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Sample GSM1002313 Query DataSets for GSM1002313
Status Public on Aug 21, 2013
Title Slide 27_Aerobic culture_iCORM-3_biol rep 2_Cy3 5 Cy5 0
Sample type RNA
 
Channel 1
Source name Continuous aerobically grown cultures in Evans medium, prior to CORM-3 addition
Organism Escherichia coli
Characteristics strain: Wild type strain MG1655
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy5
Label protocol cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).
 
Channel 2
Source name Continuous aerobically grown cultures in Evans medium, exposed to 40uM iCORM-3 for 5min
Organism Escherichia coli
Characteristics strain: Wild type strain MG1655
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
Label Cy3
Label protocol cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).
 
 
Hybridization protocol For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).
Scan protocol Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology
Description The labelling procedure uses equal quantities of RNA from adequate CORM-3 samples and samples prior to addition of CORM-3
Data processing Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Sep 12, 2012
Last update date Aug 21, 2013
Contact name Robert Poole
E-mail(s) R.poole@shef.ac.uk
Phone 01142224447
Organization name University of Sheffield
Department Molecular Biology & Biotechnology
Lab F13
Street address Firth Court, Western Bank
City Sheffield
State/province South Yorkshire
ZIP/Postal code S10 2TN
Country United Kingdom
 
Platform ID GPL16048
Series (1)
GSE40811 Transcriptional profiling of Escherichia coli after addition of CORM-3 and iCORM-3 to aerobically and anaerobically growing cells

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]
INV_VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE INV_VALUE
1 0.000000000e+000 0.000000000e+000
2 0.000000000e+000 0.000000000e+000
3 0.000000000e+000 0.000000000e+000
4 0.234428 -2.344281465e-001
5 0.099039 -9.903900502e-002
6 0.000000000e+000 0.000000000e+000
7 -0.103658 1.036580221e-001
8 0.012768 -1.276799785e-002
9 0.2379 -2.378997017e-001
10 -0.0325598 3.255982459e-002
11 -0.120868 1.208681544e-001
12 0.0452491 -4.524910192e-002
13 -0.536994 5.369938912e-001
14 -0.130513 1.305131910e-001
15 0.142678 -1.426784555e-001
16 0.17338 -1.733796369e-001
17 0.00334182 -3.341817803e-003
18 -0.253893 2.538929434e-001
19 0.192795 -1.927952384e-001
20 -0.0689754 6.897544579e-002

Total number of rows: 15744

Table truncated, full table size 513 Kbytes.




Supplementary file Size Download File type/resource
GSM1002313_US11033869_252941210027_S01_GE2_1010_Sep10_1_4.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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