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| Status |
Public on Apr 11, 2018 |
| Title |
PAO1_FBI (exposed to hexadecane-water interface for 1h)_1 |
| Sample type |
SRA |
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| Source name |
Stationary phase microbial culture
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| Organism |
Pseudomonas aeruginosa PAO1 |
| Characteristics |
strain: PAO1
culture: 16h culture
cell type: whole cell
stress: exposed to hexadecane-water interface for 1h
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| Extracted molecule |
total RNA |
| Extraction protocol |
To evaluate changes in the transcriptional profile of cells after interfacial confinement, PAO1 and PA14 cells were exposed to the hexadecane-water interface and the cells total RNA were isolated. First the cells were grown for 16 h in the LB medium, washed and resuspended in 154 mM NaCl solution as described above. To form the FBIs, 5 mL of suspensions and 5 mL of hexadecane were introduced in 25 mL glass vials. The vials were rotated at 60 rpm for 2 h using a Rugged Rotator (Glas-Col, Terre Haute, USA) for 1 h and the emulsions were collected in microcentrifuge tubes, then centrifuges at 15,000 g for 2.5 min at 4C to remove cells, which are not attached to the FBIs. The FBIs were collected from the hexadecane water interfaces, introduced in a vial and stored at 80C for RNA isolation. Similarly, the control cells, which were only suspended in 154 mM NaCl solution, were collected by centrifugation and stored at 80C for RNA extraction. Three independent samples were prepared for the control experiments. The RNeasy Mini Kit (Qiagen, CA, USA), which includes on-column DNase, was employed to extract the total RNA of cells following a protocol previously developed. The total RNA of PA14 and PAO1 FBIs as well as the untreated controls (PAO1 and PA14 in suspension) were isolated and bioanalyzed for their quality. The RNA samples were sent to the Penn Next-Generation Sequencing Core to acquire the transcriptional profile of the cells using RNA sequencing.
Illumina's TruSeq Stranded Total RNA Sample Preparation protocol with Ribo-Zero rRNA removal was used to construct libraries. All steps conformed to as listed in manufacturer's sample preparation guide.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PAO1_TranscriptRawReadCounts.txt
replicate 1
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| Data processing |
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to Pseudomonas aeruginosa genomes PAO1 and PA14, the Refseq transcriptome, and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: PAO1 - NCBI Build ASM676v1 (GCF_000006765.1), PA14 - NCBI Build Pseu_aeru_PA14_V1 (GCF_000404265.1)
Supplementary_files_format_and_content: transcript raw read counts of each sample
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| Submission date |
Apr 10, 2018 |
| Last update date |
Apr 11, 2018 |
| Contact name |
Tagbo Niepa |
| E-mail(s) |
[email protected]
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| Phone |
4123834265
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| Organization name |
University of Pittsburgh
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| Department |
Chemical and Petroleum Engineering
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| Lab |
MicroBiointerface Lab
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| Street address |
3700 OHara Street, 926 Benedum Hall
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platform ID |
GPL18782 |
| Series (1) |
| GSE112911 |
Genome-wide analysis of Differential Responses of Pseudomonas aeruginosa PAO1 and PA14 cells to Interfacial Stress |
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| Relations |
| BioSample |
SAMN08905348 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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