|
| Status |
Public on May 17, 2021 |
| Title |
H78hfq mutant rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Pseudomonas protegens H78hfq mutant
|
| Organism |
Pseudomonas protegens |
| Characteristics |
strain: H78hfq mutant
growth phase: the late exponential phase
genotype: H78hfq mutant
|
| Growth protocol |
Pseudomonas protegens H78 and its hfq mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNeasy Mini Kit (Cat.4106), purified by the Qiagen RNeasy micro kit (Cat.74004) and the Qiagen RNase-Free DNase Set (Cat.79254)
According to standard Illumina protocols, mRNA was enriched by removing rRNA and further fragmented to be used for synthesizing the first and second strands of cDNAs and constructing the sequencing library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Hfq3
|
| Data processing |
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed by Trimmomatic（v0.30） for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pseudomonas protegens H78 whole genome using tophat (v2.0.9 ).
Fragments Per Kilobase per Megabase of library size (FPKM) were calculated using Htseq(V 0.6.1).
Genome_build: Pseudomonas protegens H78 (Genbank Accession No. CP013184)
Supplementary_files_format_and_content: Excel file include FPKM values for each sample and differential expression analysis of all genes in the hfq mutant relative to the wild-type H78 strain...
|
| |
|
| Submission date |
Dec 06, 2019 |
| Last update date |
May 17, 2021 |
| Contact name |
Xianqing Huang |
| E-mail(s) |
xqhuang66@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Life Sciences and Biotechnology
|
| Street address |
DongChuan RD, Minhang District
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL22592 |
| Series (1) |
| GSE141556 |
Comparison of transcriptomic profiles of Pseudomonas protegens H78 and its hfq mutant (H78Δhfq) |
|
| Relations |
| BioSample |
SAMN13496598 |
| SRA |
SRX7278096 |
