|
| Status |
Public on May 24, 2023 |
| Title |
HN878 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HN878
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: HN878
genotype: wild type
morphotype: rough
|
| Growth protocol |
Bacterial strains were cultured in triplicate in 30 mL of Middlebrook 7H9 liquid medium (Difco) containing ADC (0.2% dextrose, 0.5% BSA fraction V, 0.0003% beef catalase) and 0.05% Tween 80 at 37°C without agitation. Cultures were harvested when reaching the exponential phase of growth with a final OD at 600nm between 0.5 and 0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using a Trizol RNA isolation protocol (Invitrogen) and a mechanical lysis in Lysing Matrix B tubes (MP Biomedicals, Fisher Scientific) via rapid agitation in a Bead Mill 24 Homogenizer (Fisherbrand, Thermo Fisher Scientific). RNA extracts were then treated with the Turbo DNase (Ambion) and cleaned up using the RNeasy mini kit (Qiagen). RNA integrity and quality was monitored with a Bioanalyzer RNA nano assay (Agilent Technologies) to ensure that the RNA Integrity Number (RIN) was greater than 9.
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 |
HN878_1
|
| 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, and differential expression analysis was performed using a FDR of 0.05.
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 |
Apr 13, 2023 |
| Last update date |
May 24, 2023 |
| 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 |
GPL33344 |
| Series (1) |
| GSE229680 |
Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli |
|
| Relations |
| SRA |
SRX19961298 |
| BioSample |
SAMN34175027 |
