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Series GSE164017 Query DataSets for GSE164017
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
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.
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.
Contributor(s) Smyth GK, Chen Y, Pal B, Visvader JE
Citation(s) 34187545, 37994351
Submission date Dec 29, 2020
Last update date Dec 07, 2023
Contact name Gordon K Smyth
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (18)
GSM4994960 Embryonic mammary
GSM4994961 Embryonic adjacent skin
GSM4994962 Early postnatal
BioProject PRJNA688522
SRA SRP299699

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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
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Raw data are available in SRA
Processed data provided as supplementary file

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