ASPERGILLUS experiment annotation
2-4-2007
Annotations were compiled by Daniela Albrecht and Franziska Leßing. They were checked for compliance with MIAPE Gel-Electrophoresis V.1.2. but go beyond this standard.
2D_gel_common_annotatios
General_features
19001 -
Date_of_entry_day
19002 -
Date_of_entry_month
19003 -
Date_of_entry_year
19004 -
Responsible_person
19001 - Olaf_Kniemeyer
19002 - Franziska_Lessing
19003 - Andre_Schmidt
19004 - Martin_Voedisch
19005 - Silke_Steinbach
19005 -
Institutional_adress_and_email
19006 - Hans_Knoell_Institute_(HKI),_Beutenbergstrasse_11a,_07745_Jena,_mailto:firstname.surname(at)hki-jena.de
19006 -
Electrophoresis_type
19007 - Difference_gel_electrophoresis_(2D_DIGE)
19008 - Two-dimensional_(2D_standard)
Sample
19007 -
Organism
19009 - Aspergillus_fumigatus
19008 -
Strain
19010 - Af293
19011 - WT_ATCC_46645
19012 - ATCCDyap1
19013 - ATCCDskn7
19014 - ATCCDyap1/Dskn7
19015 - ATCC(CEA17)PksP
19016 - ATCCKu80Daif
19017 - pooled_standard
19009 -
Type
19018 - control
19019 - test
19020 - standard
19010 -
Label
19021 - coomassie
19022 - silver
19023 - Cy2
19024 - Cy3
19025 - Cy5
19026 - Sypro_Ruby
Loading_buffer
19011 -
Components
19027 - bromphenole_blue_(comassie)
19028 - lysis_buffer_3+40mM_DTT+3.2%Servalyt_(DIGE)
19012 -
Volume
19029 - 10_mikrol
19030 - 4_x_sample
19013 -
Amount_of_protein
microg
Gel
First_dimension_(IEF)
19014 -
Description
19031 - IPG_strip_native
19032 - IPG_strip_gradient
19015 -
Model_name
19033 - Immobiline_Drystrip_(GE_Healthcare)
19016 -
Model_number_(enter_NA_if_unknown)
19017 -
Batch_number_(enter_NA_if_unknown)
19018 -
Length
cm
19019 -
pH_range_and_distribution
19034 - 3-7_linear
19035 - 3-7_nonlinear
19036 - 3-10_linear
19037 - 3-10_nonlinear
19038 - 4-7_linear
19039 - 7-10_nonlinear
Acrylamide_concentration
19020 -
Type
19040 - fixed
19041 - linear
19042 - stepped
19021 -
Miminum
%
19022 -
Maximum
%
19023 -
Sample_application
19043 - rehydration-loading
19044 - cup-loading_anode
19045 - cup-loading_catode
19046 - cup_loading_middle
Acrylamide:Crosslinker_ratio
19024 -
Name_of_crosslinker
19047 - bis-acrylamide
19025 -
Ratio_(e.g._0.5)_(enter_NA_if_unknown)
19026 -
Additional_substances_in_gel
19048 - none_(0M)
19027 -
Number_of_Gel_lanes_and_Sample_loading_per_lane
19049 - not_applicable
Electrophoresis_protocol
19028 -
Running_buffer
19050 - none
19029 -
Additional_buffers
19051 - rehydration_buffer_3_(7M_urea,_2M_thiourea,_2%_Chaps,_1%_Zwittergent,_bromphenol_blue)
19030 -
Conditions
19052 - 7cm_protocol_(hold-200V-10min_hold-500V-10min_gradient-to-3500V-1.5h_hold-3500V-1.5h,_room_temperature)
19053 - 24cm_protocol_(gradient-to-300V-4h_gradient-to-600V-3(4)h_gradient-to_1000V-4h_gradient-to-8000V-4h,_hold8000V-3h,_room_temperature)
Inter-dimension_process
19031 -
Name
19054 - equilibration
19032 -
Buffer
19055 - equilibration_buffer_(in_200ml_72g_urea,_69ml_glycerol,_4g_SDS,_10ml_tris-hcl_buffer_pH_8.8+1%DTT_(fist_step)_or_+2.5%_iodacetamid_(second_step))
19033 -
Additional_reagents
19056 - none
19034 -
Special_equipment_and_protocols
19057 - none
Second_dimension_(SDS_PAGE)
19035 -
Description
19058 - SDS_gel_native
19059 - SDS_gel_gradient
19036 -
Manufacturer
19060 - HKI_(12.5%_gele,_125ml_acrylamid-bisacrylamid,_75ml_1.5M_trisbuffer_ph_8.8,_68ml_water,_25ml_Rhinohyde,_3ml_10%_SDS,_75microl_TEMED,_3.7ml_10%_APS)
