|
Affymetrix data set from SCRI, April - December 2006
Accession number: GN124
Barley1 Embryo MAS 5.0 SCRI (Dec 06) - integrated probe set value for each gene has been calculated using MAS 5.0 algorithm which uses pixel values from both, PM and MM probes. Descriptions of probe set signal calculation can be found on this page below, section 'About Data Processing'.
Summary:
The SCRI barley data set provides estimates of mRNA abundance in doubled haploid recombinant lines of cultivated barley. Embryo-derived tissues at four days after imbibition (150 lines) and seedling leaves at 12 days after imbibition (subset of 34 lines) and three biological replicates of each parental cultivar (Steptoe and Morex) for each tissue were used for the isolation of total RNA and hybridization to the Barley1 22K GeneChip.
About the lines used to generate this set of data:
The SM cross was originally made to map barley grain quality traits; Steptoe is high-yielding barley cultivar used for animal feeding, but Morex has good malting barley characteristics (Hayes et al 1993). Many agronomic quality traits have been mapped using this population (for the lists see BeerGenes web-site http://gnome.agrenv.mcgill.ca/bg/).
The sample used in this study consists of 150 Steptoe x Morex doubled haploid recombinant lines (Kleinhofs et al. 1993) was used to obtain embryo-derived tissue. For the seedling leaf tissue a subset of 35 lines was used. This subset was selected based on evenly spaced crossovers along each of seven barley chromosomes. The expression data of 11 DH lines has been removed from both, embryo and leaf, leaving for the analysis 129 lines with embryo expression data and a subset of 30 lines with seedling leaf expression data. The lines were removed from the analysis after error checking; discrepancies with genotyping data were found. We left all 150 lines in the embryo Apr06 data set and the full data set is available from the ArrayExpress. The following table lists line IDs and corresponding CEL file IDs, also indicating:
1)
pedigree; shows the direction of the cross that was used to produce the original F1. The parental plants were given letter codes of A - Z. For example, SM1 was derived from an F1 that was generated by crossing Steptoe plant "B" as a female with Morex plant "F" as a male.
2)
'minimapper' subset - MINI;
3) lines that have expression data removed - ERROR:
| Order # |
Line ID |
Permanent Oregon ID |
Cross direction |
CEL file names |
Mini-mapper set |
Error check |
| embryo data-set |
leaf data-set |
embryo data-set |
leaf data-set |
| 1 |
SM001 |
2907001 |
