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Series GSE152405 Query DataSets for GSE152405
Status Public on Jun 13, 2020
Title ConnecTF: A platform to integrate validated transcription factor-target interactions to build and refine gene regulatory networks
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media 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 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 16 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) 33631799
Submission date Jun 12, 2020
Last update date Jun 03, 2021
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 (56)
GSM4614459 AT5G04340 ZAT6 Rep3 Batch1
GSM4614460 AT5G43840 HSFA6A Rep3 Batch1
GSM4614461 AT1G49720 ABF1 Rep3 Batch1
BioProject PRJNA639173
SRA SRP267137

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

Supplementary file Size Download File type/resource
GSE152405_RAW.tar 6.6 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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