19061 - HKI_(ready_to_use_Biometra_kit_(Laemmli_Chemie))
19037 -
Model_name
19062 - HKI_self_made_native
19063 - HKI_self_made_gradient
19038 -
Model_number_(enter_NA_if_unknown)
19039 -
Batch_number_(enter_NA_if_unknown)
Physical_dimensions
19040 -
Width_(distance_from_anode_to_catode)
cm
19041 -
Length
cm
19042 -
Depth
cm
19043 -
Molecular_weight_range_and_distribution
19064 - 8-150kDa_logarithmic_apparent
19065 - 8-200kDa_logarithmic_apparent
19066 - 20-150kDa_logarithmic_apparent
19067 - 20-200kDa_logarithmic_apparent
Acrylamide_concentration
19044 -
Type
19068 - fixed
19069 - stepped
19070 - linear
19045 -
Miminum
%
19046 -
Maximum
%
19047 -
Sample_application
19071 - standard_procedure_combining_strip_and_gel
Acrylamide:Crosslinker_ratio
19048 -
Name_of_crosslinker
19072 - bis-acrylamide
19049 -
Ratio_(e.g._0.5)_(enter_NA_if_unknown)
19050 -
Additional_substances_in_gel
19073 - none_(0M)
19051 -
Number_of_Gel_lanes_and_Sample_loading_per_lane
19074 - not_applicable
19052 -
Running_buffer
19075 - 10_x_SDS_running_buffer_(in_1l_water_30g_tris,_144g_glycin,_10g_SDS,_upper_chamber_2_x_SDS,_lower_chamber_1_x_SDS)
19053 -
Additional_buffers
19076 - none
19054 -
Conditions
19077 - 1W/gel-1h_15W/gel-3.5h,_20_degC
19078 - 5W/gel-0.5h_17W/gel-3.5h,_20_degC
Protein_Finding
Detection
19055 -
Direct_detection_process
19079 - visible_staining
19080 - fluorescent_staining
19056 -
Manufacturer_of_detection_agents
19081 - Roth
19082 - GE_Healthcare
19057 -
Detection_agent
19083 - coomassie
19084 - silver
19085 - Cy2
19086 - Cy3
19087 - Cy5
19088 - Sypro_Ruby
19058 -
Volume_(enter_NA_if_unknown)
microl
19059 -
Concentration_(enter_NA_if_unknown)
mM
19060 -
Additional_reagents_and_buffers
19089 - none
19061 -
Special_equipment_and_protocols
19090 - none
19062 -
Protocol
19091 - scanning
19063 -
Indirect_detection
19092 - none
Image_acquisition
19064 -
Type_of_equipment
19093 - laser_scanner
19094 - light_scanner
19065 -
Name_of_equipment
19095 - Typhoon_9200
19066 -
Software
19096 - ImageScanner_II_(Amersham_Biosciences)
19097 - Labscan_(comes_together_with_Image_Master_2D_Platinum)
19098 - Scan_Control_(comes_together_with_Typhoon_9200)
19067 -
Calibration
19099 - automatic
19100 - manual
19068 -
Protocol
19101 - scanning_gel_matrix_of_second_dimension
19069 -
Imaging_software
19102 - DeCyder_6.5_(GE_Healthcare)
19103 - ImageMaster_2D_Platinum_5.0_(GE_Healthcare)
19104 - Delta2D_3.4_(Decodon)
Image
19070 -
ID
19071 -
Format
19105 - tiff
Dimensions
19072 -
length_(pH_direction)
pixels
19073 -
width_(MW_direction)
pixels
19074 -
Resolution_(enter_NA_if_unknown)
microm/pixel
19075 -
Bit-depth_(enter_NA_if_unknown)
19076 -
Location
19106 - local_server_at_HKI_(T)
19107 - local_users_pc_at_HKI
19077 -
Orientation
19108 - standard_(highest_MW_top,_highest_pH_right)
Post_gel_annotations
Protein_identification
19113 -
Spot_picking
19158 - manual
19159 - automatic_(Proteineer_sp)
19114 -
Digestion
19160 - manual
19161 - automatic_(Proteineer_dg)
19115 -
Ms_device
19162 - ESI_ion_trap
19163 - ESI_triple_quadrupole_spectrometers
19164 - ESI_sector_field_spectrometer
19165 - Bruker_Ultraflex_1_MALDI_TOF/TOF_spectrometer
19116 -
Software
19166 - Mascot_Proteinscape
Data_preprocessing
19117 -
background_subtraction
19167 - none
19168 - automatically_(DeCyder)
19169 - automatically_(Image_Master_Platinum)
19170 - automatically_(Delta2D)
Normalisation
19118 -