Steptoe/Morex(BxF) |
AD_SCRI_82.CEL |
|
|
OK |
|
| 2 |
SM002 |
2907002 |
Steptoe/Morex(BxF) |
AD_SCRI_1.CEL |
|
|
OK |
|
| 3 |
SM003 |
2907003 |
Morex/Steptoe(CxF) |
AD_SCRI_19.CEL |
|
|
OK |
|
| 4 |
SM004 |
2907004 |
Morex/Steptoe(CxF) |
AD_SCRI_3.CEL |
0521-1_SetA1.CEL |
SMmini |
OK |
OK |
| 5 |
SM005 |
2907005 |
Steptoe/Morex(BxH) |
AD_SCRI_88.CEL |
|
|
OK |
|
| 6 |
SM006 |
2907006 |
Morex/Steptoe(CxF) |
AD_SCRI_48.CEL |
|
|
OK |
|
| 7 |
SM007 |
2907007 |
Steptoe/Morex(BxH) |
AD_SCRI_35.CEL |
0521-2_SetA2.CEL |
SMmini |
OK |
OK |
| 8 |
SM009 |
2907009 |
Steptoe/Morex(BxF) |
AD_SCRI_2.CEL |
|
|
OK |
|
| 9 |
SM010 |
2907010 |
Morex/Steptoe(IxE) |
AD_SCRI_42.CEL |
|
|
OK |
|
| 10 |
SM011 |
2907011 |
Steptoe/Morex(QxG) |
AD_SCRI_10.CEL |
|
|
OK |
|
| 11 |
SM012 |
2907012 |
Morex/Steptoe(CxF) |
AD_SCRI_45.CEL |
0521-3_SetA3.CEL |
SMmini |
ERROR |
ERROR |
| 12 |
SM013 |
2907013 |
Morex/Steptoe(IxE) |
AD_SCRI_78.CEL |
0521-4_SetA4.CEL |
SMmini |
ERROR |
ERROR |
| 13 |
SM014 |
2907014 |
Steptoe/Morex(BxH) |
AD_SCRI_18.CEL |
|
|
OK |
|
| 14 |
SM015 |
2907015 |
Steptoe/Morex(BxH) |
AD_SCRI_5.CEL |
|
|
OK |
|
| 15 |
SM016 |
2907016 |
Steptoe/Morex(BxH) |
AD_SCRI_21.CEL |
|
|
OK |
|
| 16 |
SM020 |
2907020 |
Steptoe/Morex(OxJ) |
AD_SCRI_77.CEL |
|
|
OK |
|
| 17 |
SM021 |
2907021 |
Morex/Steptoe(IxE) |
AD_SCRI_30.CEL |
|
|
OK |
|
| 18 |
SM022 |
2907022 |
Morex/Steptoe(IxE) |
AD_SCRI_31.CEL |
0521-5_SetA5.CEL |
SMmini |
OK |
OK |
| 19 |
SM023 |
2907023 |
Steptoe/Morex(BxH) |
AD_SCRI_32.CEL |
|
|
OK |
|
| 20 |
SM024 |
2907024 |
Morex/Steptoe(IxE) |
AD_SCRI_33.CEL |
0521-6_SetA6.CEL |
SMmini |
OK |
OK |
| 21 |
SM025 |
2907025 |
Morex/Steptoe(CxF) |
AD_SCRI_34.CEL |
|
|
OK |
|
| 22 |
SM027 |
2907027 |
Steptoe/Morex(OxJ) |
AD_SCRI_12.CEL |
0521-7_SetA7.CEL |
SMmini |
OK |
OK |
| 23 |
SM030 |
2907030 |
Morex/Steptoe(IxE) |
AD_SCRI_79.CEL |
|
|
OK |
|
| 24 |
SM031 |
2907031 |
Steptoe/Morex(OxJ) |
AD_SCRI_16.CEL |
|
|
OK |
|
| 25 |
SM032 |
2907032 |
Morex/Steptoe(IxE) |
AD_SCRI_13.CEL |
|
|
OK |
|
| 26 |
SM035 |
2907035 |
Morex/Steptoe(CxF) |
AD_SCRI_15.CEL |
|
|
ERROR |
|
| 27 |
SM039 |
2907039 |
Morex/Steptoe(CxF) |
AD_SCRI_41.CEL |
|
|
OK |
|
| 28 |
SM040 |
2907040 |
Steptoe/Morex(BxH) |
AD_SCRI_83.CEL |
|
|
OK |
|
| 29 |
SM041 |
2907041 |
Steptoe/Morex(OxJ) |
AD_SCRI_11_redo.CEL |
0521-8_SetA8.CEL |
SMmini |
OK |
OK |
| 30 |
SM042 |
2907042 |
Morex/Steptoe(CxF) |
AD_SCRI_57.CEL |
|
|
OK |
|
| 31 |
SM043 |
2907043 |
Morex/Steptoe(JxE) |
AD_SCRI_49.CEL |
0521-9_SetA9.CEL |
SMmini |
OK |
OK |
| 32 |
SM044 |
2907044 |
Steptoe/Morex(OxJ) |
AD_SCRI_50.CEL |
0521-10_SetA10.CEL |
