ARABIDOPSIS experiment annotation

10-4-2001
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance.

Organism specific part by Marcel Scheideler and Nikolaus Schlaich, who considered the complete list to satisfy MIAME2 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
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

3035 - ecotype

transgenes_ordered_by_no_in_y1_genes

3036 - genetic_variation
3037 - transgeneno_in_y1_genes
3038 - 2nd_genetic_variation
3039 - 2nd_transgeneno_in_y1_genes
3040 - 3rd_genetic_variation
3041 - 3rd_transgeneno_in_y1_genes
3042 - 4th_genetic_variation
3043 - 4th_transgeneno_in_y1_genes
3044 - 5th_genetic_variation
3045 - 5th_transgeneno_in_y1_genes

markers_transposons_tags

3113 - active_transposon

growth_conditions

3107 - experimentator_growth_conditions

field

3052 - begin_after_germinationd
3053 - end_after_germinationd
3054 - soil

greenhouse

3055 - begin_after_germinationd
3056 - end_after_germinationd
3057 - soil%
3058 - sand%
3059 - compost%
3060 - perlite%
3061 - vermiculite%

phytochamber

3062 - begin_after_germinationd
3063 - end_after_germinationd
3108 - light_per_dayh
3109 - light_intensitymol/m2/s PAR
3110 - light_source
3111 - day_temperaturedeg.C
3112 - night_temperaturedeg.C

in_vitro

3065 - begin_after_germinationd
3066 - end_after_germinationd
3067 - culture
3068 - light
3069 - saccharosemM
3070 - vitamine_B5mM
3072 - light_per_dayh
3073 - light_intensitymol/m2/s PAR
3074 - light_source
3075 - day_temperaturedeg.C
3076 - night_temperaturedeg.C

treatment

3106 - experimentator_treatment_and_sampling

mechanical_stress

3077 - wounding_type
3078 - wounding_where
3079 - wounding_amountmm

auxins

3080 - IAA_delivery
3081 - IAA_period_begin_after_germinationd
3082 - IAA_period_durationd
3083 - IAA_periodicity
3084 - IAA_application_begin_after_dawnh
3091 - IAA_concentrationmM
3085 - 2_4_D_delivery
3086 - 2_4_D_period_begin_after_germinationd
3087 - 2_4_D_period_durationd
3088 - 2_4_D_periodicity
3089 - 2_4_D_application_begin_after_dawnh
3090 - 2_4_D_concentrationmM

cytokinins

3092 - benzyladenine_delivery
3093 - benzyladenine_period_begin_after_germinationd
3094 - benzyladenine_period_durationd
3095 - benzyladenine_periodicity
3096 - benzyladenine_application_begin_after_dawnh
3097 - benzyladenine_concentrationmM

pathogens

3098 - bacteria_application_preparation
3099 - bacteria_application
3100 - bacteria
3101 - bacteria_titercfu_per_ml

sampling

when

3102 - after_germinationd
3103 - after_dawnh
3104 - exact_timepoint_after_treatmentmin

what

3105 - organ