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Sample GSM1239090 Query DataSets for GSM1239090
Status Public on Mar 05, 2014
Title Control-ChIP-Seq
Sample type SRA
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
line: p35S::GFP (GFP OE)
tissue: 10d-old seedling
chip antibody: GFP
chip antibody vendor: abcam
chip antibody cat. #: ab290
Treatment protocol No treatment
Growth protocol Arabidopsis thaliana plants (ecotype Col-0) were grown at 22°C and a 16-h photoperiod (65 μE m−2 s−1) on half-strength MS medium and 0.7 % plant tissue culture agar. Entire seedlings were collected at 10 days after sowing.
Extracted molecule genomic DNA
Extraction protocol ChIP DNA pooled from three independent ChIP experiments were subjected to end repair and A-base addition, followed by ligation with adapters, Mltplx_Short and Mltplx_Long (Dataset S7). Gel purified ligated libraries were amplified by Phusion Taq (New England Biolabs) with 18 cycles by using MltplxPCR1.0 and two different primers, PCR2.0_indx2 for IBH1OE or PCR2.0_indx6 for Col-0, respectively.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing CASAVA version 1.8.2 was used to generate fastq files and demultiplexing.
ChIP-seq reads were aligned to the TAIR9 genome assembly using Bowtie with a default parameters except three mismatch allowed.
The uniquely aligned data was subjected to perform the Model-based Analysis of ChIP-Seq (MACS) (version 1.4.0beta) for finding peaks (P<10-5, no duplicated fragments allowed).
Genome_build: TAIR9
Supplementary_files_format_and_content: MACS (version 1.4.0beta) generated BED files, 110328_c4_peaks.bed and 110328_c4_summits.bed, by comparison of IBL1-ChIP-Seq and Control-ChIP-Seq and WIG files,110328_c4_treat_afterfiting_all.wig.gz and 110328_c4_control_afterfiting_all.wig.gz for peak distributions of IBL1-ChIP-Seq and Control-ChIP-Seq, respectively.
Submission date Sep 24, 2013
Last update date May 15, 2019
Contact name Kengo Morohashi
Phone 614-688-4954
Organization name The Ohio State University
Department Molecular Genetics
Lab Erich Grotewold
Street address 1060 Carmack Rd
City Columbus
State/province OH
ZIP/Postal code 43210
Country USA
Platform ID GPL11221
Series (2)
GSE51120 A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [ChIP-seq]
GSE51121 A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal
BioSample SAMN02363363
SRA SRX359426

Supplementary file Size Download File type/resource
GSM1239090_110328_c4_control_afterfiting_all.wig.gz 15.0 Mb (ftp)(http) WIG
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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