BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/9749?version=1
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BioDare_metadata.json
Format: JSON document
Size: 52.6 KB
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"comment": "System generated on 17-Oct-2014"
},
"desc": {
"experiment_type": "Literature data",
"id": "13790751359110",
"status": "described",
"name": "Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, prr5, toc1;prr5",
"purpose": "In Arabidopsis thaliana, many circadian clock-associated genes have been identified. Among them, the eveningexpressed TOC1 (TIMING OF CAB EXPRESSION 1)\ngene plays a role by forming a transcriptional feedback core loop together with the morning-expressed CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene and its homologous LHY (LATE ELONGATED HYPOCOTYL) gene. TOC1 encodes a member of the PSEUDORESPONSE REGULATOR (PRR) family, including PRR9, PRR7, PRR5, PRR3,and PRR1/TOC1. The PRR genes other than TOC1 (or PRR1) also appear to be crucial for certain circadian-associated events. To clarify missing genetic linkages amongst these PRR genes, here we constructed a toc1 prr5 double knockdown mutant. In freerunning circadian rhythms, the resulting toc1-2 prr5-11 mutant plants showed an extremely short period and reduced amplitude phenotype, which was more severe than that of the toc1-2 single mutant plant, suggesting a non-linear genetic interaction between TOC1 and PRR5. Surprisingly, the hallmark early flowering phenotype of toc1-2 in the shortday conditions had been converted to a markedly late flowering phenotype in the long-day conditions, when combined with the prr5-11 allele, which itself showed a subtle flowering phenotype. This unexpected genetic result (i.e. phenotypic sign conversion) suggested that the TOC1 and PRR5 genes are coordinately implicated in a non-linear and closed genetic circuitry. In the toc1-2 prr5-11 double mutant, the diurnal expression profile of CDF1 (CYCLING DOF FACTOR 1) was markedly de-repressed in the evening in the long-day conditions. These and other results of this study led us to propose the novel view that TOC1 might play bipartite roles in the control of flowering time within a closed circuitry; the one is a GI (GIGANTEA)-dependent negative role through CCA1/LHY, and the other is a CDF1-dependent positive role through cooperating closely with PRR5.",
"pubmed_id": "18178585",
"provenance": {
"site": "Mizuno",
"author": "Ito, S.",
"start_date": "2008-01-04"
},
"growth_condition": [
{
"name": "Ito2008_LD",
"medium": "MS 1% sucrose",
"stratification": "3 days at 4C",
"duration": "10.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "10",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "10",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: LD 16:00:08:00",
"light_channel": {
"spectrum": "white",
"intensity": "90-100",
"source": "LED",
"env_conditions": {
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"label": "LD 16:00:08:00",
"duration": "10",
"env_day": {
"type": "diurnal_light",
"label": "diurnal light",
"duration": "10",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "16:00"
}
}
}
}
}
},
{
"name": "Ito2008_SD",
"medium": "MS 1% sucrose",
"stratification": "3 days at 4C",
"duration": "7.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "7",
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"label": "constant temperature",
"duration": "7",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
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"label": "W: LD 10:00:14:00",
"light_channel": {
"spectrum": "white",
"intensity": "120-150",
"source": "LED",
"env_conditions": {
"type": "diurnal_light",
"label": "LD 10:00:14:00",
"duration": "7",
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"type": "diurnal_light",
"label": "diurnal light",
"duration": "7",
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"base_value": "0.0",
"second_value": "100.0",
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"duration": "10:00"
}
}
}
}
}
}
],
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"name": "Ito2008_LD",
"medium": "MS 1% sucrose",
"duration": "1.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "1",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "1",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: LD 16:00:08:00",
"light_channel": {
"spectrum": "white",
"intensity": "90-100",
"source": "LED",
"env_conditions": {
"type": "diurnal_light",
"label": "LD 16:00:08:00",
"duration": "1",
"env_day": {
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
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{
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"label": "const. 22.0C",
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"label": "const. 22.0C",
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"cycle_length": "24",
"base_value": "22.0",
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}
}
},
"light_conditions": {
"label": "W: LD 10:00:14:00",
"light_channel": {
"spectrum": "white",
"intensity": "120-150",
"source": "LED",
"env_conditions": {
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"label": "LD 10:00:14:00",
"duration": "1",
"env_day": {
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
"cycle_length": "24",
"base_value": "0.0",
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"env_period": {
"start_time": "0:00",
"duration": "10:00"
}
}
}
}
}
}
],
"measurement": {
"technique": "RT-PCR",
"param": [
{
"@name": "RD error_type",
"@value": "none"
},
{
"@name": "RD first_data_col",
"@value": "2"
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{
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"sample_preparation": {
