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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
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 (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
BioProject PRJNA952209

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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)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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