YEAST annotation definitions ---------------------------- 6-4-2001 Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance. Organism specific part by Nicole Hauser, who considered the complete list to satisfy MIAME2 standard. References, images (tiff format), a list of array elements incl. controls (including gene/clone IDs, array location, descriptions and functional catalogue entries for each spot) as well as normalization strategies and algorithms are not included here but will be available in the results section or directly from the authors. heading1no heading1 heading2no heading2 heading3no heading3 1 common_annotations 1 array 1 - 1 common_annotations 2 hybridisation 2 RNA_preparation 1 common_annotations 2 hybridisation 3 labeling 1 common_annotations 2 hybridisation 4 hybridisation_conditions 1 common_annotations 2 hybridisation 5 stringency_wash 1 common_annotations 2 hybridisation 6 detection 1 common_annotations 3 sample 7 - 1 common_annotations 4 submission 8 - 2 organism_specific_annotations 5 genotype 9 - 2 organism_specific_annotations 5 genotype 10 transgenes_ordered_by_no_in_y1_genes 2 organism_specific_annotations 5 genotype 11 auxotrophic_marker 2 organism_specific_annotations 6 growth_conditions 12 - 2 organism_specific_annotations 7 medium 13 - 2 organism_specific_annotations 7 medium 14 C_source 2 organism_specific_annotations 7 medium 15 additive lastheadingno ano nextano annotation vno nextvno value 1 1 2 array_source 10 11 self_made 1 1 2 array_source 11 12 genome_systems 1 1 2 array_source 12 13 clontech 1 1 2 array_source 13 14 research_genetics 1 2 3 array_series 0 0 [] 1 3 4 array_individual 0 0 [] 1 4 67 array_support 14 15 nylon 1 4 67 array_support 15 16 polypropylene 1 4 67 array_support 16 117 glass 1 67 68 array_support_width 0 0 [mm] 1 68 41 array_support_length 0 0 [mm] 1 41 42 array_surface_chemistry 117 118 unknown_positive_charge 1 41 42 array_surface_chemistry 118 119 poly_L_lysine 1 41 42 array_surface_chemistry 119 120 aldehyde 1 41 42 array_surface_chemistry 120 121 aminosilane 1 42 43 support_manufacturer 121 122 Hybond 1 42 43 support_manufacturer 122 123 Pall 1 42 43 support_manufacturer 123 124 TeleChem 1 42 43 support_manufacturer 124 125 Corning 1 42 43 support_manufacturer 125 126 diehl 1 42 43 support_manufacturer 126 127 stephan 1 43 44 Hybond_support_brand 127 128 non_Hybond 1 43 44 Hybond_support_brand 128 129 N+ 1 44 45 Pall_support_brand 129 130 non_Pall 1 44 45 Pall_support_brand 130 131 Biodyne_B 1 45 46 Corning_support_brand 131 132 non_Corning 1 45 46 Corning_support_brand 132 133 CMT_GAPS 1 46 5 TeleChem_support_brand 133 134 non_TeleChem 1 46 5 TeleChem_support_brand 134 135 Aldehyde 1 46 5 TeleChem_support_brand 135 17 SuperAldehyde 1 5 69 spotted_material 17 18 PCR 1 5 69 spotted_material 18 19 colonies 1 5 69 spotted_material 19 20 DNA-oligo 1 5 69 spotted_material 20 200 PNA-oligo 1 69 70 spotted_material_property 200 201 single_stranded 1 69 70 spotted_material_property 201 202 double_stranded 1 70 71 number_of_elements_on_array_(without_duplicates) 0 0 [] 1 71 47 elements_spotted_as 202 203 single 1 71 47 elements_spotted_as 203 204 duplicate 1 71 47 elements_spotted_as 204 136 triplicate 