Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing

Miura, Asaka; Kitayama, Tomomi; Ouchi, Yuya; Saga, Kotaro; Shimbo, Takashi; Tamai, Katsuto

doi:https://doi.org/10.1016/j.bbrc.2024.151159

Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing

Miura, Asaka; Kitayama, Tomomi; Ouchi, Yuya et al.

Biochemical and Biophysical Research Communications, 2025, 743, 151159

Number of Access:121（2025-06-12 18:22 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/100385

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Title	Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing
Creator	CreatorName Miura, Asaka
	CreatorName Kitayama, Tomomi
	CreatorName Ouchi, Yuya
	NRID 1000000563389 1000000563389 researchmap permalink sksksksksksksksksksk sksksksksksksksksksk Scopus Author ID 35082564300 35082564300 CreatorName Saga, Kotaro
	NRID 1000070780609 1000070780609 researchmap permalink shimbot shimbot Scopus Author ID 35082618100 35082618100 CreatorName Shimbo, Takashi
	NRID 1000020236730 1000020236730 researchmap permalink 20236730 20236730 Scopus Author ID 7102107355 7102107355 CreatorName Tamai, Katsuto
Subject	Keratinocytes
	Single-cell transcriptome
	Skin
	Transcriptomics
Description	Miura A., Kitayama T., Ouchi Y., et al. Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing. Biochemical and Biophysical Research Communications 743, 151159 (2025); https://doi.org/10.1016/j.bbrc.2024.151159.
Abstract	The skin is primarily composed of keratinocytes and forms an effective barrier between the organism and external environment. Neonatal skin analysis is essential for understanding developmental processes and rare skin diseases. However, efficient single-cell dissociation methods for the neonatal mouse epidermis remain underexplored. Here, three enzymes (Trypsin, TrypLE, and Liberase) used for tissue dissociation were compared to optimize single-cell RNA sequencing (scRNA-seq) of the mouse neonatal epidermis. scRNA-seq revealed distinct differences in cell recovery between the enzymes, with Liberase enriching suprabasal keratinocytes and Trypsin/TrypLE favoring basal keratinocytes. Although all enzymes produced comparable data quality, the observed bias in cell population recovery highlights the significant impact of dissociation protocols on the scRNA-seq results. These findings highlight the importance and optimal selection of enzymes for the analysis of unbiased neonatal epidermis.
Publisher	Elsevier B.V.
Source Title	Biochemical and Biophysical Research Communications
Volume (Issue)	743
Page	151159
Date of Issued	2025-01-01
Language	English
Handle URL	https://hdl.handle.net/11094/100385
PISSN	0006291X
eISSN	10902104
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1016/j.bbrc.2024.151159
Access Rights	open access
CopyRight	This article is licensed under a Creative Commons Attribution 4.0 International License.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Biochemical and Biophysical Research Communications. 2025, 743, p. 151159
DC.title	Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing
DC.creator	Miura, Asaka
	Kitayama, Tomomi
	Ouchi, Yuya
	Saga, Kotaro
	Shimbo, Takashi
	Tamai, Katsuto
DC.publisher	Elsevier B.V.
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2025-01-01
DC.identifier	https://doi.org/10.1016/j.bbrc.2024.151159
DC.subject	Keratinocytes
	Single-cell transcriptome
	Skin
	Transcriptomics
DC.description	Miura A., Kitayama T., Ouchi Y., et al. Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing. Biochemical and Biophysical Research Communications 743, 151159 (2025); https://doi.org/10.1016/j.bbrc.2024.151159.
DCTERMS.abstract	The skin is primarily composed of keratinocytes and forms an effective barrier between the organism and external environment. Neonatal skin analysis is essential for understanding developmental processes and rare skin diseases. However, efficient single-cell dissociation methods for the neonatal mouse epidermis remain underexplored. Here, three enzymes (Trypsin, TrypLE, and Liberase) used for tissue dissociation were compared to optimize single-cell RNA sequencing (scRNA-seq) of the mouse neonatal epidermis. scRNA-seq revealed distinct differences in cell recovery between the enzymes, with Liberase enriching suprabasal keratinocytes and Trypsin/TrypLE favoring basal keratinocytes. Although all enzymes produced comparable data quality, the observed bias in cell population recovery highlights the significant impact of dissociation protocols on the scRNA-seq results. These findings highlight the importance and optimal selection of enzymes for the analysis of unbiased neonatal epidermis.
DC.rights	This article is licensed under a Creative Commons Attribution 4.0 International License.
DC.format	100385
citation_title	Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing
citation_author	Miura, Asaka
	Kitayama, Tomomi
	Ouchi, Yuya
	Saga, Kotaro
	Shimbo, Takashi
	Tamai, Katsuto
citation_publisher	Elsevier B.V.
citation_language	English
citation_date	2025-01-01
citation_journal_title	Biochemical and Biophysical Research Communications
citation_volume	743
citation_firstpage	151159
citation_doi	https://doi.org/10.1016/j.bbrc.2024.151159
citation_public_url	https://hdl.handle.net/11094/100385

Evaluation of the digestion protocol of mouse neonatal epidermis for single-cell RNA sequencing

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