GEO DataSets

(Submitter supplied) Mammary ducts and alveoli are composed of basal and luminal cells, with the fate and differentiation of secreting cells being controlled by hormones through specific transcription factors. This study establishes the essential role of the histone H3 lysine 27 trimethylation (H3K27me3) demethylase KDM6A (UTX) in a balanced basal and luminal cell compartment. Disproportionate formation of basal cells in the absence of KDM6A resulted in disorganized mammary ducts and alveoli and lactation failure. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

13 Samples

Download data: BEDGRAPH

(Submitter supplied) Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factor STAT5. As pregnancy progresses mammary signature genes are activated in a defined temporal order, which coincides with the recruitment of STAT5 to respective regulatory sequences. This study addressed the question whether the methyltransferase and transcriptional co-activator EZH2 controls the differentiation clock of mammary epithelium. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

41 Samples

Download data: BEDGRAPH, BIGWIG

(Submitter supplied) 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:

GPL24247

28 Samples

Download data: BW, WIG

(Submitter supplied) To determine the contribution of H3K27me3 demethylases to intestinal homeostasis, an inducible mouse model was used to simultaneously ablate Kdm6a and Kdm6b expression from the intestinal epithelium. We then performed RNA-Seq gene expression analysis at two timepoints (7 days and 5 months) following induction of Kdm6a and Kdm6b ablation. Differential H3K27me3 regions were also identified using ChIP-Seq at one time point (7 days) following gene ablation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: CSV, WIG

(Submitter supplied) To determine the contribution of H3K27me3 demethylases to intestinal homeostasis, an inducible mouse model was used to simultaneously ablate Kdm6a and Kdm6b expression from the intestinal epithelium. We then performed RNA-Seq gene expression analysis at two timepoints (7 days and 5 months) following induction of Kdm6a and Kdm6b ablation. Differential H3K27me3 regions were also identified using ChIP-Seq at one time point (7 days) following gene ablation.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

20 Samples

Download data: BW, CSV

(Submitter supplied) BACKGROUND & AIMS: Although genomic analysis have recently discovered the malignant subtype of human pancreatic ductal adenocarcinoma (PDAC) characterized by frequent mutations of a histone modifier KDM6A, the biological and molecular roles still remain obscure. We herein elucidated the clinical and biological impacts of KDM6A deficiency on human PDAC and identified the therapeutic potential by pathological and molecular evaluation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

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

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

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

Platform:

GPL32507

24 Samples

Download data: BIGWIG, TXT

(Submitter supplied) KDM6A, which regulates gene expression by demethylation of the repressive histone mark H3K27me3, has a higher level in mammalian females than in males because the Kdm6a gene escapes X chromosome inactivation. Here, we report that maternal and paternal alleles of a number of genes throughout the genome are differentially regulated by KDM6A. Knockout of KDM6A in male and female embryonic stem cells derived from F1 hybrid mice results in downregulation of maternal alleles more frequently than paternal alleles. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32507

12 Samples

Download data: TXT

(Submitter supplied) KDM6A, which regulates gene expression by demethylation of the repressive histone mark H3K27me3, has a higher level in mammalian females than in males because the Kdm6a gene escapes X chromosome inactivation. Here, we report that maternal and paternal alleles of a number of genes throughout the genome are differentially regulated by KDM6A. Knockout of KDM6A in male and female embryonic stem cells derived from F1 hybrid mice results in downregulation of maternal alleles more frequently than paternal alleles. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32507

8 Samples

Download data: BIGWIG

(Submitter supplied) KDM6A, which regulates gene expression by demethylation of the repressive histone mark H3K27me3, has a higher level in mammalian females than in males because the Kdm6a gene escapes X chromosome inactivation. Here, we report that maternal and paternal alleles of a number of genes throughout the genome are differentially regulated by KDM6A. Knockout of KDM6A in male and female embryonic stem cells derived from F1 hybrid mice results in downregulation of maternal alleles more frequently than paternal alleles. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL32507

4 Samples

Download data: BIGWIG

(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) 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 purpose of this study was to elucidate the molecular changes of the mammary epithelium induced by luminal cell specific RANK deletion. We have characterized the phenotypic consequences of RANK deletion in the luminal lineage of the mammary epithelium, and uncovered that Rank KO luminal cells have reduced long term renewal following sucessive pregnancies. Lineage tracing analysis has demonstrated that during pregnancy 2, Rank deleted luminal cells are repleace by a wt luminal cell population, derived from the basal epithelium. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

30 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:

GPL17021

83 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and activate mammary genes required for the nutrition of the offspring. Exploiting progressive differentiation during lactation, we investigated how hormonal cues shape an evolving enhancer landscape and impact the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: TXT

(Submitter supplied) The mammary luminal lineage relies on the common cytokine-sensing transcription factor STAT5 to establish super-enhancers during pregnancy and activate mammary genes required for the nutrition of the offspring. Exploiting progressive differentiation during lactation, we investigated how hormonal cues shape an evolving enhancer landscape and impact the biology of mammary cells. Employing ChIP-seq, we uncover a changing transcription factor occupancy at mammary enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

76 Samples

Download data: BEDGRAPH

(Submitter supplied) As a histone hallmark for transcription repression, Histone H3 lysine 27 trimethylation (H3K27me3) plays important roles in mammalian embryo development and induced pluripotent stem cells (iPSCs) generation. However, the expression profile and roles of H3K27me3 in bovine somatic cell nuclear transfer (SCNT) reprogramming remain poorly understood. In this study, we find SCNT embryos exhibit global hypermethylation of H3K27me3 from two-cell to eight-cell stage and its removal by ectopically expressed H3K27me3 demethylase-KDM6A could greatly improves SCNT efficiency. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

9 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

27 Samples

Download data: BED, BIGWIG, TXT