|
| Status |
Public on Oct 09, 2022 |
| Title |
Co_6715_2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cell lysate
|
| Organisms |
Streptococcus sobrinus; Streptococcus mutans UA159 |
| Characteristics |
strain: UA159 + NIDR 6715
treatment: grown in coculture (TYG) to OD600 nm = 0.5
molecule subtype: enriched mRNA
|
| Treatment protocol |
Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.
|
| Growth protocol |
Bacterial cells used for extraction of RNA were grown in TYG medium, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.5)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen).
cDNA libraries were constructed by MiGS
RNA-Seq: single-ended short reads were obtained from a set of bar-coded cDNA libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
repeat 2 of 3
|
| Data processing |
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: FastQC
Step 4: Map with Bowtie2
Step 5: sort
Step 6: featurecounts (see our publication for details)
Assembly: Streptococcus mutans: NC_004350.2
Supplementary files format and content: Counts obtained from step 6: featurecounts, listed along side each open reading frame
Supplementary files format and content: Read counts for monoculture, coculture with NIDR 6715, 4646 and 14266, and quadculture conditions, in triplicate.
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Oct 09, 2022 |
| Contact name |
Justin Ray Kaspar |
| E-mail(s) |
[email protected]
|
| Phone |
6142923773
|
| Organization name |
The Ohio State University
|
| Department |
Biosciences
|
| Lab |
Kaspar
|
| Street address |
305 W 12th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL32730 |
| Series (1) |
| GSE209925 |
Interactions with Commensal or Non-commensal Streptococci Alter Streptococcus mutans Transcriptome and Behaviors |
|
| Relations |
| BioSample |
SAMN31208495 |
| SRA |
SRX17828014 |
