|
| Status |
Public on Aug 10, 2020 |
| Title |
AB5075 adeB::T26 rep P2b |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: AB5075
genotype: single knockout mutant
|
| Growth protocol |
Cells were grown in LB broth until mid-exponential phase (OD600 = 0.5-0.6)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using hot phenol method. High quality total RNA was further processed by removing 23S and 16S rRNAs using the MicrobExpress bacterial mRNA enrichment kit (Life Technologies, USA). Final concentrations and purity grades of the samples were determined using Bioanalyzer 2100 (Agilent, USA). Samples with the amount at least 0.5-1 µg were used for library construction and RNA sequencing.
Libraries of depleted RNA were prepared using the Illumina TruSeq RNA LT v2 kit according to the manufacturer's instructions. RNA libraries were prepared for sequencing using Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark), with default settings, based on their proprietary algorithms.
Pairwise comparison of the expression results was performed using the total mapping results for deletion mutants vs wild type.
Differential gene lists were created with 2-fold expression cutoff and significant p-values of <0.05 to identify genes that were up- or down-regulated under each condition.
Genome_build: Raw sequence reads were mapped to the A. baumannii AB5075-UW genome (Accession# CP008706.1)
Supplementary_files_format_and_content: txt files with RPKM values for each sample
Supplementary_files_format_and_content: fastq raw data for each sample
|
| |
|
| Submission date |
Jul 09, 2020 |
| Last update date |
Aug 11, 2020 |
| Contact name |
Justyna Weronika Adamiak |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oklahoma
|
| Department |
Chemistry and Biochemistry
|
| Street address |
101 Stephenson Parkway
|
| City |
Norman |
| State/province |
OK |
| ZIP/Postal code |
73019 |
| Country |
USA |
| |
|
| Platform ID |
GPL19442 |
| Series (1) |
| GSE154070 |
Inactivation of AdeABC and AdeIJK efflux pumps elicits specific non-overlapping transcriptional and phenotypic responses in Acinetobacter baumannii |
|
| Relations |
| BioSample |
SAMN15489509 |
| SRA |
SRX8696867 |
