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| Status |
Public on Sep 08, 2023 |
| Title |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_ATAC] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| 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.
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| Overall design |
We then performed ATAC-seq on mouse epithelial mammary gland cell types in the basal compartment: sorted Tspan8+ (quiescent basal, Qba, Lin-/CD29hi/CD24+/Tspan8+) and Tspan8- (active basal, ABa, Lin-/CD29hi/CD24+/Tspan8+) cellular populations from adult mice in duplicate.
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| 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
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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
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (4)
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| GSM7143100 |
Tspan8- Basal cells, biol rep 1 [P6_ATAC_1] |
| GSM7143101 |
Tspan8- Basal cells, biol rep 2 [P6_ATAC_2] |
| GSM7143102 |
Tspan8+ Basal cells, biol rep 1 [P7_ATAC_1] |
| GSM7143103 |
Tspan8+ Basal cells, biol rep 2 [P7_ATAC_2] |
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| This SubSeries is part of SuperSeries: |
| GSE227750 |
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells |
|
| Relations |
| BioProject |
PRJNA952230 |
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