1 47 48 spotted_material_purification 136 137 non 1 47 48 spotted_material_purification 137 138 isopropanol_precipitation 1 47 48 spotted_material_purification 138 139 QIAquick 1 47 48 spotted_material_purification 139 140 Multiscreen_NU_Millipore 1 48 49 spotting_buffer 140 141 1.5M_NaCl_0.5M_NaOH 1 48 49 spotting_buffer 141 142 28mM_EDC_4.4volpromill_NMI 1 48 49 spotting_buffer 142 143 spottingsolution_by_diehl 1 48 49 spotting_buffer 143 144 MicroSpotting_solution_TeleChem 1 48 49 spotting_buffer 144 145 3xSSC 1 48 49 spotting_buffer 145 146 3xSSC_50%DMSO 1 49 50 spotting_robot 146 147 SDDC-2_ESI 1 49 50 spotting_robot 147 148 Biogrid_Biorobotics 1 49 50 spotting_robot 148 149 Microgrid_II_Biorobotics 1 49 50 spotting_robot 149 150 Omnigrid_Genemachines 1 49 50 spotting_robot 150 151 QArray_Genetix 1 50 51 spotting_pins 151 152 solid 1 50 51 spotting_pins 152 153 SMP-3_Telechem 1 50 51 spotting_pins 153 154 Biogrid_Biorobotics 1 51 52 relative_humidity 154 155 defined 1 51 52 relative_humidity 155 156 estimated 1 51 52 relative_humidity 156 157 unknown(enter_0%) 1 52 53 relative_humidity 0 0 [%] 1 53 54 temperature 157 158 defined 1 53 54 temperature 158 159 estimated 1 53 54 temperature 159 160 unknown(enter_0deg.C) 1 54 55 temperature 0 0 [deg.C] 1 55 6 postprocessing 160 161 neutralizing_by_1.5MNaCL_0.5MTrispH7.5_1mMEDTA 1 55 6 postprocessing 161 162 2h_at_65deg.C 1 55 6 postprocessing 162 163 succinic_anhydride_Stanford_protocol 1 55 6 postprocessing 163 164 succinic_anhydride_protocol_by_diehl 1 55 6 postprocessing 164 165 BSA_Tigr_protocol 1 55 6 postprocessing 165 21 NaBH4_Telechem_protocol 1 6 7 readfile 0 0 [] 1 7 8 array_hybridisation 0 0 [] 2 8 9 material_source 21 22 fresh 2 8 9 material_source 22 23 frozen 2 8 9 material_source 23 94 RNA_later 2 8 9 material_source 94 24 cDNA_subtraction 2 9 10 preparation_of_total_RNA 24 25 trizol 2 9 10 preparation_of_total_RNA 25 26 columns 2 9 10 preparation_of_total_RNA 26 95 phenol 2 9 10 preparation_of_total_RNA 95 27 not_applicable 2 10 11 preparation_of_PolyA+ 27 28 none 2 10 11 preparation_of_PolyA+ 28 29 dynabeads 2 10 11 preparation_of_PolyA+ 29 30 oligotex 2 10 11 preparation_of_PolyA+ 30 96 cellulose 2 10 11 preparation_of_PolyA+ 96 31 not_applicable 3 11 40 amount_of_RNA 0 0 [microgram] 3 40 12 amount_of_cDNA 0 0 [microgram] 3 12 13 enzym 31 32 superscript 3 12 13 enzym 32 33 AMV 3 12 13 enzym 33 166 M-MLV 3 12 13 enzym 166 97 OmniScript 3 12 13 enzym 97 34 klenow 3 13 14 priming 34 35 oligo_dT 3 13 14 priming 35 36 anchored_oligo_dT 3 13 14 priming 36 37 random_hexamer 3 13 14 priming 37 98 combined_oligo_dT-random_hexamer 3 13 14 priming 98 38 pcr_select 3 14 56 nucleotide 38 39 dCTP 3 14 56 nucleotide 39 167 dATP 3 14 56 nucleotide 167 168 aa-dUTP 3 14 56 nucleotide 168 169 dUTP 3 56 15 nucleotide_removal 169 170 G50_Pharmacia 3 56 15 nucleotide_removal 170 171 ammium_acetate_isopropanol_precipitation 3 56 15 nucleotide_removal 171 172 QIAquick_Qiagen 3 56 15 nucleotide_removal 172 173 GFX_columns_Pharmacia 3 56 15 nucleotide_removal 173 40 YM30_Amicon 3 15 66 label 40 41 33P 3 15 66 label 41 42 32P 3 15 66 label 42 43 Cy3 3 15 66 label 43 174 Cy5 3 15 66 label 174 175 Alexa488 3 15 66 