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Series GSE90848 Query DataSets for GSE90848
Status Public on Apr 18, 2017
Title Epithelial-Mesenchymal Micro-Niches Govern Stem Cell Lineage Choices (SC RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Adult tissue stem cells (SCs) reside in niches, which through intercellular contacts and signaling, influence SC behavior. Once activated, SCs typically give rise to short-lived transit-amplifying cells (TACs), which then progress to differentiate into their lineages. Here, using single cell RNA-sequencing, we unearth unexpected heterogeneity among SCs and TACs of hair follicles. We trace the roots of this heterogeneity to micro-niches along epithelial-mesenchymal interfaces, where progenitors display molecular signatures reflective of spatially distinct local signals and intercellular interactions. Using lineage-tracing, temporal single cell analyses and chromatin landscaping, we show that SC plasticity becomes restricted in a sequentially and spatially choreographed program, culminating in seven spatially arranged uni-lineage progenitors within TACs of mature follicles. By compartmentalizing SCs into micro-niches, tissues gain precise control over morphogenesis and regeneration: Some progenitors specify lineages immediately; others retain potency, preserving self-renewing features established early while progressively restricting lineages as they experience dynamic changes in microenvironment.
Overall design Mouse bulge hair follicle stem cell, hair germ, basal transient amplifying cells (TACs) and dermal papilla at the indicated hair cycle were FACS-purified for single cell RNA-seq.

The cell type of each sample is available in the file "GSE90848_cell_type_definitions.txt.gz" on the series record.
Contributor(s) Yang H, Fuchs E
Citation(s) 28413068
Submission date Dec 04, 2016
Last update date May 15, 2019
Contact name Hanseul Yang
Organization name Rockefeller University
Lab Fuchs lab
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (1119)
GSM2415061 819b_A10
GSM2415062 819b_A11
GSM2415063 819b_A1
This SubSeries is part of SuperSeries:
GSE90850 Epithelial-Mesenchymal Micro-Niches Govern Stem Cell Lineage Choices
BioProject PRJNA356168
SRA SRP094526

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
GSE90848_Ana6_DP_TPM.txt.gz 6.3 Mb (ftp)(http) TXT
GSE90848_Ana6_basal_hair_bulb_TPM.txt.gz 8.1 Mb (ftp)(http) TXT
GSE90848_Tel_Ana1_Ana2_bulge_HG_basal_HB_TPM.txt.gz 7.3 Mb (ftp)(http) TXT
GSE90848_cell_type_definitions.txt.gz 3.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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