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Series GSE128209 Query DataSets for GSE128209
Status Public on Mar 14, 2019
Title Nitrogen and cycloheximide effects on protoplast and TF-target identification in the TARGET assay
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The effects of nitrogen and cycloheximide treatments on nitrogen response and TF-target identification was tested in the cell-based TARGET assay. For protoplast experiments, Arabidopsis plants were grown on low nitrogen (1mM KNO3) and after 10 days protoplasts were generated from root tissue. Cells were transfected with a vector containing the GR-TGA4 fusion or GR-only empty vector and incubated overnight. In the morning, samples were pre-treated with nitrogen as specified for 2 hours, and +/-cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. 3 hours after dex treatment samples were FACS sorted into RNA extraction buffer. For whole roots, Arabidopsis were grown in liquid media with low nitrogen (1 mM KNO3) in Phytatrays for 11 days. In the morning and at the same time as the protoplasts, the plants were transferred to fresh media containing either 20 mM KCL or 20mM KNO3 + 20mM NH4NO3 for 5 hours. Roots were harvested and immediately frozen in liquid N2.
Overall design Three replicates were used for effect of cycloheximide and nitrogen source/dose on TGA4-target identification, control samples were transfected with a GR-only vector. Four replicates were collected for root vs. protoplast N-response.
Contributor(s) Brooks MD, Coruzzi G
Citation(s) 30952851
Submission date Mar 12, 2019
Last update date Apr 17, 2019
Contact name Matthew D. Brooks
Organization name USDA
Department GCPRU
Street address 1201 W Gregory Drive
City Urbana
State/province Illinois
ZIP/Postal code 61801
Country USA
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (46)
GSM3667110 EV_0N_Rep1
GSM3667111 EV_0N_Rep2
GSM3667112 EV_0N_Rep3
BioProject PRJNA526775
SRA SRP188270

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Supplementary file Size Download File type/resource
GSE128209_RAW.tar 5.3 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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