title: f2#348 versus pool Mouse Brain tissue set 2


title: f2#343 versus pool Mouse Brain tissue set 2

status: Public on Aug 10 2009

type: RNA

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

country: USA

institute: UCLA

description: Brain tissue from 292 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Brain tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Mus musculus

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Female

source_name: pool

tag: Strain:C57BL/6J and C3H/HeJ  Age:24 weeks (150 randomly selected F2)


title: f2#341 versus pool Mouse Brain tissue set 2


title: f2#362 versus pool Mouse Brain tissue set 2


title: f2#326 versus pool Mouse Brain tissue set 2


title: f2#217 versus pool Mouse Brain tissue set 2

tag: Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Male


title: f2#342 versus pool Mouse Brain tissue set 2


title: f2#335 versus pool Mouse Brain tissue set 2


title: f2#356 versus pool Mouse Brain tissue set 2


title: f2#333 versus pool Mouse Brain tissue set 2


title: f2#340 versus pool Mouse Brain tissue set 2


title: f2#325 versus pool Mouse Brain tissue set 2


title: f2#315 versus pool Mouse Brain tissue set 2


title: f2#332 versus pool Mouse Brain tissue set 2


title: f2#331 versus pool Mouse Brain tissue set 2


title: f2#330 versus pool Mouse Brain tissue set 2


title: f2#360 versus pool Mouse Brain tissue set 2


title: f2#334 versus pool Mouse Brain tissue set 2


title: f2#323 versus pool Mouse Brain tissue set 2


title: f2#324 versus pool Mouse Brain tissue set 2


title: f2#350 versus pool Mouse Brain tissue set 2


title: f2#314 versus pool Mouse Brain tissue set 2


title: f2#311 versus pool Mouse Brain tissue set 2


title: f2#287 versus pool Mouse Brain tissue set 2


title: f2#284 versus pool Mouse Brain tissue set 2


title: f2#285 versus pool Mouse Brain tissue set 2


title: f2#294 versus pool Mouse Brain tissue set 2


title: f2#273 versus pool Mouse Brain tissue set 2


title: f2#304 versus pool Mouse Brain tissue set 2


title: f2#286 versus pool Mouse Brain tissue set 2


title: f2#310 versus pool Mouse Brain tissue set 2


title: f2#262 versus pool Mouse Brain tissue set 2


title: f2#292 versus pool Mouse Brain tissue set 2


title: f2#271 versus pool Mouse Brain tissue set 2


title: f2#313 versus pool Mouse Brain tissue set 2


title: f2#291 versus pool Mouse Brain tissue set 2


title: f2#261 versus pool Mouse Brain tissue set 2


title: f2#256 versus pool Mouse Brain tissue set 2


title: f2#270 versus pool Mouse Brain tissue set 2


title: f2#272 versus pool Mouse Brain tissue set 2


title: f2#274 versus pool Mouse Brain tissue set 2


title: f2#250 versus pool Mouse Brain tissue set 2


title: f2#252 versus pool Mouse Brain tissue set 2


title: f2#251 versus pool Mouse Brain tissue set 2


title: f2#249 versus pool Mouse Brain tissue set 2


title: f2#312 versus pool Mouse Brain tissue set 2


title: f2#245 versus pool Mouse Brain tissue set 2


title: f2#244 versus pool Mouse Brain tissue set 2


title: f2#239 versus pool Mouse Brain tissue set 2


title: f2#227 versus pool Mouse Brain tissue set 2


title: f2#238 versus pool Mouse Brain tissue set 2


title: f2#226 versus pool Mouse Brain tissue set 2


title: f2#237 versus pool Mouse Brain tissue set 2


title: f2#228 versus pool Mouse Brain tissue set 2


title: f2#225 versus pool Mouse Brain tissue set 2


title: f2#221 versus pool Mouse Brain tissue set 2


title: f2#213 versus pool Mouse Brain tissue set 2


title: f2#236 versus pool Mouse Brain tissue set 2


title: f2#220 versus pool Mouse Brain tissue set 2


title: f2#209 versus pool Mouse Brain tissue set 2

description: Brain tissue from 292 F2 Female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Brain tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#216 versus pool Mouse Brain tissue set 2