SMmini |
OK |
OK |
| 33 |
SM045 |
2907045 |
Steptoe/Morex(BxH) |
AD_SCRI_51.CEL |
|
|
OK |
|
| 34 |
SM046 |
2907046 |
Steptoe/Morex(OxJ) |
AD_SCRI_52.CEL |
0521-11_SetA11.CEL |
SMmini |
OK |
OK |
| 35 |
SM048 |
2907048 |
Steptoe/Morex(BxF) |
AD_SCRI_53.CEL |
|
|
ERROR |
|
| 36 |
SM050 |
2907050 |
Morex/Steptoe(IxE) |
AD_SCRI_46.CEL |
|
|
OK |
|
| 37 |
SM054 |
2907054 |
Morex/Steptoe(CxF) |
AD_SCRI_60.CEL |
|
|
OK |
|
| 38 |
SM055 |
2907055 |
Steptoe/Morex(OxJ) |
AD_SCRI_55.CEL |
|
|
OK |
|
| 39 |
SM056 |
2907056 |
Steptoe/Morex(BxH) |
AD_SCRI_23.CEL |
|
|
OK |
|
| 40 |
SM057 |
2907057 |
Morex/Steptoe(CxF) |
AD_SCRI_24.CEL |
|
|
OK |
|
| 41 |
SM058 |
2907058 |
Steptoe/Morex(BxF) |
AD_SCRI_22.CEL |
|
|
OK |
|
| 42 |
SM059 |
2907059 |
Steptoe/Morex(BxH) |
AD_SCRI_27.CEL |
|
|
OK |
|
| 43 |
SM061 |
2907061 |
Morex/Steptoe(LxF) |
AD_SCRI_81.CEL |
0521-12_SetA12.CEL |
SMmini |
OK |
OK |
| 44 |
SM062 |
2907062 |
Morex/Steptoe(CxF) |
AD_SCRI_44.CEL |
|
|
OK |
|
| 45 |
SM063 |
2907063 |
Steptoe/Morex(OxJ) |
AD_SCRI_40.CEL |
0521-13_SetA13.CEL |
SMmini |
OK |
OK |
| 46 |
SM064 |
2907064 |
Morex/Steptoe(CxF) |
AD_SCRI_87_redo.CEL |
|
|
OK |
|
| 47 |
SM065 |
2907065 |
Morex/Steptoe(CxF) |
AD_SCRI_54.CEL |
|
|
OK |
|
| 48 |
SM067 |
2907067 |
Steptoe/Morex(OxJ) |
AD_SCRI_73.CEL |
|
|
OK |
|
| 49 |
SM068 |
2907068 |
Steptoe/Morex(OxG) |
AD_SCRI_56.CEL |
|
|
ERROR |
|
| 50 |
SM069 |
2907069 |
Steptoe/Morex(BxH) |
AD_SCRI_71.CEL |
|
|
OK |
|
| 51 |
SM070 |
2907070 |
Steptoe/Morex(BxF) |
AD_SCRI_64.CEL |
|
|
OK |
|
| 52 |
SM071 |
2907071 |
Steptoe/Morex(BxH) |
AD_SCRI_58.CEL |
|
|
OK |
|
| 53 |
SM072 |
2907072 |
Morex/Steptoe(CxF) |
AD_SCRI_59.CEL |
|
|
OK |
|
| 54 |
SM073 |
2907073 |
Steptoe/Morex(BxF) |
AD_SCRI_74.CEL |
0521-14_SetA14.CEL |
SMmini |
OK |
ERROR |
| 55 |
SM074 |
2907074 |
Morex/Steptoe(CxF) |
AD_SCRI_25.CEL |
0521-15_SetA15.CEL |
SMmini |
OK |
OK |
| 56 |
SM075 |
2907075 |
Steptoe/Morex(QxG) |
AD_SCRI_120.CEL |
|
|
OK |
|
| 57 |
SM076 |
2907076 |
Steptoe/Morex(BxF) |
AD_SCRI_112.CEL |
|
|
OK |
|
| 58 |
SM077 |
2907077 |
Morex/Steptoe(CxF) |
AD_SCRI_142.CEL |
|
|
OK |
|
| 59 |
SM078 |
2907078 |
Steptoe/Morex(BxF) |
AD_SCRI_86.CEL |
|
|
OK |
|
| 60 |
SM079 |
2907079 |
Morex/Steptoe(CxF) |
AD_SCRI_153.CEL |
0521-16_SetA16.CEL |
SMmini |
OK |
ERROR |
| 61 |
SM080 |
2907080 |
Steptoe/Morex(BxF) |
AD_SCRI_107.CEL |
|
|
OK |
|
| 62 |
SM081 |
2907081 |
Morex/Steptoe(CxF) |
AD_SCRI_105.CEL |
|
|
OK |
|
| 63 |
SM082 |
2907082 |
Steptoe/Morex(BxF) |
AD_SCRI_97.CEL |
|
|
OK |
|
| 64 |
SM083 |
2907083 |
Steptoe/Morex(BxF) |
AD_SCRI_89.CEL |
|
|
OK |
|
| 65 |
SM084 |
2907084 |
