TRYPANOSOMA BRUCEI annotation definitions ----------------------------------------- 29-4-2001 Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl; Organism specific part by Susanne Grahlmann. 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 2 organism_specific_annotations 6 growth_conditions 11 - 2 organism_specific_annotations 6 growth_conditions 12 in_vitro 2 organism_specific_annotations 6 growth_conditions 13 mouse 2 organism_specific_annotations 6 growth_conditions 14 fly 2 organism_specific_annotations 7 treatment 15 chemical_stimulation 2 organism_specific_annotations 7 treatment 16 temperature_shock 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 41 array_support 14 15 nylon 1 4 41 array_support 15 16 polypropylene 1 4 41 array_support 16 117 glass 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 47 spotted_material 17 18 PCR 1 5 47 spotted_material 18 19 colonies 1 5 47 spotted_material 19 20 DNA-oligo 1 5 47 spotted_material 20 136 PNA-oligo 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 church 4 18 57 buffer 45 46 denhardts 4 18 57 buffer 46 47 SSarc 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 20 competitors 49 50 none 4 19 20 competitors 50 51 tRNA 4 19 20 competitors 51 52 Cot1 4 19 20 competitors 52 53 dA40 4 19 20 competitors 53 99 salmon_sperm 4 19 20 competitors 99 100 dA40_Cot1_salmonsperm 4 19 20 competitors 100 101 dA40_Cot1_tRNA_salmonsperm 4 19 20 competitors 101 102 dA40_Cot1_specificoligos_salmonsperm 4 19 20 competitors 102 178 dA40_Cot1_specificoligos_tRNA_salmonsperm 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 61 measuring_device 58 59 MD_storm860_phos 6 28 61 measuring_device 59 60 MD_storm860_red 6 28 61 measuring_device 60 113 MD_storm860_blue 6 28 61 measuring_device 113 114 MD_425 6 28 61 measuring_device 114 61 MD_475A_phos 6 28 61 measuring_device 61 109 Fuji_BAS1500 6 28 61 measuring_device 109 62 Fuji_FLA3000 6 28 61 measuring_device 62 63 BioRad 6 28 61 measuring_device 63 182 ScanArray3000_GSI_Lumonics 6 28 61 measuring_device 182 183 ScanArray5000_GSI_Lumonics 6 28 61 measuring_device 183 184 Axon_4000a_Axon 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 32 spot_detection 74 75 all_spots 6 31 32 spot_detection 75 76 only_positive_spots 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 yeast 7 34 35 organism 82 83 arabidopsis 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 b_subtilis 7 34 35 organism 192 87 trypanosoma_brucei 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 4035 experimentator 104 115 bastuk 8 39 4035 experimentator 115 105 becerra 8 39 4035 experimentator 105 88 bier 8 39 4035 experimentator 88 190 boer 8 39 4035 experimentator 190 191 diehl 8 39 4035 experimentator 191 87 grahlmann 8 39 4035 experimentator 87 91 hauser 8 39 4035 experimentator 91 112 kornacker 8 39 4035 experimentator 112 107 lagorce 8 39 4035 experimentator 107 90 lombardia 8 39 4035 experimentator 90 108 lutz 8 39 4035 experimentator 108 92 meijer 8 39 4035 experimentator 92 111 mendel 8 39 4035 experimentator 111 110 steiner 8 39 4035 experimentator 110 106 sueltmann 8 39 4035 experimentator 106 89 tournu 8 39 4035 experimentator 89 93 wilmer 8 39 4035 experimentator 93 116 wittig 8 39 4035 experimentator 116 4010 yin 9 4035 4036 subspecies 4010 4011 brucei 9 4035 4036 subspecies 4011 4012 gambiense 9 4035 4036 subspecies 4012 4013 rhodesiense 9 4036 4037 strain 4013 4014 TREU927_4 9 