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Sample GSM838186 Query DataSets for GSM838186
Status Public on Nov 30, 2011
Title Pf0-1_whole_genome_array_wildtype_adnA_rep4
Sample type RNA
 
Source name Pseudomonas fluorescens Pf0-1 wild-type
Organism Pseudomonas fluorescens Pf0-1
Characteristics genotype: Wild-type
phenotype: normal
Growth protocol Pseudomonas fluorescens Pf0-1 (adnA+) was grown overnight in 50 mL of Pseudomonas Minimal Medium (PMM) Kirner, S., S et. al. 1996. Microbiology 142 ( Pt 8):2129-2135.
Extracted molecule total RNA
Extraction protocol Samples were treated with the RNAprotect reagent (Qiagen Inc., Valencia, CA, USA) and the total RNA was extracted using the RNeasy Mini kit (Qiagen). RNA was treated with RQ1 RNase free DNase (Promega Corporation, Madison, WI, USA). RNA samples were quantified using a NanoDrop Spectrophotometer (Isogen Life Science, The Netherlands). The quality of the RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) at Tufts University Core Facility (Tufts University School of Medicine, Boston, MA, USA). First strand cDNA was synthesized from 10 mg total RNA with random hexamer primers from Invitrogen (Carlsbad, CA) using SuperScript Double-Stranded cDNA Synthesis kits (Invitrogen Corporation, Carlsbad, California, USA). The cDNA synthesis was carried out according to the NimbleGen protocol for synthesis of doublestranded cDNA.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description This sample is of wild-type Pseudomonas fluorescens Pf0-1. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Nov 22, 2011
Last update date Nov 30, 2011
Contact name Matthew Mastropaolo
E-mail(s) Matthew.Mastropaolo@tufts.edu
Organization name Tufts Universicty School of Medicine
Department Molecular Biology and Microbiology
Lab Center for Adaptation Genetics and Drug Resistance, Levy Lab
Street address 136 Harrison Ave
City Boston
State/province MA
ZIP/Postal code 02111
Country USA
 
Platform ID GPL14909
Series (1)
GSE33865 Expression analysis of the AdnA regulon in Pseudomonas fluorescens Pf0-1

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
TI205922P00000013_BLOCK1 582.06
TI205922P00000011_BLOCK1 280.58
TI205922P00000008_BLOCK1 1948.71
TI205922P00000005_BLOCK1 2475.16
TI205922P00000010_BLOCK1 146.17
TI205922P00000009_BLOCK1 3090.25
TI205922P00000012_BLOCK1 996.10
TI205922P00000004_BLOCK1 2324.18
TI205922P00000001_BLOCK1 6410.54
TI205922P00000007_BLOCK1 1885.68
TI205922P00000006_BLOCK1 2727.23
TI205922P00000003_BLOCK1 2609.95
TI205922P00000002_BLOCK1 2746.69
TI205922P00000013_BLOCK2 1180.94
TI205922P00000011_BLOCK2 159.18
TI205922P00000008_BLOCK2 2311.56
TI205922P00000005_BLOCK2 1725.17
TI205922P00000010_BLOCK2 199.41
TI205922P00000009_BLOCK2 2147.95
TI205922P00000012_BLOCK2 508.27

Total number of rows: 372840

Table truncated, full table size 11585 Kbytes.




Supplementary file Size Download File type/resource
GSM838186_6396402_532_norm_RMA_pair.txt.gz 7.0 Mb (ftp)(http) TXT
GSM838186_6396402_532_pair.txt.gz 6.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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