S17.
T12627 4444-4447 DT denotes The
T12629 4448-4456 JJ denotes complete
T12630 4457-4465 NN denotes pairwise
T12631 4466-4476 NNP denotes Affymetrix
T12632 4477-4487 NN denotes microarray
T12628 4488-4496 NNS denotes datasets
T12633 4497-4500 VBP denotes are
T12634 4501-4510 JJ denotes available
T12635 4511-4513 IN denotes in
T12636 4514-4520 NNS denotes Tables
T12637 4521-4524 NN denotes S15
T12638 4524-4525 SYM denotes –
T12639 4525-4528 NN denotes S17
T12640 4528-4529 . denotes .
R7796 T11829 T11830 amod Individual,samples
R7797 T11830 T11833 nsubjpass samples,derived
R7798 T11831 T11830 amod total,samples
R7799 T11832 T11830 compound RNA,samples
R7800 T11834 T11833 auxpass were,derived
R7801 T11835 T11833 prep from,derived
R7802 T11836 T11837 nummod four,retinas
R7803 T11837 T11835 pobj retinas,from
R7804 T11838 T11837 punct (,retinas
R7805 T11839 T11837 acl pooled,retinas
R7806 T11840 T11839 prep from,pooled
R7807 T11841 T11842 nummod two,animals
R7808 T11842 T11840 pobj animals,from
R7809 T11843 T11833 punct ),derived
R7810 T11844 T11833 punct .,derived
R7811 T11846 T11847 det All,experiments
R7812 T11847 T11849 nsubjpass experiments,performed
R7813 T11848 T11847 compound microarray,experiments
R7814 T11850 T11849 auxpass were,performed
R7815 T11851 T11849 prep in,performed
R7816 T11852 T11851 pobj triplicate,in
R7817 T11853 T11849 punct ", ",performed
R7818 T11854 T11855 prep in,with
R7819 T11855 T11849 prep with,performed
R7820 T11856 T11857 det each,case
R7821 T11857 T11854 pobj case,in
R7822 T11858 T11859 amod separate,preparations
R7823 T11859 T11855 pobj preparations,with
R7824 T11860 T11859 compound RNA,preparations
R7825 T11861 T11849 punct .,performed
R7826 T11863 T11864 compound Microarray,experiments
R7827 T11864 T11865 nsubjpass experiments,performed
R7828 T11866 T11864 prep with,experiments
R7829 T11867 T11866 pobj cDNAs,with
R7830 T11868 T11865 auxpass were,performed
R7831 T11869 T11865 prep with,performed
R7832 T11870 T11871 det the,samples
R7833 T11871 T11869 pobj samples,with
R7834 T11872 T11873 npadvmod P0,derived
R7835 T11873 T11871 amod derived,samples
R7836 T11874 T11872 punct ", ",P0
R7837 T11875 T11872 conj P6,P0
R7838 T11876 T11875 punct ", ",P6
R7839 T11877 T11875 cc and,P6
R7840 T11878 T11875 conj P14,P6
R7841 T11879 T11865 punct .,performed
R7842 T11881 T11882 nsubjpass Probes,labeled
R7843 T11883 T11882 auxpass were,labeled
R7844 T11884 T11882 prep with,labeled
R7845 T11885 T11886 preconj either,Cy3
R7846 T11886 T11884 pobj Cy3,with
R7847 T11887 T11886 cc or,Cy3
R7848 T11888 T11886 conj Cy5,Cy3
R7849 T11889 T11882 advcl using,labeled
R7850 T11890 T11891 det the,kit
R7851 T11891 T11889 dobj kit,using
R7852 T11892 T11891 nmod Array,kit
R7853 T11893 T11892 nummod 900,Array
R7854 T11894 T11891 prep from,kit
R7855 T11895 T11894 pobj Genisphere,from
R7856 T11896 T11897 punct (,Hatfield
R7857 T11897 T11895 parataxis Hatfield,Genisphere
R7858 T11898 T11897 punct ", ",Hatfield
R7859 T11899 T11897 npadvmod Pennsylvania,Hatfield
R7860 T11900 T11897 punct ", ",Hatfield
R7861 T11901 T11902 compound United,States
R7862 T11902 T11897 npadvmod States,Hatfield
R7863 T11903 T11897 punct ),Hatfield
R7864 T11904 T11882 advcl starting,labeled
R7865 T11905 T11904 prep with,starting
R7866 T11906 T11907 nummod 5,μg
R7867 T11907 T11905 pobj μg,with
R7868 T11908 T11907 prep of,μg
R7869 T11909 T11910 amod total,RNA
R7870 T11910 T11908 pobj RNA,of
R7871 T11911 T11904 prep according,starting
R7872 T11912 T11911 prep to,according
R7873 T11913 T11914 det the,manufacturer
R7874 T11914 T11915 poss manufacturer,instructions
R7875 T11915 T11912 pobj instructions,to
R7876 T11916 T11914 case 's,manufacturer
R7877 T11917 T11882 punct .,labeled
R7878 T11919 T11920 amod Wild,type
R7879 T11920 T11922 compound type,probes
R7880 T11921 T11920 punct -,type
R7881 T11922 T11924 nsubjpass probes,compared
R7882 T11923 T11922 compound control,probes
R7883 T11925 T11924 auxpass were,compared
R7884 T11926 T11924 prep to,compared
