|
| Status |
Public on Sep 25, 2024 |
| Title |
H37Rv WT Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H37Rv
|
| Organism |
Mycobacterium tuberculosis H37Rv |
| Characteristics |
strain: H37Rv
genotype: wild type
batch: B2
replicate: R3
growth medium: 7H9
|
| Growth protocol |
Bacterial strains were cultured in triplicate in Middlebrook 7H9 broth supplemented with 10% OADC (oleic acid, albumin, dextrose, and catalase, BD) and 0.05% Tween 80 at 37°C. Cultures were harvested when reaching the exponential phase of growth with a final OD at 600 nm between 0.4 and 0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial strains were pelleted and bead beated in 1 mL of TRIzol (Life Technologies) with 0.1 mm silica beads (MP Biomedicals). After centrifugation, supernatants were extracted with chloroform, and RNA was precipitated with isopropanol and glycogen. RNA pellets were washed with 75% ethanol and dissolved in RNase-free water. Contaminant DNA was removed by incubation with DNase (TURBO DNA-free kit, Life Technologies). RNA cleanup was performed with the RNeasy Mini Kit (Qiagen). RNA integrity and quality were assessed with an Agilent Bioanalyzer device (Agilent Technologies).
RNA-seq libraries were prepared using the Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit (Illumina) and sequenced using a NextSeq 2000 device (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
H37Rv_3
|
| Data processing |
Reads were mapped against the reference genome of M. tuberculosis H37Rv using BWA-MEM v0.7.17-r1188 (parameters: -M; -h 1000).
Uniquely-mapped reads were extracted from the alignment maps according to the XA tag using the Python wrapper pysam v0.20.0 of SAMtools.
Reads mapped on gene features were counted using featureCounts v2.0.4 (parameters: -s 2; --primary).
Read counts were normalized and transformed by regularized logarithm using DESeq2 v1.38.3.
Assembly: Mycobacterium tuberculosis H37Rv AL123456.3
Supplementary files format and content: Tab-delimited matrix file containing the raw read counts for each gene (rows) for all samples (columns) determined by featureCounts
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Sep 25, 2024 |
| Contact name |
Mickael Orgeur |
| Organization name |
Institut Pasteur
|
| Street address |
25-28 rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL34550 |
| Series (2) |
| GSE269918 |
Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 [whiB6_RNA-seq] |
| GSE269919 |
Role of whiB6 and kdpDE in the successful multidrug-resistant clone Mycobacterium tuberculosis B0/W148 |
|
| Relations |
| BioSample |
SAMN41846233 |
| SRA |
SRX24935632 |
