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SRX391992: GSM1289376: DS21513; Arabidopsis thaliana; DNase-Hypersensitivity
1 ILLUMINA (Illumina HiSeq 2000) run: 21.1M spots, 1.5G bases, 982.5Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Mapping and dynamics of regulatory DNA in A. thaliana tissues and cell types across developmental transitions
show Abstracthide Abstract
We performed DNase-seq on root tissue, root epidermal cell types, seed coat epidermal cells at two developmental stages, and open and closed flowers. 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
Sample: DS21513 DNaseI-seq root hair cell 7 day
SAMN02444264 • SRS515202 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: DNase-Hypersensitivity
Source: GENOMIC
Selection: DNase
Layout: PAIRED
Construction 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
Experiment attributes:
GEO Accession: GSM1289376
Links:
External link:
Runs: 1 run, 21.1M spots, 1.5G bases, 982.5Mb
Run# of Spots# of BasesSizePublished
SRR104980821,138,2631.5G982.5Mb2015-09-01

ID:
562835

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