GEO DataSets

(Submitter supplied) The Bone Morphogenetic Protein (BMP) signaling pathway functions in lung development and the regeneration of adult tracheal epithelium from basal stem cells. Here, we explore its role in the alveolar region, where Type 2 epithelial cells (AT2s) and Pdgfrα+ Type 2 - associated stromal cells (TASCs) are components of the stem cell niche. We utilize both organoid assays and in vivo alveolar regrowth after pneumonectomy (PNX) - a process requiring proliferation of AT2s and differentiation into Type 1 cells (AT1). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) The conducting airway epithelium of the rodent and human lung is underlaid by mesenchymal cells that include vasculature, smooth muscle, fibroblasts and cartilage. The goal of this project is to identify cellular and molecular changes in the mesenchyme after injury to the epithelium by exposure to SO2 and which may participate in repair of the epithelium We used Affymetrix microarray analysis to compare transcripts in tracheal mesenchyme before and after SO2 injury.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) The conducting airway epithelium of the rodent and human lung is made up of about equal proportions of ciliated and secretory cells. In addition, in regions where the epithelium is pseudostratfied, ~30% of the epithelium consists of undifferentiated basal cells (BCs). Evidence suggests that these BCs are multipotent stem cells that can self renew over the long term and give rise to both ciliated and secretory lineages. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Conditional Bmp4 overexpression (Bmp4 OE), using a tetracycline regulated Bmp4 gain of function allele, resulted in facial skeletal changes that were most dramatic after an E10.5 Bmp4 induction. We identified a number of genes predominantly transcriptional regulators controlling self-renewal, osteoblast differentiation, and negative Bmp autoregulation whose expression were change after Bmp4 overexpression in the cranial neural crest cells.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6845

4 Samples

Download data: GPR

(Submitter supplied) Bone morphogenic proteins (BMPs) function in virtually all tissues with cell-type specific outcomes. Since there are a relatively small number of BMP receptors this exquisite signaling specificity requires additional molecules to regulate the output of this pathway. We demonstrated that the receptor tyrosine kinase MuSK that is selectively expressed in muscle and plays a critical role in synapse formation and maintenance binds to BMP4 and related BMPs. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

24 Samples

Download data: CEL

(Submitter supplied) The transition from progenitor to differentiated cells is critical for successful organogenesis; subtle alterations in this process can lead to developmental disorders. The anterior heart field (AHF) encompasses a niche in which cardiac progenitors maintain their multipotent and undifferentiated nature by signals from the surrounding tissues, which thus far have been poorly defined. Using systems biology approaches and perturbations of signaling molecules in chick embryos, we revealed a tight crosstalk between the bone morphogenic protein (BMP) and fibroblast growth factor (FGF) signaling pathways within the AHF: BMP4 promotes myofibrillar gene expression and cardiomyocyte contractions, by blocking FGF signaling. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3213

9 Samples

Download data: CEL

(Submitter supplied) Alveologenesis is the culmination of lung development and involves the correct temporal and spatial signals to generate the delicate gas exchange interface. Using a novel Wnt signaling reporter system, we have identified a Wnt-responsive alveolar epithelial sublineage arising during alveologenesis called the axin2+ alveolar type 2 cell or AT2Aaxin2. The number of AT2Aaxin2 sublineage cells increases substantially during late lung development, revealing a wave of Wnt signaling during alveologenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

10 Samples

Download data: CEL

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Lung epithelia cells were collected after 10 days of treatment by pseudomonas aeruginosa (PA), RNA-Seq and qRT-PCR were applied to analyze the high-throughput data Results: In general, the mutant type II-like cells expressed higher levels of type I cell markers and lower levels of type II cell markers