title: f2#212 versus pool Mouse Brain tissue set 2


title: f2#211 versus pool Mouse Brain tissue set 2


title: f2#208 versus pool Mouse Brain tissue set 2


title: f2#206 versus pool Mouse Brain tissue set 2


title: f2#222 versus pool Mouse Brain tissue set 2


title: f2#205 versus pool Mouse Brain tissue set 2


title: f2#215 versus pool Mouse Brain tissue set 2


title: f2#203 versus pool Mouse Brain tissue set 2


title: f2#204 versus pool Mouse Brain tissue set 2


title: f2#207 versus pool Mouse Brain tissue set 2


title: f2#201 versus pool Mouse Brain tissue set 2


title: f2#200 versus pool Mouse Brain tissue set 2


title: f2#202 versus pool Mouse Brain tissue set 2


title: f2#188 versus pool Mouse Brain tissue set 2


title: f2#178 versus pool Mouse Brain tissue set 2


title: f2#198 versus pool Mouse Brain tissue set 2


title: f2#189 versus pool Mouse Brain tissue set 2


title: f2#187 versus pool Mouse Brain tissue set 2


title: f2#199 versus pool Mouse Brain tissue set 2


title: f2#167 versus pool Mouse Brain tissue set 2


title: f2#173 versus pool Mouse Brain tissue set 2


title: f2#166 versus pool Mouse Brain tissue set 2


title: f2#181 versus pool Mouse Brain tissue set 2


title: f2#159 versus pool Mouse Brain tissue set 2


title: f2#158 versus pool Mouse Brain tissue set 2


title: f2#149 versus pool Mouse Brain tissue set 2


title: f2#177 versus pool Mouse Brain tissue set 2


title: f2#165 versus pool Mouse Brain tissue set 2


title: f2#150 versus pool Mouse Brain tissue set 2


title: f2#171 versus pool Mouse Brain tissue set 2


title: f2#170 versus pool Mouse Brain tissue set 2


title: f2#210 versus pool Mouse Brain tissue set 2


title: f2#172 versus pool Mouse Brain tissue set 2


title: f2#293 versus pool Mouse Brain tissue set 2


title: f2#151 versus pool Mouse Brain tissue set 2


title: f2#140 versus pool Mouse Brain tissue set 2


title: f2#148 versus pool Mouse Brain tissue set 2


title: f2#129 versus pool Mouse Brain tissue set 2


title: f2#139 versus pool Mouse Brain tissue set 2


title: f2#126 versus pool Mouse Brain tissue set 2


title: f2#133 versus pool Mouse Brain tissue set 2


title: f2#124 versus pool Mouse Brain tissue set 2


title: f2#134 versus pool Mouse Brain tissue set 2


title: f2#125 versus pool Mouse Brain tissue set 2


title: f2#157 versus pool Mouse Brain tissue set 2


title: f2#123 versus pool Mouse Brain tissue set 2


title: f2#96 versus pool Mouse Brain tissue set 2


title: f2#101 versus pool Mouse Brain tissue set 2


title: f2#117 versus pool Mouse Brain tissue set 2


title: f2#88 versus pool Mouse Brain tissue set 2


title: f2#120 versus pool Mouse Brain tissue set 2


title: f2#118 versus pool Mouse Brain tissue set 2


title: f2#97 versus pool Mouse Brain tissue set 2


title: f2#93 versus pool Mouse Brain tissue set 2


title: f2#119 versus pool Mouse Brain tissue set 2


title: f2#69 versus pool Mouse Brain tissue set 2


title: f2#109 versus pool Mouse Brain tissue set 2


title: f2#100 versus pool Mouse Brain tissue set 2


title: f2#116 versus pool Mouse Brain tissue set 2


title: f2#95 versus pool Mouse Brain tissue set 2


title: f2#102 versus pool Mouse Brain tissue set 2


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title: f2#78 versus pool Mouse Brain tissue set 2