R7885 T11927 T11926 pobj mutant,to
R7886 T11928 T11924 prep on,compared
R7887 T11929 T11930 det the,microarray
R7888 T11930 T11928 pobj microarray,on
R7889 T11931 T11930 amod same,microarray
R7890 T11932 T11924 punct .,compared
R7891 T11934 T11935 prep In,labeled
R7892 T11936 T11937 quantmod two,three
R7893 T11937 T11940 nummod three,replicates
R7894 T11938 T11937 quantmod of,three
R7895 T11939 T11937 quantmod the,three
R7896 T11940 T11934 pobj replicates,In
R7897 T11941 T11935 punct ", ",labeled
R7898 T11942 T11943 det the,probe
R7899 T11943 T11935 nsubjpass probe,labeled
R7900 T11944 T11943 compound mutant,probe
R7901 T11945 T11935 auxpass was,labeled
R7902 T11946 T11935 prep with,labeled
R7903 T11947 T11946 pobj Cy3,with
R7904 T11948 T11935 cc and,labeled
R7905 T11949 T11950 det the,type
R7906 T11950 T11935 conj type,labeled
R7907 T11951 T11950 amod wild,type
R7908 T11952 T11950 prep with,type
R7909 T11953 T11952 pobj Cy5,with
R7910 T11954 T11935 punct ", ",labeled
R7911 T11955 T11935 cc and,labeled
R7912 T11956 T11957 prep in,swapped
R7913 T11957 T11935 conj swapped,labeled
R7914 T11958 T11959 det the,replicate
R7915 T11959 T11956 pobj replicate,in
R7916 T11960 T11959 amod third,replicate
R7917 T11961 T11962 det the,dyes
R7918 T11962 T11957 nsubjpass dyes,swapped
R7919 T11963 T11957 auxpass were,swapped
R7920 T11964 T11957 punct .,swapped
R7921 T11966 T11967 amod Labeled,probe
R7922 T11967 T11968 nsubjpass probe,hybridized
R7923 T11969 T11968 auxpass was,hybridized
R7924 T11970 T11968 prep to,hybridized
R7925 T11971 T11972 compound microarray,slides
R7926 T11972 T11970 pobj slides,to
R7927 T11973 T11972 acl spotted,slides
R7928 T11974 T11973 prep with,spotted
R7929 T11975 T11976 advmod approximately,"11,500"
R7930 T11976 T11977 nummod "11,500",clones
R7931 T11977 T11974 pobj clones,with
R7932 T11978 T11977 compound cDNA,clones
R7933 T11979 T11977 prep from,clones
R7934 T11980 T11981 det the,library
R7935 T11981 T11979 pobj library,from
R7936 T11982 T11983 nmod brain,anatomy
R7937 T11983 T11981 compound anatomy,library
R7938 T11984 T11983 amod molecular,anatomy
R7939 T11985 T11981 compound project,library
R7940 T11986 T11987 punct (,gift
R7941 T11987 T11977 parataxis gift,clones
R7942 T11988 T11987 compound kind,gift
R7943 T11989 T11987 prep of,gift
R7944 T11990 T11991 compound B.,Soares
R7945 T11991 T11989 pobj Soares,of
R7946 T11992 T11991 punct ", ",Soares
R7947 T11993 T11991 npadvmod University,Soares
R7948 T11994 T11993 prep of,University
R7949 T11995 T11994 pobj Iowa,of
R7950 T11996 T11987 punct ;,gift
R7951 T11997 T11987 advcl see,gift
R7952 T11998 T11997 dobj http://trans.nih.gov/bmap/index.htm,see
R7953 T11999 T11997 prep for,see
R7954 T12000 T11999 pobj details,for
R7955 T12001 T11987 punct ),gift
R7956 T12002 T11977 cc and,clones
R7957 T12003 T12004 nummod 500,clones
R7958 T12004 T11977 conj clones,clones
R7959 T12005 T12004 compound cDNA,clones
R7960 T12006 T12004 prep from,clones
R7961 T12007 T12008 poss our,collection
R7962 T12008 T12006 pobj collection,from
R7963 T12009 T12008 compound lab,collection
R7964 T12010 T11968 punct .,hybridized
R7965 T12012 T12013 nsubjpass Slides,printed
R7966 T12014 T12013 auxpass were,printed
R7967 T12015 T12013 cc and,printed
R7968 T12016 T12013 conj hybridized,printed
R7969 T12017 T12018 mark as,described
R7970 T12018 T12016 advcl described,hybridized
R7971 T12019 T12020 punct [,60
R7972 T12020 T12016 parataxis 60,hybridized
R7973 T12021 T12020 nummod 59,60
R7974 T12022 T12020 punct ",",60
R7975 T12023 T12020 punct ],60
R7976 T12024 T12013 punct .,printed
R7977 T12026 T12027 prep After,scanned
R7978 T12028 T12026 pobj hybridization,After
R7979 T12029 T12028 cc and,hybridization
R7980 T12030 T12028 conj washing,hybridization
R7981 T12031 T12028 prep of,hybridization
R7982 T12032 T12031 pobj slides,of
R7983 T12033 T12028 prep according,hybridization
R7984 T12034 T12033 prep to,according
R7985 T12035 T12036 det the,manufacturer
R7986 T12036 T12037 poss manufacturer,instructions
