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| Status |
Public on Dec 15, 2013 |
| Title |
Mapping and dynamics of regulatory DNA in A. thaliana accessions |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We performed DNase-seq on 7-day-old seedlings from four A. thaliana accessions: Bur-0, Tsu-0, Bay-0, Est-1 using INTACT constructs (Deal and Henikoff, Developmental Cell, 2010) driven by the UBQ10 promoter.
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| Overall design |
Chromatin accessibility profiling (Dnase I-seq) of 7-day-old seedlings of A. thaliana accessions: Bur-0, Tsu-0, Bay-0 & Est-1 grown in LD conditions (16hr light 22°C, 8hr dark 20°C).
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| Contributor(s) |
Urton J, Sullivan AM, Bubb KL, Arsovski AA, Sabo PJ, Sandstrom R, Thurman R, Neph S, Reynolds AP, Johnson AK, Haugen E, Dargiel A, Neri J, Weaver M, Diegel M, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
John A Stamatoyannopoulos |
| E-mail(s) |
jstam@altius.org
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| Organization name |
Altius Institute / University of Washington
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| Department |
Genome Sciences
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| Lab |
Stamatoyannopoulos
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| Street address |
2211 Elliott Avenue, 4th Floor
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| City |
SEATTLE |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (4)
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| GSM1289370 |
DS23077 DNaseI-seq Bur-0, 7 day old seedling |
| GSM1289371 |
DS22973 DNaseI-seq Bay-0, 7 day old seedling |
| GSM1289372 |
DS22974 DNaseI-seq Est-1, 7 day old seedling |
| GSM1289373 |
DS22968 DNaseI-seq Tsu-1, 7 day old seedling |
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| Relations |
| BioProject |
PRJNA231718 |
| SRA |
SRP034155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53323_RAW.tar |
60.1 Mb |
(http)(custom) |
TAR (of BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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