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Series GSE147372 Query DataSets for GSE147372
Status Public on Apr 20, 2021
Title Tracing the origin of hair follicle stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The scRNA-seq data are an integral part of the manuscript with the above title. Using a photo-labelling technique and RamDA-seq as described in the overall design, we obtained accurate scRNA-seq data from developing hair follicles (HFs), reflecting the spatiotemporal dynamics of cellular state transition during HF morphogenesis. Single cell transcriptome analysis identified cell types, which cannot be distinguished by known makers, their signature markers, and transcriptional state changes in developing HFs. By integration of the data from single cell live imaging, our findings revealed the origin and developmental trajectories of tissue stem cells (SCs), leading to a new model of HF development and SC induction with unprecedented resolution.
Overall design Embryonic skin tissues contain a mix of different HF types at different developmental stages, rendering separation and transcriptional profiling of HFs at specific developmental stages difficult. We thus developed a transgenic mouse line expressing a photo-convertible fluorescent protein, nuclear Kikume Green-Red, which enables identification and photo-labelling of target HFs under a confocal microscope. Entire single whisker HFs at E12.0, E13.0, E13.5, E14.0, E15.0, and E17.0 were photo-converted. Basal epidermal cells of each photo-labelled HF (E12.0–E17.0, ITGA6+/CD31-/kikGR-red+ cells; E11.5, ITGA6+/CD31- cells) were isolated as single cells by FACS. All scRNA-seq libraries were constructed for RamDA-seq, a novel sensitive and accurate total scRNA-seq method. We obtained single cell full-length total RNA sequencing of developing whisker HFs as follows: E11.5, 94 cells; E12.0, 280 cells; E13.0, 276 cells; E13.5, 189 cells; E14.0, 183 cells; E15.0, 362 cells; E17.0, 282 cells (total: 1,666 single cells).

Please note that total 1,666 samples were included in the data analysis, however, the processed data file contains only 1614 data columns due to low-quality samples (indicated as the sample 'characteristics: data quality = low').
Contributor(s) Morita R, Hayashi T, Umeda M, Yoshimura M, Nikaido I, Fujiwara H
Citation(s) 34108685
Submission date Mar 23, 2020
Last update date Jun 25, 2021
Contact name Hironobu Fujiwara
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Tissue Microenvironment
Street address 2-2-3 Minatojima-minamimachi
City Chuo-ku, Kobe
ZIP/Postal code 6500047
Country Japan
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (1666)
GSM4427544 E11_FJW180312003_CA01
GSM4427545 E11_FJW180312003_CA02
GSM4427546 E11_FJW180312003_CA03
BioProject PRJNA614454
SRA SRP253687

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE147372_countsf_analysis_tpm_genesymbol_sum.txt.gz 152.4 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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