|
| Status |
Public on Jun 16, 2021 |
| Title |
0h_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
mycobacteria marinum 1218R OE WhiB4
|
| Organism |
Mycobacterium marinum |
| Characteristics |
strain: mycobacteria marinum 1218R OE WhiB4
chip antibody: Anti-FLAG® M2 Magnetic Beads (Sigma)
treatment: 7 days hypoxia
|
| Growth protocol |
For ChIP-seq, 50 ml M. marinum cultures grown to log phase (OD600=0.8) under normoxia, or 100 ml M. marinum cultures grown under hypoxia (7 days) or 0.5 h after reaeration.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated bacteria and protein-DNA complexes were isolated with antibody.
DNA was purified using phenol–chloroform extraction.Sequencing was performed on the Illumina HiSeq platform. Coverage along the genome was calculated using Bowtie2(Langmead & Salzberg, 2012). Input genomic DNA without IP was used as a control.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
whiB4-0h.q0.05_peaks.narrowPeak.annotation
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the M.marinum genome assembly using Bowtie2
Data were filtered using the IDR
The peaks were significantly enriched in ChIP samples compared with input genomic DNA, as determined by MACS2(Zhang et al, 2008) with a cutoff of enrichment fold larger than 1.5, q-value<0.05.
Genome_build: NC_010612.1
Supplementary_files_format_and_content: narrowPeak
|
| |
|
| Submission date |
Jun 15, 2021 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Chen Lin |
| E-mail(s) |
[email protected]
|
| Organization name |
Fudan university
|
| Street address |
NO.2005 Songhu road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL21992 |
| Series (2) |
| GSE178190 |
WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish [ChIP-Seq] |
| GSE178191 |
WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish |
|
| Relations |
| BioSample |
SAMN19707176 |
| SRA |
SRX11145481 |
