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| Status |
Public on Sep 01, 2015 |
| Title |
Mapping and dynamics of regulatory DNA in A. thaliana tissues and cell types across developmental transitions |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We performed DNase-seq on root tissue, root epidermal cell types, seed coat epidermal cells at two developmental stages, and open and closed flowers.
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| Overall design |
Root: We performed chromatin profiling (DNase-seq) on whole root (all cell types), or root epidermal cell types (hair cell, non-hair cell). Seed coat: We performed chromatin profiling on seed coat epidermal cells from siliques at two developmental stages (4 days past anthesis, 7 days past anthesis). We preformed chromatin profiling (DNase-seq) on flowers at two developmental time points (open and closed flowers). All plants were grown on plates (roots only) or in soild in LD conditions (16hr light 22°C, 8hr dark 20°C).
The following processed data files are pooled short read data from 2 biological replicates (GSM1289379 [DS21306] and GSM1824051 [DS20134]):
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.peaks.bed
The following processed data files are pooled short read data from 2 biological replicates (GSM1824052 [DS20131] and GSM1824053 [DS20132]):
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.peaks.bed
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.signal.bw
Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.peaks.bed
The following processed data files are pooled pooled short read data from 2 biological replicates (GSM1824054 [DS19056] and GSM1824055 [DS21512]):
Col-0.Root.Hair.DNase.pooled.6.8M.signal.bw
Col-0.Root.Hair.DNase.pooled.6.8M.peaks.bed
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| Contributor(s) |
Sullivan AM, Arsovski AA, Bubb KL, 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(s) |
25220462, 31798605 |
| Submission date |
Dec 14, 2013 |
| Last update date |
Dec 10, 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 (17)
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| GSM1289374 |
DS21511 DNaseI-seq whole root 7 day |
| GSM1289375 |
DS16398 DNaseI-seq root non hair cell 10 day |
| GSM1289376 |
DS21513 DNaseI-seq root hair cell 7 day |
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| Relations |
| BioProject |
PRJNA231717 |
| SRA |
SRP034156 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53324_Col-0.Root.Hair.DNase.pooled.6.8M.peaks.bed.gz |
302.1 Kb |
(ftp)(http) |
BED |
| GSE53324_Col-0.Root.Hair.DNase.pooled.6.8M.signal.bw |
13.8 Mb |
(ftp)(http) |
BW |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.peaks.bed.gz |
336.7 Kb |
(ftp)(http) |
BED |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.signal.bw |
12.5 Mb |
(ftp)(http) |
BW |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.peaks.bed.gz |
340.4 Kb |
(ftp)(http) |
BED |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.signal.bw |
13.3 Mb |
(ftp)(http) |
BW |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.peaks.bed.gz |
324.9 Kb |
(ftp)(http) |
BED |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.signal.bw |
13.7 Mb |
(ftp)(http) |
BW |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.peaks.bed.gz |
322.5 Kb |
(ftp)(http) |
BED |
| GSE53324_Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.signal.bw |
14.9 Mb |
(ftp)(http) |
BW |
| GSE53324_RAW.tar |
258.1 Mb |
(http)(custom) |
TAR (of BED, BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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