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Series GSE104781 Query DataSets for GSE104781
Status Public on Jan 23, 2019
Title DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [WGBS_Mm]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary The crosstalk between H3K4 monomethylation and DNA methylation has been receiving little attention to date. We investigated a mouse model harboring a loss-of-function mutation of lysine methyltransferase 2D (KMT2D), which catalyzes the monomethylation of lysine 4 on histone H3. We performed H3K4me1 ChIP-seq in spleen B cells with the wild type (WT) KMT2D as well as heterozygous (HET) and homozygous (HOM) chr15: 98,835,228 A>T KMT2D mutation. Alongside, using WGBS, we performed genome-wide DNA methylation profiling in spleen B cells with the WT KMT2D as well as HET and HOM chr15: 98,835,228 A>T KMT2D mutation.
 
Overall design Genome-wide analysis of DNA methylation using WGBS in B cells and blood from mice with the wild type KMT2D, heterozygous Ile5482Asn KMT2D mutation and homozygous Ile5482Asn KMT2D mutation.
 
Contributor(s) Skvortsova K, Masle-Farquhar E, Luu P, Clark SJ, Stirzaker C
Citation(s) 30753827
Submission date Oct 10, 2017
Last update date Jul 25, 2021
Contact name Ksenia Skvortsova
E-mail(s) k.skvortsova@garvan.org.au
Phone 478135210
Organization name Garvan Institute
Department Genomics and Epigenetics
Lab Developmental Epigenomics
Street address 384 Victoria St, Darlinghurst
City Sydney
State/province NSW
ZIP/Postal code 2010
Country Australia
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (9)
GSM2807805 mBcells_KMT2D_WT_WGBS
GSM2807806 mBcells_KMT2D_HET_WGBS
GSM2807807 mBcells_KMT2D_HOM_WGBS
This SubSeries is part of SuperSeries:
GSE104791 DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 mono-methylation patterns.
Relations
BioProject PRJNA413838
SRA SRP119705

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Supplementary file Size Download File type/resource
GSE104781_RAW.tar 1.4 Gb (http)(custom) TAR (of BW)
GSE104781_mouse_KMT2Dmut_WGBS_bigTable.tsv.gz 158.7 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data provided as supplementary file

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