Morex/Steptoe(CxF) |
AD_SCRI_155.CEL |
|
|
OK |
|
| 66 |
SM085 |
2907085 |
Morex/Steptoe(IxE) |
AD_SCRI_149.CEL |
0521-17_SetA17.CEL |
SMmini |
OK |
OK |
| 67 |
SM087 |
2907087 |
Steptoe/Morex(OxJ) |
AD_SCRI_113.CEL |
|
|
OK |
|
| 68 |
SM088 |
2907088 |
Morex/Steptoe(CxF) |
AD_SCRI_93.CEL |
0521-18_SetA18.CEL |
SMmini |
OK |
OK |
| 69 |
SM089 |
2907089 |
Steptoe/Morex(OxJ) |
AD_SCRI_148.CEL |
0521-19_SetA19.CEL |
SMmini |
OK |
OK |
| 70 |
SM091 |
2907091 |
Morex/Steptoe(CxF) |
AD_SCRI_110.CEL |
|
|
OK |
|
| 71 |
SM092 |
2907092 |
Steptoe/Morex(OxJ) |
AD_SCRI_7.CEL |
|
|
OK |
|
| 72 |
SM093 |
2907093 |
Steptoe/Morex(BxF) |
AD_SCRI_122.CEL |
|
|
OK |
|
| 73 |
SM094 |
2907094 |
Morex/Steptoe(CxF) |
AD_SCRI_150.CEL |
|
|
OK |
|
| 74 |
SM097 |
2907097 |
Morex/Steptoe(CxF) |
AD_SCRI_158.CEL |
|
|
OK |
|
| 75 |
SM098 |
2907098 |
Morex/Steptoe(CxF) |
AD_SCRI_121.CEL |
|
|
OK |
|
| 76 |
SM099 |
2907099 |
Steptoe/Morex(QxG) |
AD_SCRI_137.CEL |
|
|
OK |
|
| 77 |
SM103 |
2907103 |
Morex/Steptoe(IxE) |
AD_SCRI_156.CEL |
|
|
OK |
|
| 78 |
SM104 |
2907104 |
Steptoe/Morex(BxH) |
AD_SCRI_70.CEL |
|
|
ERROR |
|
| 79 |
SM105 |
2907105 |
Morex/Steptoe(IxE) |
AD_SCRI_69.CEL |
|
|
OK |
|
| 80 |
SM110 |
2907110 |
Morex/Steptoe(CxF) |
AD_SCRI_75.CEL |
|
|
ERROR |
|
| 81 |
SM112 |
2907112 |
Steptoe/Morex(BxF) |
AD_SCRI_84.CEL |
|
|
OK |
|
| 82 |
SM116 |
2907116 |
Morex/Steptoe(CxF) |
AD_SCRI_117.CEL |
0521-20_SetA20.CEL |
SMmini |
OK |
OK |
| 83 |
SM120 |
2907120 |
Steptoe/Morex(OxJ) |
AD_SCRI_138.CEL |
|
|
OK |
|
| 84 |
SM124 |
2907124 |
Steptoe/Morex(BxF) |
AD_SCRI_146.CEL |
|
|
OK |
|
| 85 |
SM125 |
2907125 |
Morex/Steptoe(IxE) |
AD_SCRI_43.CEL |
|
|
OK |
|
| 86 |
SM126 |
2907126 |
Steptoe/Morex(OxJ) |
AD_SCRI_144_redo.CEL |
|
|
OK |
|
| 87 |
SM127 |
2907127 |
Steptoe/Morex(BxH) |
AD_SCRI_129.CEL |
|
|
OK |
|
| 88 |
SM129 |
2907129 |
Steptoe/Morex(OxJ) |
AD_SCRI_132.CEL |
|
|
OK |
|
| 89 |
SM130 |
2907130 |
Morex/Steptoe(CxF) |
AD_SCRI_101.CEL |
0521-21_SetA21.CEL |
SMmini |
OK |
OK |
| 90 |
SM131 |
2907131 |
Steptoe/Morex(OxJ) |
AD_SCRI_102.CEL |
|
|
OK |
|
| 91 |
SM132 |
2907132 |
Steptoe/Morex(QxG) |
AD_SCRI_4_redo.CEL |
|
|
OK |
|
| 92 |
SM133 |
2907133 |
Morex/Steptoe(CxF) |
AD_SCRI_157.CEL |
|
|
OK |
|
| 93 |
SM134 |
2907134 |
Morex/Steptoe(IxE) |
AD_SCRI_159.CEL |
|
|
OK |
|
| 94 |
SM135 |
2907135 |
Steptoe/Morex(BxF) |
AD_SCRI_72.CEL |
0521-22_SetA22.CEL |
SMmini |
OK |
OK |
| 95 |
SM136 |
2907136 |
Steptoe/Morex(QxG) |
AD_SCRI_123.CEL |
0521-23_SetA23.CEL |
SMmini |
OK |
OK |
| 96 |
SM137 |
2907137 |
Steptoe/Morex(BxH) |
AD_SCRI_39.CEL |
|
|
OK |
|
| 97 |
SM139 |