R7987 T12037 T12034 pobj instructions,to
R7988 T12038 T12036 case 's,manufacturer
R7989 T12039 T12040 punct (,Genisphere
R7990 T12040 T12037 parataxis Genisphere,instructions
R7991 T12041 T12040 punct ),Genisphere
R7992 T12042 T12027 punct ", ",scanned
R7993 T12043 T12044 det the,slides
R7994 T12044 T12027 nsubjpass slides,scanned
R7995 T12045 T12027 auxpass were,scanned
R7996 T12046 T12027 prep on,scanned
R7997 T12047 T12048 det an,scanner
R7998 T12048 T12046 pobj scanner,on
R7999 T12049 T12050 nmod Axon,Instruments
R8000 T12050 T12048 nmod Instruments,scanner
R8001 T12051 T12052 punct (,City
R8002 T12052 T12050 parataxis City,Instruments
R8003 T12053 T12052 compound Union,City
R8004 T12054 T12052 punct ", ",City
R8005 T12055 T12052 npadvmod California,City
R8006 T12056 T12052 punct ", ",City
R8007 T12057 T12058 compound United,States
R8008 T12058 T12052 npadvmod States,City
R8009 T12059 T12052 punct ),City
R8010 T12060 T12048 nmod GenePix,scanner
R8011 T12061 T12060 nummod 4000,GenePix
R8012 T12062 T12027 cc and,scanned
R8013 T12063 T12064 nsubjpass images,analyzed
R8014 T12064 T12027 conj analyzed,scanned
R8015 T12065 T12064 auxpass were,analyzed
R8016 T12066 T12064 advcl using,analyzed
R8017 T12067 T12068 det the,package
R8018 T12068 T12066 dobj package,using
R8019 T12069 T12068 amod accompanying,package
R8020 T12070 T12071 compound GenePix,Pro
R8021 T12071 T12068 compound Pro,package
R8022 T12072 T12068 compound software,package
R8023 T12073 T12027 punct .,scanned
R8024 T12075 T12076 det The,set
R8025 T12076 T12082 nsubj set,are
R8026 T12077 T12076 amod complete,set
R8027 T12078 T12076 amod raw,set
R8028 T12079 T12080 compound cDNA,microarray
R8029 T12080 T12076 compound microarray,set
R8030 T12081 T12076 compound data,set
R8031 T12083 T12082 acomp available,are
R8032 T12084 T12082 prep in,are
R8033 T12085 T12086 compound Tables,S6
R8034 T12086 T12084 pobj S6,in
R8035 T12087 T12088 punct –,S14
R8036 T12088 T12086 prep S14,S6
R8037 T12089 T12082 punct .,are
R8038 T12091 T12092 nummod Two,types
R8039 T12092 T12093 nsubjpass types,performed
R8040 T12094 T12092 prep of,types
R8041 T12095 T12094 pobj normalization,of
R8042 T12096 T12093 auxpass were,performed
R8043 T12097 T12093 prep on,performed
R8044 T12098 T12099 det the,scores
R8045 T12099 T12097 pobj scores,on
R8046 T12100 T12099 amod raw,scores
R8047 T12101 T12099 compound intensity,scores
R8048 T12102 T12099 acl derived,scores
R8049 T12103 T12102 prep from,derived
R8050 T12104 T12105 det the,analysis
R8051 T12105 T12103 pobj analysis,from
R8052 T12106 T12107 compound GenePix,Pro
R8053 T12107 T12105 compound Pro,analysis
R8054 T12108 T12093 punct .,performed
R8055 T12110 T12111 advmod First,normalized
R8056 T12112 T12111 punct ", ",normalized
R8057 T12113 T12111 prep for,normalized
R8058 T12114 T12115 det a,experiment
R8059 T12115 T12113 pobj experiment,for
R8060 T12116 T12115 amod given,experiment
R8061 T12117 T12111 punct ", ",normalized
R8062 T12118 T12119 det the,intensity
R8063 T12119 T12111 nsubjpass intensity,normalized
R8064 T12120 T12119 amod average,intensity
R8065 T12121 T12119 prep of,intensity
R8066 T12122 T12123 predet all,spots
R8067 T12123 T12121 pobj spots,of
R8068 T12124 T12123 det the,spots
R8069 T12125 T12123 prep in,spots
R8070 T12126 T12127 det the,weaker
R8071 T12127 T12125 pobj weaker,in
R8072 T12128 T12127 prep of,weaker
R8073 T12129 T12130 det the,channels
R8074 T12130 T12128 pobj channels,of
R8075 T12131 T12130 nummod two,channels
R8076 T12132 T12133 punct (,Cy3
R8077 T12133 T12130 parataxis Cy3,channels
R8078 T12134 T12133 cc or,Cy3
R8079 T12135 T12133 conj Cy5,Cy3
R8080 T12136 T12133 punct ),Cy3
R8081 T12137 T12111 auxpass was,normalized
R8082 T12138 T12111 prep to,normalized
R8083 T12139 T12138 pobj those,to
R8084 T12140 T12139 prep in,those
R8085 T12141 T12142 det the,channel
R8086 T12142 T12140 pobj channel,in
R8087 T12143 T12142 amod stronger,channel
R8088 T12144 T12111 punct .,normalized