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT

(Submitter supplied) Idiopathic pulmonary fibrosis (IPF) is a common form of interstitial lung disease (ILD) resulting in alveolar remodeling and progressive loss of pulmonary function due to chronic alveolar injury and failure to regenerate the respiratory epithelium. Histologically, fibrotic lesions and honeycomb structures expressing atypical proximal airway epithelial markers replace alveolar structures, the latter normally lined by alveolar type 1 (AT1) and AT2 cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2 Samples

Download data: TXT

(Submitter supplied) We used microfluidic single cell RNA-seq on 47 individual mouse lung mesenchymal cells at adulthood to measure the transcriptional state. We were able to classify these cells into distinct populations as well as map their signaling interactions with the distal lung epithelium and endothelium. In this manner, single cell RNA-seq can be used to unbiasedly determine the signals the dictate construction and maintenance of the alveolus.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

48 Samples

Download data: FPKM_TRACKING

(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:

GPL11002

11 Samples

Download data: BED, BW

(Submitter supplied) Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naïve or primed states, we revisit the roles of BMP signaling in mESCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BED, BW

(Submitter supplied) Carrying out both RNA-seq and Smad1/5 genome-wide chromatin immunoprecipitation and sequencing (ChIP-seq) analyses of mESCs in the naïve or primed states, we revisit the roles of BMP signaling in mESCs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

5 Samples

Download data: BW, TXT

(Submitter supplied) The pulmonary alveolar epithelium which play key role in lung biological function is mainly composed of two types of epithelial cells: alveolar type I (AT1) and type II (AT2) cells. We know very little about developmental heterogeneity of the AT1 cell population. By using 10X genomics “Chromium Single Cell” technology, we performed single-cell RNA-seq (scRNA-seq) analyses of AT1 cells at postnatal day 3 (P3), P15, and P60, along with AT2 cells (P60) in mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: CSV

(Submitter supplied) Transgenic mice in two control (SftpCreERT2/+; Tomatoflox/flox) and Experimental (SftpCreERT2/+; Fgfr2bflox/flox; Tomatoflox/flox) groups were treated with tamoxifen (1mg/ml) in drinking water. The lungs were harvested at different time points (d4,d7 and d14) following tamoxifen treatment. RNA was isolated from AT2 cells sorted by FACS. FACS analysis showed two different Alveolar epithelial type 2 cells population with low and high RFP levels. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

8 Samples

Download data: GPR

(Submitter supplied) Alveolar epithelial cell fate decisions drive lung development and regeneration. Using transcriptomic and epigenetic profiling coupled with genetic mouse and organoid models, we identified Klf5 as a critical regulator of alveolar epithelial cell fate across the lifespan. During prenatal lung development and alveologenesis, Klf5 enforces alveolar epithelial type 1 (AT1) cell lineage fidelity. While it is dispensable for both adult AT1 and alveolar epithelial type 2 (AT2) cell homeostasis, Klf5 regulates AT2 cell plasticity after injury. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: CSV

(Submitter supplied) The mouse incisor is a remarkable tooth that grows throughout the animal’s lifetime. This continuous renewal is fueled by epithelial stem cells that give rise to ameloblasts, which generate enamel, and little is known about the function of specific miRNAs in this process. Here we describe the role of a novel Pitx2:miR-200c/141:Noggin regulatory pathway in dental epithelial cell differentiation. miR-200c repressed noggin, an antagonist of Bmp signaling. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL15409 GPL5973

6 Samples

Download data: TXT

(Submitter supplied) To define the role of Yap/Taz in alveolar epithelial regeneration, we deleted Yap/Taz in mouse lung Spc-expressing ATII cells by using Spc-CreERT2, Yap fl/fl, Taz fl/fl, R26R-mTmG mice. This data set contains the microarrays examining gene expression in the lineage-labeled Spc-expressing ATII cells before and after Streptococcus pneumoniae infection.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16570

4 Samples

Download data: CEL

(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

Platforms:

GPL19057 GPL24247

78 Samples

Download data: BED, BEDGRAPH, BROADPEAK, CLOUPE, CSV, H5, NARROWPEAK, TBI, TSV