Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Faculty Publications Article Faculty Publications -Articles Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Creator An entity primarily responsible for making the resource Lee, Han-Sol; Han, Jong-Eun; Shim, Donghwan; Choi, Bae Young; Cho, Hyunwoo; Murthy, Hosakatte Niranjana; Park, So-Young Title A name given to the resource Comprehensive transcriptomic and functional characterization of protoplast regeneration in Angelica gigas Nakai Date A point or period of time associated with an event in the lifecycle of the resource 01-01-2026 Source A related resource from which the described resource is derived BMC Plant Biology;Volume;26;Issue;1;Article No.;208; Identifier An unambiguous reference to the resource within a given context <a href="https://doi.org/10.1186/s12870-025-08075-4" target="_blank" rel="noreferrer noopener">https://doi.org/10.1186/s12870-025-08075-4</a> <br /><br /><a href="https://www.scopus.com/pages/publications/105029171322?origin=resultslist" target="_blank" rel="noreferrer noopener">https://www.scopus.com/pages/publications/105029171322?origin=resultslist</a> Coverage The spatial or temporal topic of the resource, the spatial applicability of the resource, or the jurisdiction under which the resource is relevant Lee H.-S., Department of Horticultural Science, Chungbuk National University, Cheongju, 28644, South Korea; Han J.-E., Department of Horticultural Science, Chungbuk National University, Cheongju, 28644, South Korea; Shim D., Department of Biological Sciences, Chungnam National University, Daejeon, 34134, South Korea; Choi B.Y., Department of Biological Sciences, Chungnam National University, Daejeon, 34134, South Korea, School of Liberal Arts and Sciences, Korea National University of Transportation, Chungju, 27469, South Korea; Cho H., Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 28644, South Korea; Murthy H.N., Department of Horticultural Science, Chungbuk National University, Cheongju, 28644, South Korea, Department of Life Sciences, Christ University, Central Campus, Bengaluru, 560029, India; Park S.-Y., Department of Horticultural Science, Chungbuk National University, Cheongju, 28644, South Korea Description An account of the resource Background: Protoplasts that are isolated from various plant sources, including leaf mesophyll tissue, callus, will continue to have the ability to take part in cell wall regeneration, division, and expression of totipotency. In model systems like Arabidopsis thaliana, it has been thoroughly established. Meanwhile, the fate of protoplasts isolated from both embryogenic (EC) and non-embryogenic callus (NEC) in other plants is unknown. Thus, we conducted transcriptome analyses of protoplasts produced from both EC and NEC in Angelica gigas in the present investigation. To achieve this, three stages of RNA sequencing were carried out: (1) EC, (2) freshly isolated protoplasts (Pt), and (3) cells undergoing cell division (CD) during A. gigas in vitro protoplast regeneration. Different gene expression programs were identified across stages through transcriptome profiling, which highlighted early stress responses, transcriptional changes, and the acquisition of stem cell identity following protoplast isolation. Results: A pre-existing stem cell-like condition was shown by the strong expression of WUSCHEL-RELATED HOMEOBOX5 (WOX5) and CUP-SHAPED COTYLEDON2 (CUC2) genes at the EC stage. Important genes linked to stress reactions and cellular transcriptional changes, as WOX13 and WOUND INDUCED DEDIFFERENTIATION1 (WIND1), were significantly elevated at the Pt stage. Additionally, during this phase, genes associated with the cell cycle, auxin and cytokinin signaling, and cell wall regeneration were also active, indicating a dynamic shift toward regaining stem cell identity. Key regulators of stem cell maintenance and proliferation, such as LATERAL ORGAN BOUNDARIES DOMAIN16 (LBD16) and ENHANCER OF SHOOT REGENERATION2 (ESR2), were then substantially expressed at the CD stage, encouraging the start of cell division. The dynamic regulation of embryogenesis-related genes, including SOMACTIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2 (SERK2), LBD29, ESR2, LBD16, D-TYPE CYCLINS (CYCD3-2), and WOX1, during protoplast culture was validated by real-time quantitative polymerase chain reaction (RT-qPCR). Conclusions: WOX5 and CUC2 genes were found to be significantly expressed at the EC stage, suggesting a pre-existing stem cell-like state. Important genes linked to stress reactions and cellular transcriptional changes, as WOX13 and WIND1, were clearly elevated at the Pt stage. The activation of genes linked to cell wall renewal, auxin and cytokinin signaling, and the cell cycle during this phase also suggested a dynamic transition toward regaining stem cell identity. Additionally, the findings previously reported show that the EC-derived protoplasts successfully underwent cell division and contributed to the development of somatic embryos. Although the NEC-generated protoplasts did not divide upon culture, these results show that embryogenic cells maintain their embryogenic potential even after protoplast isolation and culture. The Author(s) 2026. Subject The topic of the resource Angelica gigas; Cell identity transition; Protoplast regeneration; Stem cell; Totipotency; Transcriptional transition Publisher An entity responsible for making the resource available BioMed Central Ltd Relation A related resource ISSN: 14712229; Language A language of the resource English Type The nature or genre of the resource Article Rights Information about rights held in and over the resource All Open Access; Gold Open Access; Green Open Access Format The file format, physical medium, or dimensions of the resource online