R8089 T12146 T12147 advmod Second,normalized
R8090 T12148 T12147 punct ", ",normalized
R8091 T12149 T12147 prep in,normalized
R8092 T12150 T12151 det a,set
R8093 T12151 T12149 pobj set,in
R8094 T12152 T12151 amod given,set
R8095 T12153 T12151 prep of,set
R8096 T12154 T12153 pobj experiments,of
R8097 T12155 T12154 acl done,experiments
R8098 T12156 T12155 prep in,done
R8099 T12157 T12156 pobj triplicate,in
R8100 T12158 T12155 prep at,done
R8101 T12159 T12160 det a,point
R8102 T12160 T12158 pobj point,at
R8103 T12161 T12160 amod particular,point
R8104 T12162 T12160 compound time,point
R8105 T12163 T12147 punct ", ",normalized
R8106 T12164 T12165 det the,experiments
R8107 T12165 T12147 nsubjpass experiments,normalized
R8108 T12166 T12165 nummod two,experiments
R8109 T12167 T12165 prep with,experiments
R8110 T12168 T12169 det the,intensity
R8111 T12169 T12167 pobj intensity,with
R8112 T12170 T12169 amod weaker,intensity
R8113 T12171 T12169 amod average,intensity
R8114 T12172 T12169 compound signal,intensity
R8115 T12173 T12169 prep over,intensity
R8116 T12174 T12175 det all,spots
R8117 T12175 T12173 pobj spots,over
R8118 T12176 T12147 auxpass were,normalized
R8119 T12177 T12147 prep to,normalized
R8120 T12178 T12177 pobj those,to
R8121 T12179 T12178 prep in,those
R8122 T12180 T12181 det the,microarray
R8123 T12181 T12179 pobj microarray,in
R8124 T12182 T12181 amod third,microarray
R8125 T12183 T12178 prep with,those
R8126 T12184 T12185 det the,intensity
R8127 T12185 T12183 pobj intensity,with
R8128 T12186 T12185 amod strongest,intensity
R8129 T12187 T12185 amod average,intensity
R8130 T12188 T12185 compound signal,intensity
R8131 T12189 T12147 punct .,normalized
R8132 T12191 T12192 det All,spots
R8133 T12192 T12193 nsubjpass spots,removed
R8134 T12194 T12192 prep with,spots
R8135 T12195 T12196 compound signal,levels
R8136 T12196 T12194 pobj levels,with
R8137 T12197 T12196 amod equal,levels
R8138 T12198 T12197 prep to,equal
R8139 T12199 T12197 cc or,equal
R8140 T12200 T12201 prep below,background
R8141 T12201 T12197 conj background,equal
R8142 T12202 T12193 auxpass were,removed
R8143 T12203 T12193 prep from,removed
R8144 T12204 T12205 det the,analysis
R8145 T12205 T12203 pobj analysis,from
R8146 T12206 T12193 punct .,removed
R8147 T12208 T12209 det The,files
R8148 T12209 T12211 nsubj files,contained
R8149 T12210 T12209 amod resulting,files
R8150 T12212 T12211 prep on,contained
R8151 T12213 T12212 amod average,on
R8152 T12214 T12215 quantmod about,"6,000"
R8153 T12215 T12216 nummod "6,000",spots
R8154 T12216 T12211 dobj spots,contained
R8155 T12217 T12211 punct .,contained
R8156 T12219 T12220 det These,files
R8157 T12220 T12221 nsubjpass files,sorted
R8158 T12222 T12221 auxpass were,sorted
R8159 T12223 T12221 advmod then,sorted
R8160 T12224 T12221 prep according,sorted
R8161 T12225 T12224 prep to,according
R8162 T12226 T12227 compound Cy3,Cy5
R8163 T12227 T12229 compound Cy5,intensity
R8164 T12228 T12227 punct /,Cy5
R8165 T12229 T12225 pobj intensity,to
R8166 T12230 T12229 compound signal,intensity
R8167 T12231 T12221 punct ", ",sorted
R8168 T12232 T12221 cc and,sorted
R8169 T12233 T12234 det those,spots
R8170 T12234 T12235 nsubjpass spots,compared
R8171 T12235 T12221 conj compared,sorted
R8172 T12236 T12234 prep with,spots
R8173 T12237 T12238 det the,ratios
R8174 T12238 T12236 pobj ratios,with
R8175 T12239 T12240 nummod 10,%
R8176 T12240 T12241 npadvmod %,highest
R8177 T12241 T12238 amod highest,ratios
R8178 T12242 T12241 cc and,highest
R8179 T12243 T12244 nummod 10,%
R8180 T12244 T12245 npadvmod %,lowest
R8181 T12245 T12241 conj lowest,highest
R8182 T12246 T12238 compound intensity,ratios
R8183 T12247 T12248 punct (,spots
R8184 T12248 T12234 parataxis spots,spots
R8185 T12249 T12250 advmod approximately,600
R8186 T12250 T12248 nummod 600,spots
R8187 T12251 T12252 punct /,experiment
R8188 T12252 T12248 prep experiment,spots
R8189 T12253 T12248 punct ),spots
R8190 T12254 T12235 auxpass were,compared
R8191 T12255 T12235 prep across,compared
