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Series GSE99530 Query DataSets for GSE99530
Status Public on Sep 13, 2018
Title Promoter bivalency favors an open architecture of the stem cell genome
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary In embryonic stem cells (ESCs), bivalency characterizes the chromatin state of developmental gene promoters, simultaneously modified by Mll2 and Polycomb complexes. Despite its essential role in embryogenesis, the function of bivalency is currently unclear. Here we show that Mll2 plays a central role in stem cell genome organization. We generate a catalog of bona-fide bivalent genes in mESCs and demonstrate that loss of Mll2 leads to increased Polycomb occupancy. Consequently, promoters lose accessibility and long-range interactions become redistributed, affecting ESC differentiation. We propose that bivalency balances accessibility and long-range connectivity of promoters to modulate developmental gene expression.
Overall design List of ChIPseq samples (Mll2 wt and mutant), ATACseq samples (Mll2 wt and mutant) and RNAseq samples (differentiation in embryoid bodies, day0, day3, day6 and day9).
List of new ChIPseq samples and PROseq samples (Mll2 wt and mutant).
List of HiC samples. Conditional MLL2 KO samples: OH means WT and TAM means KO. Catalytic inactive MLL2 samples: WT means WT and CD means Catalytic Dead.
Contributor(s) Mas G, Blanco E, Marti-Renom M, DiCroce L
Citation(s) 30224650
Submission date May 31, 2017
Last update date Jul 25, 2021
Contact name Enrique Blanco
Phone +34 93 316 01 00
Organization name Center for Genomic Regulation (CRG)
Department Gene Regulation, Stem Cells and Cancer
Lab Epigenetic Events in Cancer (L. Di Croce's lab)
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (80)
GSM2645495 ChIP_H3K4me3_WT
GSM2645496 ChIP_H3K4me3_KO
GSM2645497 ChIP_H3K27me3_WT
BioProject PRJNA388716
SRA SRP108392

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
GSE99530_CD_interaction_matrices_100Kb.tar.gz 18.6 Mb (ftp)(http) TAR
GSE99530_CD_interaction_matrices_50Kb.tar.gz 47.0 Mb (ftp)(http) TAR
GSE99530_Day0_OH-TAM_FPKMs.txt.gz 688.1 Kb (ftp)(http) TXT
GSE99530_Day3_OH-TAM_FPKMs.txt.gz 680.6 Kb (ftp)(http) TXT
GSE99530_Day6_OH-TAM_FPKMs.txt.gz 686.8 Kb (ftp)(http) TXT
GSE99530_Day9_OH-TAM_FPKMs.txt.gz 695.9 Kb (ftp)(http) TXT
GSE99530_OH_interaction_matrices_100Kb.tar.gz 20.7 Mb (ftp)(http) TAR
GSE99530_OH_interaction_matrices_50Kb.tar.gz 53.7 Mb (ftp)(http) TAR
GSE99530_PROseq_OH1-OH2-TAM1-TAM2_FPKMs.txt.gz 721.7 Kb (ftp)(http) TXT
GSE99530_RAW.tar 5.6 Gb (http)(custom) TAR (of BED, BEDGRAPH)
GSE99530_TAM_interaction_matrices_100Kb.tar.gz 20.1 Mb (ftp)(http) TAR
GSE99530_TAM_interaction_matrices_50Kb.tar.gz 51.6 Mb (ftp)(http) TAR
GSE99530_WT_interaction_matrices_100Kb.tar.gz 19.0 Mb (ftp)(http) TAR
GSE99530_WT_interaction_matrices_50Kb.tar.gz 48.3 Mb (ftp)(http) TAR
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Raw data are available in SRA
Processed data provided as supplementary file
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