HYDRACTINIA annotation definitions ---------------------------------- 23-5-2002 Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance. Organism specific part by Marcus Frohme. 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 parental_information 9 father_of_animal_in_experiment 2 organism_specific_annotations 5 parental_information 10 mother_of_animal_in_experiment 2 organism_specific_annotations 5 parental_information 11 mating_yield 2 organism_specific_annotations 6 animal_in_experiment 12 basic_information 2 organism_specific_annotations 6 animal_in_experiment 13 strain_or_phenotype 2 organism_specific_annotations 7 culture_conditions 14 preparation 2 organism_specific_annotations 7 culture_conditions 15 feeding 2 organism_specific_annotations 8 experimental_settings 16 basic_tissue_information 2 organism_specific_annotations 8 experimental_settings 17 experimental_category 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 130 223 Biodyne_B 1 44 45 Pall_support_brand 223 131 polypropylene 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 145 227 3xSSC_50%DMSO 1 48 49 spotting_buffer 227 228 150mM_sodiumphosphate_pH8.5 1 48 49 spotting_buffer 228 146 150mM_sodiumphosphate_pH8.5_0.01%SDS 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 77 postprocessing 160 161 neutralizing_by_1.5MNaCL_0.5MTrispH7.5_1mMEDTA 1 55 77 postprocessing 161 162 2h_at_65deg.C 1 55 77 postprocessing 162 163 succinic_anhydride_Stanford_protocol 1 55 77 postprocessing 163 164 succinic_anhydride_protocol_by_diehl 1 55 77 postprocessing 164 165 BSA_Tigr_protocol 1 55 77 postprocessing 165 224 NaBH4_Telechem_protocol 1 77 78 uv_crosslink_applicable 224 225 no(enter_0) 1 77 78 uv_crosslink_applicable 225 21 yes 1 78 6 uv_crosslink_energy 0 0 [x100microJpercm2] 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 170 226 ammium_acetate_isopropanol_precipitation 3 56 15 nucleotide_removal 226 171 Na_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 44 229 0.5M_Na_phosphate_pH7.2_7%_SDS 4 18 57 buffer 229 230 5x_SSC_0.1%_SDS 4 18 57 buffer 230 231 Genisphere3DNA 4 18 57 buffer 231 232 Genisphere3DNAformamide 4 18 57 buffer 232 45 3x_SSC_2.5x_denhardts_0.08%_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 48 221 ambion_Northern_max 4 18 57 buffer 221 176 3x_SSC_5x_denhardts_1%_SDS_5%_dextransulfate_50%_formamide 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 51 217 Cot1 4 19 75 competitors 217 52 dA20 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_TeleChem 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 56 222 0.2xSSC_0.1%SDS 5 23 24 wash_buffer 222 233 0.2xSSC 5 23 24 wash_buffer 233 234 0.1xSSC 5 23 24 wash_buffer 234 57 0.06xSSC 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 199 220 Candida_albicans 7 34 35 organism 220 218 Neurospora_crassa 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 [] 3 39 9035 experimentator 218 104 aign 8 39 9035 experimentator 104 235 bastuk 8 39 9035 experimentator 235 115 bauer 8 39 9035 experimentator 115 105 becerra 8 39 9035 experimentator 105 88 bier 8 39 9035 experimentator 88 190 boer 8 39 9035 experimentator 190 196 diehl 8 39 9035 experimentator 196 191 fischer 8 39 9035 experimentator 191 219 grahlmann 8 39 9035 experimentator 219 87 grees 8 39 9035 experimentator 87 91 hauser 8 39 9035 experimentator 91 112 kornacker 8 39 9035 experimentator 112 107 lagorce 8 39 9035 experimentator 107 90 lombardia 8 39 9035 experimentator 90 108 lutz 8 39 9035 experimentator 108 92 meijer 8 39 9035 experimentator 92 198 mendel 8 39 9035 experimentator 198 195 reile 8 39 9035 experimentator 195 197 scheideler 8 39 9035 experimentator 197 111 schrenk 8 39 9035 experimentator 111 110 steiner 8 39 9035 experimentator 110 106 sueltmann 8 39 9035 experimentator 106 89 tournu 8 39 9035 experimentator 89 93 wilmer 8 39 9035 experimentator 93 116 wittig 8 39 9035 experimentator 116 9087 yin 9 9035 9036 