title: f2#71 versus pool Mouse Brain tissue set 2


title: f2#92 versus pool Mouse Brain tissue set 2


title: f2#70 versus pool Mouse Brain tissue set 2


title: f2#87 versus pool Mouse Brain tissue set 2


title: f2#77 versus pool Mouse Brain tissue set 2


title: f2#68 versus pool Mouse Brain tissue set 2


title: f2#60 versus pool Mouse Brain tissue set 2


title: f2#63 versus pool Mouse Brain tissue set 2


title: f2#61 versus pool Mouse Brain tissue set 2


title: f2#55 versus pool Mouse Brain tissue set 2


title: f2#196 versus pool Mouse Brain tissue set 2


title: f2#192 versus pool Mouse Brain tissue set 2


title: f2#54 versus pool Mouse Brain tissue set 2


title: f2#191 versus pool Mouse Brain tissue set 2


title: f2#186 versus pool Mouse Brain tissue set 2


title: f2#56 versus pool Mouse Brain tissue set 2


title: f2#194 versus pool Mouse Brain tissue set 2


title: f2#57 versus pool Mouse Brain tissue set 2


title: f2#59 versus pool Mouse Brain tissue set 2


title: f2#195 versus pool Mouse Brain tissue set 2


title: f2#175 versus pool Mouse Brain tissue set 2


title: f2#183 versus pool Mouse Brain tissue set 2


title: f2#179 versus pool Mouse Brain tissue set 2


title: f2#180 versus pool Mouse Brain tissue set 2


title: f2#176 versus pool Mouse Brain tissue set 2


title: f2#174 versus pool Mouse Brain tissue set 2


title: f2#169 versus pool Mouse Brain tissue set 2


title: f2#168 versus pool Mouse Brain tissue set 2


title: f2#185 versus pool Mouse Brain tissue set 2


title: f2#163 versus pool Mouse Brain tissue set 2


title: f2#164 versus pool Mouse Brain tissue set 2


title: f2#67 versus pool Mouse Brain tissue set 2


title: f2#156 versus pool Mouse Brain tissue set 2


title: f2#160 versus pool Mouse Brain tissue set 2


title: f2#154 versus pool Mouse Brain tissue set 2


title: f2#144 versus pool Mouse Brain tissue set 2


title: f2#136 versus pool Mouse Brain tissue set 2


title: f2#137 versus pool Mouse Brain tissue set 2


title: f2#131 versus pool Mouse Brain tissue set 2


title: f2#132 versus pool Mouse Brain tissue set 2


title: f2#193 versus pool Mouse Brain tissue set 2


title: f2#184 versus pool Mouse Brain tissue set 2


title: f2#135 versus pool Mouse Brain tissue set 2


title: f2#153 versus pool Mouse Brain tissue set 2


title: f2#155 versus pool Mouse Brain tissue set 2


title: f2#143 versus pool Mouse Brain tissue set 2


title: f2#128 versus pool Mouse Brain tissue set 2


title: f2#147 versus pool Mouse Brain tissue set 2


title: f2#127 versus pool Mouse Brain tissue set 2


title: f2#138 versus pool Mouse Brain tissue set 2


title: f2#146 versus pool Mouse Brain tissue set 2


title: f2#130 versus pool Mouse Brain tissue set 2


title: f2#121 versus pool Mouse Brain tissue set 2


title: f2#142 versus pool Mouse Brain tissue set 2


title: f2#115 versus pool Mouse Brain tissue set 2


title: f2#122 versus pool Mouse Brain tissue set 2


title: f2#112 versus pool Mouse Brain tissue set 2


title: f2#113 versus pool Mouse Brain tissue set 2


title: f2#114 versus pool Mouse Brain tissue set 2


title: f2#111 versus pool Mouse Brain tissue set 2


title: f2#110 versus pool Mouse Brain tissue set 2


title: f2#108 versus pool Mouse Brain tissue set 2


title: f2#107 versus pool Mouse Brain tissue set 2


title: f2#105 versus pool Mouse Brain tissue set 2


title: f2#84 versus pool Mouse Brain tissue set 2


title: f2#79 versus pool Mouse Brain tissue set 2


title: f2#99 versus pool Mouse Brain tissue set 2


title: f2#85 versus pool Mouse Brain tissue set 2


title: f2#106 versus pool Mouse Brain tissue set 2


title: f2#104 versus pool Mouse Brain tissue set 2


title: f2#98 versus pool Mouse Brain tissue set 2


title: f2#89 versus pool Mouse Brain tissue set 2


title: f2#90 versus pool Mouse Brain tissue set 2


