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Sample GSM4933293 Query DataSets for GSM4933293
Status Public on Jun 07, 2021
Title T1, biological replicate1
Sample type SRA
 
Source name Exponential phase bacterial culture of Staphylococcus aureus treated by TRQ
Organism Staphylococcus aureus
Characteristics treatment: TRQ-treated in lB medium
phase: Exponential phase
genotype/variation: wild type
Treatment protocol Bacterial cells were collected and kept on ice to extract RNA.
Growth protocol Bacterial cells were grown for 12 hr at 37C.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description Gene expression data from TRQ-treated Staphylococcus aureus grown till exponential phase
Data processing The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT.
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method Bowtie2 and RSEM were used for differential expression analysis
Genome_build: Staphylococcus aureus COL
 
Submission date Nov 24, 2020
Last update date Jun 07, 2021
Contact name Qing Wei
E-mail(s) vubwqing@hotmail.com
Organization name Institute of Microbiology, Chinese Academy of Sciences
Lab Biofilm Research Group
Street address NO.1 Beichen West Road, Chaoyang District
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL29442
Series (1)
GSE162107 Transcriptional responses of Tanreqing treated Staphylococcus aureus cells
Relations
BioSample SAMN16885738
SRA SRX9569480

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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