<h2>CCA1 ChIP-Seq experiment</h2>

<p>This directory contains processed data files from</p>

<p><a href=
"http://www.pnas.org/content/early/2015/08/05/1513609112.full.pdf">Genome-wide
identification of CCA1 targets uncovers an expanded clock network in
Arabidopsis</a></p>

<h4>Experiment Design</h4>

<p>CCA1, a transcriptional regulator with a central role in plant circadian
clocks was fused to GFP and the chimeric protein driven by the CCA1
promoter. Arabidopsis seedlings containing these CCA1::CCA1-GFP constructs
were grown in 12h:12h light:dark cycles at constant temperature. The plants
were harvested two hours after dawn (LD) or, after shifting the plants to
constant light conditions were harvested at ZT26 (LL) or ZT38 (ZT14).
ChIP-Seq was performed and the resulting reads were mapped to the Col-0
genome. Peaks were called using HOMER and IDR.</p>

<h4>Samples</h4>

<p>This experiment includes 2 replicates of the LD samples. There are 3
replicates of the ZT26 (LL) samples. ZT26 (26 hours after zeitgeber time)
corresponds to 2 hours after dawn. Peaks were called for the LL samples and
LD samples.</p>

<p>The ZT38 sample (38 hours after zeitgeber time) correspond to 14 hours
after dawn. CCA1 is less abundant in the evening. The ZT38 sample had
minimal pull down and only one library was created. No peak calls were made
for the ZT38 (ZT14) sample.</p>

<p>The experiment included a single input sample.</p>

<h4>Contact</h4>

<p>For questions about this data set, please contact Colleen Doherty at
cjdohert@ncsu.edu or Steve Kay at stevekay@dornsife.usc.edu.</p>

<p>The peak files were converted to bed detail format for this quickload
site using a script called MakeBed (below). All other data processing steps
were carried out by the authors of the paper.</p>

	Name	Last modified	Size	Description
	Parent Directory		-
	Input.bam	2017-07-25 15:01	1.3G
	Input.bam.bai	2017-07-25 15:00	340K
	Input.ucsc.bedGraph.gz	2017-07-25 15:00	65M	Annotation or junction file
	Input.ucsc.bedGraph.gz.tbi	2017-07-25 15:01	108K	Tabix index file
	LD.peaks.bed.gz	2017-07-25 15:01	87K	Annotation or junction file
	LD.peaks.bed.gz.tbi	2017-07-25 15:01	13K	Tabix index file
	LD1.sort.bam	2017-07-25 15:01	2.0G
	LD1.sort.bam.bai	2017-07-25 15:01	260K
	LD1.ucsc.bedGraph.gz	2017-07-25 15:00	8.4M	Annotation or junction file
	LD1.ucsc.bedGraph.gz.tbi	2017-07-25 15:00	76K	Tabix index file
	LD2.sort.bam	2017-07-25 15:02	2.1G
	LD2.sort.bam.bai	2017-07-25 15:01	278K
	LD2.ucsc.bedGraph.gz	2017-07-25 15:02	18M	Annotation or junction file
	LD2.ucsc.bedGraph.gz.tbi	2017-07-25 15:00	88K	Tabix index file
	LL.peaks.bed.gz	2017-07-25 15:01	76K	Annotation or junction file
	LL.peaks.bed.gz.tbi	2017-07-25 15:01	13K	Tabix index file
	LL1.sort.bam	2017-07-25 15:01	654M
	LL1.sort.bam.bai	2017-07-25 15:01	249K
	LL1.ucsc.bedGraph.gz	2017-07-25 15:01	4.5M	Annotation or junction file
	LL1.ucsc.bedGraph.gz.tbi	2017-07-25 15:01	71K	Tabix index file
	LL2.sort.bam	2017-07-25 15:00	1.5G
	LL2.sort.bam.bai	2017-07-25 15:02	250K
	LL2.ucsc.bedGraph.gz	2017-07-25 15:01	4.1M	Annotation or junction file
	LL2.ucsc.bedGraph.gz.tbi	2017-07-25 15:00	66K	Tabix index file
	LL3.sort.bam	2017-07-25 15:01	715M
	LL3.sort.bam.bai	2017-07-25 15:00	237K
	LL3.ucsc.bedGraph.gz	2017-07-25 15:00	1.5M	Annotation or junction file
	LL3.ucsc.bedGraph.gz.tbi	2017-07-25 15:00	63K	Tabix index file
	ZT14.sort.bam	2017-07-25 15:02	139M
	ZT14.sort.bam.bai	2017-07-25 15:01	227K
	ZT14.ucsc.bedGraph.gz	2017-07-25 15:01	186K	Annotation or junction file
	ZT14.ucsc.bedGraph.gz.tbi	2017-07-25 15:00	47K	Tabix index file
	annotsEntriesToAdd.xml	2017-07-25 15:02	4.6K