NEUROSPORA CRASSA annotation definitions ---------------------------------------- 29-4-2001 Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl; Organism specific part by Verena Aign. 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 6 growth_conditions 10 - 2 organism_specific_annotations 6 growth_conditions 11 light_periods 2 organism_specific_annotations 7 medium 12 - 2 organism_specific_annotations 7 medium 13 C_source 2 organism_specific_annotations 7 medium 14 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 5035 experimentator 104 115 bastuk 8 39 5035 experimentator 115 105 becerra 8 39 5035 experimentator 105 88 bier 8 39 5035 experimentator 88 190 boer 8 39 5035 experimentator 190 196 diehl 8 39 5035 experimentator 196 191 fischer 8 39 5035 experimentator 191 87 grahlmann 8 39 5035 experimentator 87 91 hauser 8 39 5035 experimentator 91 112 kornacker 8 39 5035 experimentator 112 107 lagorce 8 39 5035 experimentator 107 90 lombardia 8 39 5035 experimentator 90 108 lutz 8 39 5035 experimentator 108 92 meijer 8 39 5035 experimentator 92 198 mendel 8 39 5035 experimentator 198 195 reile 8 39 5035 experimentator 195 197 scheideler 8 39 5035 experimentator 197 111 schrenk 8 39 5035 experimentator 111 110 steiner 8 39 5035 experimentator 110 106 sueltmann 8 39 5035 experimentator 106 89 tournu 8 39 5035 experimentator 89 93 wilmer 8 39 5035 experimentator 93 116 wittig 8 39 5035 experimentator 116 1087 yin 9 5035 5036 strain 5035 5036 740R23_1A 9 5035 5036 strain 5036 5037 deltaWC_1 9 5035 5036 strain 5037 5038 deltaWC_2 9 5036 5037 genetic_variation 5038 5039 WT 9 5036 5037 genetic_variation 5039 5040 mutation 9 5036 5037 genetic_variation 5040 5041 ko 9 5036 5037 genetic_variation 5041 5042 overexpression 9 5036 5037 genetic_variation 5042 5043 inducible_promoter 9 5037 5038 transgene 0 0 [no_in_y1_genes] 10 5038 5039 culture 5043 5044 liquid 10 5038 5039 culture 5044 5045 solid 10 5039 5040 growth_phase 5045 5046 conidial 10 5039 5040 growth_phase 5046 5047 mycedial 10 5039 5040 growth_phase 5047 5048 perithecial 10 5040 5041 temperature 0 0 [deg.C] 11 5041 5042 first_period 5048 5049 light 11 5041 5042 first_period 5049 5050 dark 11 5042 5043 first_period_duration 0 0 [h] 11 5043 5044 second_period 5050 5051 light 11 5043 5044 second_period 5051 5052 dark 11 5044 5045 second_period_duration 0 0 [h] 12 5045 5046 base 5052 5053 Vogels_minimal 13 5046 5047 glucose 0 0 [%] 13 5047 5048 galactose 0 0 [%] 13 5048 5049 ethanol 0 0 [%] 13 5049 5050 glycerol 0 0 [%] 13 5050 5051 sucrose 0 0 [%] 13 5051 5052 lactate 0 0 [%] 14 5052 5053 temporary_additive 5053 5054 H2O2 14 5052 5053 temporary_additive 5054 5055 NaCl 14 5052 5053 temporary_additive 5055 5056 calcium 14 5052 5053 temporary_additive 5056 5057 isoamylalcohol 14 5052 5053 temporary_additive 5057 5058 sorbitol 14 5052 5053 temporary_additive 5058 5059 ammonium_sulfate 14 5052 5053 temporary_additive 5059 5060 glucose 14 5052 5053 temporary_additive 5060 -1 none 14 5053 5054 concentration 0 0 [mM] 14 5054 -1 incubation_period 0 0 [min]