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Sample GSM1325797

Query DataSets for GSM1325797

Status

Public on Jan 11, 2015

Title

(Negative Control for SVP-ChIPSeq) 35S:GFP rep1

Sample type

SRA

Source name

Seedlings

Organism

Arabidopsis thaliana

Characteristics

tissue: seedlings
ecotype: Columbia-0 FRI
chip antibody: anti-GFP (Ab290)

Growth protocol

2 weeks seedling grown in Long days photoperiod

Extracted molecule

genomic DNA

Extraction protocol

Ovation Ultralow DR Multiplex System

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Data processing

We followed recommended guidelines in the analysis of ChIP-seq data for quality control, read mapping, normalization, peak-calling, assessment of reproducibility among biological replicates, and post-processing of peaks (Bailey et al., PLoS Computational Biology 2013, DOI: 10.1371/journal.pcbi.1003326).
Basecalls were performed using CASAVA version 1.8.
Low-quality reads in the raw data (fastq files) were filtered out using Parallel-QC 1.0 (Zhou et al., PLoS ONE 2013). Low-quality reads were defined as those not having Phred quality scores ≥ 13 in the bases called.
Reads kept were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 2.0.2, under default mode parameters.
Peak calling was done in each biological replicate separately using MACS version 2 (Feng et al., Nature Protocols 2012) with a p-value cutoff 1e-3, followed by an Irreproducible Discovery Rate (IDR) analysis (Li et al., Annals of Applied Statatistics 2011). Using the code provided in https://sites.google.com/site/anshulkundaje/projects/idr, a conservative estimate number of peaks for each experiment was selected as the maximum number of reproducible peaks for IDR ≤ 0.05 found at any pair-wise comparison between biological replicates.
We further post-processed the peaks using shape analysis implemented in the Bioconductor package NarrowPeaks v1.4.0 (http://www.bioconductor.org/). Only MACS peaks confirmed also by NarrowPeaks are reported. Duplicated reads were not considered during peak calling in order to achieve a better specificity (Bailey et al., PLoS Computational Biology 2013).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-separated values .csv files containing peak definitions: chromosome, peak start, peak end, peak summit (0-based offset from peak start), fold enrichment, -log10(p-value), and genes with a peak summit in a region spanning from 3kb upstream to 1kb downstream the gene body.

Submission date

Feb 11, 2014

Last update date

May 15, 2019

Contact name

Julieta Mateos

E-mail(s)

jmateos@leloir.org.ar

Phone

+054 11 5238-7500

Organization name

Max Planck Institute for Plant Breeding Research