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| Status |
Public on Jun 01, 2015 |
| Title |
XIP_15_I |
| Sample type |
SRA |
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| Source name |
bacterial culture
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| Organism |
Streptococcus mutans UA159 |
| Characteristics |
treatment: XIP
time after treatment (min): 15
replicate: 1
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| Treatment protocol |
Overnight cultures of the S. mutans UA 159 wildtype grown in THBY were diluted to an OD of 0.1 in CDM and cultivated at 37°C and 5% CO2 until the culture had reached an OD of 0.175. Subsequently the culture was divided into three equal parts, one part was treated with 2 µM synthetic XIP, one with 2 µM synthetic CSP and the third part was used as an uninduced control. Samples were taken at 5, 15, 30, 60 and 120 min post addition of the synthetic peptides. The samples were immediately transferred into an equal volume of RNA Protect and incubated for 5 min at RT. Subsequently the bacteria were pelleted (13000 rpm, 2 min, RT), the supernatant was removed and the pellet was frozen at -70°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted bacteria were washed with 500 µl nuclease free water and centrifuged for 2 min at 13.000 rpm. The supernatant was removed and the pellet resuspended in LM-lysis buffer containing 2.5 mg lysozyme and 100 U mutanolysin (pH=7.4). The resuspension was shaken in a heating block at 25°C and 1400 rpm for 45 min. 700 µl of Qiazol Lysis solution (Qiagen, Germany) was added and the mixture transferred to a falcon tube containing sterile 0.1 µm glass beads (Carl Roth, Germany). The falcon tubes were vortexed for 3 min and centrifuged at 6000 rpm at RT to pellet the glass beads. The supernatant was transferred to a new tube and 200 µl of chloroform was added. Samples were vortexed for 15 sec, incubated for 2 min at RT and centrifuged for 20 min at 13.000 rpm and 4°C. The upper aqueous phase (approximately 550 µl) was transferred to a new tube and 870 µl of ethanol was added and mixed thoroughly. RNA extraction was carried out using the MiRNeasy Kit (Qiagen, Germany) according to the manufacturer’s instructions. To remove genomic DNA the optional on-column DNAseI digestion using the DNAse I Kit (Qiagen, Germany) was performed for 45 min. After the washing steps the RNA was eluted in 50 µl of nuclease free water supplied with the kit. To test the integrity of the isolated total RNA and the enriched mRNA, samples were analyzed using the Agilent 2100 Bioanalyzer and the RNA 6000 Pico Kit (Agilent, Germany).
The Illumina ScriptSeq™ v2 RNA-Seq Library Preparation Kit was used according to the manufacturers protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
fastQ-mcf was used to clip adapter sequences and bases with a quality score below 20 from the raw reads
Rockhopper version 2.0.2 (http://cs.wellesley.edu/~btjaden/Rockhopper/index.html) was used to map the clipped reads to the genome of S. Mutans UA159 using the default parameters.
Genome_build: NC_004350.2
Supplementary_files_format_and_content: tab-delimited textfile including mapped reads per ORF
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| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jürgen Tomasch |
| E-mail(s) |
[email protected]
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| Organization name |
Center Algatech, Institute of Microbiology of the Czech Academy of Science
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| Lab |
Anoxygenic Phototrophs
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| Street address |
Novohradská 237
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| City |
Třeboň |
| ZIP/Postal code |
37901 |
| Country |
Czech Republic |
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| Platform ID |
GPL19789 |
| Series (1) |
| GSE65982 |
Transcriptional response of Streptococcus mutans in chemically defined medium (CDM) towards the autoinducers CSP and XIP |
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| Relations |
| BioSample |
SAMN03351738 |
| SRA |
SRX878848 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1611975_Raw.Counts.X15.Replicate.1.txt.gz |
10.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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