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Status |
Public on Jul 02, 2021 |
Title |
10X Genomics scRNA-seq profiling of mammary gland cells from mice at different life stages |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Background: Heterogeneity within the mouse mammary epithelium has been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary development, we profiled single cells from different developmental stages including late embryogenesis, early postnatal, prepuberty, resting adult, mid-pregnancy, late-pregnancy, lactation and post-involution. We also compared the transcriptomes and chromatin accessibility of micro-dissected ducts versus terminal endbuds (TEBs) to help decipher the molecular properties of these specialized units that drive morphogenesis. Results: The single cell transcriptomes of 110,726 cells isolated from different stages were determined on the 10x Chromium platform and integrative analyses were performed to compare specific time-points. The mammary rudiment at E18.5 aligned more closely with the basal than the luminal lineage, while prepubertal epithelial cells at 2 weeks exhibited lineage segregation but to a less differentiated state than their adult counterparts. Integrated analysis of five stages spanning the pregnancy cycle revealed a novel alveolar progenitor that arises in late-pregnancy and stage-specific expression profiles. A continuum of states was uncovered along the basal-luminal progenitor cell axis following interrogation with >3,200 lineage-specific signature genes. Finally, exploration of micro-dissected TEBs and ducts showed that luminal cells within TEBs harbored intermediate expression profiles, and that ductal basal cells exhibited a higher level of accessible chromatin than their counterparts in TEBs.
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Overall design |
The data provides 18 biologically independent scRNA-seq profiles comprising a total of 149,371 cells supported by at least 500 sequence reads assigned to genes.
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Contributor(s) |
Smyth GK, Chen Y, Pal B, Visvader JE |
Citation(s) |
34187545, 37994351 |
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Submission date |
Dec 29, 2020 |
Last update date |
Dec 07, 2023 |
Contact name |
Gordon K Smyth |
E-mail(s) |
smyth@wehi.edu.au
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Phone |
(+61 3) 9345 2326
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Fax |
(+61 3) 9347 0852
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URL |
http://www.wehi.edu.au
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Organization name |
Walter and Eliza Hall Institute of Medical Research
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Department |
Bioinformatics
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Lab |
Smyth
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Street address |
1G Royal Pde
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City |
Parkville |
State/province |
Vic |
ZIP/Postal code |
3052 |
Country |
Australia |
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Platforms (1) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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Samples (18)
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Relations |
BioProject |
PRJNA688522 |
SRA |
SRP299699 |
Supplementary file |
Size |
Download |
File type/resource |
GSE164017_RAW.tar |
909.8 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
GSE164017_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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