label 175 193 Alexa594 3 66 38 days_from_calibration_date_applicable 193 194 yes 3 66 38 days_from_calibration_date_applicable 194 44 no(enter_0d) 3 38 16 days_from_calibration_date 0 0 [d] 3 16 17 label_incorporation_rate 0 0 [%] 3 17 18 total_activity 0 0 [cpm] 4 18 57 buffer 44 45 0.5M_Na_phosphate_pH7.2_7%_SDS 4 18 57 buffer 45 46 5x_SSC_5x_denhardts_0.5%_SDS 4 18 57 buffer 46 47 4x_SSC_7.2%_Na_sarcosyl 4 18 57 buffer 47 48 Clontech_Express_hyb 4 18 57 buffer 48 176 ambion_Northern_max 4 57 19 prehybridization_without_target 176 177 no 4 57 19 prehybridization_without_target 177 49 yes 4 19 75 competitors 49 50 none 4 19 75 competitors 50 51 tRNA 4 19 75 competitors 51 52 Cot1 4 19 75 competitors 52 53 dA40 4 19 75 competitors 53 99 salmon_sperm 4 19 75 competitors 99 100 dA40_Cot1_salmonsperm 4 19 75 competitors 100 101 dA40_Cot1_tRNA_salmonsperm 4 19 75 competitors 101 102 dA40_Cot1_specificoligos_salmonsperm 4 19 75 competitors 102 211 dA40_Cot1_specificoligos_tRNA_salmonsperm 4 75 76 hybridisation_device 211 212 water_bath 4 75 76 hybridisation_device 212 213 rotating_oven 4 76 20 hybridisation_instrument 213 214 hybridisation_bottle 4 76 20 hybridisation_instrument 214 215 hybridisation_chamber_corning 4 76 20 hybridisation_instrument 215 216 hybridisation_chamber_ArrayIt 4 76 20 hybridisation_instrument 216 178 hybridisation_chamber_ClonTech 4 20 21 hybridisation_temp 0 0 [deg.C] 4 21 58 buffer_volume 0 0 [ml] 4 58 59 coverslip_used 178 179 no_(enter_size_0) 4 58 59 coverslip_used 179 54 yes 4 59 22 coverslip_size 0 0 [mmxmm] 4 22 23 hybridisation_length 0 0 [h] 5 23 24 wash_buffer 54 55 0.1xSSC_0.1%SDS 5 23 24 wash_buffer 55 56 0.6xSSC_1%SDS 5 23 24 wash_buffer 56 57 0.2xSSC_0.1%SDS 5 23 24 wash_buffer 57 180 40mMNaPipH7_0.1%SDS 5 24 25 times 0 0 [] 5 25 26 wash_length 0 0 [min] 5 26 60 temperature 0 0 [deg.C] 6 60 27 exposure_time_applicable 180 181 yes 6 60 27 exposure_time_applicable 181 58 no_(enter_0h) 6 27 28 exposure_time 0 0 [h] 6 28 72 measuring_device 58 59 MD_storm860_phos 6 28 72 measuring_device 59 60 MD_storm860_red 6 28 72 measuring_device 60 113 MD_storm860_blue 6 28 72 measuring_device 113 114 MD_425 6 28 72 measuring_device 114 61 MD_475A_phos 6 28 72 measuring_device 61 109 Fuji_BAS1500 6 28 72 measuring_device 109 62 Fuji_FLA3000 6 28 72 measuring_device 62 63 BioRad 6 28 72 measuring_device 63 182 ScanArray3000_GSI_Lumonics 6 28 72 measuring_device 182 183 ScanArray5000_GSI_Lumonics 6 28 72 measuring_device 183 205 Axon_4000a_Axon 6 72 73 scanning_software 205 206 Fuji_Image_Reader_FLA3000_3000G_V1.0 6 72 73 scanning_software 206 207 BAS_reader_V2.26beta 6 72 73 scanning_software 207 208 Storm_scanner_control 6 72 73 scanning_software 208 209 Typhoon_scanner_control_V1.0 6 72 73 scanning_software 209 210 Scan_Array3000_V3.11_Controller_V2.03 6 72 73 scanning_software 210 184 Scan Array_V2.1 6 73 61 spacial_resolution 0 0 [microm] 6 61 62 pixelsize 0 0 [micromxmicrom] 6 62 63 PMT_setting_applicable 184 185 no(enter_0%) 6 62 63 PMT_setting_applicable 185 186 yes 6 63 64 PMT_setting 0 0 [%] 6 64 65 laser_power_setting_applicable 186 187 no(enter_0%) 6 64 65 laser_power_setting_applicable 187 64 yes 6 65 29 laser_power_setting 