|
| Status |
Public on Apr 03, 2018 |
| Title |
hypoxia_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hypoxia
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
genotype: CDC1551
stress condition: hypoxia
|
| Growth protocol |
Bacteria were grown to log phase in rich medium (7H9) and reimmersed in PBS/0.05% Tween-80 (PBS), Dubos-Tween-Albumin (hypoxia), or 7H9 medium without phosphate (Phosphate-depleted). See Methods section of papers for additional details.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were spun down at 4C and immersed in Trizol. Mixture was then beat-beated for 4 minutes. Chloroform:Isoamyl (24:1) was used to extract the RNA. Turbo DNAse was used to remove remaining gDNA.
RNA was converted to cDNA and an NGS library was constructed using the Encore Complete Prokaryotic RNA-Seq DR Mulitplex Systems 1-8 and 9-16 kit from NuGen (Part No. 0326 and 0327).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calls performed using Casava v1.8.2.
EDGE-pro v1.3.1 with default settings was used to align reads to the CDC1551 genome and output *.rpkm files. bash was used to concatenate the multiple files (one per contig) into a single *.rpkm file per sample. The edgeToDeseq.perl script provided with EDGE-pro was used to combine these *.rpkm files into a single deseqFile (for input into DESeq2).
R with DESeq2 v1.16.1 was used to compute log2FC and p-values for all comparisons.
Genome_build: Mycobacterium tuberculosis CDC1551 (GenBank assembly accession: GCA_000669715.1)
Supplementary_files_format_and_content: *.rpkm files are plain text and contain counts of reads mapping to each gene (and RPKM) as generated by EDGE-pro (concatenated with bash). *.csv files are plain text (comma-separated-values format) generated by custom R scripts with DESeq2. The *.csv files report high-level comparisons between the stress conditions (PBS, hypoxia, phosphate-depletion) and rich medium condition (7H9) along with other useful information.
|
| |
|
| Submission date |
Oct 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Petros Constantine Karakousis |
| E-mail(s) |
petros@jhmi.edu
|
| Phone |
4105028233
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Department of Infectious Diseases
|
| Lab |
Center for TB Research
|
| Street address |
733 North Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21202 |
| Country |
USA |
| |
|
| Platform ID |
GPL18768 |
| Series (1) |
| GSE104599 |
Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance |
|
| Relations |
| BioSample |
SAMN07738090 |
| SRA |
SRX3243869 |