2907139 |
Morex/Steptoe(CxF) |
AD_SCRI_133.CEL |
|
|
OK |
|
| 98 |
SM140 |
2907140 |
Morex/Steptoe(CxF) |
AD_SCRI_134.CEL |
0521-24_SetA24.CEL |
SMmini |
OK |
OK |
| 99 |
SM141 |
2907141 |
Steptoe/Morex(BxH) |
AD_SCRI_136.CEL |
0521-25_SetA25.CEL |
SMmini |
OK |
OK |
| 100 |
SM142 |
2907142 |
Morex/Steptoe(IxE) |
AD_SCRI_6.CEL |
|
|
OK |
|
| 101 |
SM143 |
2907143 |
Steptoe/Morex(BxH) |
AD_SCRI_145.CEL |
|
|
OK |
|
| 102 |
SM144 |
2907144 |
Steptoe/Morex(BxF) |
AD_SCRI_103.CEL |
|
|
OK |
|
| 103 |
SM145 |
2907145 |
Steptoe/Morex(QxG) |
AD_SCRI_108.CEL |
|
|
OK |
|
| 104 |
SM146 |
2907146 |
Morex/Steptoe(BxF) |
AD_SCRI_91.CEL |
0521-26_SetA26.CEL |
SMmini |
OK |
OK |
| 105 |
SM147 |
2907147 |
Steptoe/Morex(OxJ) |
AD_SCRI_139.CEL |
|
|
OK |
|
| 106 |
SM149 |
2907149 |
Steptoe/Morex(BxF) |
AD_SCRI_131.CEL |
|
|
ERROR |
|
| 107 |
SM150 |
2907150 |
Morex/Steptoe(CxF) |
AD_SCRI_37.CEL |
|
|
OK |
|
| 108 |
SM151 |
2907151 |
Morex/Steptoe(IxE) |
AD_SCRI_28.CEL |
|
|
OK |
|
| 109 |
SM152 |
2907152 |
Steptoe/Morex(BxH) |
AD_SCRI_9_redo.CEL |
0521-27_SetA27.CEL |
SMmini |
OK |
OK |
| 110 |
SM153 |
2907153 |
Steptoe/Morex(BxH) |
AD_SCRI_135.CEL |
|
|
OK |
|
| 111 |
SM154 |
2907154 |
Steptoe/Morex(BxH) |
AD_SCRI_114.CEL |
|
|
OK |
|
| 112 |
SM155 |
2907155 |
Steptoe/Morex(BxH) |
AD_SCRI_119.CEL |
0521-28_SetA28.CEL |
SMmini |
OK |
OK |
| 113 |
SM156 |
2907156 |
Steptoe/Morex(BxH) |
AD_SCRI_140.CEL |
|
|
OK |
|
| 114 |
SM157 |
2907157 |
Morex/Steptoe(CxF) |
AD_SCRI_106_redo.CEL |
|
|
OK |
|
| 115 |
SM158 |
2907158 |
Morex/Steptoe(CxF) |
AD_SCRI_65.CEL |
|
|
OK |
|
| 116 |
SM159 |
2907159 |
Morex/Steptoe(IxE) |
AD_SCRI_168.CEL |
|
|
OK |
|
| 117 |
SM160 |
2907160 |
Steptoe/Morex(OxJ) |
AD_SCRI_47.CEL |
0521-29_SetA29.CEL |
SMmini |
OK |
ERROR |
| 118 |
SM161 |
2907161 |
Steptoe/Morex(BxH) |
AD_SCRI_76.CEL |
|
|
ERROR |
|
| 119 |
SM162 |
2907162 |
Morex/Steptoe(CxF) |
AD_SCRI_147.CEL |
|
|
OK |
|
| 120 |
SM164 |
2907164 |
Steptoe/Morex(OxJ) |
AD_SCRI_128.CEL |
|
|
OK |
|
| 121 |
SM165 |
2907165 |
Steptoe/Morex(BxH) |
AD_SCRI_143.CEL |
|
|
OK |
OK |
| 122 |
SM166 |
2907166 |
Morex/Steptoe(CxF) |
AD_SCRI_115.CEL |
|
|
OK |
|
| 123 |
SM167 |
2907167 |
Steptoe/Morex(BxH) |
AD_SCRI_127.CEL |
0521-30_SetA30.CEL |
SMmini |
OK |
OK |
| 124 |
SM168 |
2907168 |
Steptoe/Morex(BxH) |
AD_SCRI_130.CEL |
|
|
OK |
|
| 125 |
SM169 |
2907169 |
Morex/Steptoe(CxF) |
AD_SCRI_118.CEL |
0521-31_SetA31.CEL |
SMmini |
OK |
OK |
| 126 |
SM170 |
2907170 |
Steptoe/Morex(BxF) |
AD_SCRI_151.CEL |
|
|
OK |
|
| 127 |
SM171 |
2907171 |
Steptoe/Morex(BxF) |
AD_SCRI_165.CEL |
|
|
ERROR |
|
| 128 |
SM172 |
2907172 |
