|
| Status |
Public on Mar 04, 2019 |
| Title |
08_Msm_916_uninduced |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Mycolicibacterium smegmatis |
| Characteristics |
strain: mc2155
genotype: MSM pDTCF-MSMEG_0916 uninduced
time point: 4 hour
agent: 0 ng/ml ATc
|
| Treatment protocol |
induced samples treated with 100 ng/ml Atc for overexpression of MSMEG_0916
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biological triplicate cultures of M. smegmatis containing pDTCF-MSMEG_0916 in 7H9 media, were grown as 10 mL cultures in 50mL flasks, at 37ºC, 5%CO2, for 4 hours in the presence or absence of 100 ng/ml anhydrotetracycline. After harvesting, cells were spun down, resuspended in Trizol, and frozen at -80 until RNA isolation. Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using the Direct-zol RNA MicroPrep kit (Zymol Research) according to manufacturer’s instruction with on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium smegmatis mc2155 ASM1500v1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample
|
| |
|
| Submission date |
Jun 20, 2018 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Eliza Peterson |
| Organization name |
Institute for Systems Biology
|
| Lab |
Baliga
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL25202 |
| Series (2) |
| GSE116027 |
Path-seq identifies essential mycolate remodeling program for mycobacterial adaptation in host cells [RNA-seq] |
| GSE116085 |
An essential mycolate remodeling program for mycobacterial adaptation in host cells |
|
| Relations |
| BioSample |
SAMN09460737 |
