|
| Status |
Public on Aug 03, 2021 |
| Title |
2P24-2-6h |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells
|
| Organism |
Pseudomonas fluorescens |
| Characteristics |
strain: 2P24
age: 6 h
genotype: wild type
|
| Growth protocol |
Strains 2P24 and 2P24ΔinvF were grown on KB plates with 50 μg/mL ampicillin at 28℃. Fresh lawns were suspended in 5 mL of KB and incubated at 28℃ overnight with 200 rpm shaking. Bacterial suspension was diluted in 50 mL of MG medium in flasks to a final OD600 of 0.1. The cultures were incubated at 28°C at 200 rpm on a rotary shaker for 6 h/12 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cell fractions were separated by centrifugation at 10, 000 rpm for 5 min at 4°C. Total RNA was isolated using a E.Z.N.A.® Bacterial RNA Kit (Omega Bio‐tek, USA) as described by the manufacturer for RNA-seq. A prokaryotic chain specific sequencing library was constructed using a NEBNext Ultra Directional RNA Library Prep Kit and then sequenced on an Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard protocols of NEBNext Ultra Directional RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The sequencing data quality was evaluated by FastQC (V0.10.1).
The Cutadapt (version 1.9.1) is used to preprocess the original data, filter the low quality data, remove the pollution and the joint sequence.
The Clean Data and the reference genome were compared and analyzed by using BowtiE2 (V2.1.9) software with default parameters.
Samtools (V0.1.18) software was used for MPileup processing, so as to obtain the possible SNV results of each sample, and then Annovar (V2013.02.11) software was used for annotation.
Htseq software (V 0.6.1) was used to calculate gene expression levels.
DESeq2 (V1.6.3) of Bioconductor software package was used to analyze the genetic differences.
Genome_build: GenBank: CP025542.1
Supplementary_files_format_and_content: Gene counts and FPKM of all samples at 6 h and 12 h
Supplementary_files_format_and_content: Differentially expressed genes (DEGs) of 2P24ΔinvF compared with 2P24 at 6 h and 12 h
|
| |
|
| Submission date |
Aug 01, 2021 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Jing Wang |
| E-mail(s) |
[email protected]
|
| Phone |
15130192723
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
12 Zhongguancun South St
|
| City |
Beijing |
| State/province |
Not applicable |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL30468 |
| Series (1) |
| GSE181272 |
Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Wild Type and invF Deficient Mutant of Pseudomonas fluorescens 2P24 |
|
| Relations |
| BioSample |
SAMN20515202 |
| SRA |
SRX11623638 |
