|
| Status |
Public on Apr 14, 2020 |
| Title |
PDO300_1 |
| Sample type |
SRA |
| |
|
| Source name |
PDO300_1
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
genotype: mucA22
group: mucoid
|
| Treatment protocol |
2 ml aliquots from each culture were added directly to 10ml of RNAlater, stored at 4°C for 24 hours, and then transferred to -80°C until samples were processed.
|
| Growth protocol |
Overnight cultures of the P. aeruginosa strains were grown in 3ml MOPS-succinate, cultures were back diluted to an OD600 of 0.01 in 20 ml MOPS-succinate and allowed to grow to exponential phase, shaking at 200 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed by bead beating and RNA was precipitated using chloroform and isopropanol. Pellets were washed with ethanol and quantified using NanoDrop.
mRNA was enriched using Ambion MICROBExpress kit. Enriched mRNA was fragmented using NEBNext Fragmentation Module kit and libraries were prepared using NEBNext Multiplex Small RNA Library Prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
RNAseq reads were trimmed using cutadapt v2.3 with a minimum length cutoff of 18bp. The reads were then mapped to PAO1 refseq genome NC_002516.2 using bowtie2 v2.3.5 with end-to-end alignment. The number of reads mapped to each genomic feature was calculated using HTSeq v11.1 and features with less than 10 mapped reads were discarded
Genome_build: PAO1 refseq genome NC_002516.2
Supplementary_files_format_and_content: .count.txt files contain the number of reads mapped to each genomic feature calculated using HTSeq
|
| |
|
| Submission date |
Apr 13, 2020 |
| Last update date |
Apr 15, 2020 |
| Contact name |
Joanna B Goldberg |
| E-mail(s) |
joanna.goldberg@emory.edu
|
| Organization name |
Emory University
|
| Lab |
Goldberg Lab
|
| Street address |
O. Wayne Rollins Research Center, Room 3009 1510 Clifton Road NE
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL28386 |
| Series (1) |
| GSE148593 |
The histone-like protein AlgP regulon is distinct in nonmucoid and mucoid Pseudomonas aeruginosa and does not include alginate biosynthesis genes |
|
| Relations |
| BioSample |
SAMN14592740 |
| SRA |
SRX8111266 |
