GEO DataSets

(Submitter supplied) To investigate the possible changes of genes expression during muscle atrophy, we performed bulk RNA-seq of skeletal muscle from C57 BL/6 mice with or without denervation (2 weeks).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, XLSX

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL21103

10 Samples

Download data: BED, BW, MTX, TSV

(Submitter supplied) Current atlas of regulatory sequences controlling skeletal muscle atrophy are still incomplete and lack cell type resolution. We applied single-cell chromatin accessibility assays (snATAC) to normal and denervated skeletal muscle from mice. We integrated these snATAC datasets with our single-nucleus RNA-sequence dataset to reveal the status of open chromatin. Using these datasets, we delineated chromatin accessibility maps in both normal and atrophic muscles and identified cis-regulatory elements (CREs) in all type of cell in skeletal muscle that may regulating muscle protein metabolism, energy metabolism and transcription activities, thus, provided a rich resource for understanding gene regulatory programs in skeletal muscle and related disorders.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: BED, MTX, TSV

(Submitter supplied) The epigenomic regulation is a part of Gene Regulatory Network (GRN). During we study the reprogramming of GRN adaptive to atrophic stimulation in skeletal muscle, we performed Histone 3 lysine 27 (H3K27) acetylation (H3K27ac) ChIP-seq assay using mouse skeletal muscle with or without denervation. This dataset combining with our snATAC datasets enable us to infer the candidate enhancer that could regulate muscle protein metabolism and energy metabolism during atrophy.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: BW

(Submitter supplied) Skeletal muscle exhibits remarkably plasticity under both physiological and pathological conditions. We used adult mice with sciatic denervation as model of muscle atrophy. SnRNA-seq was performed to generate single-nucleus transcriptome profiles of gastrocnemius from normal and denervation mice. Our results define the myonuclear transition, metabolic remodeling and gene regulation networks associated with muscle atrophy induced by denervation and illustrated the molecular basis of heterogeneity and plasticity of muscle cells in response to muscle atrophy, thus providing a resource for exploring molecular mechanisms leading to muscle atrophy

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: RDS, TAR

(Submitter supplied) RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with pooled siRNAs targeting YAP1 and TAZ (WWTR1), or non-targeting control siRNA (siCon)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: XLSX

(Submitter supplied) RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with pooled siRNAs targeting KLF4, or non-targeting control siRNA (siCon)

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: XLSX

(Submitter supplied) RNA sequencing (RNAseq) of N/TERT2G keratinocytes transduced with TEAD inhibitor protein (TEADi) or control GFP for 12, 24 and 48 hs

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: XLSX

(Submitter supplied) Regulation of organ size is important for development and tissue homeostasis. In Drosophila, Hippo signaling controls organ size by regulating the activity of a TEAD transcription factor, Scalloped, through modulation of its coactivator protein Yki. The role of mammalian Tead proteins in growth regulation, however, remains unknown. Here we examined the role of mouse Tead proteins in growth regulation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 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:

GPL21103 GPL17021

40 Samples

Download data: WIG

(Submitter supplied) Defining the function of TEAD transcription factors in myogenic differentiation has proved elusive due to overlapping expression and functional redundancy. Here, we show that siRNA silencing of either Tead1, Tead2 or Tead4 did not effect differentiation of primary myoblasts (PMs) while their simultaneous knockdown strongly impaired differentiation. In contrast in C2C12 cells, silencing of Tead1 or Tead4 impaired differentiation showing a differential requirement for these factors in PMs and C2C12 cells that involved both differential regulation of their expression and intracellular localisation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: TXT

(Submitter supplied) Defining the function of TEAD transcription factors in myogenic differentiation has proved elusive due to overlapping expression and functional redundancy. Here, we show that siRNA silencing of either Tead1, Tead2 or Tead4 did not effect differentiation of primary myoblasts (PMs) while their simultaneous knockdown strongly impaired differentiation. In contrast in C2C12 cells, silencing of Tead1 or Tead4 impaired differentiation showing a differential requirement for these factors in PMs and C2C12 cells that involved both differential regulation of their expression and intracellular localisation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL21103

16 Samples

Download data: WIG

(Submitter supplied) The initial aim of the study was to determine the mechanisms underlying the positive effect of AICAR on the phenotype of HSALR mice, a well-known model for DM1. We have previously shown that treatment with AICAR reduces myotonia and mis-splicing in the HSALR mice. We here aimed to identify splicing and transcriptional changes in gastrocnemius muscle from HSALR mice treated or not with AICAR, as compared to FVB control mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: TXT

(Submitter supplied) In order to investigate the effect of Hippo pathway in pancreatic endorince specification and differentiaion, single nucleus RNA seq was performed using mouse pancreatic tissues with Lats1&2 deletion in NGN3+ cells (NL mice). Wild type mice pancreatic tissues were also subject to same analysis as a control.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: H5

(Submitter supplied) YAP and TAZ are transcriptional co-activators and downstream effectors of the Hippo pathway, which play crucial roles in organ size control and cancer pathogenesis. Genetic deletion of YAP/TAZ has revealed their critical importance for embryonic development of the heart, vasculature and gastrointestinal mesenchyme. The aim of this study was to determine the functional role of YAP/TAZ in adult smooth muscle cell in vivo.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

12 Samples

Download data: TSV

(Submitter supplied) YAP1 gene fusions have been observed in a subset of paediatric ependymomas. Here we show that ectopic expression of active nuclear YAP1 (nlsYAP5SA) in ventricular zone neural progenitor cells using conditionally-induced NEX/NeuroD6-Cre is sufficient to drive brain tumour formation in mice. Neuronal differentiation is inhibited in the hippocampus. Deletion of YAP1’s negative regulators LATS1 and LATS2 kinases in NEX-Cre lineage in double conditional knockout mice also generates similar tumours, which are rescued by deletion of YAP1 and its paralog TAZ. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

13 Samples

Download data: TXT

(Submitter supplied) YAP1/TEAD1 ChIP was performed in N/TERT2G human keratinocytes

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

3 Samples

Download data: BW

(Submitter supplied) RNA sequencing (RNAseq) of primary keratinocytes from mouse basal cell carcinoma mice (BCC) transduced with pooled siRNAs targeting YAP1 and TAZ (siYT) or non-targeting control siRNA (siCon), and with TEADi or GFP as control

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: XLSX

(Submitter supplied) To identify atrophy genes directly targeted by Bcl-3 transactivator at a genome wide level, we performed whole transcript expression array and ChIP-seq for muscles from weight bearing or 5-day hind limb unloaded mice. Genes that showed increased expression with unloading and a Bcl-3 peak in the promoter (from ChIP-seq data) were considered as Bcl-3 direct targets during disuse atrophy. Using ChIP array, we identified 241 direct targets for Bcl-3. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11078

8 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

70 Samples

Download data: TXT