|
| Status |
Public on May 20, 2022 |
| Title |
9hour_no_mero_1 |
| Sample type |
SRA |
| |
|
| Source name |
ATCC 17978
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: ATCC 17978
treatment: untreated
time point: 9 hours
|
| Treatment protocol |
Cultures were washed and stored in RNAlater (sigma).
|
| Growth protocol |
An overnight culture of A. baumannii strain ATCC 17978 was backdiluted 1:10 in fresh, pre-warmed BH broth containing meropenem or equivalent volume of water. Cultres were incubated at 37 degress for 0.5, 3, and 9 h in triplicate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-Zol RNA MiniPrep kit (Zymo Research) was used to extract total RNA from cultures. Turbo DNA-free DNA removal kit (Invitrogen) was used to remove genomic DNA contamination.
Done at MiGS - rRNA depletion was done using RiboZero Plus. Libraries were prepared using stranded library prep and 12 M paired end reads were obtained for each sample using Illumina NextSeq 550..
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
CLC genomic workbench software (Qiagen) was used to process reads
Reads were aligned to the A. baumannii ATCC 17978 genome annotations lue.
The RPKM expression values and the weighted proportions fold change of expression values between meropenem treated and treated samples at the same timepoint were calcualted.
Baggerley’s test on proportions was used to generate a false discovery rate adjusted P-value.
Genome_build: GCA_000015425.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 08, 2021 |
| Last update date |
May 21, 2022 |
| Contact name |
Joseph Michael Boll |
| Organization name |
University of Texas at Dallas
|
| Department |
Biological Sciences
|
| Lab |
BSB 12.302
|
| Street address |
800 W Campbell
|
| City |
Richardson |
| State/province |
TX |
| ZIP/Postal code |
75080 |
| Country |
USA |
| |
|
| Platform ID |
GPL31042 |
| Series (1) |
| GSE190441 |
Transcriptional response to carbapenem treatment in Acinetobacter baumannii |
|
| Relations |
| BioSample |
SAMN23787661 |
| SRA |
SRX13351576 |
