|
| Status |
Public on Feb 01, 2023 |
| Title |
S. mutans/V.p dual biofilm +copper ions 500µM |
| Sample type |
SRA |
| |
|
| Source name |
S. mutans strain UA159/V. parvula PK1910
|
| Organism |
Streptococcus mutans |
| Characteristics |
strain: S. mutans strain UA159/V. parvula PK1910
treatment: copper ions 500µM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Invitrogen(Invitrogen). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SAMPLES 4
|
| Data processing |
Illumina Hiseq4000
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina Hiseq4000 benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genome using Bowtie2 software
By using GO database, a gene or a group of genes were classified and annotated in terms of biological process, molecular function and cellular component according to their reference
Gene expression levels were calculated by the number of sequences (clean reads) that were mapped to genomic regions. According to the comparison results between all samples and reference genomes, the FPKM value of each gene/transcript in the sample was calculated, and this value was used as the gene/transcript expression quantity in the sample. Finally, the significance analysis of differences in the expression of all genes/transcripts in each group of samples was conducted to find out the relative differentially expressed genes/transcripts, and the visualization analysis was carried out
Supplementary files format and content: Excel files and mat files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Yun Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China
|
| Street address |
Qingyang District first Ring Road west second section
|
| City |
Chengdu |
| ZIP/Postal code |
610072 |
| Country |
China |
| |
|
| Platform ID |
GPL28465 |
| Series (1) |
| GSE222218 |
Copper ions inhibit Streptococcus mutans-Veillonella parvula dual biofilm by activating Streptococcus-mutans reactive nitrogen species |
|
| Relations |
| BioSample |
SAMN32602907 |
| SRA |
SRX18945510 |
