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Sample GSM65626 Query DataSets for GSM65626
Status Public on Jul 27, 2005
Title dam mutS treat replicate 3
Sample type RNA
 
Source name E. coli dam mutS mutant strain GM5556
Organism Escherichia coli
Characteristics As GM3819 dam-16::Kan but mutS215::Tn10
Growth protocol Overnight culture was diluted 1000-fold with fresh LB medium and cultured further. Log phase culture was diluted to a cell density of 2 X 108 cells/ml in M9 salts containing 150 uM cisplatin and incubated at 37°C for two hours, after which it was resuspended in LB broth for 90 minutes.
Extracted molecule total RNA
Extraction protocol Epicentre MasterPure RNA Purification kit
Label PEO-iodeacetyl-Biotin
Label protocol Affymetrix protocol for E. coli sense genome arrays
 
Description Overnight culture was diluted 1000-fold with fresh LB medium and cultured further. Log phase culture was diluted to a cell density of 2 X 108 cells/ml in M9 salts containing 150 uM cisplatin and incubated at 37°C for two hours, after which it was resuspended in LB broth for 90 minutes. Total RNA was isolated from cells by extraction using the MasterPure RNA Purification Kit (Epicentre Technologies) followed by DNAse digestion according to the manufacturer’s protocol. The isolated total RNA was quantitated by absorption at 260 nm (typical yield from a 15 ml culture was 250-500 µg of total RNA), and the purity was determined by the ratio of absorption values at 260/280nm. RNA quality was determined by formaldehyde agarose gel electrophoresis (1.2% agarose in FA Buffer pH 7.0 (20 mM 3-[N-morpholino]propanesulfonic acid, 5 mM sodium acetate, 1 mM ethylenadiaminetetraacetic acide (EDTA))) or by analysis on an Agilent 2100 Bioanalyzer. All samples visualized by gel electrophoresis or by the bioanalyzer electropherogram showed clear distinct bands correlating to 16S and 23S ribosomal RNA, indicating that no detectable RNA degradation occurred and that RNA integrity was maintained throughout the RNA isolation procedure. mRNA was enriched from total RNA as described in the Affymetrix GeneChip Expression Analysis Technical Manual for GeneChip E. coli Sense Genome Arrays.
Data processing GCRMA normalization using the Array Analyzer module version 2.0.2 in S-Plus version 6.2 (Insightful)
 
Submission date Jul 25, 2005
Last update date Oct 28, 2005
Contact name Jennifer Robbins
E-mail(s) [email protected]
Organization name Massachusetts Institute of Technology
Department Biological Engineering
Lab John Essigmann
Street address 77 Massachusetts Ave.
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL73
Series (1)
GSE2999 Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli

Data table header descriptions
ID_REF
VALUE dam mutS treat replicate 3

Data table
ID_REF VALUE
AFFX-BioB-5_st 4.307590001
AFFX-BioC-3_st 3.987770001
AFFX-CreX-3_st 4.48056
AFFX-CreX-5_st 5.285120001
AFFX-DapX-3_st 5.797159999
AFFX-DapX-5_st 5.960820002
AFFX-DapX-M_st 6.685460001
AFFX-HXB2_3_st 5.814880002
AFFX-HXB2_5_st 7.042650002
AFFX-HXB2_M_st 5.731589998
AFFX-LysX-3_st 10.2575
AFFX-LysX-5_st 8.083830002
AFFX-LysX-M_st 6.129900001
AFFX-PheX-3_st 5.570680001
AFFX-PheX-5_st 7.373880002
AFFX-PheX-M_st 6.435629998
AFFX-ThrX-3_st 4.921350001
AFFX-ThrX-5_st 5.177280001
AFFX-ThrX-M_st 5.645949998
AFFX-TrpnX-3_st 5.640609999

Total number of rows: 7312

Table truncated, full table size 215 Kbytes.




Supplementary data files not provided

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