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| Status |
Public on May 25, 2022 |
| Title |
mycelia - H3K4me3_set1_rep2_IP |
| Sample type |
SRA |
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| Source name |
mycelia
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| Organism |
Ustilaginoidea virens |
| Characteristics |
isolate: mutant UvKmt2
growth_condition: potato sucrose agar
treatment: H3K4me3
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| Treatment protocol |
The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.
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| Growth protocol |
The WT and all transformed strains derived from the WT were cultured on PSA (potato sucrose agar, potato 200 g/L, sucrose 20 g/L and agar 20 g/L) plates at 28°C under dark conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After the cross-linking was stopped with 125 mM glycine, the mycelia were ground in liquid nitrogen and suspended with the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM sodium butyrate, 400 mM sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol and 1 × proteinase inhibitors). The precipitated nuclei were treated with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM sodium butyrate, 0.1% deoxycholate, 1% Triton X-100, 0.1% SDS, 1mM PMSF and 1 × Roche protease inhibitor cocktail) and broken into DNA fragments between 200 -500 bp using Diagenode Vioruptor. After pretreating with 10 μL protein A beads (Thermofisher, 10001D), the supernatant was incubated with anti-H3K4me3 antibody (Abcam, ab1012) for 1 h. Then 20 μL protein A beads were added into the above reaction system to bind anti-H3K4me3 antibody. 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).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| 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) , and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (Version 1.9).
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: UV-8b
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph
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| Submission date |
May 18, 2022 |
| Last update date |
May 25, 2022 |
| Contact name |
Chuyu Lin |
| E-mail(s) |
[email protected]
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| Phone |
+86 13588301175
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| Organization name |
Zhejiang University
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| Department |
College of Agriculture and Biotechnology
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| Lab |
Tao’s Lab
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| Street address |
866#, Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL27887 |
| Series (1) |
| GSE203326 |
Genome-wide mapping of H3K4 tri-methylation in ΔUvkmt2 mutant strain of Ustilaginoidea virens |
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| Relations |
| BioSample |
SAMN28534738 |
| SRA |
SRX15337202 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6166515_set1-2-IP_sorted_mapped_TagDir.ucsc.bedGraph.gz |
104.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM6166515_set1_vs_background_H3K4me3_DE_Peaks.txt.gz |
171.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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