Smart-seq3xpress scRNA-seq data from human skin across 4 donors and 4 body sites
https://doi.org/10.48723/y92n-w439
Smart-seq3xpress scRNA-seq datasets from 4 donors, covering 4 bodysites each. Healthy human skin biopsies were obtained from four adult donors, including two female and two male donors aged 30–45 years. From each donor, biopsies were collected from four anatomical sites: upper back, occipital scalp, plantar skin and inner upper arm. Skin samples were collected using a 4 mm punch biopsy. Next, tissue was dissociated with Miltenyi Whole Skin Dissociation Kit and these isolated cells were sorted (only live cell) into separate wells in 384-well lysis plates (28 or 32 plates per donor) for Smart-Seq3Xpress library preparation and subsequent sequencing. Prepared libraries were sequenced using BGI DNBSEQ-T7 and BGI DNBSEQ-G400 platforms. Sequencing reads were aligned to the human GRCh38 reference genome and processed using zUMIs.
The dataset contains 64 sequencing files at a total of 2.5 TB
Documentation files
Documentation files
Citation and access
Citation and access
Data access level:
Creator/Principal investigator(s):
Research principal:
Data contains personal data:
Yes
Type of personal data:
These data contain human sequence data generated from skin biopsies using the Smart-Seq3Xpress library preparation method. The uploaded files contain raw mRNA sequencing reads.
Code key exists:
Yes
Sensitive personal data:
Yes
Citation:
Language:
Method and outcome
Method and outcome
Unit of analysis:
Population:
Healthy adult human skin donors, 2 female, 2 male, aged 30–45 years, from whom skin biopsies were collected from multiple anatomical body sites.
Time method:
Study design:
- Observational study
Description of study design:
This is a cross-sectional observational study of healthy adult human skin samples, with experimental single-cell RNA-seq profiling of dissociated skin cells. No intervention, treatment allocation or randomization was performed.
Sampling procedure:
Description of sampling:
Skin biopsies were collected from four healthy adult donors selected according to study inclusion criteria. Sampling was non-random and criterion-based.
From each donor, biopsies were collected from four predefined anatomical body sites: upper back, occipital scalp, plantar skin and inner upper arm.
Time period(s) investigated:
Number of individuals/objects:
4
Weighting:
None
Data format/data structure:
Data collection - Biological tests
Data collection - Biological tests
Mode of collection:
Biological tests
Description of the mode of collection:
Skin biopsies from four anatomical body sites were collected using 4 mm punch biopsies and kept in PBS on ice. The biopsies were then dissociated using the Miltenyi Whole Skin Dissociation Kit (Miltenyi Biotec, 130-101-540) with a GentleMACS Dissociator to obtain single-cell suspensions. Live cells were sorted by flow cytometry using a BD FACSAria Fusion (BD Biosciences) into individual wells of 384-well Smart-seq3xpress lysis plates. Prepared libraries were sequenced using BGI DNBSEQ-T7 and BGI DNBSEQ-G400 platforms (MGI Tech Co., Ltd., Shenzhen, China).
Time period(s) for data collection:
2021-09-29 - 2021-11-10
Data collector:
- Karolinska University Hospital
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ROR
Sample size:
4
Number of responses:
4
Source of the data:
- Biological samples
Instrument
Instrument
Name:
4 mm biopsy punch
Type:
Technical instrument(s)
Description of the instrument:
Sterile punch tool used to collect standardized 4 mm skin biopsies.
Name:
Whole Skin Dissociation Kit with GentleMACS Dissociator
Type:
Technical instrument(s)
Description of the instrument:
Enzymatic and mechanical tissue dissociation system used to generate single-cell suspensions from skin biopsies.
Name:
BD FACSAria Fusion
Type:
Technical instrument(s)
Description of the instrument:
Flow cytometer/cell sorter used to isolate live single cells into 384-well plates.
Name:
Smart-seq3xpress
Type:
Technical instrument(s)
Description of the instrument:
Plate-based single-cell RNA-seq library preparation method used to generate sequencing-ready libraries from individual cells.
Name:
DNBSEQ-T7 and DNBSEQ-G400
Type:
Technical instrument(s)
Description of the instrument:
High-throughput sequencing platforms used to sequence the prepared Smart-seq3xpress libraries.
Geographic coverage
Geographic coverage
Geographic location:
Administrative information
Administrative information
Responsible department/unit:
Department of Cell and Molecular Biology [C5]
Other research principals:
Contributor(s):
Ethical Review
Ethical Review
Reviewer:
- Swedish Ethical Review Authority
components.catalogue.resource.content.administrativeInformation.ethicalReview.rorId.srText
ROR
Registration number:
2021-01568
Funding
Funding
Funding agency:
- LEO Foundation
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ROR
Award number:
LF-OC-19-000225
Award title:
Molecular body map of human skin: the key for understanding human skin diseases
Funding information:
Skin is the largest human organ and contains an intricate variety of cell types that assure tissue architecture and proper skin function, such as thermoregulation and hair growth.
An imbalance of cell types and/or molecular signalling often results in disease. Across the body, skin composition differs in thickness, hair growth, sebaceous and sweat gland density, microbiota exposure and disease susceptibility.
However, a molecular understanding of how cell types and genetic programs vary with skin regions, and molecular alterations in disease, is currently lacking.
Previously, my lab pioneered the use of single-cell RNA-seq (scRNA-seq) in mouse skin by generating a comprehensive molecular and spatial atlas of epithelial and mesenchymal cells during hair growth and rest (Joost et al. 2016; Joost et al. 2019). Building upon our expertise, we will molecularly dissect human skin, initially through a body map that spans various body sites of healthy donors, to identify cell types and sub types in human skin and also to investigate important cell type differences and alterations compared to mouse skin. Subsequently, the body map will be the foundation for molecular analyses of skin diseases, including immune-triggered psoriasis.
A carefully constructed and annotated human skin atlas, with spatial and molecular precision, would have enormous value for the scientific community and propel our molecular understanding of skin in health and disease.
