|
| Status |
Public on Nov 09, 2021 |
| Title |
drna2 |
| Sample type |
SRA |
| |
|
| Source name |
S. Typhimurium culture
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: 14028s delta-rna
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 |
SAMN21441933 |
| SRA |
SRX12194866 |