title: f2#91 versus pool Mouse Brain tissue set 2


title: f2#76 versus pool Mouse Brain tissue set 2


title: f2#82 versus pool Mouse Brain tissue set 2


title: f2#80 versus pool Mouse Brain tissue set 2


title: f2#83 versus pool Mouse Brain tissue set 2


title: f2#74 versus pool Mouse Brain tissue set 2


title: f2#75 versus pool Mouse Brain tissue set 2


title: OriC-null, yabA-null untreated sample replicate 2

status: Public on Sep 01 2009

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

department: Biology

institute: MIT

description: Investigating the effects of replication arrest on OriC-null, yabA-null cells

hyb_protocol: see: A transcriptional response to replication status mediated by the conserved bacterial replication protein DnaA. Goranov AI, Katz L, Breier AM, Burge CB, Grossman AD. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12932-7. PMID: 16120674

data_processing: Arrays were normalized by setting the total signal of both channels to unity. Goranov et al. 2005.

organism: Bacillus subtilis

source_name: AIG185 RNA

growth_protocol: defined minimal medium. Exponentially growing

tag: strain

value: AIG185, yabA-null, OriC-null

tag: sample type

value: RNA from untreated yabA, OriC-null

source_name: reference RNA

value: pooled reference RNA


title: f2#145 versus pool Mouse Brain tissue set 2


title: f2#161 versus pool Mouse Brain tissue set 2


title: f2#73 versus pool Mouse Brain tissue set 2


title: f2#58 versus pool Mouse Brain tissue set 2


title: f2#352 versus pool Mouse Muscle tissue

description: Muscle tissue from 285 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Muscle tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#359 versus pool Mouse Muscle tissue


title: f2#51 versus pool Mouse Brain tissue set 2


title: f2#347 versus pool Mouse Muscle tissue


title: f2#53 versus pool Mouse Brain tissue set 2


title: f2#65 versus pool Mouse Brain tissue set 2


title: f2#66 versus pool Mouse Brain tissue set 2


title: f2#358 versus pool Mouse Muscle tissue


title: f2#339 versus pool Mouse Muscle tissue


title: f2#357 versus pool Mouse Muscle tissue


title: f2#64 versus pool Mouse Brain tissue set 2


title: f2#345 versus pool Mouse Muscle tissue


title: f2#337 versus pool Mouse Muscle tissue


title: f2#338 versus pool Mouse Muscle tissue


title: f2#346 versus pool Mouse Muscle tissue


title: f2#329 versus pool Mouse Muscle tissue


title: f2#336 versus pool Mouse Muscle tissue


title: f2#327 versus pool Mouse Muscle tissue


title: f2#353 versus pool Mouse Muscle tissue


title: f2#354 versus pool Mouse Muscle tissue


title: f2#328 versus pool Mouse Muscle tissue


title: f2#351 versus pool Mouse Muscle tissue


title: f2#322 versus pool Mouse Muscle tissue


title: f2#319 versus pool Mouse Muscle tissue


title: f2#320 versus pool Mouse Muscle tissue


title: f2#318 versus pool Mouse Muscle tissue


title: f2#317 versus pool Mouse Muscle tissue


title: f2#321 versus pool Mouse Muscle tissue


title: f2#316 versus pool Mouse Muscle tissue


title: f2#303 versus pool Mouse Muscle tissue


title: f2#299 versus pool Mouse Muscle tissue


title: f2#296 versus pool Mouse Muscle tissue


title: f2#307 versus pool Mouse Muscle tissue


title: f2#308 versus pool Mouse Muscle tissue


title: f2#281 versus pool Mouse Muscle tissue


title: f2#282 versus pool Mouse Muscle tissue


title: f2#283 versus pool Mouse Muscle tissue


title: f2#297 versus pool Mouse Muscle tissue


title: f2#300 versus pool Mouse Muscle tissue


title: f2#301 versus pool Mouse Muscle tissue


title: f2#288 versus pool Mouse Muscle tissue


title: f2#280 versus pool Mouse Muscle tissue


title: f2#289 versus pool Mouse Muscle tissue


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title: f2#309 versus pool Mouse Muscle tissue


title: f2#295 versus pool Mouse Muscle tissue


title: f2#306 versus pool Mouse Muscle tissue


title: f2#278 versus pool Mouse Muscle tissue


title: f2#279 versus pool Mouse Muscle tissue


title: f2#268 versus pool Mouse Muscle tissue


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title: f2#266 versus pool Mouse Muscle tissue


title: f2#277 versus pool Mouse Muscle tissue


title: f2#258 versus pool Mouse Muscle tissue


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title: f2#263 versus pool Mouse Muscle tissue


title: f2#248 versus pool Mouse Muscle tissue


title: f2#257 versus pool Mouse Muscle tissue


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title: f2#255 versus pool Mouse Muscle tissue


title: f2#241 versus pool Mouse Muscle tissue


title: f2#247 versus pool Mouse Muscle tissue


title: f2#276 versus pool Mouse Muscle tissue


title: f2#253 versus pool Mouse Muscle tissue


title: f2#290 versus pool Mouse Muscle tissue


title: f2#254 versus pool Mouse Muscle tissue


title: f2#242 versus pool Mouse Muscle tissue


title: f2#235 versus pool Mouse Muscle tissue


title: f2#240 versus pool Mouse Muscle tissue


title: f2#231 versus pool Mouse Muscle tissue


title: f2#223 versus pool Mouse Muscle tissue (2)


title: f2#219 versus pool Mouse Muscle tissue


title: f2#234 versus pool Mouse Muscle tissue


title: f2#302 versus pool Mouse Muscle tissue


title: f2#217 versus pool Mouse Muscle tissue


title: f2#356 versus pool Mouse Muscle tissue


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title: f2#230 versus pool Mouse Muscle tissue


title: f2#348 versus pool Mouse Muscle tissue


title: f2#342 versus pool Mouse Muscle tissue


title: f2#360 versus pool Mouse Muscle tissue


title: f2#362 versus pool Mouse Muscle tissue


title: f2#224 versus pool Mouse Muscle tissue


title: f2#355 versus pool Mouse Muscle tissue


title: f2#335 versus pool Mouse Muscle tissue


title: f2#350 versus pool Mouse Muscle tissue


title: f2#334 versus pool Mouse Muscle tissue


title: f2#333 versus pool Mouse Muscle tissue


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title: f2#341 versus pool Mouse Muscle tissue


title: f2#343 versus pool Mouse Muscle tissue


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title: f2#361 versus pool Mouse Muscle tissue


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title: f2#312 versus pool Mouse Muscle tissue


title: f2#291 versus pool Mouse Muscle tissue


title: f2#310 versus pool Mouse Muscle tissue


title: f2#292 versus pool Mouse Muscle tissue


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title: f2#313 versus pool Mouse Muscle tissue


title: f2#287 versus pool Mouse Muscle tissue


title: f2#305 versus pool Mouse Muscle tissue


title: f2#294 versus pool Mouse Muscle tissue


title: f2#284 versus pool Mouse Muscle tissue


title: f2#304 versus pool Mouse Muscle tissue


title: f2#293 versus pool Mouse Muscle tissue


title: f2#285 versus pool Mouse Muscle tissue


title: f2#275 versus pool Mouse Muscle tissue


title: f2#273 versus pool Mouse Muscle tissue


title: f2#274 versus pool Mouse Muscle tissue


title: f2#286 versus pool Mouse Muscle tissue


title: f2#272 versus pool Mouse Muscle tissue


title: f2#256 versus pool Mouse Muscle tissue


title: f2#245 versus pool Mouse Muscle tissue


title: f2#249 versus pool Mouse Muscle tissue


title: f2#244 versus pool Mouse Muscle tissue


title: f2#271 versus pool Mouse Muscle tissue


title: f2#237 versus pool Mouse Muscle tissue


title: f2#239 versus pool Mouse Muscle tissue (2)


