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Sample GSM3243128 Query DataSets for GSM3243128
Status Public on Dec 10, 2018
Title Ecoli_MG1655_T0_rep2_re-analysis
Sample type RNA
 
Source name Ecoli_MG1655_T0
Organism Escherichia coli str. K-12 substr. MG1655
Characteristics genotype/variation: wild type
sampling time point: before rifampicin addition
repetition: repetition 2
Treatment protocol Three hours after the stationary phase of growth was reached, samples were collected for transcriptomic analysis; this time point was also the reference time point (T0) for the half-life determination procedure.
Growth protocol The laboratory strain E. coli K12 MG1655 and two mutant strains E. coli MG1655_rnr) and E. coli MG1655_pnp) were grown in baffled flasks in LB medium at 37 °C and 180 rpm. Initial pH was set to 7. All cultures were inoculated at OD 0.1 from overnight pre-cultures performed in similar conditions. Biomass was estimated from absorbance at 600 nm. Cultures were performed in triplicate.
Extracted molecule total RNA
Extraction protocol After thawing and centrifugation steps, total RNA was extracted with TRIZOL® Reagent (Ambion) according to the manufacturer’s instructions. DNA contamination was eliminated with Turbo DNase kit (Ambion). Total RNA concentration and integrity were measured using a Nanodrop® spectrophotometer and Agilent BioAnalyzer, respectively. Total RNA extraction profiles were checked to be similar for all the three tested strains.
Label Cy3
Label protocol According to manufacturer instructions, 1 µg of cDNA was labeled using one color DNA labeling kit
 
Hybridization protocol According to manufacturer instructions, 2 µg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) during 17 h at 42 °C.
Scan protocol Arrays were later washed and scanned using MS200 Microarray Scanner (Nimblegen, Roche). Pictures were analyzed with DEVA 1.2.1 software.
Description SAMPLE 2
the cells were in stationary phase, the sampling was performed just before rifampicin addition. It is the second of three biological replicates used in this experiment, each from separate cultures.
Data processing Raw probe intensities ( .pair files three replicates for each strain) were processed and analyzed with R computing environment using the affy and limma package of Bioconductor. Raw probe intensities were processed and analyzed with the R computing environment using the affy and limma packages of Bioconductor. Raw data were submitted to a RMA-based background correction [Irizarry et al, 2003, Biostatistics 4(2): 249-264]. After background correction, intra-replicate quantile normalization was performed for each strain. A set of probes in the background for which the ranks were roughly invariant across all nine arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure [Irizarry et al, 2003, Biostatistics 4(2): 249-264] within each condition. Intensity values were multiplied by the total RNA extraction yield (in µg total RNA per mg of dry cell weight) to provide the mRNA concentration value in arbitrary units per mg of dry cell weight.
 
Submission date Jul 03, 2018
Last update date Dec 10, 2018
Contact name Laurence Girbal
E-mail(s) girbal@insa-toulouse.fr
Phone 33 5 61 55 97 24
Organization name TBI
Street address 135 avenue de rangueil
City Toulouse
ZIP/Postal code 31077
Country France
 
Platform ID GPL14649
Series (2)
GSE116577 Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [transcriptome]
GSE116652 Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase
Relations
Reanalysis of GSM3243096

Data table header descriptions
ID_REF
VALUE After normalization, in each array, transcript-specific intensity was computed as the median value of the 16 targeting probe intensities.

Data table
ID_REF VALUE
b0001071000000001 4.216405542
b0002071000000002 4.756936658
b0003071000000003 17.44384574
b0004071000000004 3.079047172
b0005071000000005 1.744620204
b0006071000000006 1.675986092
b0007071000000007 3.475914673
b0008071000000008 8.521161362
b0009071000000009 3.506388723
b0010071000000010 2.003443713
b0011071000000011 1.594947102
b0013071000000012 1.273951546
b0014071000000013 76.05049225
b0015071000000014 52.86466702
b0016071000000015 7.295479488
b0018071000000016 1.598944164
b0019071000000018 8.905817135
b0020071000000019 2.727662974
b0021071000000020 2.199954023
b0022071000000021 5.435262832

Total number of rows: 4254

Table truncated, full table size 124 Kbytes.




Supplementary file Size Download File type/resource
GSM3243128_Ecoli_MG1655_T0_rep2.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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