|
| Status |
Public on Apr 21, 2020 |
| Title |
PAO1_T2.5_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture
|
| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
strain: PAO1
genotype: wild type
|
| Treatment protocol |
PAO1 was exposed to the presence of 2.5 um testosterone or vehicle control (EtOH).
|
| Growth protocol |
PAO1 was cultured for 24 hours in TSB broth.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1ml of culture was treated with RNAprotect reagent and total RNA extracted using the Rneasy kit. Ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RRNA-depleted RNA
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to PAO1 genome (NC_002516) and assessed using the Rockhopper RNAseq analysis pipline (Tjaden et al 2013, Genome biology)
Genome_build: PAO1 NC_002516
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each experimental condition.
|
| |
|
| Submission date |
Apr 20, 2020 |
| Last update date |
Apr 22, 2020 |
| Contact name |
Micheal Mac Aogain |
| Organization name |
Nanyang Technological University
|
| Department |
Lee Kong Chian School of Medicine
|
| Street address |
308232, 11 Mandalay Rd, Singapore
|
| City |
Singapore |
| ZIP/Postal code |
308232 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18782 |
| Series (1) |
| GSE148955 |
RNA-Seq analysis of Pseudomonas aeruginosa response to testosterone |
|
| Relations |
| BioSample |
SAMN14646042 |
| SRA |
SRX8143229 |
