{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE331nnn/GSE331340/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Arabidopsis thaliana"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE331340"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Hormone-treatment (ABA, SA) timecourse of Arabidopsis thaliana root","description":"Profiling of binding sites for hundreds of A. thaliana transcription factors genome-wide revealed an unexpected enrichment of conserved TF binding sites (TFBSs) in coding sequence (CDS) for specific TF families, yet little association with cell type-specific gene expression. To differentiate between possible explanations for this, gene expression was profiled using bulk RNA-seq in response to hormone-induced stress. Abscisic Acid (ABA) treatment time-course data revealed that TFs known to activate transcription in response to ABA were significantly up-regulated, and most target genes of these TFs were upregulated as well - with the exception being target genes with TFBSs exclusively in coding sequence, which showed no significant expression change. Salicylic acid (SA) treatment further confirmed that target genes of known SA-responsive activators were induced only when TFBSs were found outside the coding region. However a key SA-responsive repressor (ABR1) showed strong repression of genes with CDS binding sites, suggesting a mechanism for rapid antagonistic response. Moreover, integration with chromatin accessibility data from the same tissues revealed strong links between constitutive TFBS accessibility and stress-induced target gene expression, suggesting that rapid, tissue-wide regulatory responses might preferentially operate through constitutively accessible sites primarily located close to transcription start sites.","dates":{"publication":"2026/06/24"},"accession":"GSE331340","cross_references":{"GSM":["GSM9744249","GSM9744244","GSM9744243","GSM9744242","GSM9744241","GSM9744248","GSM9744247","GSM9744246","GSM9744245","GSM9744240","GSM9744139","GSM9744253","GSM9744252","GSM9744138","GSM9744251","GSM9744250","GSM9744229","GSM9744228","GSM9744227","GSM9744189","GSM9744222","GSM9744221","GSM9744188","GSM9744187","GSM9744220","GSM9744186","GSM9744226","GSM9744225","GSM9744224","GSM9744223","GSM9744181","GSM9744180","GSM9744185","GSM9744184","GSM9744183","GSM9744182","GSM9744239","GSM9744238","GSM9744233","GSM9744232","GSM9744199","GSM9744198","GSM9744231","GSM9744230","GSM9744197","GSM9744237","GSM9744236","GSM9744235","GSM9744234","GSM9744192","GSM9744191","GSM9744190","GSM9744196","GSM9744195","GSM9744194","GSM9744193","GSM9744208","GSM9744207","GSM9744206","GSM9744205","GSM9744209","GSM9744167","GSM9744200","GSM9744166","GSM9744165","GSM9744164","GSM9744204","GSM9744203","GSM9744169","GSM9744202","GSM9744201","GSM9744168","GSM9744163","GSM9744162","GSM9744161","GSM9744160","GSM9744219","GSM9744218","GSM9744217","GSM9744216","GSM9744178","GSM9744211","GSM9744210","GSM9744177","GSM9744176","GSM9744175","GSM9744215","GSM9744214","GSM9744213","GSM9744212","GSM9744179","GSM9744170","GSM9744174","GSM9744173","GSM9744172","GSM9744171","GSM9744145","GSM9744144","GSM9744143","GSM9744142","GSM9744149","GSM9744148","GSM9744147","GSM9744146","GSM9744141","GSM9744140","GSM9744156","GSM9744155","GSM9744154","GSM9744153","GSM9744159","GSM9744158","GSM9744157","GSM9744152","GSM9744151","GSM9744150"],"GPL":["26208"],"GSE":["331340"],"taxon":["Arabidopsis thaliana"]}}