|
| Status |
Public on Sep 22, 2021 |
| Title |
wt_N_1 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type strain without zinc treatment rep1
|
| Organism |
Mycobacterium tuberculosis variant bovis BCG |
| Characteristics |
genotype: wildtype
|
| Treatment protocol |
Wild-type or cmtR-deleted strains of Mycobacterium bovis BCG were cultured in 7H9 medium with shaking at 160 rpm at 37 ? until the mid-logarithmic phase. Then, the cells were treated with 0 mM and 0.5 mM Zinc for 24 h, respectively, and harvested from each sample (each strain in three biological replicates).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAprep Pure Cell/Bacteria Kit (Qiagen, Germany) according to the manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mycobacterium_tuberculosis_variant_bovis_BCG_Pasteur_1173P2 whole genome using bowtie2 v2-2.0.5
Fragments per kilobase of exon per million fragments mapped(FPKM). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium tuberculosis variant bovis BCG Pasteur 1173P2
Supplementary_files_format_and_content: gene_fpkm.xls file includes FPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 12, 2021 |
| Last update date |
Sep 22, 2021 |
| Contact name |
Liu Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Life Science and Technology
|
| Lab |
State Key Laboratory of Agricultural Microbiology
|
| Street address |
No.1 Shizishan Street, Hongshan District, Wuhan, Hubei Province, China
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL30387 |
| Series (1) |
| GSE179966 |
Next Generation Sequencing Facilitates Quantitative Analysis of Zinc treated Wild-Type or CmtR-deleted strains of Mycobacterium bovis BCG Transcriptomes |
|
| Relations |
| BioSample |
SAMN20178000 |
| SRA |
SRX11417021 |
