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Series GSE174369 Query DataSets for GSE174369
Status Public on May 11, 2024
Title Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Muscle groups throughout the body are specialized in function and are specified during development by position specific gene regulatory networks. In developed tissue, myopathies affect muscle groups differently. Facioscapulohumeral muscular dystrophy, FSHD, affects upper body and tibialis anterior (TA) muscles earlier and more severely than others such as quadriceps. To investigate an epigenetic basis for susceptibility of certain muscle groups to disease, we perform DNA methylation and RNA sequencing on primary patient derived myoblasts from TA and quadricep for both control and FSHD2 as well as RNA-seq for myoblasts from FSHD1 deltoid, bicep and TA over a time course of differentiation. We find that TA and quadricep retain methylation and expression differences in transcription factors that are key to muscle group specification during embryogenesis. FSHD2 patients have differences in DNA methylation and expression related to SMCHD1 mutations and FGF signaling. Genes induced specifically in FSHD are more highly expressed in more commonly affected muscle groups. We find a set of genes that distinguish more susceptible muscle groups including developmental associated TFs and genes involved in WNT signaling. Adult muscle groups therefore retain transcriptional and DNA methylation differences associated with development, which may contribute to susceptibility in FSHD.
Overall design Time-course of primary FSHD2 myoblasts from tibialis anterior and quadricep, control myoblasts from tibialis anterior and quadricep.
Contributor(s) Williams KE, Mortazavi SA
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Submission date May 12, 2021
Last update date May 11, 2024
Contact name Ali Mortazavi
Organization name UC Irvine
Street address 2300E Biological Sciences 3
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (48)
GSM5293107 Day_0_Control_1_R1 [methylation]
GSM5293108 Day_0_Control_1_R2 [methylation]
GSM5293109 Day_3_Control_1_R1 [methylation]
This SubSeries is part of SuperSeries:
GSE174370 Muscle group specific transcriptomic and DNA methylation differences related to developmental patterning influence FSHD
BioProject PRJNA729574
SRA SRP319580

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Supplementary file Size Download File type/resource
GSE174369_PerMeth.AllRegions.csv.gz 71.2 Mb (ftp)(http) CSV
GSE174369_RAW.tar 2.5 Gb (http)(custom) TAR (of COV)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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