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Status |
Public on Mar 13, 2020 |
Title |
STZ_JA_2hr_ChIPseq_rep1 |
Sample type |
SRA |
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|
Source name |
Three day old etiolated seedlings
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: Three day old etiolated seedlings genotype: Col-0 STZ::STZ-Ypet treatment: JA treatment for 2h chip antibody: Goat anti-GFP (from David Dreschel)
|
Treatment protocol |
Air or JA treated for 2h
|
Growth protocol |
Seeds were sterilised using bleach then plated on 1.2% agar Linsmaier and Skoog medium plates. Stratification was at 4 celsius in the dark for three days. Plates were exposed to the light at room temperature for 2 h to induce germinaiton, then returned to the dark at 22 celsius. Plates were incubated for three days, after which treatments were conducted.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Conducted as described in O'Malley et al. 2016 (doi: 10.1016/j.cell.2016.04.038) and Chang et al. 2013 (10.7554/eLife.00675). Harvested seedlings were crosslinked with 1% formaldehyde under vacuum for 20 minutes then snap-frozen in liquid nitrogen. Nuclei were extracted from frozen, ground seedlings according to Qiao et al. 2016 (10.1126/science.1225974) then sonicated according to Chang et al .2016 using a Diagenode bioruptor to yield an average DNA fragment size of approximately 150-300 bases. Transcription-factor DNA complexes were isolated by immunoprecipitation with polyclonal anti-GFP raised in goat from David Dreschel (Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany) or, for non-transgenic controls, IgG from goat. These complexes were then retrieved using Protein G Dynabeads (Life Technologies). Conducted as described in Chang et al. 2013 (10.7554/eLife.00675) with one modification. Size selection was performed on SPRI beads, instead of on gels, with upper and lower cut-offs to yield a fragment size-range of 150-500 nucleotides. Sequencing was conducted on the Illumina HiSeq 2500 platform.
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
ChIPSeq_Sample 38
|
Data processing |
base-calling using RTA 2.7.7 Reads were aligned by bowtie2 v2.0.5 using only the first 65 bases against the Arabidopsis thaliana TAIR10 reference genome. Shiftsize was calculated using phantompeakqualtools and default parameters Peaks called with MACS2 version 2.0.10 with parameters "callpeak -c --format=SAM --gsize=1.19e8 -p 99e-2 --nomodel --shiftsize=[from phantompeakqualtools] --down-sample --call-summits". A concatenated file of all non-transgenic control IP reads was used as the control in peak calling ChIPPeakAnno was used for annotation. gene ontology enrichment was assessed using clusterProfiler Genome_build: TAIR10 Supplementary_files_format_and_content: Summit region output created by MACS2 in bed format.
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Submission date |
Jul 18, 2019 |
Last update date |
Mar 14, 2020 |
Contact name |
Joseph R Ecker |
E-mail(s) |
ecker@salk.edu
|
Phone |
8584534100
|
Organization name |
HHMI-Salk-Institute
|
Department |
Genomic Analysis Laboratory
|
Lab |
Ecker lab
|
Street address |
10010 North Torrey Pines Road
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL17639 |
Series (1) |
GSE133408 |
The jasmonate-response genome regulatory program is defined by the direct targets of transcription factors MYC2 and MYC3, chromatin modification and gene expression changes |
|
Relations |
BioSample |
SAMN12308542 |
SRA |
SRX6460111 |