YEAST experiment annotation

6-4-2001
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl and have been checked for MIAME2 compliance.

Organism specific part by Nicole Hauser, 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
number of previous hybs on this particular slide plus one

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

1035 - strain
1036 - mating_type

transgenes_ordered_by_no_in_y1_genes

1037 - genetic_variation
1038 - transgeneno_in_y1_genes
1056 - 2nd_genetic_variation
1057 - 2nd_transgeneno_in_y1_genes
1058 - 3rd_genetic_variation
1059 - 3rd_transgeneno_in_y1_genes
1060 - 4th_genetic_variation
1061 - 4th_transgeneno_in_y1_genes
1062 - 5th_genetic_variation
1063 - 5th_transgeneno_in_y1_genes

auxotrophic_marker

1039 - LEU2
1040 - URA3
1041 - TRP1
1042 - HIS3
1043 - LYS2
1044 - ADE2

growth_conditions

1066 - culture
1045 - growth_phase
1046 - temperaturedeg.C
1064 - temperature_shift_incubation_periodmin
1047 - energy_metabolism

medium

1048 - base

C_source

1049 - glucose%
1050 - galactose%
1051 - ethanol%
1052 - glycerol%
1065 - sucrose%
1067 - lactate%

additive

1053 - temporary_additive
1054 - concentrationmM
1055 - incubation_periodmin