|
Status |
Public on Aug 25, 2016 |
Title |
Starvation day4 rep2 |
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 |
S4-2_S5
|
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 |
SAMN03407391 |
SRA |
SRX956451 |