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Series GSE228930 Query DataSets for GSE228930
Status Public on Sep 08, 2023
Title 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [MEC_Omni-C]
Organism Mus musculus
Experiment type Other
Summary In order to understand gene regulation of epithelial cells in the mouse mammary gland, we have generated a comprehensive epigenetic atlas from freshly sorted myoepithelial (basal), luminal progenitor (LP) and mature luminal (ML) from adult mice (9 week-old) encompassing gene expression profiling, histone and polymerase II CUT&Tag sequencing, chromatin accessibility via ATAC-seq and chromatin interactions. We further studied the basal compartment by sorting to additional cell type population: Tspan8+ (quiescent basal, QBa) and Tspan8- (active basal, ABa) cells.
 
Overall design We then performed Omni-CTM, a DNase-based HiC protocol which measures the interaction frequency of all loci in the genome in duplicate of each of the sorted cellular populations from adult mice: myoepithelial (basal, Lin-/CD29hi/CD24+), luminal progenitor (LP, Lin-/CD29low/CD24+/CD61hi) and mature luminal (ML, Lin-/CD29low/CD24+/CD61low).
 
Contributor(s) Smyth GK, Coughlan HD, Milevskiy M
Citation(s) 38020976
Submission date Apr 04, 2023
Last update date Dec 08, 2023
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
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 (6)
GSM7142991 Basal cells, biol rep 1 [Ba1]
GSM7142992 Basal cells, biol rep 2 [Ba2]
GSM7142993 LP cells, biol rep 1 [LP1]
This SubSeries is part of SuperSeries:
GSE227750 3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells
Relations
BioProject PRJNA952209

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
GSE228930_GenomicRegions.bed.gz 382.8 Kb (ftp)(http) BED
GSE228930_RAW.tar 505.5 Mb (http)(custom) TAR (of MTX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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