Comment[GEAAccession]	E-GEAD-654
MAGE-TAB Version	1.1
Investigation Title	Timecourse transcriptome analysis (mRNA-seq) of calli of Madake bamboo under osmotic stresses
Experiment Description	We conducted mRNA sequencing (mRNA-seq) on cultivated cell lines from Madake bamboo (Phyllostachys bambusoides) at multiple timepoints following treatment with either air drying or high osmolytes, such as glucose and sucrose.
Experimental Design	case control design	replicate design
Experimental Factor Name	treatment
Experimental Factor Type	treatment
Person Last Name	Kim
Person First Name	June-Sik
Person Affiliation	Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science
Person Roles	submitter
Public Release Date	2024-09-26
Publication DOI	10.1038/s41597-025-04518-7
Protocol Name	P-GEAD-2030	P-GEAD-2031	P-GEAD-2032	P-GEAD-2033	P-GEAD-2034	P-GEAD-2035
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol	high throughput sequence alignment protocol
Protocol Description	Cultivated calli were collected and stored in dry ice.	RNA was harvested using Rneasy mini plus kit (Qiagen). 2~5 ug of total RNA was used for the construction of sequencing libraries.	RNA libraries for RNA-seq were prepared using NEXTflex Rapid Directional RNA-seq kit (v2.0; PerkinElmer) following manufacturer's protocols.	NGS	The STAR resultant toTranscriptome.out.bam files were subjected to RSEM (version 1.3.1) analysis to evalaute the expression level for each transcript isoform with default parameters.	The clean reads were aligned to the PHO1 (Zhao et al., 2018) reference genome by STAR (version 2.7.9a) with default parameters.
SDRF File	E-GEAD-654.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB16709
Comment[Last Update Date]	2025-02-04