title: f2#251 versus pool Mouse Muscle tissue


title: f2#214 versus pool Mouse Muscle tissue


title: f2#250 versus pool Mouse Muscle tissue


title: f2#225 versus pool Mouse Muscle tissue


title: f2#228 versus pool Mouse Muscle tissue


title: f2#262 versus pool Mouse Muscle tissue


title: f2#252 versus pool Mouse Muscle tissue


title: f2#261 versus pool Mouse Muscle tissue


title: f2#220 versus pool Mouse Muscle tissue


title: f2#216 versus pool Mouse Muscle tissue


title: f2#221 versus pool Mouse Muscle tissue


title: f2#222 versus pool Mouse Muscle tissue


title: f2#227 versus pool Mouse Muscle tissue


title: f2#236 versus pool Mouse Muscle tissue


title: f2#215 versus pool Mouse Muscle tissue


title: f2#226 versus pool Mouse Muscle tissue


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title: f2#205 versus pool Mouse Muscle tissue


title: f2#201 versus pool Mouse Muscle tissue


title: f2#324 versus pool Mouse Muscle tissue


title: f2#207 versus pool Mouse Muscle tissue


title: f2#167 versus pool Mouse Muscle tissue


title: f2#159 versus pool Mouse Muscle tissue


title: f2#270 versus pool Mouse Muscle tissue


title: f2#158 versus pool Mouse Muscle tissue


title: f2#166 versus pool Mouse Muscle tissue


title: f2#172 versus pool Mouse Muscle tissue


title: f2#150 versus pool Mouse Muscle tissue


title: f2#171 versus pool Mouse Muscle tissue


title: f2#177 versus pool Mouse Muscle tissue


title: f2#157 versus pool Mouse Muscle tissue


title: f2#187 versus pool Mouse Muscle tissue


title: f2#152 versus pool Mouse Muscle tissue


title: f2#170 versus pool Mouse Muscle tissue


title: f2#165 versus pool Mouse Muscle tissue


title: f2#151 versus pool Mouse Muscle tissue


title: f2#181 versus pool Mouse Muscle tissue


title: f2#198 versus pool Mouse Muscle tissue


title: f2#178 versus pool Mouse Muscle tissue


title: f2#148 versus pool Mouse Muscle tissue


title: f2#173 versus pool Mouse Muscle tissue


title: f2#190 versus pool Mouse Muscle tissue


title: f2#189 versus pool Mouse Muscle tissue (2)


title: f2#134 versus pool Mouse Muscle tissue


title: f2#149 versus pool Mouse Muscle tissue


title: f2#139 versus pool Mouse Muscle tissue


title: f2#202 versus pool Mouse Muscle tissue


title: f2#188 versus pool Mouse Muscle tissue


title: f2#203 versus pool Mouse Muscle tissue (2)


title: f2#199 versus pool Mouse Muscle tissue


title: f2#200 versus pool Mouse Muscle tissue


title: f2#123 versus pool Mouse Muscle tissue


title: f2#126 versus pool Mouse Muscle tissue


title: f2#92 versus pool Mouse Muscle tissue


title: f2#109 versus pool Mouse Muscle tissue


title: f2#116 versus pool Mouse Muscle tissue


title: f2#119 versus pool Mouse Muscle tissue


title: f2#118 versus pool Mouse Muscle tissue


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title: f2#95 versus pool Mouse Muscle tissue


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title: f2#96 versus pool Mouse Muscle tissue


