NEUROSPORA CRASSA experiment annotation
29-4-2001
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance.
Organism specific part by Verena Aign.
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
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
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
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
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
45 - 5x_SSC_5x_denhardts_0.5%_SDS
46 - 4x_SSC_7.2%_Na_sarcosyl
47 - Clontech_Express_hyb
48 - ambion_Northern_max
57 -
prehybridization_without_target
176 - no
177 - yes
19 -
competitors
49 - none
50 - tRNA
51 - Cot1
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_ArrayIt
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
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
submission
35 -
date_of_entry_day
36 -
date_of_entry_month
37 -
date_of_entry_year
39 -
experimentator
104 - bastuk
115 - becerra
105 - bier
88 - boer
190 - diehl
196 - fischer
191 - grahlmann
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
genotype
5035 -
strain
5035 - 740R23_1A
5036 - deltaWC_1
5037 - deltaWC_2
5036 -
genetic_variation
5038 - WT
5039 - mutation
5040 - ko
5041 - overexpression
5042 - inducible_promoter
5037 -
transgene
no_in_y1_genes
growth_conditions
5038 -
culture
5043 - liquid
5044 - solid
5039 -
growth_phase
5045 - conidial
5046 - mycedial
5047 - perithecial
5040 -
temperature
deg.C
light_periods
5041 -
first_period
5048 - light
5049 - dark
5042 -
first_period_duration
h
5043 -
second_period
5050 - light
5051 - dark
5044 -
second_period_duration
h
medium
5045 -
base
5052 - Vogels_minimal
C_source
5046 -
glucose
%
5047 -
galactose
%
5048 -
ethanol
%
5049 -
glycerol
%
5050 -
sucrose
%
5051 -
lactate
%
additive
5052 -
temporary_additive
5053 - H2O2
5054 - NaCl
5055 - calcium
5056 - isoamylalcohol
5057 - sorbitol
5058 - ammonium_sulfate
5059 - glucose
5060 - none
5053 -
concentration
mM
5054 -
incubation_period
min