|
| Status |
Public on Oct 01, 2024 |
| Title |
LS1 |
| Sample type |
SRA |
| |
|
| Source name |
Serratia marcescens FY and Lactobacillus plantarum FY1
|
| Organisms |
Serratia marcescens; Lactiplantibacillus plantarum |
| Characteristics |
strain: Serratia marcescens FY and Lactobacillus plantarum FY1
genotype: WT
treatment: bacteria co-cultured
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
replicate=LS group biological replicate 1
|
| Data processing |
For annotation, the genome of S. marcescens (GCF_013122155.1) and L. plantarum (GCF_032436005.1) was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: txt files include gene count values for each Sample
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
Oct 01, 2024 |
| Contact name |
sheng zhang |
| E-mail(s) |
zhangs1308@outlook.com
|
| Organization name |
anhui agriculture university
|
| Street address |
Shushan District
|
| City |
Hefe |
| State/province |
Anhui Province |
| ZIP/Postal code |
241000 |
| Country |
China |
| |
|
| Platform ID |
GPL34033 |
| Series (2) |
| GSE251781 |
Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [bulkRNA-seq] |
| GSE251783 |
Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions |
|
| Relations |
| BioSample |
SAMN39051765 |
| SRA |
SRX22995613 |
