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Series GSE77260 Query DataSets for GSE77260
Status Public on Jan 28, 2016
Title E2F1 orchestrates transcriptomics and oxidative metabolism in Wharton’s jelly derived mesenchymal stem cells from growth-restricted neonates
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Wharton’s jelly derived Mesenchymal Stem Cells (MSCs) isolated from newborns with intrauterine fetal growth restriction were previously shown to exert anabolic features including insulin hypersensitivity. Here, we extend these observations and demonstrate that MSCs from small for gestational age (SGA) individuals have decreased mitochondrial oxygen consumption rates. Comparing normally grown and SGA MSCs using next generation sequencing studies, we measured global transcriptomic and epigenetic profiles and identified in SGA, E2F1 as an over-expressed transcription factor regulating oxidative metabolism. We further show that E2F1 regulates the differential transcriptome found in SGA and is associated with the activating histone marks H3K27ac and H3K4me3. One of the key genes regulated by E2F1 was found to be the fatty acid elongase ELOVL2, a gene involved in the endogenous synthesis of docosahexaenoic acid (DHA).
 
Overall design ChIP-seq of E2F1, H3K27ac, H3K27me3, H3K36me3, H3K4me1 and H3K4me3 in MSCs from 3 AGA and 3 SGA samples. RNA-seq of basal, siCTRL and siE2F1 conditions in the same 6 MSC lines.
 
Contributor(s) Tan PY, Chang CW, Duan K, Poidinger M, Ng KL, Chong YS, Gluckman PD, Stünkel W
Citation(s) 27631473
Submission date Jan 26, 2016
Last update date Jun 27, 2019
Contact name Walter Stunkel
E-mail(s) walter_stunkel@sics.a-star.edu.sg
Phone 64070689
Organization name Singapore Institute for Clinical Sciences
Street address 30 Medical Drive, Brenner Centre Lvl 4
City Singapore
ZIP/Postal code 117609
Country Singapore
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (60)
GSM2046831 ID01.E2F1
GSM2046832 ID56.E2F1
GSM2046833 ID75.E2F1
Relations
BioProject PRJNA309966
SRA SRP068942

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
GSE77260_AGA.E2F1.bigWig 334.0 Mb (ftp)(http) BIGWIG
GSE77260_AGA.H3K27ac.bigWig 392.7 Mb (ftp)(http) BIGWIG
GSE77260_AGA.H3K27me3.bigWig 400.8 Mb (ftp)(http) BIGWIG
GSE77260_AGA.H3K36me3.bigWig 390.4 Mb (ftp)(http) BIGWIG
GSE77260_AGA.H3K4me1.bigWig 393.5 Mb (ftp)(http) BIGWIG
GSE77260_AGA.H3K4me3.bigWig 356.6 Mb (ftp)(http) BIGWIG
GSE77260_E2F1_consensus.bed.gz 296.0 Kb (ftp)(http) BED
GSE77260_RAW.tar 11.8 Gb (http)(custom) TAR (of BIGWIG)
GSE77260_SGA.E2F1.bigWig 355.0 Mb (ftp)(http) BIGWIG
GSE77260_SGA.H3K27ac.bigWig 369.1 Mb (ftp)(http) BIGWIG
GSE77260_SGA.H3K27me3.bigWig 414.0 Mb (ftp)(http) BIGWIG
GSE77260_SGA.H3K36me3.bigWig 392.9 Mb (ftp)(http) BIGWIG
GSE77260_SGA.H3K4me1.bigWig 391.7 Mb (ftp)(http) BIGWIG
GSE77260_SGA.H3K4me3.bigWig 369.8 Mb (ftp)(http) BIGWIG
GSE77260_genecounts.xls.gz 1.5 Mb (ftp)(http) XLS
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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