0 0 [%] 6 29 30 imaging_software 64 65 AIS 6 29 30 imaging_software 65 66 HDG 6 29 30 imaging_software 66 67 XDotsReader 6 29 30 imaging_software 67 68 imagene 6 29 30 imaging_software 68 188 Xdigitise 6 29 30 imaging_software 188 189 GenePixPro 6 29 30 imaging_software 189 69 QuantArray 6 30 31 background_correction 69 70 none 6 30 31 background_correction 70 71 local_background 6 30 31 background_correction 71 72 block_background 6 30 31 background_correction 72 73 empty_spots_average 6 30 31 background_correction 73 74 empty_spots_per_block 6 31 74 spot_detection 74 75 all_spots 6 31 74 spot_detection 75 76 only_positive_spots 6 74 32 spot_dimension_(diameter) 0 0 [microm] 6 32 33 spot_size 76 77 fixed 6 32 33 spot_size 77 78 variable 6 33 34 intensity_measurement 78 79 highest_value_in_spot_centre 6 33 34 intensity_measurement 79 80 sum_of_pixels_within_boundary 6 33 34 intensity_measurement 80 81 mean_of_pixels_within_boundary 7 34 35 organism 81 82 Saccharomyces_cerevisiae 7 34 35 organism 82 83 Arabidopsis_thaliana 7 34 35 organism 83 103 murine_biopsy 7 34 35 organism 103 84 murine_cell_line 7 34 35 organism 84 85 human_biopsy 7 34 35 organism 85 86 human_cell_line 7 34 35 organism 86 192 Bacillus_subtilis 7 34 35 organism 192 199 Trypanosoma_brucei 7 34 35 organism 199 87 Candida_albicans 8 35 36 date_of_entry_day 0 0 [] 8 36 37 date_of_entry_month 0 0 [] 8 37 39 date_of_entry_year 0 0 [] 8 39 1035 experimentator 104 115 bastuk 8 39 1035 experimentator 115 105 becerra 8 39 1035 experimentator 105 88 bier 8 39 1035 experimentator 88 190 boer 8 39 1035 experimentator 190 196 diehl 8 39 1035 experimentator 196 191 fischer 8 39 1035 experimentator 191 87 grahlmann 8 39 1035 experimentator 87 91 hauser 8 39 1035 experimentator 91 112 kornacker 8 39 1035 experimentator 112 107 lagorce 8 39 1035 experimentator 107 90 lombardia 8 39 1035 experimentator 90 108 lutz 8 39 1035 experimentator 108 92 meijer 8 39 1035 experimentator 92 198 mendel 8 39 1035 experimentator 198 195 reile 8 39 1035 experimentator 195 197 scheideler 8 39 1035 experimentator 197 111 schrenk 8 39 1035 experimentator 111 110 steiner 8 39 1035 experimentator 110 106 sueltmann 8 39 1035 experimentator 106 89 tournu 8 39 1035 experimentator 89 93 wilmer 8 39 1035 experimentator 93 116 wittig 8 39 1035 experimentator 116 1087 yin 9 1035 1036 strain 1087 1088 FY1679 9 1035 1036 strain 1088 1089 RS453 9 1035 1036 strain 1089 1090 Y546 9 1035 1036 strain 1090 1091 CEN_PK2 9 1035 1036 strain 1091 1092 3E2 9 1035 1036 strain 1092 1124 702 9 1035 1036 strain 1124 1125 MYC730 9 1035 1036 strain 1125 1126 T73 9 1035 1036 strain 1126 1127 WC4alpha 9 1035 1036 strain 1127 1128 YSH2alpha 9 1035 1036 strain 1128 1129 FY73 9 1035 1036 strain 1129 1130 L5528 9 1035 1036 strain 1130 1139 L5743 9 1035 1036 strain 1139 1140 W303 9 1035 1036 strain 1140 1141 FY834 9 1035 1036 strain 1141 1142 AR27 9 1035 1036 strain 1142 1143 X2180 9 1035 1036 strain 1143 1093 aGH1 9 1036 1037 mating_type 1093 1094 a 9 1036 1037 mating_type 1094 1095 alpha 9 1036 1037 mating_type 1095 1100 both 10 1037 1038 genetic_variation 1100 1096 WT 10 1037 1038 genetic_variation 1096 1097 mutation 10 1037 1038 genetic_variation 1097 