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Status |
Public on Mar 19, 2020 |
Title |
SOB3-GFP ChIP replicate 1 |
Sample type |
SRA |
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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)
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
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Description |
ChIP-seq for SOB3-GFP replicate 1
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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
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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 |
|
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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 |
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Relations |
BioSample |
SAMN10414060 |
SRA |
SRX5001348 |