|
| Status |
Public on Jan 14, 2019 |
| Title |
Mut_2 |
| Sample type |
SRA |
| |
|
| Source name |
∆trxA
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
genotype/variation: thioredoxin-A knockout
growth phase: Mid-log
|
| Growth protocol |
Bacteria were grown to mid-log phase
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation using a PureLink RNA Mini Kit (Ambion). RNA was then enriched for mRNA by removing rRNA from the total RNA using a MICROBExpress Kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Mut_2_S5_L001
|
| Data processing |
The sequencing reads were preprocessed by the Trim Galore program with default parameters to remove adapters and low-quality sequences
The reads were then aligned to Acinetobacter baumannii strain CI79 reference genome ASM51663v2 using HISAT2 with default settings
The reads were counted using the featureCounts program
After eliminating genes with low expression (< 1 counts per million (CPM) in more than three samples across the dataset), the raw expression value was normalized using the calcNormFactors function implemented in the edgeR program
Differentially expressed genes (DEGs) were then determined by quasi-likelihood F-test using glmQLFit function implemented in the edgeR package. Genes with FDR-adjusted P-value (≤0.05) and fold change ≥2 (or ≤-2) were considered to be differentially expressed in this study
Heatmaps and the volcano plot were generated using R functions.
Genome_build: GenBank assembly accession: GCA_000516635.2
Supplementary_files_format_and_content: csv files show raw counts and statistics for each sample
|
| |
|
| Submission date |
Jan 13, 2019 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Bernard Arulanandam |
| Organization name |
University of Texas at San Antonio
|
| Department |
Biology
|
| Street address |
1 UTSA Cir
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78249 |
| Country |
USA |
| |
|
| Platform ID |
GPL26038 |
| Series (1) |
| GSE125017 |
Next Generation Sequencing of Wildtype and Thioredoxin-A knockout of a clinical isolate of Acinetobacter baumannii |
|
| Relations |
| BioSample |
SAMN10737736 |
| SRA |
SRX5245807 |
