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Sample GSM3466753 Query DataSets for GSM3466753
Status Public on Mar 19, 2020
Title SOB3-GFP ChIP replicate 2
Sample type SRA
 
Source name SOB3-GFP ChIP
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia (Col-0)
genotype/variation: ProSOB3::SOB3-GFP sob3-4
age: 14 days old
time of harvest: ZT4
tissue: whole plant
chip antibody: Anti-GFP antibody - ChIP Grade (ab290, Abcam)
Growth protocol 22°C constant temperature with long-day photoperiod (16h light/8h darkness) under white fluorescent light (~35-55 μmol/m2/sec) on sucrose-free 1X MS medium containing 0.8% Gelzan CM
Extracted molecule genomic DNA
Extraction protocol Frozen samples were ground using mortar and pestle. Ground tissue was mixed with fixation buffer and formaldehyde added to 1% final concentration. Fixation was stopped after 10 minutes by addition of glycine. Solution was filtered twice through miracloth and then centrifuged to pellet cells. Pellet was resuspended in extraction buffer containing 1% Triton X-100 to lyse cells and centrifuged to pellet nuclei. Pellet with nuclei was resuspended in nuclei separation buffer containing 1.7 M sucrose and centrifuged to separate nuclei from debris. Nuclei were resuspended in nuclei lysis buffer containing 1% SDS and flash frozen twice in liquid nitrogen in order to lyse nuclei. Subsequently, chromatin was sonicated in a Bioruptor (Diagenode) to an average size of approximately 200-400 bp.
Libraries were constructed from input or ChIPed DNA using the TruSeq ChIP Library Preparation Kit (Illumina) according to manufacturer's instructions, with the exception of the "Purify Ligation Products" step, which was skipped. Library quality was validated using the Agilant 2200 TapeStation with D1000 ScreenTape & Reagents. Qubit dsDNA HS Assay Kit was used with the Qubit 2.0 Fluorometer (Invitrogen) for quantitation of DNA.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description ChIP-seq for SOB3-GFP replicate 2
Data processing Generation of fastq files: Raw data files (bcl format) were converted to fastq files by BaseSpace Sequence Hub (Illumina) or bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 0.12.9 with the setting "-m 1".
Peak-calling: Peaks were called using the "callpeak" command in MACS2 with the following parameters: "-g 119480000 -m 2 50 -B --SPMR -q 0.05".
Generation of bigwig files: Fold-enrichment bdg format files were generated by using the treatment pileup and control lambda output files generated from "callpeak" as inputs for the MACS2 "bdgcmp" command with the setting "-m FE". The bdg files were converted to bigwig format using the "bedGraphToBigWig" program (UCSC).
Genome_build: TAIR10
Supplementary_files_format_and_content: Fold enrichment bigwig files (ChIP vs Input); peak calls in BED format from MACS2
 
Submission date Nov 13, 2018
Last update date Mar 19, 2020
Contact name David Seth Favero
E-mail(s) davefavero@gmail.com
Phone +81-45-503-9575
Organization name RIKEN
Department CSRS
Lab Keiko Sugimoto
Street address 1-7-22 Suehirocho, Tsurumi-ku
City Yokohama
State/province International
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL19580
Series (2)
GSE122455 AT-hook transcription factors repress petiole growth by antagonizing PIF4 [ChIP-seq]
GSE122456 AT-hook transcription factors repress petiole growth by antagonizing PIF4
Relations
BioSample SAMN10414059
SRA SRX5001349

Supplementary file Size Download File type/resource
GSM3466753_SOB3-GFP_ChIP_Rep2.narrowPeak.gz 114.9 Kb (ftp)(http) NARROWPEAK
GSM3466753_SOB3-GFP_ChIP_Rep2_FE.bw 205.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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