R8192 T12256 T12257 det the,experiments
R8193 T12257 T12255 pobj experiments,across
R8194 T12258 T12257 nummod three,experiments
R8195 T12259 T12235 prep at,compared
R8196 T12260 T12261 det a,point
R8197 T12261 T12259 pobj point,at
R8198 T12262 T12261 amod given,point
R8199 T12263 T12261 compound time,point
R8200 T12264 T12235 advcl using,compared
R8201 T12265 T12266 compound custom,scripts
R8202 T12266 T12264 dobj scripts,using
R8203 T12267 T12266 compound Perl,scripts
R8204 T12268 T12266 punct (,scripts
R8205 T12269 T12266 relcl available,scripts
R8206 T12270 T12269 prep upon,available
R8207 T12271 T12270 pobj request,upon
R8208 T12272 T12269 prep from,available
R8209 T12273 T12272 pobj JCC,from
R8210 T12274 T12235 punct ),compared
R8211 T12275 T12235 punct .,compared
R8212 T12277 T12278 det All,spots
R8213 T12278 T12279 nsubjpass spots,recorded
R8214 T12280 T12281 dep which,were
R8215 T12281 T12278 relcl were,spots
R8216 T12282 T12281 acomp present,were
R8217 T12283 T12281 prep in,were
R8218 T12284 T12285 det the,%
R8219 T12285 T12288 nmod %,genes
R8220 T12286 T12285 amod top,%
R8221 T12287 T12285 nummod 10,%
R8222 T12288 T12283 pobj genes,in
R8223 T12289 T12290 advmod most,regulated
R8224 T12290 T12288 amod regulated,genes
R8225 T12291 T12290 advmod up,regulated
R8226 T12292 T12291 punct -,up
R8227 T12293 T12291 cc or,up
R8228 T12294 T12291 conj down,up
R8229 T12295 T12290 punct -,regulated
R8230 T12296 T12281 prep in,were
R8231 T12297 T12298 quantmod two,three
R8232 T12298 T12301 nummod three,experiments
R8233 T12299 T12298 quantmod out,three
R8234 T12300 T12298 quantmod of,three
R8235 T12301 T12296 pobj experiments,in
R8236 T12302 T12298 cc or,three
R8237 T12303 T12304 quantmod three,three
R8238 T12304 T12298 conj three,three
R8239 T12305 T12304 quantmod out,three
R8240 T12306 T12304 quantmod of,three
R8241 T12307 T12279 auxpass were,recorded
R8242 T12308 T12309 punct (,listed
R8243 T12309 T12279 parataxis listed,recorded
R8244 T12310 T12311 det the,latter
R8245 T12311 T12309 nsubjpass latter,listed
R8246 T12312 T12309 auxpass are,listed
R8247 T12313 T12309 prep in,listed
R8248 T12314 T12315 compound Table,S3
R8249 T12315 T12313 pobj S3,in
R8250 T12316 T12309 punct ),listed
R8251 T12317 T12279 punct .,recorded
R8252 T12319 T12320 compound Microarray,analysis
R8253 T12320 T12321 nsubjpass analysis,performed
R8254 T12322 T12320 prep of,analysis
R8255 T12323 T12324 det the,retinas
R8256 T12324 T12322 pobj retinas,of
R8257 T12325 T12324 compound P21,retinas
R8258 T12326 T12321 auxpass was,performed
R8259 T12327 T12321 prep on,performed
R8260 T12328 T12329 nmod Affymetrix,array
R8261 T12329 T12327 pobj array,on
R8262 T12330 T12331 nmod mouse,genome
R8263 T12331 T12329 nmod genome,array
R8264 T12332 T12331 nummod 430,genome
R8265 T12333 T12334 nummod 2.0,GeneChip
R8266 T12334 T12329 compound GeneChip,array
R8267 T12335 T12336 punct (,Affymetrix
R8268 T12336 T12329 parataxis Affymetrix,array
R8269 T12337 T12336 punct ", ",Affymetrix
R8270 T12338 T12339 compound Santa,Clara
R8271 T12339 T12336 npadvmod Clara,Affymetrix
R8272 T12340 T12336 punct ", ",Affymetrix
R8273 T12341 T12336 npadvmod California,Affymetrix
R8274 T12342 T12336 punct ", ",Affymetrix
R8275 T12343 T12344 compound United,States
R8276 T12344 T12336 npadvmod States,Affymetrix
R8277 T12345 T12336 punct ),Affymetrix
R8278 T12346 T12321 punct .,performed
R8279 T12348 T12349 quantmod A,six
R8280 T12349 T12352 nummod six,hybridizations
R8281 T12350 T12349 quantmod total,six
R8282 T12351 T12349 quantmod of,six
R8283 T12352 T12354 nsubjpass hybridizations,performed
R8284 T12353 T12352 compound microarray,hybridizations
R8285 T12355 T12354 auxpass were,performed
R8286 T12356 T12354 punct : ,performed
R8287 T12357 T12354 dobj three,performed
R8288 T12358 T12357 prep with,three
R8289 T12359 T12358 pobj probes,with
R8290 T12360 T12359 acl derived,probes
R8291 T12361 T12360 prep from,derived
R8292 T12362 T12363 compound mutant,RNA
R8293 T12363 T12361 pobj RNA,from
