CANDIDA ALBICANS experiment annotation

20-11-2001
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance.

Organism specific part by Nicole Hauser, who considered the complete list to satisfy MIAME 1.0 standard.

References, images (tiff format), a list of array elements incl. controls (including gene/clone IDs, array location, descriptions and functional catalogue entries for each spot) as well as normalization strategies and algorithms are not included here but will be available in the results section or directly from the authors.


common_annotations

array

1 - array_source
2 - array_series
3 - array_individual
4 - array_support
67 - array_support_widthmm
68 - array_support_lengthmm
41 - array_surface_chemistry
42 - support_manufacturer
43 - Hybond_support_brand
44 - Pall_support_brand
45 - Corning_support_brand
46 - TeleChem_support_brand
5 - spotted_material
69 - spotted_material_property
70 - number_of_elements_on_array_(without_duplicates)
71 - elements_spotted_as
47 - spotted_material_purification
48 - spotting_buffer
49 - spotting_robot
50 - spotting_pins
51 - relative_humidity
52 - relative_humidity%
53 - temperature
54 - temperaturedeg.C
55 - postprocessing
77 - uv_crosslink_applicable
78 - uv_crosslink_energyx100microJpercm2
6 - readfile
7 - array_hybridisation

hybridisation

RNA_preparation

8 - material_source
9 - preparation_of_total_RNA
10 - preparation_of_PolyA+

labeling

11 - amount_of_RNAmicrogram
40 - amount_of_cDNAmicrogram
12 - enzym
13 - priming
14 - nucleotide
56 - nucleotide_removal
15 - label
66 - days_from_calibration_date_applicable
38 - days_from_calibration_dated
16 - label_incorporation_rate%
17 - total_activitycpm

hybridisation_conditions

18 - buffer
57 - prehybridization_without_target
19 - competitors
75 - hybridisation_device
76 - hybridisation_instrument
20 - hybridisation_tempdeg.C
21 - buffer_volumeml
58 - coverslip_used
59 - coverslip_sizemmxmm
22 - hybridisation_lengthh

stringency_wash

23 - wash_buffer
24 - times
25 - wash_lengthmin
26 - temperaturedeg.C

detection

60 - exposure_time_applicable
27 - exposure_timeh
28 - measuring_device
72 - scanning_software
73 - spacial_resolutionmicrom
61 - pixelsizemicromxmicrom
62 - PMT_setting_applicable
63 - PMT_setting%
64 - laser_power_setting_applicable
65 - laser_power_setting%
29 - imaging_software
30 - background_correction
31 - spot_detection
74 - spot_dimension_(diameter)microm
32 - spot_size
33 - intensity_measurement

sample

34 - organism

submission

35 - date_of_entry_day
36 - date_of_entry_month
37 - date_of_entry_year
39 - experimentator

organism_specific_annotations

genotype

7035 - strain
7036 - mating_type

genetic_specification

7037 - genetic_variation
7038 - transgeneno_in_y1_genes
7056 - 2nd_genetic_variation
7057 - 2nd_transgeneno_in_y1_genes
7058 - 3rd_genetic_variation
7059 - 3rd_transgeneno_in_y1_genes
7060 - 4th_genetic_variation
7061 - 4th_transgeneno_in_y1_genes
7062 - 5th_genetic_variation
7063 - 5th_transgeneno_in_y1_genes

resistance_marker

7039 - leucine
7040 - uracil
7041 - tryptophan
7042 - histidine
7043 - lysine
7044 - adenine
7068 - arginine
7069 - MPA_(mycophenolic_acid)

pre_culture

7066 - culture
7045 - growth_phase
7070 - morphology
7071 - life_cycle_status
7046 - temperaturedeg.C
7064 - pH_(enter_0_if_unknown)
7047 - energy_metabolism
7072 - light_periods
7073 - medium_base

C_source

7049 - glucose%
7050 - galactose%
7051 - ethanol%
7052 - glycerol%
7065 - sucrose%
7067 - lactate%

main_culture

7074 - culture
7075 - growth_phase
7076 - morphology
7077 - life_cycle_status
7078 - temperaturedeg.C
7079 - pH_(enter_0_if_unknown)
7080 - energy_metabolism

medium

7081 - base

C_source

7082 - glucose%
7083 - galactose%
7084 - ethanol%
7085 - glycerol%
7086 - sucrose%
7087 - lactate%

additive

7088 - temporary_additive
7089 - concentrationmM

growth_condition_shift

7090 - incubation_period_with_additivemin
7091 - incubation_period_after_temperature_shiftmin
7092 - incubation_period_after_ph_shiftmin
7093 - incubation_period_after_medium_shiftmin
7094 - incubation_period_after_C_source_shiftmin

lighting_conditions

7095 - first_period
7096 - first_period_durationh
7097 - second_period
7098 - second_period_durationh