First_normalisation
19171 - none
19172 - logarithmising
19173 - internal_standard_(division_by_Cy2,_DIGE)
19174 - variance_stabilisation_(DIGE)
19175 - loess_regression
19119 -
Second_normalisation
19176 - none
19177 - logarithmising
19178 - internal_standard_(division_by_Cy2)
19179 - variance-stabilisation
19180 - loess_regression
19120 -
Third_normalisation
19181 - none
19182 - logarithmising
19183 - internal_standard_(division_by_Cy2)
19184 - variance-stabilisation
19185 - loess_regression
19121 -
Fourth_normalisation
19186 - none
19187 - logarithmising
19188 - internal_standard_(division_by_Cy2)
19189 - variance-stabilisation
19190 - loess_regression
Filtering
19122 -
First_filter
19191 - none
19192 - Fold_Change
19193 - Z_Score
19123 -
Threshold_first_filter
19124 -
Second_filter
19194 - none
19195 - t-test_p-value
19196 - ANOVA_p-value
19197 - t-test_p-value_corrected_for_multiple_comparisons
19198 - ANOVA_p-value_corrected_for_multiple_comparisons
19125 -
Threshold_second_filter
Experiment_specific_annotations
sample_preparation
19078 -
Experimental_context
19109 - Carbon_sources
19110 - Temperature_shift
19111 - Iron-limitation
19112 - Reactive_oxygen_species
19113 - Oxygen_limitation
19114 - Drug_resistance
19079 -
Material_source
19115 - fresh
19116 - frozen
19080 -
Fractionate
19117 - none
19118 - cell_compartment-cytosol
19119 - cell_compartment-nucleus
19120 - cell_compartment-mitochondria
19121 - cell_compartment-membrane
19122 - culture_supernatant
19081 -
Purification
19123 - none
19124 - phenole_precipitation
19125 - purification_kit
19126 - TCA-precipitation
19082 -
Lysis_buffer
19127 - Lysis_buffer1_(CHAPS/Urea)
19128 - Lysis_buffer2_(CHAPS/Thiourea)
19129 - Lysis_buffer3_(CHAPS/SB3-10/Thiourea)
19130 - Lysis_buffer3_for_DIGE
19131 - Lysis_buffer4_(ASB-14/Thiourea)
19132 - Lysis_buffer5_(ASB-14/CHAPS_SB3-10/Thiourea)
19133 - Lysis_buffer6_(C7_BzO)
19134 - Lysis_buffer7_(CHAPS/C7_BzO)
Pre-culture
19083 -
Culture
19135 - liquid
19136 - solid
19137 - glycerol_stock
19084 -
Life_cycle_status
19138 - mycelia
19139 - conidia
19140 - mixed
19085 -
Temperature_(enter_NA_if_unknown)
degC
19086 -
pH_(enter_NA_if_unknown)
19087 -
Medium
19141 - AMM
19142 - CM
19143 - YEPD_complete_medium
19144 - RPMI
19088 -
Incubation_period_(enter_NA_if_unknown)
min
C_source
19089 -
Glucose
%
19090 -
Galactose
%
19091 -
Ethanol
%
19092 -
Glycerol
%
19093 -
Sucrose
%
19094 -
Lactate
%
Main-culture
19095 -
Culture
19145 - liquid
19146 - solid
19147 - glycerol_stock
19096 -
Life_cycle_status
19148 - mycelia
19149 - conidia
19150 - mixed
19097 -
Temperature_(enter_NA_if_unknown)
degC
19098 -
pH_(enter_NA_if_unknown)
19099 -
Medium
19151 - AMM
19152 - CM
19153 - YEPD_complete_medium
19154 - RPMI
C_source
19100 -
Glucose
%
19101 -
Galactose
%
19102 -
Ethanol
%
19103 -
Glycerol
%
19104 -
Sucrose
%
19105 -
Lactate
%
Temporary_additive
19106 -
Name
19155 - H2O2
19156 - diamide
19157 - farnesol
19107 -
Concentration
mM
Growth_condition_shift
19108 -
Incubation_period_with_additive_(enter_NA_if_not_applicable)
min
19109 -
Incubation_period_after_temperature_shift_(enter_NA_if_not_applicable)
min
19110 -
Incubation_period_after_pH_shift_(enter_NA_if_not_applicable)
min
19111 -
Incubation_period_after_medium_shift_(enter_NA_if_not_applicable)
min
19112 -
Incubation_period_after_C_source_shift_(enter_NA_if_not_applicable)
min