R8294 T12364 T12357 cc and,three
R8295 T12365 T12357 conj three,three
R8296 T12366 T12365 prep from,three
R8297 T12367 T12368 amod wild,type
R8298 T12368 T12366 pobj type,from
R8299 T12369 T12368 punct -,type
R8300 T12370 T12354 punct .,performed
R8301 T12372 T12373 nsubjpass Probes,synthesized
R8302 T12374 T12373 auxpass were,synthesized
R8303 T12375 T12373 advcl starting,synthesized
R8304 T12376 T12375 prep with,starting
R8305 T12377 T12378 nummod 10,μg
R8306 T12378 T12376 pobj μg,with
R8307 T12379 T12378 prep of,μg
R8308 T12380 T12381 amod total,RNA
R8309 T12381 T12379 pobj RNA,of
R8310 T12382 T12378 prep for,μg
R8311 T12383 T12384 det each,sample
R8312 T12384 T12382 pobj sample,for
R8313 T12385 T12375 prep according,starting
R8314 T12386 T12385 prep to,according
R8315 T12387 T12388 poss manufacturer,instructions
R8316 T12388 T12386 pobj instructions,to
R8317 T12389 T12387 case 's,manufacturer
R8318 T12390 T12391 punct (,Affymetrix
R8319 T12391 T12375 parataxis Affymetrix,starting
R8320 T12392 T12391 punct ),Affymetrix
R8321 T12393 T12373 punct .,synthesized
R8322 T12395 T12396 nsubjpass Hybridization,performed
R8323 T12397 T12395 punct ", ",Hybridization
R8324 T12398 T12395 conj washing,Hybridization
R8325 T12399 T12398 punct ", ",washing
R8326 T12400 T12398 cc and,washing
R8327 T12401 T12398 conj scanning,washing
R8328 T12402 T12395 prep of,Hybridization
R8329 T12403 T12404 det the,microarrays
R8330 T12404 T12402 pobj microarrays,of
R8331 T12405 T12396 auxpass were,performed
R8332 T12406 T12396 dep all,performed
R8333 T12407 T12396 prep at,performed
R8334 T12408 T12409 det the,Center
R8335 T12409 T12407 pobj Center,at
R8336 T12410 T12409 compound Bauer,Center
R8337 T12411 T12409 prep for,Center
R8338 T12412 T12413 compound Genomics,Research
R8339 T12413 T12411 pobj Research,for
R8340 T12414 T12409 prep at,Center
R8341 T12415 T12416 compound Harvard,University
R8342 T12416 T12414 pobj University,at
R8343 T12417 T12396 prep according,performed
R8344 T12418 T12417 prep to,according
R8345 T12419 T12420 poss manufacturer,instructions
R8346 T12420 T12418 pobj instructions,to
R8347 T12421 T12419 case 's,manufacturer
R8348 T12422 T12423 punct (,Affymetrix
R8349 T12423 T12396 parataxis Affymetrix,performed
R8350 T12424 T12423 punct ),Affymetrix
R8351 T12425 T12396 punct .,performed
R8352 T12427 T12428 amod Initial,analysis
R8353 T12428 T12430 nsubjpass analysis,carried
R8354 T12429 T12428 compound data,analysis
R8355 T12431 T12430 auxpass was,carried
R8356 T12432 T12430 prt out,carried
R8357 T12433 T12430 advcl using,carried
R8358 T12434 T12435 det the,software
R8359 T12435 T12433 dobj software,using
R8360 T12436 T12437 nmod GeneChip,System
R8361 T12437 T12435 nmod System,software
R8362 T12438 T12437 nmod Operating,System
R8363 T12439 T12437 punct (,System
R8364 T12440 T12437 appos GCOS,System
R8365 T12441 T12435 punct ),software
R8366 T12442 T12435 prep from,software
R8367 T12443 T12442 pobj Affymetrix,from
R8368 T12444 T12430 punct .,carried
R8369 T12446 T12447 amod Pairwise,comparisons
R8370 T12447 T12448 nsubjpass comparisons,made
R8371 T12449 T12448 auxpass were,made
R8372 T12450 T12448 prep between,made
R8373 T12451 T12452 amod individual,results
R8374 T12452 T12450 pobj results,between
R8375 T12453 T12452 compound mutant,results
R8376 T12454 T12452 compound microarray,results
R8377 T12455 T12452 cc and,results
R8378 T12456 T12452 conj controls,results
R8379 T12457 T12448 punct .,made
R8380 T12459 T12460 det All,genes
R8381 T12460 T12461 nsubjpass genes,removed
R8382 T12462 T12461 auxpass were,removed
R8383 T12463 T12461 prep from,removed
R8384 T12464 T12465 det the,analysis
R8385 T12465 T12463 pobj analysis,from
R8386 T12466 T12467 prep for,made
R8387 T12467 T12465 relcl made,analysis
R8388 T12468 T12466 pobj which,for
R8389 T12469 T12470 punct “,calls
R8390 T12470 T12467 nsubjpass calls,made
R8391 T12471 T12470 amod absent,calls
R8392 T12472 T12470 punct ”,calls
R8393 T12473 T12467 auxpass were,made
