Transcriptomic, ChIP-seq, and TARGET-seq datasets revealing NLP7 regulatory networks under nitrogen and drought stress in Arabidopsis thaliana

This dataset includes original transcriptomic and genomic sequencing data generated to study the transcription factor NIN-LIKE PROTEIN 7 (NLP7) and its role in regulating gene expression in response to nitrogen and drought in Arabidopsis thaliana.The dataset comprises three experimental approaches:Transcriptome profiling using BRB-seq and Lexogen QuantSeqTotal RNA was extracted from rosettes of Arabidopsis thaliana wild-type (Col-0) and nlp7 mutant plants grown under controlled long-day conditions (16 h light / 8 h dark, 22 C, 65 percent relative humidity). At 21 days after germination, plants were transferred to soil and subjected to two nitrogen regimes (low 0.5 mM NH4NO3 and high 10 mM NH4NO3). After two days of acclimation under these nitrogen conditions, plants were exposed to drought treatments applied in parallel -- either well-watered or deprived of irrigation for six days. Libraries were prepared using both the Bulk RNA Barcoding and Sequencing (BRB-seq) protocol and the Lexogen QuantSeq 3 mRNA-Seq Library Prep Kit for Illumina, optimized for high-throughput and multiplexed 3-end transcriptome profiling. Sequencing was performed on an Illumina platform, generating single-end reads for downstream gene expression analysis.ChIP-seq of NLP7 under drought and well-watered conditionsChIP-seq was performed on NLP7pro::GFP:NLP7 Arabidopsis plants subjected to drought stress (6 days without watering) and well-watered control conditions. Leaves were collected, crosslinked, and chromatin was sonicated. Immunoprecipitation was carried out using anti-GFP antibodies, with input DNA sequenced as control. Libraries were prepared from pooled biological replicates and sequenced as 100 bp single-end reads on an Illumina HiScanSQ platform.TARGET-seq to determine direct NLP7 targets in protoplastsLeaf protoplasts were isolated from nlp7 mutant plants and transfected with a dexamethasone-inducible NLP7-GR construct or a control vector. After overnight incubation, protoplasts were treated with dexamethasone to induce nuclear translocation of NLP7-GR in the presence of cycloheximide to block secondary transcriptional cascades. RNA was then extracted and sequenced to identify direct targets of NLP7 in leaf cells.These datasets provide a resource to explore NLP7-mediated gene regulation under defined environmental conditions, supporting future studies on the integration of nutrient and stress signals in plants.