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Series GSE119171 Query DataSets for GSE119171
Status Public on Nov 16, 2018
Title Long-range epigenetic concordance revealed by simultaneous profiling of DNA methylation and chromosomal conformation changes in bulk and single cell Methyl-HiC
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Other
Summary Genomic sequences, as well as its covalent epigenetic modifications, are spatially organized into three-dimensional structures. Here, we developed Methyl-HiC by combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture genome-wide chromosome conformation changes and DNA methylation within the same DNA molecule. Methyl-HiC generated consistent information compared with in situ Hi-C and WGBS from the same cell line. We detected long-range DNA methylation concordance in general but varied in different chromatin states. We extended Methyl-HiC to single cell level and applied it on 103 primed and 47 naïve mouse embryonic stem cells (mESCs). We revealed the heterogeneity of chromosomal conformation changes by grouping cells in their DNA methylation level alone. We also observed increases of DNA methylation stochasticity and decreases of contact frequency together in late replication timing regions. Our method here paves the road to evaluate the direct long-range effect of epigenetic alterations in different pathological and healthy conditions at genome-wide and single cell level.
 
Overall design Methyl-HiC and single cell Methyl-HiC experiments applied to mouse embryonic stem cell (F123).
Web link https://www.biorxiv.org/content/biorxiv/early/2018/11/14/470963.full.pdf
 
Contributor(s) Li G, Liu Y, Kellis M, Ren B
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Aug 28, 2018
Last update date May 14, 2019
Contact name Guoqiang Li
E-mail(s) liguoqiang.jason@gmail.com
Phone (858)822-5767
Organization name Ludwig Institute for Cancer Reaserch, San Diego
Lab Bing Ren
Street address 9500 Gilman Dr. CMM East, Room 2071
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (48)
GSM3359960 F123_Methyl-HiC_Rep1
GSM3359961 F123_Methyl-HiC_Rep2
GSM3359962 F123_Methyl-HiC_Rep3
Relations
BioProject PRJNA488313
SRA SRP159191

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
GSE119171_F123.MethylHic.mm9.calmd.cpg.filtered.sort.CG.strand.6plus2.bed.gz 228.9 Mb (ftp)(http) BED
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.10k_res.all_chr.hiccups.txt.gz 195.0 Kb (ftp)(http) TXT
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.10k_res.methy_corr.minMapQ30.methyCor.txt.gz 196.0 Kb (ftp)(http) TXT
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.25k_res.all_chr.hiccups.txt.gz 233.6 Kb (ftp)(http) TXT
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.25k_res.methy_corr.minMapQ30.methyCor.txt.gz 448.6 Kb (ftp)(http) TXT
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.5k_res.all_chr.hiccups.txt.gz 198.6 Kb (ftp)(http) TXT
GSE119171_F123.MethylHic.mm9.calmd.long.hic.mapQ30.5k_res.methy_corr.minMapQ30.methyCor.txt.gz 162.9 Kb (ftp)(http) TXT
GSE119171_F123.mESC.MethylHic.mapQ30.25k_res.enhancedHicMatrix.txt.gz 30.2 Kb (ftp)(http) TXT
GSE119171_JL.merged.sorted.nodup.long.juice.q30.hic 945.2 Mb (ftp)(http) HIC
GSE119171_RAW.tar 872.5 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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