|
| Status |
Public on Jun 02, 2021 |
| Title |
log_riboseq_2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro cultured bacterial cells
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: H37Rv
condition: Log phase
|
| Treatment protocol |
For oxidative stress, cells grown to log phase was harvested and transferred to fresh 7H9 media containing 50µM cumene hydroperoxide and incubated at 37ºC for 1 hour. For pH stress log phase cells were harvested and transferred to fresh 7H9 media whose pH was adjusted to 4.5 and incubated for 1 hour at 37ºC.
|
| Growth protocol |
Mycobacterium tuberculosis H37Rv cells were grown to log hase (OD600 0.4-0.6) in 7H9 broth at 37ºC with shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells after treatment was harvested by rapid centrifugation followed by mechanical lysis in presence of a lysis buffer containing chloramphenicol. Lysate was cleared and digested with a combination of RNAse T1 (4U) and Mnase (4U) for 45 minutes at room temperature. Monosome fractions were isolated using sucrose gradient ultracentrifugation.
Library preparation was done exactly as described in Ingolia, N., Brar, G., Rouskin, S. et al. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534–1550 (2012). https://doi.org/10.1038/nprot.2012.086.
Others (Ribo-seq)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribosome profiling data
|
| Data processing |
Casava 1.7 for base calling
Reads were mapped to M. tb genome using Bowtie2.
P site phasing was done using custom scripts written in python 3.
Read counts per gene was calculated using HTseq-count
Genome_build: ASM19595v2
Supplementary_files_format_and_content: Read counts per gene
|
| |
|
| Submission date |
Jun 03, 2020 |
| Last update date |
Jun 02, 2021 |
| Contact name |
G Aneeshkumar Arimbasseri |
| E-mail(s) |
aneesh@nii.ac.in
|
| Phone |
+91 9971986746
|
| Organization name |
National Institute of Immunology
|
| Department |
Molecular Genetics Laboratory
|
| Lab |
Molecular Genetics Laboratory
|
| Street address |
Aruna Asaf Ali Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL22688 |
| Series (1) |
| GSE151718 |
Translatome analysis of Mycobacterium tuberculosis |
|
| Relations |
| BioSample |
SAMN15095254 |
| SRA |
SRX8464043 |
