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Sample GSM940585 Query DataSets for GSM940585
Status Public on Jun 01, 2012
Title PI-GFP (AP1-GR ap1 cal) ChIPseq
Sample type SRA
Source name PI-GFP (AP1-GR ap1 cal) ChIPseq replicate 1
Organism Arabidopsis thaliana
Characteristics genotype: PI-GFP AP1-GR ap1 cal
tissue: flower
developmental stage: 4 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 4-5 flowers)
chip antibody: Anti-GFP
chip antibody manufacturer: Abcam
chip antibody catalog #: AB290
genetic background: Ler
Treatment protocol For all experiments, ~4 week-old plants were used. For the experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.
Growth protocol Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees (16 degrees for plants used for temperature-sensitive perturbation experiments) under constant illumination with cool white fluorescent light
Extracted molecule genomic DNA
Extraction protocol ChIP was performed using a modified version of previously described protocols (Gomez-Mena C, de Folter S, Costa MM, Angenent GC, & Sablowski R (2005); Development 132(3):429-438 + Kaufmann K, et al. (2010), Nat Protoc 5(3):457-472.) Library preparation was performed as described in the instructions of the Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001), whereby the adapter-oligo dilution used was 1:30 in water, the gel for DNA purification was run at low voltage (20V for > 6hrs) and gel-extraction step performed twice.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software
Data processing For each dataset, two independent alignment- and peak calling methods were performed. The main method was using the SOAPv2 short read alignment program and subsequent peak calling using the CSAR package as implemented in the Bioconductor project. These peak definitions were retained, but only if confirmed by an overlapping peak range as determined by the independent method as described below.
Main method: Arabidopsis genomic sequences were downloaded from TAIR (; files ‘TAIR10_chr1.fas’ - ‘TAIR10_chr5.fas’). Short read alignments were performed using the SOAP2 software with default settings. Data were read into R using the CSAR package. and functionality provided by various Bioconductor packages (including the IRanges v1.12.5 and GenomicRanges v1.6.4 packages) was used for data handling operations.
Peak calling was performed using the CSAR package that included a normalization and a test based on the Poisson distribution, and enriched regions were identified at a False Discovery Rate (FDR)<0.001 (with five rounds of permutations for each dataset, resulting in >600,000 permutations). Default parameters were used. Only peak regions with stretches of >50 bp were retained.
In order to validate peak regions detected by the CSAR software, the peak calling was repeated using independent short-read aligner and peak calling tools as follows: short-reads were aligned to the reference genome using BWA version 0.6.1, aligned reads were sorted and duplicated reads removed using samtools. and peak calling was performed using MACS Version 1.4.1 with default parameters. Peaks as determined by the CSAR software were then retained only if they had any overlap with peaks determined by the MACS software. In order to merge biological replicates from the PI-GFP ChIP-Seq experiments, peak definitions determined for PI-GFP replicate 2 were retained only if they showed any overlap with the PI-GFP replicate 1.
Peaks were associated with genes located in the vicinity using CSAR functionality, whereby a peak had to reside in a genomic region ranging from 3 kb upstream of a gene’s transcriptional start position to 1 kb downstream of its transcriptional end position. Gene range definitions were downloaded from TAIR (file TAIR10_GFF3_genes.gff).
Genome_build: TAIR10 Arabidopsis thaliana
Supplementary_files_format_and_content: csv formatted files, 1) file containing peak definitions (chromosome, peak start, peak end, peak position and maximal Poisson-based enrichment score) and putative direct target genes and 2) lists of putative direct target genes according to TAIR v10 genome build. The position of significantly enriched region(s) with respect to the corresponding gene is indicated by dividing the gene region into different segments (as indicated) and the maximum peak scores within these segments are shown. A value of 0 indicates that no significantly enriched peak region was detected within a given segment.
Submission date May 31, 2012
Last update date Sep 04, 2019
Contact name Samuel Elias Wuest
Phone +41 44 635 44 99
Organization name University of Zurich
Department Institute of Evolutionary Biology and Environmental Studies
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
Platform ID GPL11221
Series (2)
GSE38358 Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA (ChIP-Seq)
GSE38363 Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
Reanalyzed by GSE136843
SRA SRX150807
BioSample SAMN01001255

Supplementary file Size Download File type/resource
GSM940585_PI_directTargets.csv.gz 210.0 Kb (ftp)(http) CSV
GSM940585_PI_peaks.csv.gz 31.0 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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