|
| Status |
Public on Sep 05, 2014 |
| Title |
Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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
|
| |
|
| Overall design |
We compared WT, Mbnl1/2KO, Mbnl1/2KO/3siRNA, and Mbnl1/2KO/scrambled siRNA MEFs (n=2 for each group) to evaluate alternative polyadenylation shifts that occur due to progressive loss of Mbnl proteins. We also compared WT (1 day old, and 4 months old, n=2 each) and HSALR mouse model (4 months old, n=2) of myotonic dystrophy for developmental alternative polyadenylation defects in myotonic dystrophy. Finally, we compared control and DM1 autopsy muscle tissues (n=3) for changes in alternative polyadenylation.
We performed HITS-CLIP analysis of binding sites of Mbnl1, Mbnl2 and Mbnl3 in MEFs (n=3 each). We also performed HITS-CLIP analysis for major skeletal muscle Mbnl protein, Mbnl1 in FVB WT adult muscle (4 months, n=3). Finally we performed HITS-CLIP analysis for CPSF6 in WT and Mbnl1/2 KO MEFs (n=3 each)
Please note that the 'readme_Table.txt' describes the contents of 'Table S*.xlsx' files, and the readme_method.txt include additional details about experiemenal procedures.
|
| |
|
| Contributor(s) |
Batra R, Charizanis K, Zhang C |
| Citation(s) |
25263597 |
| Submission date |
Aug 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ranjan Batra |
| E-mail(s) |
ranjanbatra9@yahoo.com
|
| Phone |
352-222-9209
|
| Organization name |
University of California San Diego
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Yeo Lab
|
| Street address |
2880 Torrey Pines Scenic Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
|
| Samples (36)
|
|
| Relations |
| BioProject |
PRJNA258393 |
| SRA |
SRP045573 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60487_Batra_et_al_Table_S1.xlsx |
3.5 Mb |
(ftp)(http) |
XLSX |
| GSE60487_Batra_et_al_Table_S2_Rev_July_23.xlsx |
1.2 Mb |
(ftp)(http) |
XLSX |
| GSE60487_Control_pooled.wig.gz |
245.7 Kb |
(ftp)(http) |
WIG |
| GSE60487_DM_pooled.wig.gz |
173.4 Kb |
(ftp)(http) |
WIG |
| GSE60487_FVB_HSA_pooled.wig.gz |
242.9 Kb |
(ftp)(http) |
WIG |
| GSE60487_FVB_P1_pooled.wig.gz |
236.5 Kb |
(ftp)(http) |
WIG |
| GSE60487_FVB_WT_pooled.wig.gz |
231.5 Kb |
(ftp)(http) |
WIG |
| GSE60487_HITS-CLIP_MEFs_Mbnl1.wig.gz |
2.4 Mb |
(ftp)(http) |
WIG |
| GSE60487_HITS-CLIP_MEFs_Mbnl2.wig.gz |
3.0 Mb |
(ftp)(http) |
WIG |
| GSE60487_HITS-CLIP_MEFs_Mbnl3.wig.gz |
1.2 Mb |
(ftp)(http) |
WIG |
| GSE60487_MEF_DKO3si_pooled.wig.gz |
252.6 Kb |
(ftp)(http) |
WIG |
| GSE60487_MEF_DKONTsi_pooled.wig.gz |
241.8 Kb |
(ftp)(http) |
WIG |
| GSE60487_MEF_DKO_pooled.wig.gz |
257.2 Kb |
(ftp)(http) |
WIG |
| GSE60487_MEF_WT_pooled.wig.gz |
291.3 Kb |
(ftp)(http) |
WIG |
| GSE60487_MEF_dko_cpsf_pooled.bedgraph.txt.gz |
4.8 Mb |
(ftp)(http) |
TXT |
| GSE60487_MEF_wt_cpsf_pooled.bedgraph.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE60487_Mbnl1_quad_pooled.wig.gz |
1.3 Mb |
(ftp)(http) |
WIG |
| GSE60487_readme_Table.txt |
1.2 Kb |
(ftp)(http) |
TXT |
| GSE60487_readme_method.txt |
8.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...