1098 ko 10 1037 1038 genetic_variation 1098 1099 overexpression 10 1037 1038 genetic_variation 1099 1101 inducible_promoter 10 1038 1056 transgene 0 0 [no_in_y1_genes] 10 1056 1057 2nd_genetic_variation 1100 1096 WT 10 1056 1057 2nd_genetic_variation 1096 1097 mutation 10 1056 1057 2nd_genetic_variation 1097 1098 ko 10 1056 1057 2nd_genetic_variation 1098 1099 overexpression 10 1056 1057 2nd_genetic_variation 1099 1101 inducible_promoter 10 1057 1058 2nd_transgene 0 0 [no_in_y1_genes] 10 1058 1059 3rd_genetic_variation 1100 1096 WT 10 1058 1059 3rd_genetic_variation 1096 1097 mutation 10 1058 1059 3rd_genetic_variation 1097 1098 ko 10 1058 1059 3rd_genetic_variation 1098 1099 overexpression 10 1058 1059 3rd_genetic_variation 1099 1101 inducible_promoter 10 1059 1060 3rd_transgene 0 0 [no_in_y1_genes] 10 1060 1061 4th_genetic_variation 1100 1096 WT 10 1060 1061 4th_genetic_variation 1096 1097 mutation 10 1060 1061 4th_genetic_variation 1097 1098 ko 10 1060 1061 4th_genetic_variation 1098 1099 overexpression 10 1060 1061 4th_genetic_variation 1099 1101 inducible_promoter 10 1061 1062 4th_transgene 0 0 [no_in_y1_genes] 10 1062 1063 5th_genetic_variation 1100 1096 WT 10 1062 1063 5th_genetic_variation 1096 1097 mutation 10 1062 1063 5th_genetic_variation 1097 1098 ko 10 1062 1063 5th_genetic_variation 1098 1099 overexpression 10 1062 1063 5th_genetic_variation 1099 1101 inducible_promoter 10 1063 1039 5th_transgene 0 0 [no_in_y1_genes] 11 1039 1040 LEU2 1101 1102 yes 11 1039 1040 LEU2 1102 1103 no 11 1040 1041 URA3 1103 1104 yes 11 1040 1041 URA3 1104 1105 no 11 1041 1042 TRP1 1105 1106 yes 11 1041 1042 TRP1 1106 1107 no 11 1042 1043 HIS3 1107 1108 yes 11 1042 1043 HIS3 1108 1109 no 11 1043 1044 LYS2 1109 1110 yes 11 1043 1044 LYS2 1110 1111 no 11 1044 1066 ADE2 1111 1112 yes 11 1044 1066 ADE2 1112 1137 no 12 1066 1045 culture 1137 1138 liquid 12 1066 1045 culture 1138 1113 solid 12 1045 1046 growth_phase 1113 1131 exponential 12 1045 1046 growth_phase 1131 1114 pseudo_hyphal 12 1045 1046 growth_phase 1114 1147 stationary 12 1045 1046 growth_phase 1147 1115 arrested 12 1046 1064 temperature 0 0 [deg.C] 12 1064 1047 temperature_shift_incubation_period 0 0 [min] 12 1047 1048 energy_metabolism 1115 1116 aerob 12 1047 1048 energy_metabolism 1116 1117 anaerob 13 1048 1049 base 1117 1118 YPD 13 1048 1049 base 1118 1120 SDC 13 1048 1049 base 1120 1132 MV 13 1048 1049 base 1132 1133 YNB 13 1048 1049 base 1133 1134 YNB_without_aa_without_am_sulfate 13 1048 1049 base 1134 1144 YNB_without_calcium 13 1048 1049 base 1144 1121 CM 14 1049 1050 glucose 0 0 [%] 14 1050 1051 galactose 0 0 [%] 14 1051 1052 ethanol 0 0 [%] 14 1052 1065 glycerol 0 0 [%] 14 1065 1067 sucrose 0 0 [%] 14 1067 1053 lactate 0 0 [%] 15 1053 1054 temporary_additive 1121 1122 H2O2 15 1053 1054 temporary_additive 1122 1135 NaCl 15 1053 1054 temporary_additive 1135 1136 calcium 15 1053 1054 temporary_additive 1136 1145 isoamylalcohol 15 1053 1054 temporary_additive 1145 1146 sorbitol 15 1053 1054 temporary_additive 1146 1148 ammonium_sulfate 15 1053 1054 temporary_additive 1148 1123 glucose 15 1053 1054 temporary_additive 1123 -1 none 15 1054 1055 concentration 0 0 [mM] 15 1055 -1 incubation_period 0 0 [min]