|
| Status |
Public on Aug 25, 2016 |
| Title |
Starvation day4 rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Starvation day4_bacteria culture
|
| Organism |
Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 |
| Characteristics |
strain: Pasteur 1173P2
genotype/variation: wild type
treatment: Starvation 4 days
|
| Treatment protocol |
At mid-log growths, M. bovis BCG str. Pasteur 1173P2 cultures were pelleted, washed twice in Phosphate Buffered Saline (PBS) supplemented with 0.05% (v/v) tyloxapol and resuspended in the same solution. Cultures continued in roller bottles at 5 rpm and 37C.
|
| Growth protocol |
M. bovis BCG str. Pasteur 1173P2 were grown in roller bottles with 7H9 broth at 5 rpm and 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed by bead-beating in Trizol reagent (Invitrogen) and RNA purified with on-column DNaseI digest and PureLink miRNA spin columns (Ambion). The second PureLink miRNA spin column depletes tRNA. rRNA is depleted using the Ribo-ZeroTM Magnetic Kit for Bacteria (Epicentre, Illumina) as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq® RNA Sample Preparation v2 kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
S4-3_S6
|
| Data processing |
Illumina Offline BaseCaller1.9.3 software used for basecalling.
Sequence reads were mapped to NC_008796.fasta whole genome using BWA-MEM algorithm
Gene expression was calculated as gene-wised coverage of the sequencing reads
Genome_build: NC_008796.fasta;gi|121635883|ref|NC_008769.1|
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
May 19, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
|
| Organization name |
MIT
|
| Department |
Koch Institute
|
| Lab |
Bioinformatics Core
|
| Street address |
77 Massachusetts Ave
|
| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL19889 |
| Series (1) |
| GSE66883 |
Ketogenesis: An Achilles' heel of starvation-selected persistent mycobacteria |
|
| Relations |
| BioSample |
SAMN03407368 |
| SRA |
SRX956452 |
