|
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
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|
|
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
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|
|
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 |