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Series GSE117857 Query DataSets for GSE117857
Status Public on Mar 14, 2019
Title Genome-wide validation of the direct regulated targets for 33 nitrogen-early response transcription factors
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The direct targets of 33 Nitrogen-early responsive TFs were identified using the TARGET system. 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-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with 20 mM KNO3 and 20 mM NH4NO3 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 and RNA-seq libraries were generated. Transcriptional response to each TF compared to empty vector was assayed.
Overall design Genome-wide direct regulated targets of 33 TFs were determined by comparison to an empty vector control. Vectors were expressed in protoplasts isolated from root tissue, samples were done in triplicate, and sequenced using the Illumina NextSeq platform.
Contributor(s) Brooks MD, Coruzzi G
Citation(s) 30952851
Submission date Jul 30, 2018
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 (115)
GSM3311571 EV_B1Rep1
GSM3311572 ERF056_B1Rep1
GSM3311573 HSFB2A_B1Rep1
BioProject PRJNA483458
SRA SRP155742

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE117857_RAW.tar 13.6 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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