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Series GSE93916 Query DataSets for GSE93916
Status Public on Jun 02, 2017
Title MyoD and FoxO3 mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation.
 
Overall design The CRISPR/Cas9 system was used to delete hotspots (H1_KO, H23_KO, H34_KO, H3_KO) and knockout MyoD expression (Myod1_KO) in C2C12 cell line following published protocols (Ran, F. A. et al., 2013; Huang, J. et al., 2016). Double deletion of H2 and H3 was generated by deleting H3 in H2 KO cell line. Similarly, double deletion of H3 and H4 was generated by deleting H3 in H4 KO cell line. Both WT and KO C2C12 cells were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep) and processed for H3K27ac ChIP-seq.
Web link https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/28575289
 
Contributor(s) Wang H, Sun H, Peng XL, So KK, He L, Zhao Y, Zhou J
Citation(s) 28575289
Submission date Jan 22, 2017
Last update date May 15, 2019
Contact name Jiajian Zhou
E-mail(s) zhoujj2013@gmail.com
Organization name Southern Medical University
Department Dermatology Hospital
Street address No. 2 Lujing Road, Yuexiu District,
City Guangzhou
State/province Guangdong
ZIP/Postal code NA
Country China
 
Platforms (2)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (13)
GSM2464966 DM_minus24hr_H3K27ac
GSM2464967 DM_0hr_H3K27ac
GSM2464968 DM_6hr_H3K27ac
Relations
BioProject PRJNA362824
SRA SRP097582

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Supplementary file Size Download File type/resource
GSE93916_RAW.tar 16.6 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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