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Sample GSM6620250 Query DataSets for GSM6620250
Status Public on Oct 09, 2022
Title Co_Lcasei_2
Sample type SRA
 
Source name Whole cell lysate
Organisms Lacticaseibacillus casei; Streptococcus mutans UA159
Characteristics strain: UA159 + 4646
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 Kaspar
E-mail(s) kaspar.17@osu.edu
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 GPL32731
Series (1)
GSE209925 Interactions with Commensal or Non-commensal Streptococci Alter Streptococcus mutans Transcriptome and Behaviors
Relations
BioSample SAMN31208492
SRA SRX17828017

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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