Information about Samples:
Sample_titleWT(Ler)_Dark_replicate1WT(Ler)_Dark_replicate2WT(Ler)_Dark_replicate3phyAphyB_Dark_replicate1phyAphyB_Dark_replicate2phyAphyB_Dark_replicate3YHB_Dark_replicate1YHB_Dark_replicate2YHB_Dark_replicate3WT(Ler)_Rc15_replicate1WT(Ler)_Rc15_replicate2WT(Ler)_Rc50_replicate1WT(Ler)_Rc50_replicate2YHB_Rc50_replicate1YHB_Rc50_replicate2
Sample_geo_accessionGSM226267GSM226268GSM226269GSM226270GSM226271GSM226272GSM226273GSM226274GSM226275GSM226276GSM226277GSM226278GSM226279GSM226280GSM226281
Sample_typeRNARNARNARNARNARNARNARNARNARNARNARNARNARNARNA
Sample_channel_count111111111111111
Sample_source_name_ch1whole seedlingwhole seedlingwhole seedlingsWhole seedlingwhole seedlingwhole seedlingwhole seedlingwhole seedlingswhole seedlingwhole seedlingwhole seedlingwhole seedlingwhole seedlingwhole seedlingwhole seedling
Sample_organism_ch1Arabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thalianaArabidopsis thaliana
Sample_characteristics_ch1wild type (Landsberg erecta ecotype)wild type (Landsberg erecta ecotype); dark-grown; 4 days (96h) oldwild type (Landsberg erecta ecotype); dark-grown; 4 days (96h) oldphyA-201phyB-5 mutant in Ler backgroundphyA-201phyB-5 mutant in Ler backgournd; dark-grown; 4 days (96h) oldphyA-201phyB-5 mutant in Ler background; dark-grown; 4 days (96h) oldTransgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #5;transgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #5; dark-grown; 4 days (96h) oldTransgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #4; dark-grown; 4 days (96h) oldwild type (Landsberg erecta ecotype); grwon under continuous red light (Rc; light intensity = 15 umole m-2 s-1); 4 days (96h) oldwild type (Landsberg erecta ecotype); grown under continuous red light (Rc; light intensity = 15 umole m-2 s-1); 4 days (96h) oldwild type (Landsberg erecta ecotype); grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) oldwild type (Landsberg erecta ecotype); grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) oldTransgenic plant, AtPHYB(genomic)-Y276H/phyA-201phyB-5, line #4; grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) oldTransgenic plant, AtPHYB(genomic)-Y276H/phyAphyB, line #4; grown under continuous red light (Rc; light intensity = 50 umole m-2 s-1); 4 days (96h) old
Sample_characteristics_ch1Dark-grownDark-grownDark-grown;
Sample_characteristics_ch14 days (96h) old4 days (96 h) old4 days (96h) old
Sample_molecule_ch1total RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNAtotal RNA
Sample_extract_protocol_ch1QIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini KitQIAGEN RNeasy Plant Mini Kit
Sample_label_ch1BiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotinBiotin
Sample_label_protocol_ch1Affymetrix GeneChip® Expression Analysis kitsAffymetrixAffymetrixAffymetrix GeneChip® Expression Analysis kitsAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents)
Sample_taxid_ch1370237023702370237023702370237023702370237023702370237023702
Sample_hyb_protocolAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrix
Sample_scan_protocolAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrixAffymetrix
Sample_descriptionSeeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 micromol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 micromol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. For dark growth, plates were wrapped with several layers of aluminum foil and subject to a temperature cycle (12h 22 degree /12h 18 degree) during the first two days of growth to entrain and synchronize circadian clock; temperature was set at 20 degree during the second two days. Seedlings were harvested and immediately frozen in liquid nitrogen in complete darkness with the aid of Bushnell night vision goggle with a built-in infrared illuminator (model: 26-1020 (1.0 x 20)).Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 15 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 15 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 50 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 50 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 50 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.Seeds were surface sterilized and sowed on filter papers that were laid on MS medium (solidified with 0.8% agar) without sucrose. Seeds were stratified at 4 degree in darkness for 4 days. Germination was induced by exposure under ~80 umol m-2 s-1 white light for 3 hours. The SNAP-LITE lighting system (Quantum Devices Inc., Barneveld, WI) was used for red light source. Seedlings were grown for 4 days at 20 degree under 50 umol m-2 s-1 continuous red light (measured by a LI-COR quantum photometer, model LI-189). Seedlings were harvested and immediately frozen in liquid nitrogen under red light.
Sample_platform_idGPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198GPL198