HYDRACTINIA experiment annotation
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.
common_annotations
array
1 -
array_source
10 - self_made
11 - genome_systems
12 - clontech
13 - research_genetics
2 -
array_series
3 -
array_individual
4 -
array_support
14 - nylon
15 - polypropylene
16 - glass
67 -
array_support_width
mm
68 -
array_support_length
mm
41 -
array_surface_chemistry
117 - unknown_positive_charge
118 - poly_L_lysine
119 - aldehyde
120 - aminosilane
42 -
support_manufacturer
121 - Hybond
122 - Pall
123 - TeleChem
124 - Corning
125 - diehl
126 - stephan
43 -
Hybond_support_brand
127 - non_Hybond
128 - N+
44 -
Pall_support_brand
129 - non_Pall
130 - Biodyne_B
223 - polypropylene
45 -
Corning_support_brand
131 - non_Corning
132 - CMT_GAPS
46 -
TeleChem_support_brand
133 - non_TeleChem
134 - Aldehyde
135 - SuperAldehyde
5 -
spotted_material
17 - PCR
18 - colonies
19 - DNA-oligo
20 - PNA-oligo
69 -
spotted_material_property
200 - single_stranded
201 - double_stranded
70 -
number_of_elements_on_array_(without_duplicates)
71 -
elements_spotted_as
202 - single
203 - duplicate
204 - triplicate
47 -
spotted_material_purification
136 - non
137 - isopropanol_precipitation
138 - QIAquick
139 - Multiscreen_NU_Millipore
48 -
spotting_buffer
140 - 1.5M_NaCl_0.5M_NaOH
141 - 28mM_EDC_4.4volpromill_NMI
142 - spottingsolution_by_diehl
143 - MicroSpotting_solution_TeleChem
144 - 3xSSC
145 - 3xSSC_50%DMSO
227 - 150mM_sodiumphosphate_pH8.5
228 - 150mM_sodiumphosphate_pH8.5_0.01%SDS
49 -
spotting_robot
146 - SDDC-2_ESI
147 - Biogrid_Biorobotics
148 - Microgrid_II_Biorobotics
149 - Omnigrid_Genemachines
150 - QArray_Genetix
50 -
spotting_pins
151 - solid
152 - SMP-3_Telechem
153 - Biogrid_Biorobotics
51 -
relative_humidity
154 - defined
155 - estimated
156 - unknown(enter_0%)
52 -
relative_humidity
%
53 -
temperature
157 - defined
158 - estimated
159 - unknown(enter_0deg.C)
54 -
temperature
deg.C
55 -
postprocessing
160 - neutralizing_by_1.5MNaCL_0.5MTrispH7.5_1mMEDTA
161 - 2h_at_65deg.C
162 - succinic_anhydride_Stanford_protocol
163 - succinic_anhydride_protocol_by_diehl
164 - BSA_Tigr_protocol
165 - NaBH4_Telechem_protocol
77 -
uv_crosslink_applicable
224 - no(enter_0)
225 - yes
78 -
uv_crosslink_energy
x100microJpercm2
6 -
readfile
7 -
array_hybridisation
hybridisation
RNA_preparation
8 -
material_source
21 - fresh
22 - frozen
23 - RNA_later
94 - cDNA_subtraction
9 -
preparation_of_total_RNA
24 - trizol
25 - columns
26 - phenol
95 - not_applicable
10 -
preparation_of_PolyA+
27 - none
28 - dynabeads
29 - oligotex
30 - cellulose
96 - not_applicable
labeling
11 -
amount_of_RNA
microgram
40 -
amount_of_cDNA
microgram
12 -
enzym
31 - superscript
32 - AMV
33 - M-MLV
166 - OmniScript
97 - klenow
13 -
priming
34 - oligo_dT
35 - anchored_oligo_dT
36 - random_hexamer
37 - combined_oligo_dT-random_hexamer
98 - pcr_select
14 -
nucleotide
38 - dCTP
39 - dATP
167 - aa-dUTP
168 - dUTP
56 -
nucleotide_removal
