GEO DataSets

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

18 Samples

Download data: MTX, TSV

(Submitter supplied) The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted. RNA and nuclei were extracted for RNA-seq and ATAC-seq profiling using an Illumina NextSeq 500 sequencer. This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

22 Samples

Download data: TXT

(Submitter supplied) The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted and nuclei extracted for 75bp paired-end ATAC-seq profiling using an Illumina NextSeq 500 sequencer.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: BED, TXT

(Submitter supplied) The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted and RNA extracted for 75bp paired-end RNA-seq profiling using an Illumina NextSeq 500 sequencer.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

11 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BAI, MTX, TSV

(Submitter supplied) Epithelial cells were isolated by FACS from the mammary glands of pubescent (5 week old), estrus adult (10 week old) and diestrus adult (10 week old) female mice. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer using parameters recommended by 10X Genomics.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: MTX, TSV

(Submitter supplied) Epithelial cells were isolated by FACS from the mammary glands of adult (10 week old) female mice. A basal subpopulation of the epithelial cells was also isolated. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture. cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on an Illumina NextSeq500 sequencer to achieve 75 bp paired-end reads.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: BAI, MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Mammary glands were collected from female mice of various ages: pre puberty (2 weeks), pubescent (5 weeks), adult (10 weeks) and pregnant (12.5 days mid-pregnancy). Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. In some cases, cells were further sorted into basal and luminal subsets. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

1566 Samples

Download data: TXT

(Submitter supplied) Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 adult (10 week old) female mice. Basal epithelial cells were FACS sorted. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

312 Samples

Download data: TXT

(Submitter supplied) Mammary glands were collected from 8 pubescent (4.7-4.9 week-old) female mice and 8 adult (10 week old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina NextSeq 500 to achieve paired-end 75 bp reads.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

444 Samples

Download data: TXT

(Submitter supplied) Mammary glands were collected from 8 pregnant (12.5 day) mice and 8 non-pregnant adult (10 week old) female mice. Epithelial cells were FACS sorted from the pregnant mice. Cells from the adult mice were FACS sorted as basal or luminal. Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

278 Samples

Download data: TXT

(Submitter supplied) Mammary glands were collected from pre-pubescent (2 weeks old), pubescent (4.7- 4.9 weeks old) and adult (10 week-old) female mice. Freshly sorted epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under a microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100 bp paired-end reads.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

346 Samples

Download data: TXT

(Submitter supplied) Mammary glands of 8 adult (10 week-old) female mice were collected. Freshly sorted basal and luminal epithelial cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis. Cells were visualized under the microscope to ensure integrity of the captured single cells prior to cDNA preparation. Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Hiseq 2000 to achieve 100bp paired-end reads.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

186 Samples

Download data: TXT

(Submitter supplied) The mammary epithelia are mainly composed of two distinct lineages, the basal and luminal cells. Due to the limitation of traditional transcriptome analysis of bulk mammary cells, the hierarchy and heterogeneity of mammary cells within these two lineages remain unclear. Hence, we have performed single cell RNA-seq on mammary epithelial cells of virgin and pregnant mice. Based on the respective gene expression profiles, we found mammary cells are highly heterogeneous and can be classified into distinct subgroups with signature markers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

239 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: TXT

(Submitter supplied) The mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define differentiation states within the secretory type of luminal cells, which can be defined as a continuous spectrum of progenitor and mature secretory cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

3 Samples

Download data: TXT

(Submitter supplied) The mammary epithelial cell (MEC) system is a bi-layered ductal epithelial network consisting of luminal and basal cells, maintained by a lineage of stem and progenitor cell populations. Here, we used integrated single-cell transcriptomics and chromatin accessibility analysis to reconstruct the cell types of the mouse MEC system and their underlying gene regulatory features in an unbiased manner. We define differentiation states within the secretory type of luminal cells, which can be defined as a continuous spectrum of progenitor and mature secretory cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

(Submitter supplied) The mammary gland is a unique organ as it undergoes most of its development during puberty and adulthood. Characterising the hierarchy of the various mammary epithelial cells and how they are regulated in response to gestation, lactation and involution is important for understanding how breast cancer develops. Recent studies have used numerous markers to enrich, isolate and characterise the different epithelial cell compartments within the adult mammary gland. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; Rattus norvegicus; Homo sapiens

Type:

Expression profiling by RT-PCR

Platforms:

GPL10331 GPL18234

32 Samples

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(Submitter supplied) RNA samples were prepared from freshly sorted mammary cell subpopulations (MaSC/basal-enriched, luminal progenitor, mature luminal and stromal) from five sets of adult mice. High throughput RT-PCR was used to measure the global microRNA expression profiles of each cell subpopulation. The expression profiles were compared between cell subpopulations to gain insight into the regulation of lineage-restricted genes.

Organism:

Rattus norvegicus; Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL10331

14 Samples

Download data: XLS