|
| Status |
Public on Aug 11, 2011 |
| Title |
19606S_1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: ATCC19606
growth stage: mid-log
antibiotic: No selection
|
| Growth protocol |
The lpxA mutant strain 19606R was an LPS-deficient, colistin-resistant derivative of ATCC19606 described previously (30). A. baumannii cultures were grown on Mueller-Hinton (MH) agar, or in cation-adjusted MH broth at 37°C. Colistin sulfate (10 µg/ml) was added to overnight cultures where appropriate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Qiagen RNeasy Purification Kit. Sequencing was conducted on an Illumina GAIIx by the Micromon High Throughput Sequencing Facility (Monash University). ATCC19606 and 19606R cDNA samples were multiplexed into a single lane and sequenced using a 75 bp paired-end DNA-sequencing protocol as per the manufacturer's instructions (Illumina). GSM773505 had mean fragment size 154, standard deviation 31. GSM773506 had mean fragment size 238, standard deviation 48. GSM773507 had mean fragment size 158, standard deviation 40. GSM773508 had mean fragment size 319, standard deviation 56.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Read pairs were clipped of bases with quality < 20 and adaptor sequences using "nesoni" http://bioinformatics.net.au/software.nesoni.shtml, and aligned using "SHRiMP" http://compbio.cs.toronto.edu/shrimp/. Alignments to coding sequences were then counted. Where a read-pair aligned equally well to multiple locations, it was counted multiple times, but the fact that the alignment was ambiguous was noted (in count.txt).
Processed data file build: NZ_GG704572.1
|
| |
|
| Submission date |
Aug 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Francis Harrison |
| E-mail(s) |
paul.harrison@monash.edu
|
| Organization name |
Victorian Bioinformatics Consortium
|
| Department |
Microbiology
|
| Street address |
Building 76, Monash University, Wellington Rd
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL14114 |
| Series (1) |
| GSE31206 |
Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids and poly-beta-1,6-N-acetylglucosamine |
|
| Relations |
| SRA |
SRX091928 |
| BioSample |
SAMN00709468 |