title: f2#124 versus pool Mouse Muscle tissue


title: f2#94 versus pool Mouse Muscle tissue


title: f2#133 versus pool Mouse Muscle tissue


title: f2#72 versus pool Mouse Muscle tissue


title: f2#120 versus pool Mouse Muscle tissue


title: f2#86 versus pool Mouse Muscle tissue


title: f2#87 versus pool Mouse Muscle tissue


title: f2#125 versus pool Mouse Muscle tissue


title: f2#88 versus pool Mouse Muscle tissue


title: f2#77 versus pool Mouse Muscle tissue


title: f2#71 versus pool Mouse Muscle tissue


title: f2#78 versus pool Mouse Muscle tissue


title: f2#69 versus pool Mouse Muscle tissue


title: f2#70 versus pool Mouse Muscle tissue


title: f2#59 versus pool Mouse Muscle tissue


title: f2#67 versus pool Mouse Muscle tissue


title: f2#60 versus pool Mouse Muscle tissue


title: f2#61 versus pool Mouse Muscle tissue


title: f2#57 versus pool Mouse Muscle tissue


title: f2#63 versus pool Mouse Muscle tissue


title: f2#68 versus pool Mouse Muscle tissue


title: f2#54 versus pool Mouse Muscle tissue


title: f2#62 versus pool Mouse Muscle tissue


title: f2#196 versus pool Mouse Muscle tissue


title: f2#56 versus pool Mouse Muscle tissue


title: f2#192 versus pool Mouse Muscle tissue


title: f2#186 versus pool Mouse Muscle tissue


title: f2#55 versus pool Mouse Muscle tissue


title: f2#179 versus pool Mouse Muscle tissue


title: f2#176 versus pool Mouse Muscle tissue


title: f2#193 versus pool Mouse Muscle tissue


title: f2#194 versus pool Mouse Muscle tissue


title: f2#180 versus pool Mouse Muscle tissue


title: f2#195 versus pool Mouse Muscle tissue


title: f2#175 versus pool Mouse Muscle tissue


title: f2#174 versus pool Mouse Muscle tissue


title: f2#191 versus pool Mouse Muscle tissue


title: f2#197 versus pool Mouse Muscle tissue


title: f2#164 versus pool Mouse Muscle tissue


title: f2#154 versus pool Mouse Muscle tissue


title: f2#169 versus pool Mouse Muscle tissue


title: f2#168 versus pool Mouse Muscle tissue


title: f2#156 versus pool Mouse Muscle tissue


title: f2#153 versus pool Mouse Muscle tissue


title: f2#163 versus pool Mouse Muscle tissue


title: f2#144 versus pool Mouse Muscle tissue


title: f2#141 versus pool Mouse Muscle tissue


title: f2#137 versus pool Mouse Muscle tissue


title: f2#146 versus pool Mouse Muscle tissue


title: f2#135 versus pool Mouse Muscle tissue


title: f2#162 versus pool Mouse Muscle tissue


title: f2#128 versus pool Mouse Muscle tissue


title: f2#161 versus pool Mouse Muscle tissue


title: f2#131 versus pool Mouse Muscle tissue


title: f2#127 versus pool Mouse Muscle tissue


title: f2#130 versus pool Mouse Muscle tissue


title: f2#142 versus pool Mouse Muscle tissue


title: f2#155 versus pool Mouse Muscle tissue


title: f2#132 versus pool Mouse Muscle tissue


title: f2#160 versus pool Mouse Muscle tissue


title: f2#129 versus pool Mouse Muscle tissue


title: f2#101 versus pool Mouse Muscle tissue


title: f2#143 versus pool Mouse Muscle tissue


title: f2#145 versus pool Mouse Muscle tissue


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title: f2#110 versus pool Mouse Muscle tissue


title: f2#85 versus pool Mouse Muscle tissue

description: Muscle tissue from 285  F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Muscle tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#114 versus pool Mouse Muscle tissue


title: f2#107 versus pool Mouse Muscle tissue


title: f2#80 versus pool Mouse Muscle tissue


title: f2#79 versus pool Mouse Muscle tissue


title: f2#84 versus pool Mouse Muscle tissue


title: f2#83 versus pool Mouse Muscle tissue


title: f2#82 versus pool Mouse Muscle tissue


title: f2#89 versus pool Mouse Muscle tissue


title: f2#75 versus pool Mouse Muscle tissue


title: f2#108 versus pool Mouse Muscle tissue


title: f2#99 versus pool Mouse Muscle tissue


title: f2#91 versus pool Mouse Muscle tissue


title: f2#105 versus pool Mouse Muscle tissue


title: f2#74 versus pool Mouse Muscle tissue


title: f2#58 versus pool Mouse Muscle tissue


title: f2#65 versus pool Mouse Muscle tissue


title: f2#52 versus pool Mouse Muscle tissue


title: f2#359 versus pool Mouse Liver tissue

description: Liver tissue from 302 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Liver tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

tag: Strain:C57BL/6J and C3H/HeJ  Age:20 weeks (150 randomly selected F2)


