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| Status |
Public on Jun 16, 2019 |
| Title |
PAO1 in DNA, repl 3 |
| Sample type |
SRA |
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| Source name |
Whole cell
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| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
genotype: wild type
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| Growth protocol |
P. aeruginosa strains PAO1 and PASS4 were simultaneously inoculated into 5 ml of LB liquid medium from the frozen stock and grown overnight. Overnight cultures were used to inoculate 15 ml of M9 minimal medium supplemented with either L-Asparagine (20mM) or DNA (1.5 mg/ml) (Salmon sperm DNA, Sigma), both in biological triplicates. Cultures were grown until mid-exponential phase (OD600 = 0.6).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from these cultures using the miRNEasy RNA extraction kit (Qiagen) according to the manufacturer’s protocol. To remove any residual genomic DNA, the samples were treated with DNAse using the TurboDNAse kit (Invitrogen). To remo.ve highly abundant ribosomal RNA from the RNA extracts before sequencing, the samples were treated using RiboZero GN Magnetic rRNA depletion kit (Epicentre); the rRNA depleted samples were purified using RNeasy MinELute Cleanup kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
grown in DNA as a sole carbon source, replicate 3
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| Data processing |
Paired-end RNA sequence files were assessed for quality using FastQC software (Babraham Bioinformatics)
Sequenced reads were trimmed for adaptor sequence and the low-quality sequence, then mapped to the complete genome of PAO1 via EdgePro software
Differential expression calculated using DESeq software
De novo transcript assembly and differential gene expression analysis was performed for PASS4 strain using the Rockhopper 2.03 tool (54, 55) to supplement the data on PASS4 genes absent in PAO1 genome.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 21, 2017 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Anahit Penesyan |
| Organization name |
Mcquarie University
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| Street address |
E8A, Eastern road
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| City |
Macquarie University |
| State/province |
NSW |
| ZIP/Postal code |
2109 |
| Country |
Australia |
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| Platform ID |
GPL18644 |
| Series (1) |
| GSE100287 |
A Cystic Fibrosis Pseudomonas aeruginosa Isolate Specialised to Catabolise Nucleic Acids |
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| Relations |
| BioSample |
SAMN07260036 |
| SRA |
SRX2940629 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2677312_PAO1_D3_PAO1Ref_EdgePro.rpkm.txt.gz |
119.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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