NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM773508 Query DataSets for GSM773508
Status Public on Aug 11, 2011
Title 19606S_2
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 SRX091929
BioSample SAMN00709469

Supplementary file Size Download File type/resource
GSM773508_19606S_2.bam 855.9 Mb (ftp)(http) BAM
GSM773508_19606S_2.bam.bai.gz 7.2 Kb (ftp)(http) BAI
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap