|
| Status |
Public on Aug 13, 2020 |
| Title |
5_AB5075_E_GFF |
| Sample type |
SRA |
| |
|
| Source name |
LB media
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: AB5075
od: 0.5
population: VIR-O
|
| Growth protocol |
Samples were grown at 37 degrees with shaking to an OD of 0.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared from 1 ml of pelleted culture using the MasterPure RNA Purification kit (Epicentre, Madison, WI)
Libraries were prepared from 2ug of bacterial RNA using the ScriptSeq v2 Complete (Bacteria) kit. After pooling at equimolar ratios, the libraries were sequenced on a HiSeq3000 using a SR100 configuration
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Acinetobacter baumannii AB5075 genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done with htseq-count.
Normalized abundance calculation and differential expression analysis was performed with DESeq2.
Genome_build: ASM96381v1 Strain: AB5075-UW GenBank assembly accession: GCA_000963815.1
Supplementary_files_format_and_content: tab-delimited text files with raw or DESeq2 normailzed read count values for each Sample …
|
| |
|
| Submission date |
Aug 13, 2020 |
| Last update date |
Aug 14, 2020 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
[email protected]
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL26038 |
| Series (1) |
| GSE156206 |
Copy Number of an Integron-Encoded Antibiotic Resistance Locus Regulates a Virulence and Opacity Switch in Acinetobacter baumannii AB5075 |
|
| Relations |
| BioSample |
SAMN15813963 |
| SRA |
SRX8944522 |