strain_definition 9087 9088 undefined 9 9035 9036 strain_definition 9088 9089 mutant 9 9035 9036 strain_definition 9089 9090 RNAi_phenotype 10 9036 9037 strain_definition 9090 9091 undefined 10 9036 9037 strain_definition 9091 9092 mutant 10 9036 9037 strain_definition 9092 9093 RNAi_phenotype 11 9037 9038 strain_definition 9093 9094 defined 11 9037 9038 strain_definition 9094 9095 undefined 11 9037 9038 strain_definition 9095 9096 cross 12 9038 9039 type_definition 9096 9097 defined 12 9038 9039 type_definition 9097 9098 undefined 12 9039 9040 strain_definition 9098 9099 Wildtype 12 9039 9040 strain_definition 9099 9100 cross 12 9039 9040 strain_definition 9100 9101 mutant 12 9039 9040 strain_definition 9101 9102 RNAi 12 9040 9041 sex_of_experiment_animal 9102 9103 male 12 9040 9041 sex_of_experiment_animal 9103 9104 female 12 9040 9041 sex_of_experiment_animal 9104 9105 mixed 12 9040 9041 sex_of_experiment_animal 9105 9106 unknown 13 9041 9042 wildtype_ID 9106 9107 no_wildtype 13 9041 9042 wildtype_ID 9107 9108 wt_1_(stoloniferous) 13 9041 9042 wildtype_ID 9108 9109 wt_2_(plateforming) 13 9042 9043 mutant_ID 9109 9110 no_mutant 13 9042 9043 mutant_ID 9110 9111 Diss 13 9042 9043 mutant_ID 9111 9112 He-mh 13 9042 9043 mutant_ID 9112 9113 Dpp 13 9042 9043 mutant_ID 9113 9114 Gkp 13 9042 9043 mutant_ID 9114 9115 Bst 13 9043 9044 RNAi_ID 9115 9116 no_RNAi 13 9043 9044 RNAi_ID 9116 9117 act1 13 9043 9044 RNAi_ID 9117 9118 ast1 13 9043 9044 RNAi_ID 9118 9119 ast2 13 9043 9044 RNAi_ID 9119 9120 cad1 13 9044 9045 developmental_stage 9120 9121 gamet 13 9044 9045 developmental_stage 9121 9122 zygote 13 9044 9045 developmental_stage 9122 9123 gastrula 13 9044 9045 developmental_stage 9123 9124 planula 13 9044 9045 developmental_stage 9124 9125 induced_planula 13 9044 9045 developmental_stage 9125 9126 primary_polyp 13 9044 9045 developmental_stage 9126 9127 immature_colony 13 9044 9045 developmental_stage 9127 9128 mature_colony 14 9045 9046 time_of_preparation 9128 9129 morning 14 9045 9046 time_of_preparation 9129 9130 afternoon 14 9045 9046 time_of_preparation 9130 9131 evening 14 9046 9047 preparator 9131 9132 Jasna_Guduric 14 9046 9047 preparator 9132 9133 Uri_Frank 14 9046 9047 preparator 9133 9134 Brahim_Mali 14 9046 9047 preparator 9134 9135 Regina_Teo 14 9046 9047 preparator 9135 9136 Frank_Moehrlen 14 9046 9047 preparator 9136 9137 Guenter_Plickert 14 9046 9047 preparator 9137 9138 Melanie_Maniura 14 9046 9047 preparator 9138 9139 Thomas_Leitz 14 9046 9047 preparator 9139 9140 Stefanie_Seipp 15 9047 9048 fed_last_24_hours 9140 9141 yes 15 9047 9048 fed_last_24_hours 9141 9142 no 16 9048 9049 fed_last_24_hours 9142 9143 whole_animals 16 9048 9049 fed_last_24_hours 9143 9144 selected_tissues 16 9049 9050 embryonic 9144 9145 no 16 9049 9050 embryonic 9145 9146 yes 16 9050 9051 posterior_planula 9146 9147 no 16 9050 9051 posterior_planula 9147 9148 yes 16 9051 9052 anterior_planula 9148 9149 no 16 9051 9052 anterior_planula 9149 9150 yes 16 9052 9053 tentacles 9150 9151 no 16 9052 9053 tentacles 9151 9152 yes 16 9053 9054 head 9152 9153 no 16 9053 9054 head 9153 9154 yes 16 9054 9055 body_column 9154 9155 no 16 9054 9055 body_column 9155 9156 yes 16 9055 9056 stolones 9156 9157 no 16 9055 9056 stolones 9157 9158 yes 16 9056 9057 stolone_tip 9158 9159 no 16 9056 9057 stolone_tip 9159 9160 yes 16 9057 9058 stolone_mat 9160 9161 no 16 9057 9058 stolone_mat 9161 9162 yes 17 9058 9059 tissue_specificity 9162 9163 no 17 9058 9059 tissue_specificity 9163 9164 yes 17 9059 9060 development 9164 9165 no 17 9059 9060 development 9165 9166 yes 17 9060 9061 RNAi_phenotype 9166 9167 no 17 9060 9061 RNAi_phenotype 9167 9168 yes 17 9061 9062 strain_specificity 9168 9169 no 17 9061 9062 strain_specificity 9169 9170 yes 17 9062 9063 Induction_or_treatment 9170 9171 no 17 9062 9063 Induction_or_treatment 9171 9172 yes 17 9063 -1 regeneration 9172 9173 no 17 9063 -1 regeneration 9173 -1 yes