|
| Status |
Public on May 13, 2024 |
| Title |
Δfim LB3 |
| Sample type |
SRA |
| |
|
| Source name |
R51
|
| Organism |
Salmonella enterica subsp. enterica serovar Pullorum |
| Characteristics |
strain: R51
genotype: fim knockout
treatment: egg white
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of all strains was extracted with Trizol reagent, assessed using Thermo NanoDrop One and Agilent 4200 Tape Station instruments.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used for cDNA library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Δfim LB3
|
| Data processing |
Fastp v.0.19.7 was used to process the raw data in fastq format to get clean data (parameter qualified_quality_phred 15；cut_mean_quality 20；length_required 75).
Clean reads were mapped to the NCBI Rfam database, and rRNA sequences were removed by Bowtie2(v2.33)（parameter default）.
Sequence reads after ribosome removal were aligned to the Homo sapiens reference genome GRCh38 from ensembl database by Hisat2 (v2.1.0)（parameter default）.
Salmon software v1.2.1 was used to obtain the expression for each gene（parameter default）.
EdgeR software v3.20.2 was used to obtain the differentially expressed genes（parameter fold change>2;FDR<0.05）.
Assembly: GenBank accession number CP068386.1 (chromosome) and two plasmids (CP068387.1 and CP068388.1)
Supplementary files format and content: Tab_delimited txt file include raw counts for each sample
|
| |
|
| Submission date |
Feb 20, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Xiamei Kang |
| Organization name |
Zhejiang University
|
| Street address |
No. 388, Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL34216 |
| Series (1) |
| GSE256211 |
Integrated OMICs approach reveals energy metabolism pathway is vital for Salmonella Pullorum survival within the egg white |
|
| Relations |
| BioSample |
SAMN40004156 |
| SRA |
SRX23672419 |
