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Sample GSM3949140 Query DataSets for GSM3949140
Status Public on Mar 13, 2020
Title STZ_AIR_ChIPseq_rep3
Sample type SRA
 
Source name Three day old etiolated seedlings
Organism Arabidopsis thaliana
Characteristics tissue: Three day old etiolated seedlings
genotype: Col-0 STZ::STZ-Ypet
treatment: Air 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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description ChIPSeq_Sample 37
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.
 
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 SAMN12308543
SRA SRX6460110

Supplementary file Size Download File type/resource
GSM3949140_HAL_1424_AT1G27730_AIR_MGLCHIP41_160315_summits.bed.gz 425 b (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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