GEO DataSets

(Submitter supplied) The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy. Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation. To identify transcriptome-wide targets of the Celf1 protein in heart, we performed RNA-Seq of polyA+ RNA from mice inducibly expressing Celf1 in the muscle.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

15 Samples

Download data: TXT

(Submitter supplied) The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy. Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation. To identify transcriptome-wide targets of the Celf1 protein, we performed CLIP-seq against Celf1 using the 3B1 antibody, in myoblasts, heart tissue, and muscle tissue.

Organism:

synthetic construct

Type:

Other

Platform:

GPL15228

7 Samples

Download data: XLSX

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

Organism:

Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL15228 GPL9250

40 Samples

Download data: BED

(Submitter supplied) The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy. Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation. To identify transcriptome-wide targets of the Celf1 protein, we performed CLIP-seq against Celf1 using the 3B1 antibody, in myoblasts, heart tissue, and muscle tissue.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

3 Samples

Download data: BED, TXT

(Submitter supplied) The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy. Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation. To identify transcriptome-wide targets of the Celf1 protein in heart, we performed RNA-Seq of polyA+ RNA from mice inducibly expressing Celf1 in the muscle.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

15 Samples

Download data: TXT

(Submitter supplied) The CUG-BP and ETR-3-like factor 1 (Celf1) RNA binding protein plays an important role in heart and muscle development, and is over-expressed in the disease myotonic dystrophy. Celf1 has known roles in regulation of RNA splicing, RNA stability, and protein translation. To identify transcriptome-wide targets of the Celf1 protein in heart, we performed RNA-Seq of polyA+ RNA from mice inducibly expressing Celf1 in the heart.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

15 Samples

Download data: TXT

(Submitter supplied) We report on the regulation of transcripts following siRNA-mediated depletion of an RNA binding protein, CELF1, in primary chicken embryonic cardiomyocytes in culture.

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

6 Samples

Download data: TXT

(Submitter supplied) The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. more...

Organism:

Drosophila melanogaster; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

55 Samples

Download data: BED, TXT

(Submitter supplied) CELF2 is a critical regulator of alternative splicing during T cell development and during stimulation-induced T cell activation. Here we utilize RNA-seq to globally profile the functional targets of CELF2 in a monoclonal Jurkat T cell line (JSL1 cells), including transcriptome-wide splicing targets and genes regulated at other levels of mRNA processing

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) The RNA binding protein Celf1 regulates alternative splicing in the nucleus and mRNA stability and translation in the cytoplasm. Celf1 is strongly down-regulated during mouse postnatal heart development. Its re-induction in adults induced severe heart failure and reversion to fetal splicing and gene expression patterns. However, the impact of Celf1 depletion on cardiac transcriptional and posttranscriptional dynamics in neonates has not been addressed. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: TXT

(Submitter supplied) Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. more...

Organism:

Caenorhabditis elegans; Mus musculus

Type:

Other

Platforms:

GPL13657 GPL17021

2 Samples

Download data: BEDGRAPH

(Submitter supplied) In this study, CLIP-seq was used to identify sites of CELF2-mRNA interactions in JSL1 T cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

18 Samples

Download data: BED

(Submitter supplied) CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding in alternative splicing, we performed exon array analysis in C2C12 cells using expression arrays.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6193

9 Samples

Download data: CEL

(Submitter supplied) CUGBP1 and MBNL1 are developmentally regulated RNA-binding proteins that are causally associated with myotonic dystrophy type 1. Using HITS-CLIP anlysis, we found CUGBP1 and MBNL1 preferentially bind to alternatively spliced introns and exons, as well as to the 3' UTRs. To analyze more directly the role of CUGBP1/MBNL1 binding to the 3’ UTR, we performed global analysis of mRNA stability in C2C12 cells using expression arrays, and found that CUGBP1 and MBNL1 regulate decay of endogenous mRNAs.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

9 Samples

Download data: CEL

(Submitter supplied) We report mRNA profiles of subcellularly localized transcriptomes (soma and neurite) of two mouse cell lines, N2A and CAD, as well as primary cortical neurons from E18.5 mice. We also performed this fractionation and sequencing after RNAi knockdown (cell lines) or in knockout mice (primary cortical neurons) of the RNA-binding proteins muscleblind 1 and 2 (Mbnl1 and Mbnl2).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

48 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Mapping MBNL-regulated genome-wide alternative polyadenylation: We report that depletion of Mbnl proteins in mouse embryo fibroblasts (MEFs), DM mouse model quadriceps muscle, and DM-autopsy muscle tissue leads to mis-regulation of alternative polyadenylation

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11002 GPL10999

36 Samples

Download data: TXT, WIG, XLSX

(Submitter supplied) Myotonic dystrophy type 1 (DM1) is a CTG microsatellite expansion (CTGexp) disorder caused by expression of CUGexp RNAs. These mutant RNAs alter the activities of RNA processing factors, including MBNL proteins, leading to reversion to specific fetal isoforms in adult tissues and DM1 pathology. While this pathogenesis model accounts for adult-onset disease, the molecular basis of congenital DM (CDM) is unknown. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573 GPL11154

25 Samples

Download data: TXT

(Submitter supplied) Myotonic dystrophy (DM) is a multi-systemic disease that severely impacts cardiac and skeletal muscle functions as well as the central nervous system. DM is unusual because it is RNA-mediated disease due to the expression of C(C)UG expansion RNAs that inhibit the activities of the muscleblind-like (MBNL) proteins. In mice, studies using Mbnl1 and Mbnl2 single knockouts have revealed that Mbnl1 plays a predominant role in skeletal and heart muscle alternative splicing regulation while Mbnl2 performs an analogous splicing function in the brain. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

2 Samples

Download data: BED

(Submitter supplied) Myotonic dystrophy (dystrophia myotonica, DM) is caused by expansions of CTG (type 1; DM1) or CCTG (type 2; DM2) repeats in the non-coding regions of the DMPK and CNBP genes, and patients with DM1 or DM2 often suffer from sudden cardiac death due to lethal arrhythmia. Specific molecular changes that underlie DM cardiac pathology have been linked to repeat-associated depletion of Muscleblind-like (MBNL) 1 and 2 proteins and upregulation of CUGBP Elav-like family member 1. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

6 Samples

Download data: TXT

(Submitter supplied) During development the fetal heart undergoes a rapid and dramatic transition to adult function through transcriptional and post-transcriptional mechanisms, including alternative splicing (AS). We performed deep RNA-sequencing for high-resolution analysis of transcriptome changes during postnatal mouse heart development using RNA from ventricles and freshly isolated cardiomyocytes (CM) and cardiac fibroblasts (CF). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: TXT