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Sample GSM5062170 Query DataSets for GSM5062170
Status Public on Feb 05, 2021
Title WT-1: wild type BCG
Sample type SRA
 
Source name bacteria
Organism Mycobacterium tuberculosis variant bovis
Characteristics tissue: Exponentially growing bacterial culture
genotype: Wild type
Growth protocol Exponentially growing bacterial cultures (OD600 0.4-0.6) were pelleted and washed once with 7H9/Tween-80
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from wild-type and mutant strains using TRIzol reagent (Invitrogen), followed by DNase I treatment.
Approximately 1-μg total RNA samples were treated by the Ribo-Zero rRNA removal procedure (Illumina) to enrichment for mRNA.
Approximately 1μg of RNA was used for library preparation using a ScriptSeq (v2) RNA-seq kit and high-throughput sequencing on an Illumina NextSeq platform.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing All raw sequence reads by RNA-Seq were initially pre-processed by Trimmomatic (v0.36) to trim the adaptor sequences and remove low-quality sequences.
The alignment results were input into Cufflinks (v2.2.1). Unless otherwise stated, the unit of expression level in our analyses is FPKM.
Cuffdiff (v2.2.1) was used to test for differential expression. We defined genes as differentially expressed using the following criteria: FPKM > 10 and FDR < 0.001. The data for visualization was generated by R (R Development Core Team, Vienna, Austria).
Supplementary_files_format_and_content: Table S2 Differential gene expression between wild type and the ΔTCR mutant
 
Submission date Feb 04, 2021
Last update date Feb 05, 2021
Contact name siyuan feng
E-mail(s) fsy3224502@gmail.com
Organization name Sun Yat-Sen University
Street address 74 zhongshan 2nd road
City Guang zhou
ZIP/Postal code 510080
Country China
 
Platform ID GPL29695
Series (1)
GSE166137 The involvement of Mycobacterium type III-A CRISPR-Cas system in oxidative stress and intracellular fitness
Relations
BioSample SAMN17776256
SRA SRX10020373

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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