R8394 T12474 T12467 agent by,made
R8395 T12475 T12476 det the,software
R8396 T12476 T12474 pobj software,by
R8397 T12477 T12467 prep for,made
R8398 T12478 T12479 preconj both,samples
R8399 T12479 T12477 pobj samples,for
R8400 T12480 T12479 det the,samples
R8401 T12481 T12482 amod wild,type
R8402 T12482 T12479 nmod type,samples
R8403 T12483 T12482 punct -,type
R8404 T12484 T12482 cc and,type
R8405 T12485 T12482 conj mutant,type
R8406 T12486 T12487 auxpass being,compared
R8407 T12487 T12479 acl compared,samples
R8408 T12488 T12461 punct .,removed
R8409 T12490 T12491 det The,lists
R8410 T12491 T12494 nsubj lists,contained
R8411 T12492 T12491 amod remaining,lists
R8412 T12493 T12491 compound gene,lists
R8413 T12495 T12496 advmod approximately,"26,000"
R8414 T12496 T12497 nummod "26,000",transcripts
R8415 T12497 T12494 dobj transcripts,contained
R8416 T12498 T12494 punct .,contained
R8417 T12500 T12501 det These,lists
R8418 T12501 T12502 nsubjpass lists,sorted
R8419 T12503 T12502 auxpass were,sorted
R8420 T12504 T12502 advmod then,sorted
R8421 T12505 T12502 prep according,sorted
R8422 T12506 T12505 prep to,according
R8423 T12507 T12508 det the,ratio
R8424 T12508 T12506 pobj ratio,to
R8425 T12509 T12508 nmod mutant,ratio
R8426 T12510 T12509 punct -,mutant
R8427 T12511 T12509 prep to,mutant
R8428 T12512 T12511 punct -,to
R8429 T12513 T12514 amod wild,type
R8430 T12514 T12511 pobj type,to
R8431 T12515 T12514 punct -,type
R8432 T12516 T12508 punct “,ratio
R8433 T12517 T12508 amod signal,ratio
R8434 T12518 T12508 compound log,ratio
R8435 T12519 T12502 punct ”,sorted
R8436 T12520 T12502 prep in,sorted
R8437 T12521 T12520 pobj order,in
R8438 T12522 T12523 aux to,identify
R8439 T12523 T12521 acl identify,order
R8440 T12524 T12525 det the,genes
R8441 T12525 T12523 dobj genes,identify
R8442 T12526 T12527 advmod most,markedly
R8443 T12527 T12528 advmod markedly,regulated
R8444 T12528 T12525 amod regulated,genes
R8445 T12529 T12528 advmod up,regulated
R8446 T12530 T12529 punct -,up
R8447 T12531 T12529 cc and,up
R8448 T12532 T12529 conj down,up
R8449 T12533 T12528 punct -,regulated
R8450 T12534 T12502 punct .,sorted
R8451 T12536 T12537 det The,transcripts
R8452 T12537 T12547 nsubjpass transcripts,compared
R8453 T12538 T12537 amod top,transcripts
R8454 T12539 T12537 nummod 500,transcripts
R8455 T12540 T12541 advmod most,regulated
R8456 T12541 T12537 amod regulated,transcripts
R8457 T12542 T12541 advmod up,regulated
R8458 T12543 T12542 punct -,up
R8459 T12544 T12542 cc and,up
R8460 T12545 T12542 conj down,up
R8461 T12546 T12541 punct -,regulated
R8462 T12548 T12549 punct (,%
R8463 T12549 T12537 parataxis %,transcripts
R8464 T12550 T12551 advmod approximately,2
R8465 T12551 T12549 nummod 2,%
R8466 T12552 T12549 prep of,%
R8467 T12553 T12554 det all,genes
R8468 T12554 T12552 pobj genes,of
R8469 T12555 T12549 prep in,%
R8470 T12556 T12557 det each,case
R8471 T12557 T12555 pobj case,in
R8472 T12558 T12549 punct ),%
R8473 T12559 T12537 prep from,transcripts
R8474 T12560 T12559 pobj each,from
R8475 T12561 T12560 prep of,each
R8476 T12562 T12563 det the,comparisons
R8477 T12563 T12561 pobj comparisons,of
R8478 T12564 T12563 nummod three,comparisons
R8479 T12565 T12563 amod pairwise,comparisons
R8480 T12566 T12563 prep between,comparisons
R8481 T12567 T12566 pobj mutant,between
R8482 T12568 T12567 cc and,mutant
R8483 T12569 T12570 amod wild,type
R8484 T12570 T12567 conj type,mutant
R8485 T12571 T12570 punct -,type
R8486 T12572 T12547 auxpass were,compared
R8487 T12573 T12547 advcl using,compared
R8488 T12574 T12575 compound custom,scripts
R8489 T12575 T12573 dobj scripts,using
R8490 T12576 T12575 compound Perl,scripts
R8491 T12577 T12575 punct (,scripts
R8492 T12578 T12575 relcl available,scripts
R8493 T12579 T12578 prep upon,available
R8494 T12580 T12579 pobj request,upon
R8495 T12581 T12578 prep from,available
R8496 T12582 T12581 pobj JCC,from
R8497 T12583 T12547 punct ),compared
R8498 T12584 T12585 aux to,identify
