|
| Status |
Public on Sep 15, 2024 |
| Title |
Nmus_smooth_2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial biofilm,pelleted
|
| Organism |
Neisseria musculi |
| Characteristics |
strain: NW746
morphotype: smooth
genotype: wild-type
|
| Treatment protocol |
One ml of RNA laterTM solution was added to each plate and biofilms were scraped and collected in sterile microfuge tubes. The tubes were centrifuged for 3 min at 14, 000 x g at 4 °C to pellet the cells.
|
| Growth protocol |
Strains were grown as static biofilms in 90 mm petri dishes for 16 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each pellet was suspended inTris EDTA buffer pH 8.0 containing of lysozyme, incubated for 5 min at room temperature with vortexing every 1 min. RNA extraction was done using RNeasy Mini kit (Qiagen) and contaminating DNA was removed by DNase digestion using the Turbo DNA-free kit (Invitrogen).
Libraries were constructed using Illumina Truseq Stranded mRNA Library Prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
total RNA,rRNA depleted
|
| Data processing |
Illumina reads were mapped using Bowtie to Neisseria musculi strain NW831, GenBank CP060414.1. Gene expression counts for all samples were estimated using HTseq. Counts were then tabularized and imported into R studio for analyses. Differentially expressed genes were analyzed using the DESeq2 R package. Expression values for each gene were calculated as TPM values. The TPM values are presented in the excel files.
Important note: Two separate analyses were performed. One analysis was done using two replicates for each condition (GSM5582130 and GSM5582131 [smooth] and GSM5582134 and GSM5582135 [rough]) and one analysis was done using all three replicates per condition.
Samples include the normalized data for the two replicate analysis and the three replicate analysis.
Genome_build: The reference genome used for the analysis was based on GenBank CP060414.1
Supplementary_files_format_and_content: TPM values. The DESeq output files for each analysis are available on the series record.
|
| |
|
| Submission date |
Sep 15, 2021 |
| Last update date |
Sep 15, 2024 |
| Contact name |
Nathan John Weyand |
| E-mail(s) |
weyand@ohio.edu
|
| Phone |
740-593-0191
|
| Organization name |
Ohio University
|
| Department |
Biological Sciences
|
| Lab |
Weyand
|
| Street address |
7 Depot Street
|
| City |
Athens |
| State/province |
OH |
| ZIP/Postal code |
45701 |
| Country |
USA |
| |
|
| Platform ID |
GPL30638 |
| Series (1) |
| GSE184230 |
In vitro and transcriptomic variation in Neisseria musculi morphotypes correlate with colonization variability and persistence in vivo |
|
| Relations |
| BioSample |
SAMN21445317 |
| SRA |
SRX12199937 |
