|
| Status |
Public on Mar 06, 2020 |
| Title |
del-hutC_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Pseudomonas fluorescens |
| Characteristics |
strain: MU60-1
genotype: Isogenic hutC deletion mutant of SBW25
|
| Growth protocol |
Bacteria were exponentially grown in triplicate in the M9 mininmal salt medium summplemented with succinate (20 mM) and histidine (10 mM)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was preparated using the SV Total RNA Isolation System purchased from Promega (Madison, WI)
RNA libraries were prepared for sequencing by Novogene Technology Co. Ltd, using the standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
CS213
|
| Data processing |
The paired-end reads from Novogene were processed in the Geneious 9.0.5 program following the instructions
Reads were mapped to the reference genome of Pseudomonas fluorescens SBW25 (GenBank: AM181176.4)
Differentially expressed genes were determined based on transcripts comparison normalized using the Median of Gene Expression Ratios method implemented in Geneious 9.0.5.
Genome_build: Pseudomonas fluorescens SBW25 (GenBank: AM181176.4)
Supplementary_files_format_and_content: a csv file exported from Geneious containing raw read counts for both wild type and its derived del-hutC mutants, and ratios of differential expression for all genes in the genome.
|
| |
|
| Submission date |
Mar 05, 2020 |
| Last update date |
Mar 06, 2020 |
| Contact name |
Xue-Xian Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Massey University
|
| Department |
School of Natural and Computational Sciences
|
| Street address |
14.02 The Station Cre., Albany
|
| City |
Auckland |
| ZIP/Postal code |
0745 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL28231 |
| Series (1) |
| GSE146488 |
Identifying candidate genes whose expression is regulated by the HutC transcriptional repressor in Pseudomonas fluorescens SBW25 |
|
| Relations |
| BioSample |
SAMN14308918 |
| SRA |
SRX7858889 |