169 - G50_Pharmacia
170 - ammium_acetate_isopropanol_precipitation
226 - Na_acetate_isopropanol_precipitation
171 - QIAquick_Qiagen
172 - GFX_columns_Pharmacia
173 - YM30_Amicon
15 -
label
40 - 33P
41 - 32P
42 - Cy3
43 - Cy5
174 - Alexa488
175 - Alexa594
66 -
days_from_calibration_date_applicable
193 - yes
194 - no(enter_0d)
38 -
days_from_calibration_date
d
16 -
label_incorporation_rate
%
17 -
total_activity
cpm
hybridisation_conditions
18 -
buffer
44 - 0.5M_Na_phosphate_pH7.2_7%_SDS
229 - 5x_SSC_0.1%_SDS
230 - Genisphere3DNA
231 - Genisphere3DNAformamide
232 - 3x_SSC_2.5x_denhardts_0.08%_SDS
45 - 5x_SSC_5x_denhardts_0.5%_SDS
46 - 4x_SSC_7.2%_Na_sarcosyl
47 - Clontech_Express_hyb
48 - ambion_Northern_max
221 - 3x_SSC_5x_denhardts_1%_SDS_5%_dextransulfate_50%_formamide
57 -
prehybridization_without_target
176 - no
177 - yes
19 -
competitors
49 - none
50 - tRNA
51 - Cot1
217 - dA20
52 - dA40
53 - salmon_sperm
99 - dA40_Cot1_salmonsperm
100 - dA40_Cot1_tRNA_salmonsperm
101 - dA40_Cot1_specificoligos_salmonsperm
102 - dA40_Cot1_specificoligos_tRNA_salmonsperm
75 -
hybridisation_device
211 - water_bath
212 - rotating_oven
76 -
hybridisation_instrument
213 - hybridisation_bottle
214 - hybridisation_chamber_corning
215 - hybridisation_chamber_TeleChem
216 - hybridisation_chamber_ClonTech
20 -
hybridisation_temp
deg.C
21 -
buffer_volume
ml
58 -
coverslip_used
178 - no_(enter_size_0)
179 - yes
59 -
coverslip_size
mmxmm
22 -
hybridisation_length
h
stringency_wash
23 -
wash_buffer
54 - 0.1xSSC_0.1%SDS
55 - 0.6xSSC_1%SDS
56 - 0.2xSSC_0.1%SDS
222 - 0.2xSSC
233 - 0.1xSSC
234 - 0.06xSSC
57 - 40mMNaPipH7_0.1%SDS
24 -
times
25 -
wash_length
min
26 -
temperature
deg.C
detection
60 -
exposure_time_applicable
180 - yes
181 - no_(enter_0h)
27 -
exposure_time
h
28 -
measuring_device
58 - MD_storm860_phos
59 - MD_storm860_red
60 - MD_storm860_blue
113 - MD_425
114 - MD_475A_phos
61 - Fuji_BAS1500
109 - Fuji_FLA3000
62 - BioRad
63 - ScanArray3000_GSI_Lumonics
182 - ScanArray5000_GSI_Lumonics
183 - Axon_4000a_Axon
72 -
scanning_software
205 - Fuji_Image_Reader_FLA3000_3000G_V1.0
206 - BAS_reader_V2.26beta
207 - Storm_scanner_control
208 - Typhoon_scanner_control_V1.0
209 - Scan_Array3000_V3.11_Controller_V2.03
210 - Scan_Array_V2.1
73 -
spacial_resolution
microm
61 -
pixelsize
micromxmicrom
62 -
PMT_setting_applicable
184 - no(enter_0%)
185 - yes
63 -
PMT_setting
%
64 -
laser_power_setting_applicable
186 - no(enter_0%)
187 - yes
65 -
laser_power_setting
%
29 -
imaging_software
64 - AIS
65 - HDG
66 - XDotsReader
67 - imagene
68 - Xdigitise
188 - GenePixPro
189 - QuantArray
30 -
background_correction
69 - none
70 - local_background
71 - block_background
72 - empty_spots_average
73 - empty_spots_per_block
31 -
spot_detection
74 - all_spots
75 - only_positive_spots
74 -
spot_dimension_(diameter)
microm
32 -
spot_size
76 - fixed
77 - variable
33 -
intensity_measurement
78 - highest_value_in_spot_centre
