|
| Status |
Public on Apr 26, 2024 |
| Title |
mycelia - N1617GFP-ash1_rep3_IP |
| Sample type |
SRA |
| |
|
| Source name |
1617GFP/ash1
|
| Organism |
Pyricularia oryzae |
| Characteristics |
cell line: 1617GFP/ash1
cell type: mycelia
genotype: complement
treatment: GFP
|
| 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) or anti-H3K4ac (Active Motif, 39381) 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 |
Illumina NovaSeq 6000 |
| |
|
| 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).
Assembly: MG8
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph
|
| |
|
| Submission date |
Apr 25, 2024 |
| Last update date |
Apr 26, 2024 |
| Contact name |
mengting xu |
| E-mail(s) |
12116082@zju.edu.cn
|
| Phone |
19858122056
|
| Organization name |
mengtingxu
|
| Street address |
Zhejiang University
|
| City |
Hangzhou |
| State/province |
ZheJiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL32309 |
| Series (2) |
| GSE246678 |
Genome-wide mapping of a repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae |
| GSE246679 |
Repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae |
|
| Relations |
| BioSample |
SAMN41085392 |
| SRA |
SRX24372881 |