"method": "For real-time PCR, seedlings were grown on MS plates containing 1% sucrose under the conditions of LoD (16 h light/8 h dark) or ShD (10 h light/14 h dark) for 10 or 7 d. They were then harvested (3 h intervals) to quantify mRNA of genes involved in flowering regulation. Total RNA was purified by an RNeasy plant kit (Qiagen, Valencia, CA, USA). To synthesize cDNA, 1 mg of each RNA was reverse transcribed with Rever Tra Ace (TOYOBO, Osaka, Japan) and oligo(dT) primer. The synthesized cDNAs were amplified with iQ SYBR Green supermix (Bio-Rad Laboratories, Hercules, CA, USA) and a primer set using a MiniOpticon real-time PCR system (Bio-Rad Laboratories). The following standard thermal cycling\nprogram was used for all PCRs: 95oC for 120 s, 40 cycles of 95oC for 10 s, and 60oC for 60 s. Data were analyzed using Opticon Monitor version 3.1 software (Bio-Rad Laboratories). The oligonucleotide primers used in this study have all been described previously (Niwa et al. 2007)."
},
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{
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},
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},
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{
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},
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},
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{
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},
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"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD",
"ignored": "false"
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD",
"ignored": "false"
},
{
"sample_id": "20",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD",
"ignored": "false"
},
{
"sample_id": "21",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "22",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2",
"line": "unknown"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "23",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11",
"line": "unknown"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "24",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5",
"line": "unknown"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "25",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "26",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "27",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "28",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "29",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "30",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "31",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
},
{
"sample_id": "32",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5",
"line": "unknown"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD",
"ignored": "false"
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/Z:/communal/DataDescription/models/literature/model/full_literature.xsd",
"name": "Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, prr5, toc1;prr5",
"purpose": "In Arabidopsis thaliana, many circadian clock-associated genes have been identified. Among them, the eveningexpressed TOC1 (TIMING OF CAB EXPRESSION 1)\ngene plays a role by forming a transcriptional feedback core loop together with the morning-expressed CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene and its homologous LHY (LATE ELONGATED HYPOCOTYL) gene. TOC1 encodes a member of the PSEUDORESPONSE REGULATOR (PRR) family, including PRR9, PRR7, PRR5, PRR3,and PRR1/TOC1. The PRR genes other than TOC1 (or PRR1) also appear to be crucial for certain circadian-associated events. To clarify missing genetic linkages amongst these PRR genes, here we constructed a toc1 prr5 double knockdown mutant. In freerunning circadian rhythms, the resulting toc1-2 prr5-11 mutant plants showed an extremely short period and reduced amplitude phenotype, which was more severe than that of the toc1-2 single mutant plant, suggesting a non-linear genetic interaction between TOC1 and PRR5. Surprisingly, the hallmark early flowering phenotype of toc1-2 in the shortday conditions had been converted to a markedly late flowering phenotype in the long-day conditions, when combined with the prr5-11 allele, which itself showed a subtle flowering phenotype. This unexpected genetic result (i.e. phenotypic sign conversion) suggested that the TOC1 and PRR5 genes are coordinately implicated in a non-linear and closed genetic circuitry. In the toc1-2 prr5-11 double mutant, the diurnal expression profile of CDF1 (CYCLING DOF FACTOR 1) was markedly de-repressed in the evening in the long-day conditions. These and other results of this study led us to propose the novel view that TOC1 might play bipartite roles in the control of flowering time within a closed circuitry; the one is a GI (GIGANTEA)-dependent negative role through CCA1/LHY, and the other is a CDF1-dependent positive role through cooperating closely with PRR5.",
"pubmed_id": "18178585",
"provenance": {
"pub_title": "Insight into missing genetic links between two evening-expressed pseudo-response regulator genes TOC1 and PRR5 in the circadian-clock controlled circuitry in Arabidopsis thaliana.",
"first_author": "Ito, S.",
"group": "Mizuno",
"pub_date": "2008-01-04"
},
"growth_condition": [
{
"name": "Ito2008_LD",
"medium": "MS 1% sucrose",
"stratification": "3 days at 4C",
"duration": "10",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "90-100",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "16"
}
}
}
},
{
"name": "Ito2008_SD",
"medium": "MS 1% sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "120-150",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "10"
}
}
}
}
],
"experimental_condition": [
{
"name": "Ito2008_LD",
"medium": "MS 1% sucrose",
"duration": "1",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "90-100",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "16"
}
}
}
},
{
"name": "Ito2008_SD",
