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Sample GSM93999 Query DataSets for GSM93999
Status Public on Feb 15, 2006
Title Mock infected murine liver-MO30k-(B)-6 hpi
Sample type RNA
 
Channel 1
Source name Cy5 labeled Liver RNA
Organism Mus musculus
Characteristics C57/BL6 murine Liver RNA- 6 hours post-injection with 200ul PBS (Mock).
Biomaterial provider Amalfitano Lab
Treatment protocol The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Extracted molecule total RNA
Extraction protocol RNA isolation was accomplished by homogenizing liver in liquid nitrogen, then extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was purified using an RNeasy Kit (Qiagen) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Label Cy5
Label protocol The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.
 
Channel 2
Source name Murine Reference RNA
Organism Mus musculus
Characteristics Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.
Biomaterial provider Stratagene
Treatment protocol The RNA (10 µg) was a total RNA mix that was assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Extracted molecule total RNA
Label Cy3
Label protocol The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.
 
 
Hybridization protocol Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.
Description Sample is C57/Bl6 murine liver RNA extract after mock infection with 200ul if PBS at 6 hpi.
Data processing VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.
 
Submission date Jan 27, 2006
Last update date Mar 06, 2006
Contact name Zachary Conrad Hartman
E-mail(s) zch@duke.edu
Phone 919-684-9197
Organization name Duke University
Department Surgery
Lab Lyerly Lab
Street address Research Drive MSRB rm 414
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL3222
Series (2)
GSE4128 Ad vectors in C3KO mice
GSE4339 The in vivo cellular response to adenovirus and its regulation through MyD88

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
PRE_VALUE Ratio of normalized Cy5/Cy3 values
Control Control Signal from Reference RNA
Raw Raw signal from Labeled RNA
FLAGS P denotes satisfactory features
UNF_VALUE Log2 of normalized Cy5/Cy3 values

Data table
ID_REF VALUE PRE_VALUE Control Raw FLAGS UNF_VALUE
M200000001
M200000002 -2.556393349 0.17 150.7 25 P -2.556393349
M200000004 -0.120294234 0.92 152.9 141 P -0.120294234
M200000005
M200000006 -0.152003093 0.9 116.4 105 P -0.152003093
M200000007
M200000008
M200000009 -0.577766999 0.67 238.2 160 P -0.577766999
M200000010
M200000011 -0.029146346 0.98 29.46 29 P -0.029146346
M200000012 -0.304006187 0.81 81.36 66 P -0.304006187
M200000014
M200000016 0.411426246 1.33 91.84 122 P 0.411426246
M200000017
M200000019
M200000020
M200000021
M200000023 -0.577766999 0.67 66.11 44 P -0.577766999
M200000025
M200000027

Total number of rows: 31780

Table truncated, full table size 920 Kbytes.




Supplementary data files not provided

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