biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsAgnieszka Kiełbowicz-MatukIllumina HiSeq 1500RNA-seq of coding RNASolanum tuberosumSolanum tuberosumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15322Analysis of gene expression in the apical shoot parts and stolons of StBBX20-silenced and -overexpressed potato lines was carried out via RNA-seq (two biological replicates). 5- and 7-week-old apical shoot parts (Figure S3) and 3-week-old stolons (Figure S4) samples were collected at ZT6 from four plants per pot (pooled technical replicates). Total cellular RNA was prepared using TRI Reagent® RT (Molecular Research Center, Inc.) and treated with DNase I during RNA purification. The quality and quantity of RNA were verified using a DS-11 FX spectrophotometer (DeNovix Inc.). RNA integrity number (RIN) of samples sufficient for sequencing (≥ 7) and rRNA ratio (≥ 1.7) was checked using Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Inc.). cDNA library construction using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequencing using an Illumina platform with a 2 × 150 bp PE configuration were conducted by Macrogen Inc. (Seoul, Republic of Korea).biostudies-arrayexpressGrowth Protocol - Solanum tuberosum L., cv. Desirée wild-type (WT) plants and transgenic lines (amiRBBX20.2.7 and StBBX20-OE3) were propagated in vitro on solid MS medium at 20/18°C (day/night) under a 150 µmol photon m -2 s -1 PFD and a 14-hour photoperiod for three weeks. Then, four single-eye plugs from tubers were transferred to the soil (pots diameter 21 cm) and grown in the phytotron under conditions as follows: 20/18°C (day/night), 40% relative humidity, PFD of 350 µmol photons m -2 s -1 and 14-hour- light/10-hour-dark regime. The term Zeitgeber time (ZT) relates to the experimental time, where the ZT0 point corresponded to light-on (initiation of experimental dawn) and the ZT14 point to light-off (initiation of experimental dusk). Two independent experiments were conducted and two independent plant samples from each experiment were collected. 5- and 7-week-old apical shoot parts and 4-week-old stolons of S. tuberosum WT plants, and two transgenic lines: StBBX20 gene-silenced line (amiRBBX20.2.7) and StBBX20 gene-overexpressed line (StBBX20-OE3) were collected at ZT6.Sample Collection - Samples gathered in two biological replicates. Samples were taken from 5- and 7-week-old apical shoot parts and 3-week-old stolons collected at ZT6 from four plants per pot.Nucleic Acid Extraction - Total cellular RNA was prepared using TRI Reagent® RT (Molecular Research Center, Inc.) and treated with DNase I during RNA purification. The quality and quantity of RNA were verified using a DS-11 FX spectrophotometer (DeNovix Inc.). RNA integrity number (RIN) of samples sufficient for sequencing (≥ 7) and rRNA ratio (≥ 1.7) was checked using Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Inc.).Sequencing - Sequencing using an Illumina platform with a 2 × 150 bp PE configuration were conducted by Macrogen Inc. (Seoul, Republic of Korea).Library Construction - Library construction using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina)OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesAgnieszka Kiełbowicz-MatukfalseTranscriptomic analysis reveals new role of circadian-regulated StBBX20 protein in potato reproductionAnalysis of gene expression in the apical shoot parts and stolons of StBBX20-silenced and -overexpressed potato lines was carried out via RNA-seq (two biological replicates). 5- and 7-week-old apical shoot parts (Figure S3) and 3-week-old stolons (Figure S4) samples were collected at ZT6 from four plants per pot (pooled technical replicates). Total cellular RNA was prepared using TRI Reagent® RT (Molecular Research Center, Inc.) and treated with DNase I during RNA purification. The quality and quantity of RNA were verified using a DS-11 FX spectrophotometer (DeNovix Inc.). RNA integrity number (RIN) of samples sufficient for sequencing (≥ 7) and rRNA ratio (≥ 1.7) was checked using Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Inc.). cDNA library construction using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequencing using an Illumina platform with a 2 × 150 bp PE configuration were conducted by Macrogen Inc. (Seoul, Republic of Korea).2025-11-17T00:00:00Z2025-11-17T10:49:37.937Z2025-07-04T13:11:32.517ZE-MTAB-15322ERP174661EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0004184