{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Oscar Juez"],"organism":["Arabidopsis thaliana"],"software":["Illumina for base calling and demultiplexing"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16266"],"description":["Chromatin immunoprecipitation sequencing (ChIP-seq) was used to map the genome-wide binding profile of the inner nuclear envelope protein KAKU4 in Arabidopsis thaliana. A functional ProKAKU4:KAKU4-eYFP transgene (Goto et al., Plant Cell 2014), which complements the kaku4-3 mutant, and an untagged kaku4 (SALK_076754) control line were analysed. Young samples consisted of 10-day-old seedlings (n = 3 biological replicates per genotype, pooling ~12 seedlings per replicate). Old samples consisted of 120-day short-day rosettes, where senescence leaves from 3–4 plants were pooled per replicate (n = 3 replicates). Together enabling comparison of KAKU4 occupancy between juvenile and long-term aged tissues."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Arabidopsis thaliana Col-0 background plants were used to profile KAKU4 chromatin binding. A functional ProKAKU4:KAKU4-eYFP translational reporter in the kaku4-3 mutant background (homozygous T3 with stable eYFP expression) and an untagged KAKU4-deficient control (SALK_076754) were analysed. For “young” samples, seeds were germinated on ½ MS medium and grown for 10 days under long-day conditions; early cotyledon tissue from ~12 seedlings was pooled per biological replicate (n = 3 per genotype). For “old” samples, seeds were sown on soil (3–5 plants per pot) and grown for 120 days under short-day conditions (8 h light / 16 h dark); the most senescent rosette leaves 1–4 from 3–4 plants were pooled per replicate (n = 3). All tissues were harvested at ZT4, immediately froze","Library Construction - ChIP and input DNA were purified using QIAquick columns and eluted in nuclease-free water. Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645) and NEBNext Multiplex Oligos (E6440) according to the manufacturer’s protocol. Briefly, 10–15 ng of DNA was subjected to end repair, A-tailing, adaptor ligation, and USER treatment, followed by SPRIselect bead clean-up. Size selection was performed to exclude adaptor dimers and enrich fragments >150 bp (target library size ~270–500 bp including adaptors). Libraries were PCR-amplified for 8 cycles using the recommended thermocycling program, bead-cleaned, quantified by Qubit dsDNA HS assay, and assessed on an Agilent Bioanalyzer to confirm the expected size distribution.","Growth Protocol - All lines were in the Arabidopsis thaliana Col-0 background. For seedling (“young”) samples, seeds of the ProKAKU4:KAKU4-eYFP line and the untagged kaku4 control (SALK_076754) were surface-sterilized, stratified at 4 °C, and germinated on ½ MS medium. Seedlings were grown for 10 days under long-day conditions (16 h light / 8 h dark) at ~22 °C before harvesting cotyledon tissue. For rosette (“old”) samples, seeds were sown on soil (3–5 plants per pot) and grown in controlled-environment chambers for 120 days under short-day conditions (8 h light / 16 h dark) at ~22 °C. Plants were regularly watered and fertilized according to standard Arabidopsis practice. All sample collections were performed at ZT4.","Sequencing - Indexed libraries were pooled equimolarly and sequenced at the OIST Sequencing Section on an Illumina NovaSeq 6000 platform. Sequencing was performed in paired-end 2 × 150 bp mode, targeting at least 20 million read pairs per sample. Standard Illumina base calling and demultiplexing were used to generate gzipped FASTQ files for each library.","Nucleic Acid Extraction - For each replicate, 0.5 g of 10-day seedlings or 1 g of 120-day senescent rosette leaves were frozen, ground in liquid nitrogen, and resuspended in 11 mL ice-cold nuclei isolation buffer (10 mM HEPES pH 7.6, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA) freshly supplemented with formaldehyde (final 1%), Triton X-100, 2-mercaptoethanol and protease inhibitor cocktail. Crosslinking was carried out for 15 min at room temperature with gentle inversion and quenched with glycine for 5 min. Nuclei were pelleted, washed, and enriched by centrifugation through 15% Percoll, then lysed in SDS lysis buffer (50 mM Tris-HCl pH 7.8, 1% SDS, 10 mM EDTA) and diluted in ChIP buffer (50 mM HEPES-KOH pH 7.6, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM EDTA). Chromati"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Thermocycler; SPRI magnetic bead rack; Qubit fluorometer; Agilent Bioanalyzer","Controlled-environment growth chambers (long-day and short-day)","Illumina NovaSeq 6000","Dissection tools; liquid nitrogen; −80 °C freezer","Branson Digital Sonifier; refrigerated benchtop centrifuge; rotator; magnetic rack"],"study_type":["ChIP-seq"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Oscar Juez"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide KAKU4-eYFP ChIP-seq of Arabidopsis thaliana kaku4 complemented and untagged control plants at seedling (10 days) and 120-day rosette stages","description":"Chromatin immunoprecipitation sequencing (ChIP-seq) was used to map the genome-wide binding profile of the inner nuclear envelope protein KAKU4 in Arabidopsis thaliana. A functional ProKAKU4:KAKU4-eYFP transgene (Goto et al., Plant Cell 2014), which complements the kaku4-3 mutant, and an untagged kaku4 (SALK_076754) control line were analysed. Young samples consisted of 10-day-old seedlings (n = 3 biological replicates per genotype, pooling ~12 seedlings per replicate). Old samples consisted of 120-day short-day rosettes, where senescence leaves from 3–4 plants were pooled per replicate (n = 3 replicates). Together enabling comparison of KAKU4 occupancy between juvenile and long-term aged tissues.","dates":{"release":"2026-08-08T00:00:00Z","modification":"2026-08-08T01:01:02.074Z","creation":"2025-11-24T13:12:14.511Z"},"accession":"E-MTAB-16266","cross_references":{"ENA":["ERP185552"],"Biostudies":["E-MTAB-16263","E-MTAB-16251"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"]}}