|
Status |
Public on May 23, 2023 |
Title |
WT-7H9-1 |
Sample type |
SRA |
|
|
Source name |
Bacterial cell
|
Organism |
Mycobacterium tuberculosis H37Rv |
Characteristics |
cell type: Bacterial cell genotype: WT treatment: Standard 7H9
|
Growth protocol |
Standard 7H9 or 50 µM dipyridyl-treated 7H9, grown at 37 degrees shaking for 4 divisions
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted using Trizol and Zymo Direct-zol kit, NEB DNase I treatment, cleanup with Zymo Clean and Concentrate Kit Libraries were prepped using NEB Ultra II Directional RNA Library Prep Kit for Illumina following manufacturers' instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
|
|
Description |
WT-7H9-1
|
Data processing |
Reads were mapped to the M. tuberculosis H37Rv genome using Burrows-Wheeler Alignment Read-count normalization and statistical analysis of differentially expressed genes (DEGs) were calculated using DESeq2 Assembly: Genbank accession NC_000962.3 Supplementary files format and content: Tab delimited text file with raw read counts for all samples
|
|
|
Submission date |
Apr 11, 2023 |
Last update date |
May 23, 2023 |
Contact name |
Christopher Sassetti |
Organization name |
University of Massachusetts Chan Medical School
|
Street address |
55 Lake Ave North
|
City |
Worcester |
State/province |
MA |
ZIP/Postal code |
01655 |
Country |
USA |
|
|
Platform ID |
GPL29823 |
Series (1) |
GSE229446 |
The response of WT, ∆rip1, and ∆sigL strains of Mycobacterium tuberculosis to dipyridyl treatment |
|
Relations |
SRA |
SRX19935275 |
BioSample |
SAMN34146815 |