Steptoe/Morex(OxJ) |
AD_SCRI_152.CEL |
|
|
ERROR |
|
| 129 |
SM173 |
2907173 |
Steptoe/Morex(OxJ) |
AD_SCRI_104.CEL |
0521-32_SetA32.CEL |
SMmini |
OK |
OK |
| 130 |
SM174 |
2907174 |
Steptoe/Morex(BxH) |
AD_SCRI_154.CEL |
|
|
OK |
|
| 131 |
SM176 |
2907176 |
Morex/Steptoe(CxF) |
AD_SCRI_141.CEL |
|
|
OK |
|
| 132 |
SM177 |
2907177 |
Morex/Steptoe(CxF) |
AD_SCRI_111.CEL |
0521-33_SetA33.CEL |
SMmini |
OK |
OK |
| 133 |
SM179 |
2907179 |
Morex/Steptoe(CxF) |
AD_SCRI_166.CEL |
|
|
OK |
|
| 134 |
SM180 |
2907180 |
Morex/Steptoe(IxE) |
AD_SCRI_161.CEL |
|
|
OK |
|
| 135 |
SM181 |
2907181 |
Morex/Steptoe(IxE) |
AD_SCRI_162.CEL |
|
|
OK |
|
| 136 |
SM182 |
2907182 |
Morex/Steptoe(CxF) |
AD_SCRI_163.CEL |
|
|
OK |
|
| 137 |
SM183 |
2907183 |
Morex/Steptoe(CxF) |
AD_SCRI_164.CEL |
|
|
OK |
|
| 138 |
SM184 |
2907184 |
Morex/Steptoe(IxE) |
AD_SCRI_160.CEL |
0521-34_SetA34.CEL |
SMmini |
OK |
OK |
| 139 |
SM185 |
2907185 |
Morex/Steptoe(IxE) |
AD_SCRI_167.CEL |
|
|
OK |
|
| 140 |
SM186 |
2907186 |
Morex/Steptoe(IxE) |
AD_SCRI_62.CEL |
|
|
OK |
|
| 141 |
SM187 |
2907187 |
Morex/Steptoe(IxE) |
AD_SCRI_61.CEL |
|
|
OK |
|
| 142 |
SM188 |
2907188 |
Morex/Steptoe(CxF) |
AD_SCRI_63.CEL |
|
|
OK |
|
| 143 |
SM189 |
2907189 |
Steptoe/Morex(QxG) |
AD_SCRI_80.CEL |
|
|
OK |
|
| 144 |
SM193 |
2907193 |
Morex/Steptoe(IxE) |
AD_SCRI_36.CEL |
|
|
OK |
|
| 145 |
SM194 |
2907194 |
Steptoe/Morex(OxJ) |
AD_SCRI_29.CEL |
|
|
OK |
|
| 146 |
SM196 |
2907196 |
Steptoe/Morex(BxF) |
AD_SCRI_26.CEL |
|
|
OK |
|
| 147 |
SM197 |
2907197 |
Steptoe/Morex(BxF) |
AD_SCRI_85.CEL |
|
|
OK |
|
| 148 |
SM198 |
2907198 |
Morex/Steptoe(IxE) |
AD_SCRI_8.CEL |
|
|
OK |
|
| 149 |
SM199 |
2907199 |
Steptoe/Morex(BxF) |
AD_SCRI_20.CEL |
|
|
OK |
|
| 150 |
SM200 |
2907200 |
Morex/Steptoe(IxE) |
AD_SCRI_38.CEL |
0521-35_SetA35.CEL |
SMmini |
OK |
OK |
| parent |
Steptoe |
|
|
AD_SCRI_17.CEL |
0521-36_SetA36.CEL |
|
|
|
| parent |
Steptoe |
|
|
AD_SCRI_66.CEL |
0521-37_SetA37.CEL |
|
|
|
| parent |
Steptoe |
|
|
AD_SCRI_68.CEL |
0521-38_SetA38.CEL |
|
|
|
| parent |
Morex |
|
|
AD_SCRI_116.CEL |
0521-39_SetA39.CEL |
|
|
|
| parent |
Morex |
|
|
AD_SCRI_14.CEL |
0521-40_SetA40.CEL |
|
|
|
| parent |
Morex |
|
|
AD_SCRI_67.CEL |
0521-41_SetA41.CEL |
|
|
|
About tissues used to generate this set of data:
Plant material according to the current plant ontologies: Embryo-derived tissues: whole plant (PO:0000003) at the development stage 1.05-coleoptile emerged from seed (GRO:0007056); Seedling leaves: primary shoot (PO:0006341) at the developmental stage 2.02-first leaf unfolded (GRO:0007060) (Druka et al. 2006).
