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| Status |
Public on May 26, 2024 |
| Title |
NC24C |
| Sample type |
SRA |
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| Source name |
nonchronic wound
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| Organism |
Pseudomonas aeruginosa |
| Characteristics |
tissue: nonchronic wound
cell type: prokaryote
time: 24h
biological replicate: C
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| Treatment protocol |
chronic wounds were treated with inhibitors for antioxidant enzymes, catalase and GPx
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| Growth protocol |
P. aeruginosa was grown in LB and inoculated into clean db/db wounds
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit, treated with Dnase, and cleaned with vacuum grease and isopropyl alcohol
Ribosomal transcripts were removed using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and barcoded with IDT® for Illumina® RNA UD Indexes Set A Li-gation
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Quality control was processed using Fastqc. Low quality reads were trimmed using trim_galore and high quality trimmed reads were aligned to the RPA reference genome using the STAR aligner. QC data were summarized using MultiQC. Fastq-screen was used to sample each library (1 M reads) and quickly align them to known references including humans, mouse, E. coli, Arabidopsis, vectors, adapters, etc. Sortmerna was used to determine the extent of the rRNA contamination within each library. Featurecount quantified the mapped reads with a genome annotation to generate a count matrix for each transcript/gene. A differential expression analysis was performed using DESeq2.
Assembly: PRJNA1112363
Supplementary files format and content: tab delineated text file contains raw counts for each sample
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| Submission date |
May 20, 2024 |
| Last update date |
May 26, 2024 |
| Contact name |
Manuela Martins-Green |
| Organization name |
University of California, Riverside
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| Street address |
900 University Ave
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platform ID |
GPL33271 |
| Series (1) |
| GSE267862 |
Pseudomonas aeruginosa Activates Quorum Sensing, Antioxidant Enzymes and Type VI Secretion in Response to Oxidative Stress to Initiate Biofilm Formation and Wound Chronicity |
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| Relations |
| BioSample |
SAMN41455869 |
| SRA |
SRX24606725 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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