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Sample GSM506210 Query DataSets for GSM506210
Status Public on Apr 02, 2010
Title AP1-GR_uninduced_control_1
Sample type SRA
 
Source name AP1-GR ap1 cal apical meristematic tissue; uninduced
Organism Arabidopsis thaliana
Characteristics tissue: AP1-GR ap1 cal apical meristematic tissue
antibody: AP1 antibody, affinity-purified against IKC-domains
Treatment protocol For the ChIP experiments, we treated inflorescences with a solution containing 1 mM dexamethasone, 0.01% (v/v) ethanol, and 0.015% (v/v) Silwett L-77, and harvested the inflorescences after 2h induction
Growth protocol Plants were grown on a soil:vermiculite:perlite (2:1:1) mixture at 20ÂșC under constant illumination with cool white fluorescent light, unless indicated otherwise
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared using the Illumina protocol for preparation of ChIP-SEQ libraries with modifications described in Kaufmann et al., Nature Protocols 2010
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against AP1 transcription factor
Data processing Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana genome using the SOAP mapping software (soap.genomics.org.cn/). All reads mapping with two or fewer mismatches at unique positions were retained. Iteratively, one base was discarded form the 3`end of the nonmapped reads until the reads were uniquelly mapped or fell bellow a minimum length of 30 bp
 
Submission date Feb 03, 2010
Last update date Sep 04, 2019
Contact name Gerco Angenent
E-mail(s) gerco.angenent@wur.nl
Organization name Plant Research International
Street address Bornsesteeg 65
City Wageningen
ZIP/Postal code 6708 PD
Country Netherlands
 
Platform ID GPL9062
Series (1)
GSE20176 Orchestration of Floral Initiation by APETALA1
Relations
Reanalyzed by GSE136843
SRA SRX018394
BioSample SAMN00010661

Supplementary file Size Download File type/resource
GSM506210_090323_s_5_seq_WKK-2.soa.gz 9.3 Mb (ftp)(http) SOA
GSM506210_090408_s_8_seq_WKK-2.soa.gz 18.1 Mb (ftp)(http) SOA
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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