|
| Status |
Public on Jan 31, 2024 |
| Title |
microorganism,coculture,24h,rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H. alvei H4 WT + P. fluorescens ACTT13525
|
| Organisms |
Pseudomonas fluorescens; Hafnia alvei |
| Characteristics |
strain: H. alvei H4 WT + P. fluorescens ACTT13525
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was harvested from H. alvei H4WT/ΔluxI and P. fluorescens ATCC13525
Total RNA was used as input material for the RNA sample preparations. For prokaryotic samples, mRNA was purified from total RNA using probes to remove rRNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WP-H-3
|
| Data processing |
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis_x0002_natural antisense transcripts.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package and used KOBAS3 software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: 569
Supplementary files format and content: H. alvei H4WT and P. fluorescens ATCC13525
Supplementary files format and content: H. alvei H4ΔluxI and P. fluorescens ATCC13525
|
| |
|
| Submission date |
Oct 19, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Yanan Wang |
| E-mail(s) |
21173083200045@xy.dlpu.edu.cn
|
| Organization name |
Dalian Polytechnic University
|
| Lab |
School of Food Science and Technology
|
| Street address |
Ganjingzi District
|
| City |
Dalian |
| State/province |
Liaoning |
| ZIP/Postal code |
116034 |
| Country |
China |
| |
|
| Platform ID |
GPL33855 |
| Series (1) |
| GSE245811 |
Role of quorum sensing of Hafnia alvei H4 in co-culture with Pseudomonas fluorescens ATCC13525 analyzed by biological and transcriptomic |
|
| Relations |
| BioSample |
SAMN37884783 |
| SRA |
SRX22145865 |
