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Sample GSM1289381 Query DataSets for GSM1289381
Status Public on Sep 01, 2015
Title DS20434 DNaseI-seq up-open flowers
Sample type SRA
 
Source name up-open flowers
Organism Arabidopsis thaliana
Characteristics intact line: UBQ10:NTF::ACT2:birA
tissue: up-open flowers
genetic background: Col-0
experiment: DNaseI-seq
Growth protocol Root sample seedlings were planted on 1XMS, 0.8% agar, 1% sucrose, and stratified for 2-4 days before being placed vertically in an incubator with LD (16hr light, 22°C; 8hr dark, 20°C) conditions for 7 days. See coat samples were obtained by collecting whole siliques 4 or 7 days past anthesis. For the flower samples, open or unopen flowers were collected and prepped. Seed coat and flower samples were collected from soil grown plants grown in LD conditions.
Extracted molecule genomic DNA
Extraction protocol DNaseI: Nuclei were extracted and isolated with biotin-capture methods. Nuclei were then treated with 45u of DNase I for 3 minutes at 25°C. Resulting genomic DNA was size fractionated and small (double cut) fragments were sequenced using Illumina technology.
Illumina TruSeq v2
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to A. thaliana reference TAIR10 with bowtie version 0.12.7 with the following parameters: bowtie -p 8 --mm -n 2 -m 1 --best --phred33-quals
Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration except that peak thresholding was set to 95 percentile.
Genome_build: TAIR10
Supplementary_files_format_and_content: Dnase bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent per base Dnase cleavages in a 150bp window at 20bp steps across the genome.
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites
 
Submission date Dec 14, 2013
Last update date May 15, 2019
Contact name John A Stamatoyannopoulos
E-mail(s) jstam@altius.org
Organization name Altius Institute / University of Washington
Department Genome Sciences
Lab Stamatoyannopoulos
Street address 2211 Elliott Avenue, 6th Floor
City SEATTLE
State/province WA
ZIP/Postal code 98121
Country USA
 
Platform ID GPL13222
Series (1)
GSE53324 Mapping and dynamics of regulatory DNA in A. thaliana tissues and cell types across developmental transitions
Relations
BioSample SAMN02444267
SRA SRX391997

Supplementary file Size Download File type/resource
GSM1289381_Col-0.whole_plant.Unopen_flowers.DNase.DS20434.peaks.bed.txt.gz 136.3 Kb (ftp)(http) TXT
GSM1289381_Col-0.whole_plant.Unopen_flowers.DNase.DS20434.signal.bw 7.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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