Source Name Characteristics [Organism] Term Source REF Term Accession Number Description Protocol REF Protocol REF Sample Name Protocol REF Extract Name Material Type Labeled Extract Name Label Material Type Hybridization Name Array Design REF Scan Name Derived Array Data Matrix File Comment [Derived ArrayExpress FTP file] GSE5174GSM116729 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-4 GSE5174GSM116729 sample P-G5174-3 GSE5174GSM116729 extract total_RNA GSE5174GSM116729 LE biotin synthetic_RNA ein5_air_1_polyA A-AFFY-2 ein5_air_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116728 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-5 GSE5174GSM116728 sample P-G5174-3 GSE5174GSM116728 extract total_RNA GSE5174GSM116728 LE biotin synthetic_RNA ein2_ethylene_2_polyA A-AFFY-2 ein2_ethylene_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116731 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-5 GSE5174GSM116731 sample P-G5174-3 GSE5174GSM116731 extract total_RNA GSE5174GSM116731 LE biotin synthetic_RNA ein5_ethylene_1_polyA A-AFFY-2 ein5_ethylene_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116725 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Cold-treated seeds in MS plates were placed in chambers at 24oC in the dark with hydrocarbon-free airflow for three days, after which some of the chambers were connected to ethylene gas at 10 ppm while the others remained on air treatment. Four hours later the seedlings of each plate were quickly collected and frozen in liquid nitrogen. Total RNA was prepared from both air-treated and ethylene-treated etiolated seedlings of Arabidopsis Col-0, ein2-5 and ein5-1 using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Biotinylated target RNA was prepared from 16 ?g of total RNA using the procedure described by the manufacturer (Affymetrix, Santa Clara, CA). Briefly, a primer encoding a T7 RNA polymerase promoter fused to (dT)24 (Genset Oligos, La Jolla, CA) was used to prime double-stranded cDNA synthesis using the SuperScript Choice System (Life Technologies). The resulting cDNA was transcribed in vitro using the BioArray High-Yield RNA Tran-script Labeling Kit (Enzo Biochem, New York, NY) in the presence of biotinylated UTP and CTP to produce biotinylated target complementary RNA (cRNA). The labeled target cRNA was purified, fragmented, and hybridized to Arabidopsis microoarrays (Affymetrix whole genome tiling, and ATH1 gene expression arrays) according to protocols provided by the manufacturer in a hybridization oven model 640 (Affymetrix, Santa Clara, CA). The arrays were washed and stained with streptavidin-phycoerythrin using a GeneChip Fluidics Station model 400 and then scanned with a Gene Array Scanner (Hewlett-Packard, Palo Alto, CA). Scanned images were processed and quantified using GeneChip Suite 3.2. Genespring software (Silicon Genetics, Redwood City, CA) was used to manage and filter the array data. Each measurement was divided by the 50.0th percentile of all measurements in that sample. The percentile was calculated with all normalized measurements above 10. For samples where the bottom tenth percentile was less than the negative of the 50.0th percentile, it was used as a background, and subtracted from all the other genes first. Experiments were carried out in duplicate and hybridized to two sets of expression chips. Expression values were analyzed using GeneSpring™ software version 4.2 (Silicon Genetics, Redwood, California).. Strain;ein2 colmbia, Tissue; seedling, Age; 3days, Growth; on agar plate under continuous dark condition in hydrocarbon-free air P-G5174-2 P-G5174-1 GSE5174GSM116725 sample P-G5174-3 GSE5174GSM116725 extract total_RNA GSE5174GSM116725 LE biotin synthetic_RNA ein2_air_1_polyA A-AFFY-2 ein2_air_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116734 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;wild type colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-4 GSE5174GSM116734 sample P-G5174-3 GSE5174GSM116734 extract total_RNA GSE5174GSM116734 LE biotin synthetic_RNA wt_air_2_polyA A-AFFY-2 wt_air_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116733 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;wild type colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-4 GSE5174GSM116733 sample P-G5174-3 GSE5174GSM116733 extract total_RNA GSE5174GSM116733 LE biotin synthetic_RNA wt_air_1_polyA A-AFFY-2 wt_air_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116726 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-4 GSE5174GSM116726 sample P-G5174-3 GSE5174GSM116726 extract total_RNA GSE5174GSM116726 LE biotin synthetic_RNA ein2_air_2_polyA A-AFFY-2 ein2_air_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116735 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;wild type colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-6 GSE5174GSM116735 sample P-G5174-3 GSE5174GSM116735 extract total_RNA GSE5174GSM116735 LE biotin synthetic_RNA wt_ethylene_1_polyA A-AFFY-2 wt_ethylene_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116727 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-5 GSE5174GSM116727 sample P-G5174-3 GSE5174GSM116727 extract total_RNA GSE5174GSM116727 LE biotin synthetic_RNA ein2_ethylene_1_polyA A-AFFY-2 ein2_ethylene_1_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116736 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;wild type colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-6 GSE5174GSM116736 sample P-G5174-3 GSE5174GSM116736 extract total_RNA GSE5174GSM116736 LE biotin synthetic_RNA wt_ethylene_2_polyA A-AFFY-2 wt_ethylene_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116730 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-4 GSE5174GSM116730 sample P-G5174-3 GSE5174GSM116730 extract total_RNA GSE5174GSM116730 LE biotin synthetic_RNA ein5_air_2_polyA A-AFFY-2 ein5_air_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip GSE5174GSM116732 Arabidopsis thaliana EFO http://purl.org/obo/owl/NCBITaxon#NCBITaxon_3702 seedling: Arabidopsis thaliana (ecotype Columbia) seeds were surface sterilized in 75% Ethanol 10 min, rinsed in distilled water. The seeds were cold-treated at 4 degrees C for 2 days and then incubated in the dark for 5 days at 25 degrees C under ethylene treatment. Seedlings were collected which were grown as described in the Arabidopsis Biological Resources Center manual (ABRC; http://www.biosci.ohio state.edu/~plantbio/Facilities/abrc/abrchome.htm).Total RNA was isolated from whole plant tissue and leaves using the Qiagen RNeasy kit (Valencia,CA) according to the manufacturerfs instructions. The quality and quantity of RNA isolated was checked by both gel electrophoresis and spectrophotometry.Five micro g total RNA was converted into double-stranded cDNA using Affymetrix T7-oligo(dT) primers. Biotin-labeled cRNA was generated by in vitro transcription reactions, fragmented, and then approximately 15 micro g of fragmented cRNA were hybridized to the tiling arrays according to Affymetrix (Santa Clara, CA) instructions. The arrays were washed and stained using an Affymetrix fluidics station as instructed in the manufacturer's user manual. CELTM files from scanned arrays were used for further analysis.. Strain;ein2 colmbia, Tissue; seedling, Age; 5days, Growth; on agar plate under continuous dark condition P-G5174-5 GSE5174GSM116732 sample P-G5174-3 GSE5174GSM116732 extract total_RNA GSE5174GSM116732 LE biotin synthetic_RNA ein5_ethylene_2_polyA A-AFFY-2 ein5_ethylene_2_polyA E-GEOD-5174-processed-data-1628307095.txt ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E-GEOD-5174/E-GEOD-5174.processed.1.zip