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Series GSE113076 Query DataSets for GSE113076
Status Public on Aug 08, 2019
Title Genome-wide profiling of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP-seq) in wild-type, fpa mutant and bdrs triple mutant
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We used an MNase digestion of chromatin from Arabidopsis seedlings, combined or not with ChIP (native ChIP), to analyze by high-throughput sequencing the genome-wide profiles of nucleosomes (MNase-seq), and of total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIPs) in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We found that BDR proteins occupy regions of low nucleosome density. We also observed that genes upregulated in bdrs triple mutant display high levels of RNA polymerase II on their gene bodies but low levels of H3K4me3 and H3K36me3 in wild-type seedlings. For genes with the highest levels of BDR occupancy in wild-type, increased mRNA expression in bdrs mutant is associated with reduced RNA polymerase II density profile and increased H3K4me3 and H3K36me3 levels.
 
Overall design Genome-wide profiles using native (non crosslinked) chromatin from 8-day old seedlings of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP) in wild-type, fpa single mutant (fpa-7) or bdrs triple mutant were generated by deep sequencing on an Illumina NextSeq500. MNase-seq corresponds to the input chromatin sample used for the immunoprecipitation.
 
Contributor(s) Michaels SD, Martin PG, Yu X, Huang J, Ford JB
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Submission date Apr 12, 2018
Last update date Aug 10, 2019
Contact name Pascal GP Martin
E-mail(s) Pascal.Martin@inra.fr, pascmart@iu.edu
Organization name INRA
Lab ToxAlim
Street address 180 chemin de Tournefeuille, BP 93173
City Toulouse Cedex 3
ZIP/Postal code 31027
Country France
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (15)
GSM3095861 H3_WT
GSM3095862 H3K4me2_WT
GSM3095863 H3K4me3_WT
This SubSeries is part of SuperSeries:
GSE112443 RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings
Relations
BioProject PRJNA449932
SRA SRP139813

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
GSE113076_H3K36me3_optimal_peaks.txt.gz 299.5 Kb (ftp)(http) TXT
GSE113076_H3K4me2_optimal_peaks.txt.gz 577.6 Kb (ftp)(http) TXT
GSE113076_H3K4me3_optimal_peaks.txt.gz 364.7 Kb (ftp)(http) TXT
GSE113076_RAW.tar 1.7 Gb (http)(custom) TAR (of BIGWIG)
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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