{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Kota Monden"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"organism":["Arabidopsis thaliana"],"species":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15416"],"description":["Trans-zeatin (tZ)-type cytokinin (CK) positively regulates leaf size and number by translocating from root to shoot in response to nitrate signals. Our preceding study suggested that CK perception in the root may influence the long-distance transport of tZ-type CKs from root to shoot. However, the underlying mechanism and physiological significance remain unclear. Therefore, we generated grafted plants with the wild-type Col-0 (WT) as the scion and either WT or one of three CK receptor mutants - Arabidopsis histidine kinase (ahk) 2, ahk3, or ahk4 - as the rootstock (scion/rootstock: WT/WT, WT/ahk2, WT/ahk3, and WT/ahk4). We then analyzed the vegetative growth, CK concentrations, and transcriptomes of these grafted plants."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA quality was evaluated using a Qubit RNA IQ Assay Kit with a Qubit 4 Fluorometer (Thermo Fisher Scientific, Tokyo, Japan). The RNA samples for which RNA IQs were 9.5–10.0 were used for the following preparation. cDNA libraries were constructed using a NEBNext Ultra II Directional RNA Library Prep (E7760S, New England Biolabs, Ipswich, MA, USA), SPRIselect (B23317, Beckman Coulter), a NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S, New England Biolabs), and a NEBNext Multiplex Oligos for Illumina (E7710S, New England Biolabs) according to the manufacturer’s instructions.","Nucleic Acid Extraction - Frozen samples were ground with a Multi-Beads Shocker (Yasui Kikai, Osaka, Japan) using zirconia beads (diameter: 5 mm). Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen, Tokyo, Japan) according to the manufacturer's instructions with on-column DNase digestion (Qiagen).","Growth Protocol - Seeds were placed in the dark at 4˚C for 3 days to break dormancy. Seedlings were grown vertically under a PPFD of 25 µmol m⁻² s⁻¹ (16/8-h light/dark cycle) at 22˚C. Micrografting was performed aseptically using 5-day-old seedlings, which were cut perpendicularly in the hypocotyl with an injection needle tip. The obtained scion was connected with the partner rootstock in a silicon microtube. The grafted plants were incubated for 5 days under a PPDF of 50 µmol m⁻² s⁻¹ (constant light) at 27˚C. The grafted plants were horizontally grown for 7 days under a PPFD of 70 µmol m⁻² s⁻¹ (16/8-h light/dark cycle) at 22˚C in 30 mL of 1/2-Murashige and Skoog (MS) without vitamins supplemented with 0.05% (w/v) MES-KOH (pH 5.7), 1% (w/v) sucrose, and 0.8% (w/v) purified agar.","Sample Collection - Shoots and roots were harvested, immediately frozen in liquid nitrogen, and stored at - 80 °C until use. Sampling was performed independently three times, with three grafted plants pooled as one biological replicate for each sample.","Sequencing - The cDNA libraries were sequenced using NextSeq 500 (Illumina, Tokyo, Japan), and the produced bcl files were converted to fastq files using bcl2fastq (Illumina)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Kota Monden"],"additional_accession":[]},"is_claimable":false,"name":"Effects of root-specific deficiency of each cytokinin receptor AHK2, AHK3, or AHK4 on genome-wide gene expression in shoots and roots of Arabidopsis thaliana","description":"Trans-zeatin (tZ)-type cytokinin (CK) positively regulates leaf size and number by translocating from root to shoot in response to nitrate signals. Our preceding study suggested that CK perception in the root may influence the long-distance transport of tZ-type CKs from root to shoot. However, the underlying mechanism and physiological significance remain unclear. Therefore, we generated grafted plants with the wild-type Col-0 (WT) as the scion and either WT or one of three CK receptor mutants - Arabidopsis histidine kinase (ahk) 2, ahk3, or ahk4 - as the rootstock (scion/rootstock: WT/WT, WT/ahk2, WT/ahk3, and WT/ahk4). We then analyzed the vegetative growth, CK concentrations, and transcriptomes of these grafted plants.","dates":{"release":"2025-08-26T00:00:00Z","modification":"2025-07-30T14:30:49.505Z","creation":"2025-07-30T14:30:49.505Z"},"accession":"E-MTAB-15416","cross_references":{"ENA":["ERP177488"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"]}}