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| Status |
Public on Dec 04, 2023 |
| Title |
ChIP-Seq of Fusarium graminearum PH-1:H3K4me3_IP rep2 |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Fusarium graminearum PH-1 |
| Characteristics |
cell type: Mycelium
chip antibody: anti-H3K4me3 (abcam, ab8580)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
fresh mycelia of each sample were cross-linked with 1% formaldehyde for 10 min. Fixation was stopped with 125 mM glycine for 5 min. Subsequently, fixed culture samples were grounded in liquid nitrogen, and re-suspended in 10 ml of nuclear extraction buffer I (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 5mM β-mercaptoethanol, 0.1 mM PMSF, 1× protease inhibitor). DNA was sheared into 200~500 bp fragments with 30 s on and 6 min off by using a Covaris E220 DNA Sonicator (Covaris, Woburn, MA). After centrifugation, the pellets were suspended in 4 ml of nuclear extraction buffer II (1.7 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol and 1×protease inhibitor). Re-suspended samples were then centrifuged at 13,000 g for 15 min at 4 °C. The resulting pellets were re-suspended in 300 μL of nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1× protease inhibitor). Samples were then sonicated by two pulses of 30 s sonication and 1 min rest. After centrifugation at 4000 g for 5 min at 4°C, the supernatant was transformed into a clear tube, and was diluted with 10×ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0 and 167 mM NaCl). Immunoprecipitation was conducted using the monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody, anti-H3K18ac (39755, Active Motif Inc., Carlsbad, USA) antibody, or anti-H2BK11ac (ab240613, Abcam, Cambridge, UK) together with the protein A agarose beads (sc-2003, Santa Cruz, CA, USA). The beads were subsequently washed by low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE buffer. After washing, eluting, reversing the crosslinking, and removing all proteins, the resulting pellets were re-suspended in 50 μL of distilled water.
End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter; PCR amplification: PCR amplify the ligated products with specific primers; Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation. Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library; Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20.
Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters.
The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools.
BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9).
Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1
Supplementary files format and content: BPM were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.
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| Submission date |
Sep 22, 2022 |
| Last update date |
Dec 04, 2023 |
| Contact name |
zhao xiao zhen |
| E-mail(s) |
zhaoxiaozhen@ahau.edu.cn
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| Phone |
17768116791
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| Organization name |
Anhui Agricultural University
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| Street address |
Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China
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| City |
Hefei |
| ZIP/Postal code |
230036 |
| Country |
China |
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| Platform ID |
GPL32260 |
| Series (2) |
| GSE213961 |
Bivalent histone modification of BCG1 enables fungal pathogen to evade host immunity (ChIP-Seq) |
| GSE213962 |
Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion |
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| Relations |
| BioSample |
SAMN30964082 |
| SRA |
SRX17675955 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6597004_ChIP-seq_of_H3K4me3_ip2_log2BPM.bw |
27.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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