"medium": "MS 1% sucrose",
"duration": "1",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "120-150",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "10"
}
}
}
}
],
"measurement": {
"technique": "RT-PCR"
},
"sample_preparation": {
"method": "For real-time PCR, seedlings were grown on MS plates containing 1% sucrose under the conditions of LoD (16 h light/8 h dark) or ShD (10 h light/14 h dark) for 10 or 7 d. They were then harvested (3 h intervals) to quantify mRNA of genes involved in flowering regulation. Total RNA was purified by an RNeasy plant kit (Qiagen, Valencia, CA, USA). To synthesize cDNA, 1 mg of each RNA was reverse transcribed with Rever Tra Ace (TOYOBO, Osaka, Japan) and oligo(dT) primer. The synthesized cDNAs were amplified with iQ SYBR Green supermix (Bio-Rad Laboratories, Hercules, CA, USA) and a primer set using a MiniOpticon real-time PCR system (Bio-Rad Laboratories). The following standard thermal cycling\nprogram was used for all PCRs: 95oC for 120 s, 40 cycles of 95oC for 10 s, and 60oC for 60 s. Data were analyzed using Opticon Monitor version 3.1 software (Bio-Rad Laboratories). The oligonucleotide primers used in this study have all been described previously (Niwa et al. 2007)."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "GI",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "2",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "GI",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "GI",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "GI",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "5",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "FKF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "6",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "FKF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "7",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "FKF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "8",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "FKF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "9",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "10",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "11",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "12",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "13",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CO",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "14",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "CO",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "CO",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "16",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "CO",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "18",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "20",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "FT",
"growth_cond_name": "Ito2008_LD",
"experiment_cond_name": "Ito2008_LD"
},
{
"sample_id": "21",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "22",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "23",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "24",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "CDF1",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "25",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "26",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "27",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "28",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "CO",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "29",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "30",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1-2"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "31",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr5-11"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
},
{
"sample_id": "32",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "toc1;prr5"
},
"marker": "FT",
"growth_cond_name": "Ito2008_SD",
"experiment_cond_name": "Ito2008_SD"
}
]
}
},
"biblio": {
"principal": "Ito S",
"institution": "Nagoya University",
"author": [
"Ito S",
"Kawamura H",
"Niwa Y",
"Nakamichi N",
"Yamashino T",
"Mizuno T"
],
"curator": "Robert Smith"
}
}
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Views: 76 Downloads: 2
Created: 19th Jun 2026 at 15:10
Last updated: 19th Jun 2026 at 15:10
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Version 1 (earliest) Created 19th Jun 2026 at 15:10 by Daniel Thedie
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https://orcid.org/0000-0002-1352-7245Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.
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The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
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Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: Not specified
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Collection of experiments created by Ito, S. on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Ito 2007 wt LD PRR9 protein, Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, pr...
Advanced Studies list for this Data file with search and filtering
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Ito, S.
Assays: Ito 2007 wt LD PRR9 protein, Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, pr...
Advanced Assays list for this Data file with search and filtering
Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, prr5, toc1;prr5
| Property | Value |
|---|---|
| BioDare ID | 13790751359110 |
| Author | Ito, S. |
| Institution | Nagoya University |
| License | CC_BY |
Description
Purpose
In Arabidopsis thaliana, many circadian clock-associated genes have been identified. Among them, the eveningexpressed TOC1 (TIMING OF CAB EXPRESSION 1) gene plays a role by forming a transcriptional feedback core loop ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Ito, S.
Study: Unpublished
