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| Status |
Public on Feb 03, 2014 |
| Title |
DNaseI-seq 2d biological reps 1 and 2 |
| Sample type |
SRA |
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| Source name |
plant inflorescences
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Landsberg
genotype/variation: pAP1:AP1:GR ap1 cal
agent: DEX
time: 2 days
tissue: inflorescences
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| Treatment protocol |
pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 mM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Inflorescences were harvested before treatment and 2, 4 and 8 days after induction.
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| Growth protocol |
All plants were grown at 20 °C under long day condition (16 h light, 8 h dark) on rockwool.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei isolation from 0.2 g of plant material was performed according to (Zhang et al., 2007) and DNA digestion was performed according (Hesselberth et al., 2009). Two biological replicates for each time point were sequenced on Illumina HighSeq2000.
Libraries were prepared using the Illumina according to manufacture's instructions of the sample prep kit from Illumina
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
2 biological replicates
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| Data processing |
Basecalls was performed using CASAVA version 1.8
Reads were aligned to the Arabidopsis thaliana genome (TAIR10, http://www.arabidopsis.org/) using Bowtie (Langmead et al., Genome Biology 2009) version 0.12.7, allowing up to 3 mismatches.
From the aligned reads reported, uniquely mapped reads were processed according to the procedure described in (Bardet et al., Nature protocols 2012).
Target genes for genomic regions of interest were retrieved using the function 'distance2Genes' in the Bioconductor package CSAR (Muino et al., Plant Methods 2011) for genes annotated in TAIR10
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited .txt file containing peak definitions: Peak_name, chromosome, peak start, peak end, peak summit, -log10(p-value), fold enrichment, -log10(q-value) and list of genes with the peak at located at 3kb upstream to 1kb downstream of the gene.
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| Submission date |
May 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Alice Pajoro |
| E-mail(s) |
[email protected]
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| Organization name |
Wageningen University
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| Street address |
Droevendaalsesteeg 1
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| City |
Wageningen |
| ZIP/Postal code |
6708lt |
| Country |
Netherlands |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE46894 |
Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq] |
| GSE46987 |
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development |
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| Relations |
| BioSample |
SAMN02143033 |
| SRA |
SRX277580 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1139913_DNase_I_2days.txt.gz |
153.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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