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Series GSE113059 Query DataSets for GSE113059
Status Public on Aug 08, 2019
Title Genome-wide occupancy of BDR1, BDR2 and FPA (ChIP-seq)
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We generated Arabidopsis lines expressing tagged (3X Myc tag) versions of BDR1 or BDR2 driven by their endogenous promoters on a bdrs triple mutant background (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). The genome-wide distribution of BDR1 and BDR2 in 8-day old seedlings were analyzed by ChIP-seq using an anti Myc antibody. We also analyzed by ChIP-seq the genome-wide distribution of FPA (AT2G43410) in wild-type seedlings using a rabbit anti-FPA polyclonal antibody raised against the C-terminal portion (position 536-901) of the FPA protein. Controls include sequencing of input DNA for each sample and a ChIP perfomed in wild-type seedlings with the anti-Myc tag antibody. We found that BDR1 and BDR2 are enriched at the border of a large number of genes in Arabidopsis genome and that FPA localizes mostly at the 3' end of genes.
 
Overall design ChIP-seq profiles in 8-day old seedlings of FPA, Myc tag-BDR1 and Myc tag-BDR2 (Myc tag-BDR proteins expressed in bdrs triple mutant background). Controls include sequencing of input DNA for each sample as well as a ChIP perfomed in wild-type plants (not expressing a tagged protein) with the anti-Myc tag antibody.
 
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 (9)
GSM3095567 Myc_BDR1
GSM3095568 Myc_BDR2
GSM3095569 Myc_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 PRJNA449914
SRA SRP139788

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
GSE113059_RAW.tar 796.1 Mb (http)(custom) TAR (of BED, BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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