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Sample GSM5852332 Query DataSets for GSM5852332
Status Public on Feb 20, 2022
Title P. oryzae mycelia - H3K27me3_WT_rep2_IP
Sample type SRA
 
Source name mycelia
Organism Pyricularia oryzae
Characteristics isolate: wild type
growth_condition: complete medium
tissue: mycelia
antibody: anti-H3K27me3 (Abcam, ab6002)
Treatment protocol The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.
Growth protocol The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.
Extracted molecule genomic DNA
Extraction protocol The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Genome_build: MG8
Supplementary_files_format_and_content: peak text files; bedGraph
 
Submission date Feb 01, 2022
Last update date Feb 21, 2022
Contact name Chuyu Lin
E-mail(s) 12316066@zju.edu.cn
Phone +86 13588301175
Organization name Zhejiang University
Department College of Agriculture and Biotechnology
Lab Tao’s Lab
Street address 866#, Yuhangtang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platform ID GPL29717
Series (1)
GSE195863 Genome-wide mapping of H3K27 tri-methylation in PRC2 components of Pyricularia oryzae
Relations
BioSample SAMN25553324
SRA SRX14004480

Supplementary file Size Download File type/resource
GSM5852332_WT-2-IP_sorted_mapped_TagDir.ucsc.bedGraph.gz 48.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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