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Series GSE113133 Query DataSets for GSE113133
Status Public on May 29, 2018
Title Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a, and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.
 
Overall design 2 control myoblast (MB) samples, 2 control myotube (MT) samples, 2 FSHD2 MB samples, and 2 FSHD2 MT samples
Web link https://doi.org/10.1093/hmg/ddy173
 
Contributor(s) Lim J, Wong C, Yao Z, Tawil R, van der Maarel SM, Miller DG, Tapscott SJ, Filippova GN
Citation(s)
  • Lim JW, Wong CJ, Yao Z, Tawil R et al. Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures. Hum Mol Genet 2018 Aug 1;27(15):2644-2657. PMID: 29741619
Submission date Apr 13, 2018
Last update date Mar 27, 2019
Contact name Stephen Tapscott
E-mail(s) stapscot@fredhutch.org
Organization name Fred Hutch Cancer Research Center
Department Human Biology
Lab Tapscott
Street address 1100 Fairview N. Ave
City Seattle
State/province WASHINGTON
ZIP/Postal code 98103
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (10)
GSM3097757 controlA_Lenti-DUX4
GSM3097758 controlA_lenti-GFP
GSM3097759 controlA_MB
Relations
BioProject PRJNA450097
SRA SRP139954

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE113133_tapscottlab_DUX4GFP_gencode_novel.csv.gz 6.7 Mb (ftp)(http) CSV
GSE113133_tapscottlab_DUX4GFP_gencode_novel.rda.gz 29.3 Mb (ftp)(http) RDA
GSE113133_tapscottlab_MTMB_gencode19_novel.csv.gz 8.4 Mb (ftp)(http) CSV
GSE113133_tapscottlab_MTMB_gencode19_novel.rda.gz 39.2 Mb (ftp)(http) RDA
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Processed data are available on Series record

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