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Sample GSM6107522

Query DataSets for GSM6107522

Status

Public on Dec 19, 2022

Title

Staphylococcus aureus, ArlRS-, glucose+, Replicate 2

Sample type

SRA

Source name

bacterial liquid culture

Organism

Staphylococcus aureus

Characteristics

strain: Newman
cell type: bacterial liquid culture
genotype: ArlRS-
treatment: glucose+

Extracted molecule

total RNA

Extraction protocol

RNA was isolates using LETS buffer.
Ribosomal RNA was removed with the Ribozero kit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

arlRS.KO.TSB.Replicate.2

Data processing

Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adapters were trimmed from the 3' end of reads using Trimmomatic. Sequences matching the first 33 nt of the adapters used in library preparation were trimmed.
Rockhopper v2.0.3, with kentUtils v353 and SAMtools v1.9, was used for aligning reads to the genome, generating transcript counts, and predicting operons.
TMM normalization of transcript counts was performed with edgeR v3.34.0. Transcripts were filtered if they did not have at least 0.5 counts per million in all three samples of at least one experimental group. TMM normalization was re-done after filtering.
Assembly: GCF_000010465.1_ASM1046v1
Supplementary files format and content: Log-counts-per-million values after filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.
Supplementary files format and content: Raw counts before filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.

Submission date

May 05, 2022

Last update date

Dec 19, 2022

Contact name

Thomas E Kehl-Fie

Organization name

University of Illinois at Urbana-Champaign

Department

Microbiology

Street address

601 South Goodwin Avenue, MC-110