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Sample GSM22638 Query DataSets for GSM22638
Status Public on May 15, 2004
Title WT macrophages, E. coli vs. Mock, mouse 3
Sample type RNA
 
Channel 1
Source name Macrophages from wildtype mouse 3 treated with live E. coli (1 bact. per mac.) for 2 hours
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name Macrophages from wildtype mouse 3 treated with media only for 2 hours
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Bone marrow was isolated from 6-8 week old C57BL/6J wild type and MyD88-deficient mice.
Macrophages from these marrows were cultured in DMEM media supplemented with 10% FBS and 15% L929 conditioned media (a source for CSF-1) for 8 days (plated at 3 million cells per 10 cm cell culture dish).
Cells were treated for 2 hours with either 10 ng/mL re-purified LPS (from E. coli O111), live E. coli bacteria (log phase; 1 bacteria per macrophage) or media only as a reference (Mock).
High quality total RNA was purified using a combination of the TRIzol protocol (Invitrogen) and RNeasy columns (Qiagen) according to the manufacturer's instructions.
RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies).
Total RNA samples were reverse transcribed and differentially labeled with Cy3 and Cy5 dyes (Amersham) using the Atlas PowerScript Fluorescent Labeling Kit (BD Biosciences).
Labeled cDNA samples were hybridized over night in a Genomic Solutions hybridization station (Perkin-Elmer).
The hybridization buffer was 3xSSC, 50 mM Hepes buffer, 0.1% SDS, pH 7.0, 30 ng/mL salmon sperm DNA, 30 ng/mL poly-A DNA, 30 ng/mL mouse Cot-1 DNA.
The microarray slides were scanned with a GenePix 4000B microarray scanner and images quantified with the GenePix Pro 3.0 software (Axon Instruments).
All data analysis and statistical analysis was performed with BioArray Software Environment (BASE; Lund University, Sweden) and GeneSpring software (Silicon Genetics).
TIFF images can be downloaded from http://pga.mgh.harvard.edu
Keywords = Mus musculus, LPS, endotoxin, macrophages, MyD88
 
Submission date May 10, 2004
Last update date May 27, 2005
Contact name Harry Björkbacka
E-mail(s) harry.bjorkbacka@med.lu.se
URL http://www.med.lu.se/expcard
Organization name Lund University
Department Dept. of Clinical Sciences, Malmö
Lab Experimental Cardiovascular Research Unit
Street address CRC 91:12, UMAS entrance 72
City Malmö
ZIP/Postal code 205 02
Country Sweden
 
Platform ID GPL1226
Series (1)
GSE1405 LPS-induced and E. coli-induced gene expression in wildtype and MyD88-/- mouse macrophages

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of background subtracted medians defined by CH1/CH2 (LPS over Mock)
CH1_Median CH1 (F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) standard deviation of fluorescence intenisty
CH1_BG_Median CH1 (F635) background median fluorescence intensity
CH1_BG_Mean CH1 (F635) background mean fluorescence intensity
CH1_BG_SD CH1 (F635) background standard deviation of fluorescence intensity
CH2_Median CH2 (F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) standard deviation of fluorescence intenisty
CH2_BG_Median CH2 (F532) background median fluorescence intensity
CH2_BG_Mean CH2 (F532) background mean fluorescence intensity
CH2_BG_SD CH2 (F532) background standard deviation of fluorescence intensity
AREA Number of feature pixels
AREA_BG Number of feature background pixels
FLAGS 0 found feature, -50 not found feature, -75 absent feature, -100 manually flagged bad feature.

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BG_Median CH1_BG_Mean CH1_BG_SD CH2_Median CH2_MEAN CH2_SD CH2_BG_Median CH2_BG_Mean CH2_BG_SD AREA AREA_BG FLAGS
1 0.271502769 829 889 415 160 218 647 1052 1234 632 201 271 873 316 2352 0
2 0.640183149 250 291 162 155 178 152 283 292 111 199 213 84 156 1094 0
3 2.071011957 987 1022 412 149 166 94 506 524 182 200 206 68 208 1660 0
4 0.943064192 525 711 695 153 169 101 507 697 557 209 220 86 208 1502 0
5 0.280417488 715 846 516 150 168 108 905 1056 585 197 205 71 156 1140 0
6 0.331530271 1083 2519 3257 154 185 202 1329 2565 3083 208 229 169 208 1660 0
7 0.307361023 1189 1346 960 160 185 125 1478 1607 1057 218 236 108 208 1512 0
8 -6.64385619 173 195 112 176 191 104 246 257 97 224 237 84 120 820 0
9 3.883828115 6507 7420 2388 177 202 164 832 920 346 220 231 82 208 1660 0
10 4.738767999 444 557 361 177 202 135 247 263 96 234 246 92 156 1140 0
11 1.113160654 228 282 186 183 215 151 254 310 235 232 262 159 120 820 0
12 184 204 107 178 203 147 232 248 103 225 251 159 460 2620 -50
13 181 205 122 190 215 139 230 247 99 230 251 145 460 2620 -50
14 171 195 116 178 202 124 209 227 97 225 255 150 460 2620 -50
15 0.183575313 316 369 210 188 213 125 404 445 231 240 270 150 208 1660 0
16 0.969501156 292 404 334 185 214 153 308 483 447 232 262 183 316 2384 0
17 1.408840367 270 265 132 189 206 103 293 309 115 254 280 107 52 332 0
18 0.612658605 232 266 148 161 176 96 266 278 90 206 216 78 156 1130 0
19 0.022117357 4415 4703 1935 154 241 571 5931 6256 2586 196 256 497 208 1660 0
20 0.751506997 265 284 160 144 160 87 301 322 134 198 208 73 156 1140 0

Total number of rows: 13872

Table truncated, full table size 985 Kbytes.




Supplementary data files not provided

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