|
| Status |
Public on Jun 16, 2021 |
| Title |
ΔwhiB4-0_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ΔwhiB4-0
|
| Organism |
Mycobacterium marinum |
| Characteristics |
treatment: 7 days hypoxia
genotype: whiB4 mutant
|
| Treatment protocol |
cultures were sealed and incubated with slow stirring in the dark at 30°C in a conical flask for 7 days. Samples were taken 0, 0.5, 4, 24, and 48 h after reaeration
|
| Growth protocol |
Cultures of M. marinum were grown to mid-log phase (OD600 0.4–0.45), and then transferred to a hypoxia culture based on the Wayne model with a headspace ratio of 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) and purifed using the RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions.
Purifed RNA was used to construct cDNA library according to the TruSeq Stranded RNA LT Guide from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RCM_0_FPKM
|
| Data processing |
High-throughput sequencing was carried out on an Illumina HiSeq 2500 system according to the manufacturer’s instructions (Illumina HiSeq 2500 User Guide)
The raw reads were fltered by Seqtk and then mapped to the M. marinum M strain reference sequence (GenBank GCA_000018345.1) using Bowtie2 (version: 2–2.0.5)
Counting of reads per gene was performed using HTSeq followed by TMM (trimmed mean of M-values) normalization
Genome_build: M. marinum M strain reference sequence (GenBank GCA_000018345.1)
Supplementary_files_format_and_content: Excel file include FPKM values for all differential expression genes during reaeration between wild type and whiB4 mutant strain
|
| |
|
| 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) |
| GSE178188 |
WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish [bacteria RNA seq] |
| GSE178191 |
WhiB4 is required for the reactivation of latent infection of Mycobacterium marinum in zebrafish |
|
| Relations |
| BioSample |
SAMN19707154 |
| SRA |
SRX11145519 |
