|
| Status |
Public on Dec 15, 2013 |
| Title |
DS21094 PE DNaseI-seq 7 day old seedling Control |
| Sample type |
SRA |
| |
|
| Source name |
7 day old seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: Control (LD)
tissue: seedling
genetic background: Col-0
intact line: UBQ10:NTF::ACT2:birA
experiment: DNaseI-seq
|
| Treatment protocol |
Light treatments: dark grown 7 day old seedlings were moved to light conditions for the specified amounts of time. Spray control: plates were un-wrapped and lightly sprayed with 0.5% EtOH and left for 3hrs
|
| Growth protocol |
LD (16hr light, 22°C; 8hr dark, 20°C); Dark (16hr 22°C; 8hr 20°C)
|
| 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. RNA-seq 100-200mg of tissue was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), RNA was treated with DNase I and Ribo-Zero Plant leaf kit (Epicentre) and libraries were prepared using the TruSeq kit v2 (Illumina).
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
For Light/Dark DNaseI data, reads where subsampled to a uniform level of 24 million reads all subsequent processing used the subsampled set
For Heat shock DNaseI data, reads where subsampled to a uniform level of 74 million reads all subsequent processing used the subsampled set
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.
Footprints were called using the method described in PMID: 22955618
RNA-seq reads where aligned with eland_rna as part of CASAVA-1.8.2 (eland version ELANDv2e)
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: RNA bigWig (signal.bw) files were generated with BEDOPS and bedGraphToBigWig (UCSC) and represent RNA-seq read pileups
Supplementary_files_format_and_content: peak bed files were generated with Hotspot and represent DnaseI hypersensitive sites
Supplementary_files_format_and_content: footprint bed files where generated with the pipeline described in PMID 22955618 and represent transcription factor binding events
|
| |
|
| 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) |
| GSE53322 |
Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana |
|
| Relations |
| BioSample |
SAMN02444241 |
| SRA |
SRX391968 |
