|
| Status |
Public on Sep 23, 2024 |
| Title |
ACICU after 1-week desiccation (first biological replicate) |
| Sample type |
SRA |
| |
|
| Source name |
A. baumannii [NZ_CP031380.1]
|
| Organism |
Acinetobacter baumannii ACICU |
| Characteristics |
genotype: wild-type
treatment: Total RNA extraction from cells harvested after 1-week desiccation (desiccated sample)
|
| Treatment protocol |
ATCC 19606T and ACICU were washed, diluted in ultrapure distilled water to an OD600 of 1.0, and desiccated on glass Petri plates for 1 week. Before and after desiccation, samples were collected and mixed with 2 mL of RNA Protect Bacteria Reagent (Qiagen). Total RNA isolation was performed by using miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
|
| Growth protocol |
ATCC 19606T and ACICU were grown in LB and incubated at 37°C under shaking for 18 h. Bacterial cultures were sub-cultured (1:100 dilution) in a flask and incubated at 37°C under shaking for 6 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with RNeasy MiniElute Cleanup Kit (Qiagen) and RNA samples were treated with TURBO DNase (Invitrogen) to remove genomic DNA.
The RNA-seq analysis, RNA quality assessment, library preparation, sequencing, and statistical analysis of the data were performed at the GENEWIZ Biotechnology Facility (GENEWIZ, Azenta Life Sciences Company, Leipzig, Germany), as previously described [doi: 10.1128/spectrum.00961-22].
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ACICU desiccated cells (#1)
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Acinetobacter_baumannii_ATCC 19606 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. BAM files were generated because of this step. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within gene regions were counted. After the extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were defined as differentially expressed genes for each comparison.
Assembly: A. baumannii ATCC 19606T [NZ_CP058289.1]
Assembly: A. baumannii ACICU [NZ_CP031380.1]
Supplementary files format and content: Processed data: tab-delimited text files including raw counts for each sample
Supplementary files format and content: Raw data files: tab-delimited text files including RPKM values for each sample
|
| |
|
| Submission date |
Nov 30, 2023 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Massimiliano Lucidi |
| E-mail(s) |
[email protected]
|
| Phone |
+390657336346
|
| Organization name |
University of Roma Tre
|
| Department |
Sciences
|
| Street address |
Viale Guglielmo Marconi 446
|
| City |
Rome |
| State/province |
Rome |
| ZIP/Postal code |
00146 |
| Country |
Italy |
| |
|
| Platform ID |
GPL33973 |
| Series (1) |
| GSE249021 |
The response to desiccation in Acinetobacter baumannii |
|
| Relations |
| BioSample |
SAMN38526397 |
| SRA |
SRX22701057 |
