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SRX391963: GSM1289354: DS20412 SE; Arabidopsis thaliana; DNase-Hypersensitivity
1 ILLUMINA (Illumina HiSeq 2000) run: 29M spots, 1G bases, 687.8Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana
show Abstracthide Abstract
We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. Analysis of >700,000 TF footprints disclosed an extensive cis-regulatory lexicon, and enabled construction of large-scale TF cross-regulatory networks. Although the cis- and trans-regulatory repertoire is markedly distinct from mammals, the architecture of A. thaliana TF networks is strikingly similar to those of human. Analysis of the DHS landscape and TF network dynamics during heat shock and photomorphogenesis revealed thousands of conditionally-sensitive elements and enabled mapping of key regulatory circuits. Our results provide an extensive resource for understanding and enabling diverse aspects of A. thaliana biology. Overall design: Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old dark-grown seedlings exposed to 0hr light, 30min light, 3hr light or 24hr LD conditions. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old LD-grown seedlings treated with a brief sever heat shock or kept under control conditions. Replicates are included when available; controls and read-normalized samples (samples that were subsampled to the same read-depth) are also included here.
Sample: DS20412 SE DNaseI-seq 7 day old seedling Dark 3hr light
SAMN02444238 • SRS515173 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: DNase-Hypersensitivity
Source: GENOMIC
Selection: DNase
Layout: SINGLE
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. 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
Experiment attributes:
GEO Accession: GSM1289354
Links:
External link:
Runs: 1 run, 29M spots, 1G bases, 687.8Mb
Run# of Spots# of BasesSizePublished
SRR104977328,959,5121G687.8Mb2013-12-16

ID:
562806

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