HUMAN CANCER BIOPSY experiment annotation

1-4-2005
Common annotations were compiled by Nicole Hauser, Judith Boer, Rosa Arribas, Frank Diehl, and others;
Organism specific part by Judith Boer, Andrea Bauer and others.

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
92 - Eppendorf_support_brand
43 - Hybond_support_brand
44 - Pall_support_brand
45 - Corning_support_brand
46 - TeleChem_support_brand
79 - Quantifoil_support_brand
109 - Nexterion_support_brand
5 - spotted_material
69 - spotted_material_property
70 - number_of_elements_on_array_(without_duplicates)
80 - external_controls_spotted
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
110 - ribosomal_RNA
9 - preparation_of_total_RNA
98 - DNAse_digest
81 - A260_A280_ratio
10 - preparation_of_PolyA+

labeling

11 - amount_of_RNAmicrogram
40 - amount_of_cDNAmicrogram
108 - amount_of_DNAmicrogram
12 - enzyme
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
82 - pre_hyb_temperaturedeg.C
83 - pre_hyb_lengthmin
19 - competitors
75 - hybridisation_device
76 - hybridisation_instrument
20 - hybridisation_tempdeg.C
21 - buffer_volumeml
58 - coverslip_used
59 - coverslip_sizemmxmm
84 - coverslip_material
85 - coverslip_provider
86 - coverslip_spacer_thickness_(0_for_none)mm
87 - spikes_included
22 - hybridisation_lengthh

stringency_wash

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

detection

96 - days_from_washing_applicable
97 - days_from_washingd
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%
93 - CCD_camera_setting_applicable
94 - CCD_camera_exposure_times
95 - pixel_binning
29 - imaging_software
30 - background_correction
31 - spot_detection
74 - spot_dimension_(diameter)microm
32 - spot_size
33 - intensity_measurement
99 - overall_image_quality
100 - color_comparison_applicable
101 - color_comparison
102 - background_stars_abundance
103 - background_stars_occupied_area
104 - background_smere_intensity
105 - background_smere_occupied_area
106 - background_high_intensity_artifacts_(funny_pictures)
107 - background_dust_abundance

sample

34 - organism

submission

35 - date_of_entry_day
36 - date_of_entry_month
37 - date_of_entry_year
39 - experimentator_hybridization_and_washing
89 - experimentator_spotting
90 - experimentator_RNA_isolation
91 - experimentator_labeling

organism_specific_annotations

sample_id

2110 - hybridisation_length_2nd_filterh
2107 - total_activity_2nd_filtercpm
2108 - exposure_time_2nd_filterh
2109 - array_individual_2nd_filter
2105 - array_hybridisation_2nd_filter
2106 - label_incorporation_rate_2nd_filter%
2057 - cancer_express_id
2058 - sample_date_day
2059 - sample_date_month
2060 - sample_date_year
2061 - institute
2062 - institute_sample_id_firstpart
2063 - institute_sample_id_secondpart
2064 - physician
2065 - pathologist

cell_culture_(see_e.g._ATCC)

2111 - experimentator
2112 - cell_line
2138 - current_differentiation_grade_(may_or_may_not_differ_from_differentiation_grade_of_original_tumor(2092))
2113 - treatment_cis_platinmM
2114 - treatment_taxolmM
2129 - treatment_TNFalphamM
2130 - treatment_ICI.182.780mM
2136 - treatment_ValproatemM
2137 - treatment_CycloheximidemM
2115 - timepoint_after_treatmenth

patient_info

patient_characteristics_(some_also_relevant_for_cell_line_origin)

2131 - birth_date
2066 - birth_date_day
2067 - birth_date_month
2068 - birth_date_year
2069 - sex
2070 - race
2116 - smoking
2117 - alcohol_consumption
2118 - Diabetes_mellitus
2119 - jaundice
2120 - pain
2121 - weight_loss
2122 - weight_loss_in_last_4_weekskg
2123 - pancreatitis_in_history
2124 - CA_19_9units
2125 - OP_procedure
2133 - OP_date_day
2134 - OP_date_day_month
2135 - OP_date_day_year

patient_status

2071 - previous_malignancy
2072 - live_status
2132 - survival_time(put_0_both_if_unknown_or_died_in_op)months
2073 - pre_op_treatment
2074 - post_op_treatment

tumor_info

tumor_general_(also_relevant_for_cell_line_origin)

2075 - tumor_or_normal
2076 - tumor
2139 - normal
2077 - tumor_type

tumor_tnm_(also_for_cell_lines_of_well-known_origin)

2078 - pT_stage
2079 - pN_stage
2080 - pM_stage
2081 - metastasis_location

tumor_site_(also_for_cell_lines_of_well-known_origin)

2082 - tumor_site
2083 - tumor_subregion
2084 - tumor_sizecm

tumor_invasion_(also_for_cell_lines_of_very_well-known_origin)

2085 - lymphnodes_removed
2086 - lymphnodes_invaded
2087 - lymphvenes_invaded
2088 - vascular_invasion
2089 - resection_status

tumor_stage_and_histology_(also_for_cell_lines_of_well-known_origin)

2090 - WHO_stage
2091 - Duke_stage
2126 - stroma
2127 - necrosis
2128 - granulocytes
2092 - differentiation_grade_(of_tumor_biopsy_or_original_tumor_in_case_of_cell_line)

percentage_normal

2093 - percentage_normal

cytogenetics

cytogenetics_(also_for_current_status_of_cell_line)

2094 - modal_number
2095 - aberration_type
2096 - aberration_breakpoint_chromosome
2097 - aberration_breakpoint_arm
2098 - aberration_breakpoint_subregion
2099 - aberration_gain_chromosome
2100 - aberration_gain_arm
2101 - aberration_gain_subregion
2102 - aberration_loss_chromosome
2103 - aberration_loss_arm
2104 - aberration_loss_subregion