|
| Status |
Public on Dec 15, 2021 |
| Title |
T72_INH_0x_C |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain: H37Rv
drug treatment: no drug
treatment time: 72 hour
|
| Treatment protocol |
Treatment with no drug or Isoniazid at 0.18 or 1.8 μg/mL for 4, 24 or 72 h
|
| Growth protocol |
Samples grown in 7H9-rich media at 37 degrees C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In three biological replicates, M. tuberculosis cultures with or without drug treatment were harvested at 4, 24 or 72 h. Cells pellets were spun down and immediately frozen in liquid nitrogen and stored at -80 degrees C until RNA isolation. Cell pellets 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 phenol-chloroform extraction method, followed by 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 |
| |
|
| Description |
T72-0x-C_S12
|
| 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 tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM and read counts for each sample
|
| |
|
| Submission date |
Jan 26, 2021 |
| Last update date |
Dec 15, 2021 |
| 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 |
GPL22688 |
| Series (2) |
| GSE165581 |
Mycobacterium tuberculosis transcriptional response to Isoniazid |
| GSE165673 |
Transcriptome profiling of Mycobacterium tuberculosis H37Rv to primary drugs |
|
| Relations |
| BioSample |
SAMN17595036 |
| SRA |
SRX9951421 |