79 - sum_of_pixels_within_boundary
80 - mean_of_pixels_within_boundary
sample
34 -
organism
81 - Saccharomyces_cerevisiae
82 - Arabidopsis_thaliana
83 - murine_biopsy
103 - murine_cell_line
84 - human_biopsy
85 - human_cell_line
86 - Bacillus_subtilis
192 - Trypanosoma_brucei
199 - Candida_albicans
220 - Neurospora_crassa
submission
35 -
date_of_entry_day
36 -
date_of_entry_month
37 -
date_of_entry_year
39 -
experimentator
218 - aign
104 - bastuk
235 - bauer
115 - becerra
105 - bier
88 - boer
190 - diehl
196 - fischer
191 - grahlmann
219 - grees
87 - hauser
91 - kornacker
112 - lagorce
107 - lombardia
90 - lutz
108 - meijer
92 - mendel
198 - reile
195 - scheideler
197 - schrenk
111 - steiner
110 - sueltmann
106 - tournu
89 - wilmer
93 - wittig
116 - yin
organism_specific_annotations
parental_information
father_of_animal_in_experiment
9035 -
strain_definition
9087 - undefined
9088 - mutant
9089 - RNAi_phenotype
mother_of_animal_in_experiment
9036 -
strain_definition
9090 - undefined
9091 - mutant
9092 - RNAi_phenotype
mating_yield
9037 -
strain_definition
9093 - defined
9094 - undefined
9095 - cross
animal_in_experiment
basic_information
9038 -
type_definition
9096 - defined
9097 - undefined
9039 -
strain_definition
9098 - Wildtype
9099 - cross
9100 - mutant
9101 - RNAi
9040 -
sex_of_experiment_animal
9102 - male
9103 - female
9104 - mixed
9105 - unknown
strain_or_phenotype
9041 -
wildtype_ID
9106 - no_wildtype
9107 - wt_1_(stoloniferous)
9108 - wt_2_(plateforming)
9042 -
mutant_ID
9109 - no_mutant
9110 - Diss
9111 - He-mh
9112 - Dpp
9113 - Gkp
9114 - Bst
9043 -
RNAi_ID
9115 - no_RNAi
9116 - act1
9117 - ast1
9118 - ast2
9119 - cad1
9044 -
developmental_stage
9120 - gamet
9121 - zygote
9122 - gastrula
9123 - planula
9124 - induced_planula
9125 - primary_polyp
9126 - immature_colony
9127 - mature_colony
culture_conditions
preparation
9045 -
time_of_preparation
9128 - morning
9129 - afternoon
9130 - evening
9046 -
preparator
9131 - Jasna_Guduric
9132 - Uri_Frank
9133 - Brahim_Mali
9134 - Regina_Teo
9135 - Frank_Moehrlen
9136 - Guenter_Plickert
9137 - Melanie_Maniura
9138 - Thomas_Leitz
9139 - Stefanie_Seipp
feeding
9047 -
fed_last_24_hours
9140 - yes
9141 - no
experimental_settings
basic_tissue_information
9048 -
fed_last_24_hours
9142 - whole_animals
9143 - selected_tissues
9049 -
embryonic
9144 - no
9145 - yes
9050 -
posterior_planula
9146 - no
9147 - yes
9051 -
anterior_planula
9148 - no
9149 - yes
9052 -
tentacles
9150 - no
9151 - yes
9053 -
head
9152 - no
9153 - yes
9054 -
body_column
9154 - no
9155 - yes
9055 -
stolones
9156 - no
9157 - yes
9056 -
stolone_tip
9158 - no
9159 - yes
9057 -
stolone_mat
9160 - no
9161 - yes
experimental_category
9058 -
tissue_specificity
9162 - no
9163 - yes
9059 -
development
9164 - no
9165 - yes
9060 -
RNAi_phenotype
9166 - no
9167 - yes
9061 -
strain_specificity
9168 - no
9169 - yes
9062 -
Induction_or_treatment
9170 - no
9171 - yes
9063 -
regeneration
9172 - no
9173 - yes