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| Status |
Public on May 13, 2018 |
| Title |
ATCC 17978 |
| Sample type |
SRA |
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| Source name |
bacterial cells
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| Organism |
Acinetobacter baumannii ATCC 17978 |
| Characteristics |
genotype: wildtype
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| Treatment protocol |
No treatment was undertaken
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| Growth protocol |
Bacterial strains were grown at 37 degrees Celsius in Mueller-Hinton liquid broth culture to an optical density of OD 0.6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from ATCC 17978 wildtype and ∆adeRS bacterial cells was extracted according to the manufacturers' instructions using the Isolate I RNA extraction Mini Kit (Bioline, NSW, Australia)
Libraries were prepared according to the Illumina's instructions. Briefly, total RNA was treated with a Epicentre Ribo-Zero kit to deplete ribosomal RNA. RNA library barcoding was then undertaken on RNA for HiSeq analysis. Samples were run on the Illumina HiSeq platform (1X50 base pair single reads)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Wildtype bacteria
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| Data processing |
Base calling was undertaken using Illumina's software
Sequences reads were trimmed for adaptor sequence, and masked for low-complexity / low-quality sequence, and subsequently mapped to Acinetobacter baumannii ATCC 17978 genome sequence using bowtie aligner software.
Counts per gene were generated using htseq-count tool and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: Acinetobacter baumannii ATCC 17978 genome accession CP012004
Supplementary_files_format_and_content: Tab-delimited text files include gene locus names, raw counts and RPKM values generated for each gene for each sample
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| Submission date |
Aug 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Felise Adams |
| E-mail(s) |
[email protected]
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| Phone |
08 82015379
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| Organization name |
Flinders University
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| Department |
Biological Sciences
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| Lab |
Molecular microbiology
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| Street address |
Bedford Park
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| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
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| Platform ID |
GPL23922 |
| Series (1) |
| GSE102711 |
Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978 |
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| Relations |
| BioSample |
SAMN07510914 |
| SRA |
SRX3096832 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2743446_ATCC17978_wildtype.txt.gz |
40.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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