R8499 T12585 T12547 advcl identify,compared
R8500 T12586 T12587 det those,genes
R8501 T12587 T12585 dobj genes,identify
R8502 T12588 T12589 dep that,were
R8503 T12589 T12587 relcl were,genes
R8504 T12590 T12589 acomp present,were
R8505 T12591 T12589 prep in,were
R8506 T12592 T12593 quantmod two,three
R8507 T12593 T12598 nummod three,lists
R8508 T12594 T12592 cc or,two
R8509 T12595 T12592 conj three,two
R8510 T12596 T12593 quantmod out,three
R8511 T12597 T12593 quantmod of,three
R8512 T12598 T12591 pobj lists,in
R8513 T12599 T12547 punct .,compared
R8514 T12601 T12602 det Those,genes
R8515 T12602 T12603 nsubjpass genes,recorded
R8516 T12604 T12605 dep that,regulated
R8517 T12605 T12602 relcl regulated,genes
R8518 T12606 T12605 auxpass were,regulated
R8519 T12607 T12605 advmod up,regulated
R8520 T12608 T12607 punct -,up
R8521 T12609 T12607 cc or,up
R8522 T12610 T12607 conj down,up
R8523 T12611 T12605 punct -,regulated
R8524 T12612 T12605 prep in,regulated
R8525 T12613 T12614 quantmod three,three
R8526 T12614 T12617 nummod three,experiments
R8527 T12615 T12614 quantmod out,three
R8528 T12616 T12614 quantmod of,three
R8529 T12617 T12612 pobj experiments,in
R8530 T12618 T12603 auxpass were,recorded
R8531 T12619 T12620 punct (,S4
R8532 T12620 T12603 parataxis S4,recorded
R8533 T12621 T12620 compound Tables,S4
R8534 T12622 T12620 cc and,S4
R8535 T12623 T12620 conj S5,S4
R8536 T12624 T12620 punct ),S4
R8537 T12625 T12603 punct .,recorded
R8538 T12627 T12628 det The,datasets
R8539 T12628 T12633 nsubj datasets,are
R8540 T12629 T12628 amod complete,datasets
R8541 T12630 T12628 compound pairwise,datasets
R8542 T12631 T12632 compound Affymetrix,microarray
R8543 T12632 T12628 compound microarray,datasets
R8544 T12634 T12633 acomp available,are
R8545 T12635 T12633 prep in,are
R8546 T12636 T12637 compound Tables,S15
R8547 T12637 T12635 pobj S15,in
R8548 T12638 T12639 punct –,S17
R8549 T12639 T12637 prep S17,S15
R8550 T12640 T12633 punct .,are
R8555 T12761 T12762 compound Microarray,analysis
R8556 T12763 T12762 punct .,analysis
R8557 T12765 T12766 amod Total,samples
R8558 T12766 T12769 nsubjpass samples,isolated
R8559 T12767 T12766 amod retinal,samples
R8560 T12768 T12766 compound RNA,samples
R8561 T12770 T12769 auxpass were,isolated
R8562 T12771 T12769 prep from,isolated
R8563 T12772 T12773 nmod P0,mice
R8564 T12773 T12771 pobj mice,from
R8565 T12774 T12772 punct ", ",P0
R8566 T12775 T12772 conj P6,P0
R8567 T12776 T12775 punct ", ",P6
R8568 T12777 T12775 conj P14,P6
R8569 T12778 T12777 punct ", ",P14
R8570 T12779 T12777 cc and,P14
R8571 T12780 T12777 conj P21,P14
R8572 T12781 T12782 compound Nr2e3,mutant
R8573 T12782 T12773 compound mutant,mice
R8574 T12783 T12769 advcl using,isolated
R8575 T12784 T12785 det the,reagent
R8576 T12785 T12783 dobj reagent,using
R8577 T12786 T12785 compound Trizol,reagent
R8578 T12787 T12788 punct (,Gibco
R8579 T12788 T12785 parataxis Gibco,reagent
R8580 T12789 T12788 punct ", ",Gibco
R8581 T12790 T12791 compound San,Diego
R8582 T12791 T12788 npadvmod Diego,Gibco
R8583 T12792 T12788 punct ", ",Gibco
R8584 T12793 T12788 npadvmod California,Gibco
R8585 T12794 T12788 punct .,Gibco
R8586 T12795 T12796 compound United,States
R8587 T12796 T12788 npadvmod States,Gibco
R8588 T12797 T12788 punct ),Gibco
R8589 T12798 T12769 punct .,isolated
R8590 T12800 T12801 amod Total,samples
R8591 T12801 T12804 nsubjpass samples,used
R8592 T12802 T12801 amod retinal,samples
R8593 T12803 T12801 compound RNA,samples
R8594 T12805 T12801 prep from,samples
R8595 T12806 T12807 npadvmod age,matched
R8596 T12807 T12809 amod matched,mice
R8597 T12808 T12807 punct -,matched
R8598 T12809 T12805 pobj mice,from
R8599 T12810 T12811 amod wild,type
R8600 T12811 T12809 nmod type,mice
R8601 T12812 T12811 punct -,type
R8602 T12813 T12809 nmod C57BL,mice
R8603 T12814 T12813 punct /,C57BL
R8604 T12815 T12813 nummod 6,C57BL
R8605 T12816 T12804 auxpass were,used
R8606 T12817 T12804 prep as,used
R8607 T12818 T12817 pobj controls,as
R8608 T12819 T12804 punct .,used