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Sample GSM1723968 Query DataSets for GSM1723968
Status Public on Jun 27, 2015
Title Ecoli_WTnsrR_rep3
Sample type RNA
 
Source name Escherichia coli MG1655 K-12 wild-type nsrR
Organism Escherichia coli str. K-12 substr. MG1655
Characteristics genotype: nsrR deletion, leu::GUGnsrR-kan
Growth protocol The cultures were grown aerobically at 37ÂșC in L broth to mid-exponential phase (OD650nm = ~0.6).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen) and the RNAprotect reagent (Qiagen). Contaminating DNA was removed by on-column DNase digestion by the RNase-Free DNase Set (Qiagen), and RNA purity was checked by UV absorbance and by agarose gel electrophoresis.
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 Escherichia coli MG1655 K-12 containing a wild-type nsrR (GUGnsrR). It is the third of three WT strain 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., 2003, Biostatistics 4:249), quantile normalization (Bolstad et al., 2003, Bioinformatics 19:185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Jun 26, 2015
Last update date Jun 27, 2015
Contact name Stephen Spiro
E-mail(s) stephen.spiro@utdallas.edu
Phone 001-972-883-6896
Organization name University of Texas at Dallas
Department Molecular and Cell Biology
Lab Spiro Lab
Street address 800 West Campbell Road
City Richardson
State/province TX
ZIP/Postal code 75080
Country USA
 
Platform ID GPL14649
Series (1)
GSE70325 Inefficient translation of nsrR constrains behavior of the NsrR regulon in Escherichia coli

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
b0001071000000001 9.96047
b0002071000000002 12.23299
b0003071000000003 11.64618
b0004071000000004 9.57448
b0005071000000005 8.13783
b0006071000000006 9.05902
b0007071000000007 9.46617
b0008071000000008 13.36889
b0009071000000009 9.28681
b0010071000000010 7.96956
b0011071000000011 6.10724
b0013071000000012 5.75999
b0014071000000013 11.88963
b0015071000000014 9.47904
b0016071000000015 10.93026
b0018071000000016 5.66647
b0019071000000018 11.30208
b0020071000000019 8.3288
b0021071000000020 9.91437
b0022071000000021 10.91091

Total number of rows: 4294

Table truncated, full table size 109 Kbytes.




Supplementary file Size Download File type/resource
GSM1723968_62534902_532.pair.gz 1017.5 Kb (ftp)(http) PAIR
Processed data included within Sample table

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