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Sample GSM1289374 Query DataSets for GSM1289374
Status Public on Sep 01, 2015
Title DS21511 DNaseI-seq whole root 7 day
Sample type SRA
 
Source name whole root 7 day
Organism Arabidopsis thaliana
Characteristics intact line: UBQ10:NTF::ACT2:birA
tissue: whole root 7 day
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 7-10 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 30-60u 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.
Tissue and cell type DNase I data were subsampled to a uniform lebel of 6.8 million reads (excluding ChrC/ChrM), subsequent processing steps were applied to this subsampled set
4DPA and 7DPA DNase I data were subsampled to a uniform lebel of 6.65 million reads (excluding ChrC/ChrM, and centromeric regions), subsequent processing steps were applied to this subsampled set
genome build: TAIR10
processed data 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.
processed data 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, 4th 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 SAMN02444263
SRA SRX391990

Supplementary file Size Download File type/resource
GSM1289374_Col-0.Root.NA.DNase.DS21511.6.8M.peaks.bed.gz 318.8 Kb (ftp)(http) BED
GSM1289374_Col-0.Root.NA.DNase.DS21511.6.8M.signal.bw 13.7 Mb (ftp)(http) BW
GSM1289374_Col-0.Root.NA.DNase.DS21511.peaks.bed.txt.gz 351.3 Kb (ftp)(http) TXT
GSM1289374_Col-0.Root.NA.DNase.DS21511.signal.bw 17.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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