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Sample GSM5580026 Query DataSets for GSM5580026
Status Public on Nov 09, 2021
Title WT2
Sample type SRA
 
Source name S. Typhimurium culture
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics strain: 14028s
growth phase: Logarithmic
plasmid: none
Growth protocol Overnight cultures in M9 minimal medium (0.4% glucose, 0.2% casitone) were subcultured 1:100 in the same medium and grown at 37 degrees C with aeration; samples were collected at OD600 ~0.5.
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNAsnap method, treated with Dnase I, and RNA quality checked as described in Kurasz et al. 2018. J. Bacteriol. 200(23):e00476-18.
Extracted RNA was sent on dry ice to the Microbial Genome Sequencing Center (Pittsburgh, PA, USA) where all following steps, incuding data processing, were completed. 300 ng RNA for each sample were subjected to ribosomal RNA depletion using the Ribo-Zero™ Plus rRNA Removal Kit and complementary DNA (cDNA) libraries were then prepared with the Illumina Stranded RNA library preparation kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Description Total RNA depleted of rRNA
Data processing Each sample was sequenced to an approximate depth of 12 million reads.
Quality control and adapter trimming was performed with bcl2fastq (ver. 2.20.0.445) on default parameters.
RNA-Seq reads were mapped to the GenBank accession CP001363.1 using HISAT2 (version 2.2.0) on default parameters + '--very-sensitive'
Read quantification was performed using Subread’s featureCounts functionality (ver. 2.0.1) on default parameters + '-Q 20'
Read counts loaded into R (ver. 4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm (ver. 1.14.5) with default parameters.
Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (ver. 1.14.5) with default parameters.
Genome_build: The NCBI index (CP001363.1) was used for gene annotation. https://www.ncbi.nlm.nih.gov/nuccore/CP001363.1/
Supplementary_files_format_and_content: Table with raw counts for each locus and sample
Supplementary_files_format_and_content: A table containing normalized read counts for each sample (in columns) and each annotated transcript (in rows). Includes statistics for differential expression between WT samples and the 'rna' deletion strain.
 
Submission date Sep 15, 2021
Last update date Nov 09, 2021
Contact name Emily Weinert
E-mail(s) eew5225@psu.edu
Organization name Pennsylvania State University
Department Biochemistry and Molecular Biology
Street address 306 Althouse Laboratory
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL30637
Series (1)
GSE184189 Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide phosphodiesterase (CNPase) in Salmonella Typhimurium 14028s (Salmonella) I.
Relations
BioSample SAMN21441936
SRA SRX12194869

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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