|
| Status |
Public on Sep 01, 2016 |
| Title |
FA1090_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Neisseria gonorrhoeae |
| Characteristics |
growth phase: Late log
od600: 0.8 to 1.0
strain: FA1090
|
| Growth protocol |
N. gonorrhoeae strains were grown on gonococcal agar plates supplemented with Kellog’s supplements I and II or in gonococcal (GC) broth supplemented with Kellog’s supplements I and II and 0.043% (w/v) sodium bicarbonate at 37ºC with 5% CO2 and shaking at 100 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from four independent cultures of FA1090, FA1090cpxA::kan and FA1090cpxR::erm strains grown to late log phase (OD600 = 0.8-1.0) using TRIzol reagent (Invitrogen) according to the manufacturer's protocol. RNA was treated twice with the TURBO DNA-free DNase (Ambion) and the efficacy of DNase treatment was confirmed by reverse transcriptase PCR (RT-PCR) analysis and the QuantiTect SYBR green RT-PCR kit (Qiagen). Removal of rRNA from total RNA and preparation of RNA-Seq libraries were performed using the ScriptSeq Complete kit (Bacteria) (Illumina, Inc.) following the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Image analysis and base calling were performed with the HiSeq Control software and the Real Time Analysis software.
Demultiplexing was performed with the Illumina CASAVA software.
Sequenced reads were mapped with the Burrows-Wheeler Alignment tool
The total number of reads corresponding to the coding region of each gene was determined with the NGSUtils suite
Gene List was generated using an FDR cutoff of 0.1 and a fold change cutoff of 2 fold
Genome_build: AE004969
Supplementary_files_format_and_content: Excel Sheet includes RPKM values for each sample as well as calculated fold change, p-value, and FDR.
|
| |
|
| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dharanesh Gangaiah |
| E-mail(s) |
dgangaia@iupui.edu
|
| Phone |
317-278-1027
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
Spinola lab
|
| Street address |
635 Barnhill drive, MS 420
|
| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL22011 |
| Series (1) |
| GSE83341 |
Transcriptomes of FA1090,, FA1090cpxA::kan, FA1090cpxR::erm mutant strains of Neisseria gonorrhoeae in late log phase |
|
| Relations |
| BioSample |
SAMN05245226 |
| SRA |
SRX1844489 |
