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Sample GSM7163720 Query DataSets for GSM7163720
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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