4036 4037 strain 4014 4015 vATxy 10 4037 4038 genetic_variation 4015 4016 WT 10 4037 4038 genetic_variation 4016 4017 mutation 10 4037 4038 genetic_variation 4017 4018 ko 10 4037 4038 genetic_variation 4018 4019 overexpression 10 4037 4038 genetic_variation 4019 4020 inducible_promoter 10 4038 4039 transgene 0 0 [no_in_y1_genes] 10 4039 4040 2nd_genetic_variation 4015 4016 WT 10 4039 4040 2nd_genetic_variation 4016 4017 mutation 10 4039 4040 2nd_genetic_variation 4017 4018 ko 10 4039 4040 2nd_genetic_variation 4018 4019 overexpression 10 4039 4040 2nd_genetic_variation 4019 4020 inducible_promoter 10 4040 4041 2nd_transgene 0 0 [no_in_y1_genes] 10 4041 4042 3rd_genetic_variation 4015 4016 WT 10 4041 4042 3rd_genetic_variation 4016 4017 mutation 10 4041 4042 3rd_genetic_variation 4017 4018 ko 10 4041 4042 3rd_genetic_variation 4018 4019 overexpression 10 4041 4042 3rd_genetic_variation 4019 4020 inducible_promoter 10 4042 4043 3rd_transgene 0 0 [no_in_y1_genes] 10 4043 4044 4th_genetic_variation 4015 4016 WT 10 4043 4044 4th_genetic_variation 4016 4017 mutation 10 4043 4044 4th_genetic_variation 4017 4018 ko 10 4043 4044 4th_genetic_variation 4018 4019 overexpression 10 4043 4044 4th_genetic_variation 4019 4020 inducible_promoter 10 4044 4045 4th_transgene 0 0 [no_in_y1_genes] 10 4045 4046 5th_genetic_variation 4015 4016 WT 10 4045 4046 5th_genetic_variation 4016 4017 mutation 10 4045 4046 5th_genetic_variation 4017 4018 ko 10 4045 4046 5th_genetic_variation 4018 4019 overexpression 10 4045 4046 5th_genetic_variation 4019 4020 inducible_promoter 10 4046 4047 5th_transgene 0 0 [no_in_y1_genes] 11 4047 4048 stage 4020 4021 slender 11 4047 4048 stage 4021 4022 stumpy 11 4047 4048 stage 4022 4023 procyclic 11 4047 4048 stage 4023 4024 metacyclic 11 4047 4048 stage 4024 4025 epimastigote 11 4047 4048 stage 4025 4026 not_applicable 11 4048 4049 host 4026 4027 in_vitro 11 4048 4049 host 4027 4028 mouse 11 4048 4049 host 4028 4029 fly 12 4049 4050 medium 4029 4030 bloodstream 12 4049 4050 medium 4030 4031 procyclic 12 4049 4050 medium 4031 4032 agar 12 4049 4050 medium 4032 4033 not_applicable 12 4050 4051 cell_density_at_harvest 0 0 [1e6_per_ml] 12 4051 4052 temperature 0 0 [deg.C] 12 4052 4053 bottle_size 0 0 [ml] 12 4053 4054 culture_vol_per_bottle 0 0 [ml] 13 4054 4055 strain 4033 4034 C57Bl6 13 4054 4055 strain 4034 4035 not_applicable 13 4055 4056 syringe_passages 0 0 [] 13 4056 4057 organ 4035 4036 blood 13 4056 4057 organ 4036 4037 brain 13 4056 4057 organ 4037 4038 not_applicable 13 4057 4058 cell_density_at_harvest 0 0 [1e6_per_ml] 13 4058 4059 host_cell_contamination 4038 4039 estimated 13 4058 4059 host_cell_contamination 4039 4040 not_applicable 13 4059 4060 host_cell_contamination 0 0 [%] 13 4060 4061 percentage_of_stumpy_cells 0 0 [%] 13 4061 4062 harvesting_after_infection 0 0 [d] 14 4062 4063 strain 4040 4041 a 14 4062 4063 strain 4041 4042 not_applicable 14 4063 4064 passages 0 0 [] 14 4064 4065 organ 4042 4043 midgut 14 4064 4065 organ 4043 4044 salivary_gland 14 4064 4065 organ 4044 -1 total 14 4065 4066 harvesting_after_infection 0 0 [d] 15 4066 4067 CO2 0 0 [%] 15 4067 4068 cAMP 0 0 [mM] 15 4068 4069 cAMP_onset 0 0 [h] 15 4069 4070 cAMP_duration 0 0 [h] 15 4070 4071 citrate 0 0 [mM] 15 4071 4072 citrate_onset 0 0 [h] 15 4072 4073 citrate_duration 0 0 [h] 16 4073 4074 temperature 0 0 [deg.C] 16 4074 4075 temperature_onset 0 0 [h] 16 4075 -1 temperature_duration 0 0 [h]