|
| Status |
Public on Dec 01, 2022 |
| Title |
KHUD_S3.VAN.R1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-Seq of S. anginosus KHUD_S3 treated with vancomycin rep1
|
| Organism |
Streptococcus anginosus |
| Characteristics |
strain: KHUD_S3
treatment: Vancomycin treatment
|
| Treatment protocol |
S. anginosus grown to an early exponential phase (OD600 = 0.3) was divided in half. One aliquot was left untreated, while the other one was treated with 8 μg/ml vancomycin for 1 h.
|
| Growth protocol |
S. anginosus was grown in Brain Heart Infusion Broth (Difco Laboratories) at 37°C under anaerobic conditions (80% N2, 10% H2, 10% CO2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol (Invitrogen) and cleaned with RNeasy® Plus Mini Kit (QIAGEN).
To perform transcriptome sequencing (RNA-Seq) analysis, quality and integrity of the extracted total RNA was assessed by BioAnalyzer and the ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit for Bacteria (Illumina). Standard illumina sequencing system protocol (TruSeq Stranded Total RNA prep) have been used to make libraries for RNA-Seq. Around 300 bp fragments were isolated using gel electrophoresis, amplified by PCR and sequenced on the Illumina HiSeq 3000 in the paired-end sequencing mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the S. aginosus J4211 strain using Bowtie2. Uniquely and properly mapped read pairs were used for further analysis.
Expression levels of genes, the FPKM (fragments per kilobase of exon per million mapped reads) measure was calculated by cufflinks
Genome_build: S. aginosus J4211
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Dec 22, 2020 |
| Last update date |
Dec 01, 2022 |
| Contact name |
Jae-Hyung Lee |
| E-mail(s) |
jaehlee@khu.ac.kr
|
| Organization name |
Kyung Hee University
|
| Street address |
26 Kyungheedae-ro, Dongdaemun-gu
|
| City |
Seoul |
| ZIP/Postal code |
02447 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL29524 |
| Series (1) |
| GSE163717 |
RNA-Seq analysis for the antibiotics resistance between two Streptococcus anginosus strains |
|
| Relations |
| BioSample |
SAMN17138527 |
| SRA |
SRX9719075 |
