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| Status |
Public on Apr 20, 2022 |
| Title |
Wrinkly Speader1 Rep 1 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Pseudomonas fluorescens |
| Characteristics |
strain: SBW25 WS1
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| Growth protocol |
Individual colonies of bacterial strains pre-cultured on LB agar were homogenised in LB broth and spread in single lines across PM agar plates using a 1ul transfer loop. Plates were allowed to dry before applying 2 ul of suspension containing ~103 Acanthamoeba cysts µl-1 at one end of the bacterial line. Plates were incubated at 28˚C for up to 1 week and the interaction zone was collected once the amoeba had formed a visible clearing. Pseudomonas fluorescens SBW25 strains were collected with Acanthamoeba from the bacteria-protozoa interaction zone and alone from the opposite end of the culture line with a transfer loop and immediately homogenised in RNA shield (n=4
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from bacterial and amoebae cells using the Quick-RNA MiniPrep Kit (Zymo Research, USA)
Preparations were dried in GenTegra RNA tubes according to manufacturer’s instructions (Gentegra, USA) and sent to the Microbial Genome Sequencing (MiGS, USA) Center for Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion and sequencing on the NextSeq 550 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
reads were aligned to the Acanthamoeba reference genome (Acanthamoeba castellanii strain NEFF GCA_000313135.1) using HiSat2
unused reads were then aligned to the bacterial reference genome (Pseudomonas fluorescens SBW25 GCA_000009225.1) using Bowtie2
Sequence reads were assigned to genomic features using featureCounts
Differential expression using GLM and count normalisation was calculated with edgeR, Counts were normalised by library size (counts per million, CPM) with log2 transformation.
Assembly: GCA_000313135.1, GCA_000009225.1
Supplementary files format and content: tab-delimited text files include CPM values per sample
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| Submission date |
Apr 13, 2022 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Heather Hendrickson |
| E-mail(s) |
[email protected]
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| Phone |
+6433691875
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| Organization name |
University of Cantebury
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| Department |
Biological Sciences
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| Street address |
+6433691875
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| City |
Christchurch |
| ZIP/Postal code |
8140 |
| Country |
New Zealand |
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| Platform ID |
GPL28120 |
| Series (1) |
| GSE200723 |
Protozoan predation drives rapid adaptive divergence by selecting for tuned cellulose production and amyloid fibrils in Pseudomonas fluorescens SBW25 |
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| Relations |
| BioSample |
SAMN27561816 |
| SRA |
SRX14841397 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6042760_WS1_S25_counts.txt.gz |
85.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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