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Sample GSM1147617 Query DataSets for GSM1147617
Status Public on Jan 01, 2014
Title J2315_hfq2, biological rep1
Sample type RNA
 
Source name J2315 Δhfq2 with 16h growth in LB medium
Organism Burkholderia cenocepacia
Characteristics isolate: J2315 Δhfq2
Treatment protocol Bacterial cells were resuspended in RNAlater reagent (Ambion).
Growth protocol Bacterial strains were grown in 150 ml L medium contained into 250 ml Erlenmyer flasks at 37ºC, 250 r.p.m. for 16 h
Extracted molecule total RNA
Extraction protocol Total RNA extraction was carried out using the using the miRVana miRNA extraction kit (Ambion), and total RNA was enriched with the small-sized RNAs fraction, following manufacturer’s recommendation
Label biotin
Label protocol RNA was processed for use on Affymetrix custom dual species Burkholderia arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.
 
Hybridization protocol Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.
Scan protocol Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.
Description Mutation in the hfq2 gene
Data processing Scanned arrays were analyzed with Affymetrix Expression Console software for quality control. Subsequent analysis was carried out with DNA-Chip Analyzer 2010. First a digital mask was applied, leaving for analysis only the 8812 probe sets on the array representing Burkholderia cenocepacia J2315 transcripts. Then the 9 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.
 
Submission date May 23, 2013
Last update date Jan 01, 2014
Contact name Leonilde Morais Moreira
E-mail(s) lmoreira@ist.utl.pt
Phone +351 218419031
Organization name Instituto Superior Tecnico
Department Bioengineering
Lab Biological Sciences
Street address A. Rovisco Pais
City Lisboa
ZIP/Postal code 1049-001
Country Portugal
 
Platform ID GPL13356
Series (1)
GSE47344 Expression data from Burkholderia cenocepacia J2315 hfq and hfq2 mutants

Data table header descriptions
ID_REF
VALUE dChip signal values after normalization and model-based expression value computation.

Data table
ID_REF VALUE
aceE_at 629.84
acpP_at 455.09
algc_a_at 730.02
apah_at 255.36
BCAL0001_a_at 249.76
BCAL0002_a_at 538.7
BCAL0003_a_at 1401.6
BCAL0003_x_at 905.43
BCAL0004_at 536.16
BCAL0005_a_at 666.36
BCAL0005_at 187.55
BCAL0006_a_at 1020.44
BCAL0006_at 354.64
BCAL0007_a_at 412.3
BCAL0007_at 246.38
BCAL0009_at 621.53
BCAL0010_a_at 592.68
BCAL0011_x_at 446.27
BCAL0012_a_at 502.47
BCAL0012_x_at 771.19

Total number of rows: 8812

Table truncated, full table size 169 Kbytes.




Supplementary file Size Download File type/resource
GSM1147617_Bcc_mut2A.CEL.gz 885.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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