To obtain embryo-derived tissue, growth room#2, AN building, SCRI, with the standard laboratory bench positioned in the middle of the room was used to germinate sterilized seeds. Seeds were placed between three layers of wet 3MM filter paper in the 156 10 mm Petri plates. Thirty to fifty seeds per line (per Petri plate) were used. Germination was in the dark, 16 hours at 17 deg C and 8 hours at 12 deg C. After 96 hours, embryo-derived tissue (mesocotyl, coleoptile, and seminal roots) from three grains was dissected and flash frozen in the liquid nitrogen. Germination and collection was repeated two more times. Complete randomization of the Petri plates was done for each germination event. Tissues from all three germinations (collections) were bulked before RNA isolation. Three replicates of the parental cultivars were germinated for each collection.
To obtain seedling leaves, three Microclima 1000 growth chambers (Snijders Scientific B.V., Tilburg, Holland) were used for the experiment. Each cabinet accomodated 40 (13x13 cm) pots. Humidity was set to 70%, with light conditions for 16 hours light at 17C and 8 hours dark at 12C. The cycle started at 10 am with lights on. Light intensity was 337-377 mmol m-2 s-1, measured at the beginning of the experiment, 11 cm from the light source. Measurement was done using Sky Quantium light sensor at 15oC. Plants were placed 55 cm from the light source (from the bulb to the surface of the vermiculite). Ten sterilized seeds per pot were planted and 3 pots per genotype / per cabinet were used. After 12 days, leaf blade and sheath from 5-7 the same size plants was cut off, bulked and flash frozen in the liquid nitrogen.
RNA Sample Processing:
Trizol RNA isolation and RNeasy clean up protocol for whole plants (embryo-derived tissue dissected from 4 days old germinating grains) and the seedling leaves (12 days after planting).
☐ Grind tissue (9 embryos) with a mortar and pestle in liquid nitrogen
☐ Add 5 ml TRIzol (pre-heated to 60oC) to all samples, vortex until all the tissue is thawed, place in the 60oC waterbath..
☐ Incubate samples at 60oC for 10 minutes, vortexing three times.
☐ Centrifuge @ 4000 x rpm @ 4C for 30 minutes (in Eppendorf 5810R).
☐ While centrifuging, label new set of 15 ml tubes
☐ Transfer supernatant to 15 ml centrifuge tube
☐ Add 1 ml of chloroform. Vortex the sample until color shade is uniform at least 5
seconds, and incubate at room temperature for 5 minutes.
☐ Centrifuge @ 4000 x rpm for 30 minutes @ 4oC.
☐ While centrifuging, label new 15 ml tubes
☐ Collect the upper aqueous layer (there will be about 3 mls) and transfer to a new 15 ml tube.
☐ Add 0.6 volumes (2 ml) of isopropanol, mix gently, incubate at room temperature for 20 minutes.
☐ Centrifuge @ 4000 rpm for 30 minutes @ 4oC.
☐ Wash the pellet with 10 ml of cold 75% ethanol. Swirl & centrifuge at
4000 rpm for 15 minutes @ 4oC.
☐ Discard supernatant, centrifuge for 5 min, remove the rest of the ethanol
☐ Air-dry the pellet for 10 minutes, inverted on a kimwipe.
☐ Dissolve pellet in 400 ul of DEPC-treated H2O. Resuspend by pipeting up & down a
few times.
☐ Add 2 ul SuperaseIn. Incubate at 60oC for 10 minutes to resuspend.
☐ Set water bath to 37oC.
☐ Add 50 ul 10X DnaseI Buffer, 45 ul H2O and 5 ul of DnaseI, incubate at 37oC for 1 hr.
☐ Prepare Buffer RLT (Rneasy Clean-up Midi Kit) by adding b-mercaptoethanol (10ul/1ml RLT).
☐ Add 2.0 ml Buffer RLT to the RNA prep and mix thoroughly.
☐ Add 1.4 ml ethanol (96-100%) to the diluted RNA. Mix thoroughly.
☐ Label 15 ml tubes from the kit and place midi columns in them
☐ Apply sample to a Midi column, close tube gently and centrifuge for 20 min at 3000 rpm.
☐ Discard the flow-through.
☐ Add 2.5 ml Buffer RPE to the RNA easy column, close the centrifuge tube gently,
incubate for 3 min
☐ Centrifuge for 10 min at 3000 rpm. Discard the flow-through.
☐ Add another 2.5 ml Buffer RPE to the RNeasy column. Close the centrifuge tube
gently, incubate for 3 min
☐ Centrifuge for 10 min at 3000 rpm, remove flow-through
☐ Centrifuge again for another 5 min.
☐ Label new 15 ml tubes from the kit.
☐ Transfer the RNA easy column to a new tube and pipet 250 ul volume of
RNase-free water directly onto the RNeasy silica-membrane incubate for 1 min
☐ Centrifuge for 5 min at 3000 rpm.
☐ To the same tube add again 250 ul H2O, incubate for 1 min.
☐ Centrifuge for 5 min at 3000 rpm.
☐ Label two sets of 1.5 ml Eppendorf tubes.
☐ Transfer 490 ul to the one tube and 10 ul to another one. Use 10 ul tube for the RNA
Detailed descriptions of these procedures can be found under the ArrayExpress (http://www.ebi.ac.uk/aerep/?) protocol P-MEXP-4631 (Caldo et al. 2004).
Replication and Sample Balance:
3 independent replicates of both parental cultivars Steptoe and Morex were generated for both tissues, embryo and seedling leaf.
Experimental Design and Batch Structure:
Downloading complete data set:
The following are ArrayExpress (http://www.ebi.ac.uk/aerep/?) experiment IDs:
E-TABM-111 (leaf, 41 chips) and E-TABM-112 (embryo derived, 156 chips).
About the array platform:
Affymetrix 22K Barley1 GeneChip probe array (http://www.affymetrix.com/products/arrays/specific/barley.affx ; Affymetrix product #900515 GeneChip Barley Genome Array) representing 21,439 non-redundant Barley1 exemplar sequences was derived from worldwide contribution of 350,000 high-quality ESTs from 84 cDNA libraries, in addition to 1,145 barley gene sequences from the National Center for Biotechnology Information non-redundant database (Close et al 2004). Abbreviated annotations were created based on the exemplar sequence homology by Arnis Druka using data from the Harvest (http://harvest.ucr.edu/) data depository.
About data processing:
Types of the expression data-sets |
Data processing description |
Barley1 Embryo gcRMA SCRI (Dec 06)
Barley1 Leaf gcRMA SCRI (Dec 06) |
The Affymetrix' CEL files that were generated using MAS 5.0 Suite were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
|
Barley1 Embryo MAS 5.0 SCRI (Dec 06)
Barley1 Leaf MAS 5.0 SCRI (Dec 06) |
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite.
|
Barley1 Embryo0 gcRMA SCRI (Apr 06)
Barley1 Leaf gcRMAn SCRI (Dec 06) |
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure (citation of the GeneSpring normalization description):
- Values below 0.01 were set to 0.01.
- Each measurement was divided by the 50.0th percentile of all measurements in that sample.
- Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.
|
Data source acknowledgment:
Plant maintenance, tissue collection, RNA isolation, and data submission to ArrayExpress was done at SCRI by Arnis Druka with support from BBSRC/SEERAD grant
SCR/910/04
'The genetics of gene expression in barley' to Michael Kearsey (University of Birmingham, UK) and Robbie Waugh (SCRI, UK). Probe synthesis, labeling and hybridization were performed according to manufacturer’s protocols (Affymetrix, Santa Clara, CA) at the Iowa State University GeneChip Core facility (Rico Caldo and Roger Wise). ArrayExpress (EBI, UK) team members Tim Rayner, Helen Parkinson, and Alvis Brazma are acknowledged for excellent help with data submission to ArrayExpress.
Contact address:
Arnis Druka
Genetics Programme
Scottish Crop Research Institute
Invergowrie, Dundee DD2 5DA
Angus, Scotland, United Kingdom
Tel +44 01382 562731
Fax +44 01382 568587
adruka@scri.sari.ac.uk
References:
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R. (2006) An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics, Jul;6(3):202-11.
Kleinhofs A, Kilian A, Saghai Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N, Fenwick A, Blake T, Kanazin V, Ananiev E, Dahleen L, Kudrna D, Bollinger J, Knapp SJ, Liu BH, Sorrells M, Heun M, Franckowiak J, Hoffman D, Skadsen R, Steffenson B (1993) A molecular, isozyme, and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86:705-712.
Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514-2528.
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP. (2004) A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiol 134:960-968.
Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B, Blake T, Franckowiak J, Rasmusson D, Sorrells M, Ullrich SE, Wesenberg D, Kleinhofs A (1993) Quantitative trait locus effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392-401
About this text file:
This text file originally generated by Arnis Druka on May 8, 2006. Modified Aug1 by AD. Entered by RWW Aug 4, 2006. Modified by AD Jan 29, 2007, Feb 01, 2007.
|