|
| Status |
Public on Aug 21, 2021 |
| Title |
mst12_gfp_rep1_IP |
| Sample type |
SRA |
| |
|
| Source name |
liquid mycelium
|
| Organism |
Pyricularia oryzae |
| Characteristics |
strain: {delta}mst12:mst12-gfp
cell type: mycelium
background strain: Guy11
chip antibody: GFP-Trap® Agarose;monoclonal anti-Green Fluorescent Protein (GFP) single domain antibody (sdAb); Cat#gta-100; Chromotek
|
| Treatment protocol |
Two grams of mycelia were cross-linked with 1% formaldehyde for 15 min and followed by 5 mins of incubation with 125 mM glycine.
|
| Growth protocol |
ChIP seq carried out from mycelium cultures grown in CM for 48h. Mycelium cultures of Dhox7:hox73Xflag and Dmst12:Mst12-GFP. ChIP samples are after Chromatin Immunoprecipitation experiments. Input samples are Chromatin samples before IP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked mycelium samples were gound into fine powder and resuspended in Honda buffer
Libraries were prepared according to Illumina's instructions by BGI (Hong Kong)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped cleaned and aligned to M. oryzae genome v.8 using BWA aligner v. 0.5.7.
Peaks were identified by MACS2 version 2.1.1 66 with the following parameters: -g 41027733 -q 0.1 --bdg ---nomodel --extsize 180 --broad --broad-cutoff 0.1.
Sequences under the peaks were predicted ± 2kb flanks and analysed using Python
Genome_build: M. oryzae genome MG8 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002495.2)
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
Aug 21, 2021 |
| Last update date |
Aug 23, 2021 |
| Contact name |
Jitender Cheema |
| Organization name |
JIC
|
| Street address |
Colney lane
|
| City |
Norwich |
| ZIP/Postal code |
NR47UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL29553 |
| Series (1) |
| GSE182534 |
Hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzae |
|
| Relations |
| BioSample |
SAMN20923941 |
| SRA |
SRX11857189 |