title: f2#64 versus pool Mouse Muscle tissue


title: f2#51 versus pool Mouse Muscle tissue


title: f2#358 versus pool Mouse Liver tissue


title: f2#354 versus pool Mouse Liver tissue


title: f2#353 versus pool Mouse Liver tissue


title: f2#357 versus pool Mouse Liver tissue


title: f2#351 versus pool Mouse Liver tissue


title: f2#352 versus pool Mouse Liver tissue


title: f2#347 versus pool Mouse Liver tissue


title: f2#338 versus pool Mouse Liver tissue


title: f2#344 versus pool Mouse Liver tissue


title: f2#336 versus pool Mouse Liver tissue


title: f2#339 versus pool Mouse Liver tissue


title: f2#327 versus pool Mouse Liver tissue


title: f2#337 versus pool Mouse Liver tissue


title: f2#328 versus pool Mouse Liver tissue


title: f2#329 versus pool Mouse Liver tissue


title: f2#322 versus pool Mouse Liver tissue


title: f2#321 versus pool Mouse Liver tissue


title: f2#320 versus pool Mouse Liver tissue


title: f2#319 versus pool Mouse Liver tissue


title: f2#98 versus pool Mouse Muscle tissue


title: f2#317 versus pool Mouse Liver tissue


title: f2#318 versus pool Mouse Liver tissue


title: f2#81 versus pool Mouse Muscle tissue


title: f2#303 versus pool Mouse Liver tissue


title: f2#308 versus pool Mouse Liver tissue


title: f2#301 versus pool Mouse Liver tissue


title: f2#302 versus pool Mouse Liver tissue


title: f2#309 versus pool Mouse Liver tissue


title: f2#306 versus pool Mouse Liver tissue


title: f2#296 versus pool Mouse Liver tissue


title: f2#300 versus pool Mouse Liver tissue


title: f2#299 versus pool Mouse Liver tissue


title: f2#290 versus pool Mouse Liver tissue


title: f2#298 versus pool Mouse Liver tissue


title: f2#122 versus pool Mouse Muscle tissue


title: f2#288 versus pool Mouse Liver tissue


title: f2#295 versus pool Mouse Liver tissue


title: f2#316 versus pool Mouse Liver tissue


title: f2#283 versus pool Mouse Liver tissue


title: f2#307 versus pool Mouse Liver tissue


title: f2#282 versus pool Mouse Liver tissue


title: f2#289 versus pool Mouse Liver tissue


title: f2#281 versus pool Mouse Liver tissue


title: f2#73 versus pool Mouse Muscle tissue


title: f2#297 versus pool Mouse Liver tissue


title: f2#277 versus pool Mouse Liver tissue


title: f2#278 versus pool Mouse Liver tissue


title: f2#253 versus pool Mouse Liver tissue


title: f2#269 versus pool Mouse Liver tissue


title: f2#257 versus pool Mouse Liver tissue


title: f2#263 versus pool Mouse Liver tissue


title: f2#248 versus pool Mouse Liver tissue


title: f2#279 versus pool Mouse Liver tissue


title: f2#258 versus pool Mouse Liver tissue


title: f2#266 versus pool Mouse Liver tissue


title: f2#265 versus pool Mouse Liver tissue


title: f2#254 versus pool Mouse Liver tissue


title: f2#242 versus pool Mouse Liver tissue


title: f2#235 versus pool Mouse Liver tissue


title: f2#260 versus pool Mouse Liver tissue


title: f2#241 versus pool Mouse Liver tissue


title: f2#255 versus pool Mouse Liver tissue


title: f2#276 versus pool Mouse Liver tissue


title: f2#268 versus pool Mouse Liver tissue


title: f2#264 versus pool Mouse Liver tissue


title: f2#267 versus pool Mouse Liver tissue


title: f2#259 versus pool Mouse Liver tissue


title: f2#246 versus pool Mouse Liver tissue


title: f2#240 versus pool Mouse Liver tissue


title: f2#243 versus pool Mouse Liver tissue


title: f2#234 versus pool Mouse Liver tissue


title: f2#233 versus pool Mouse Liver tissue


title: f2#231 versus pool Mouse Liver tissue


title: f2#232 versus pool Mouse Liver tissue


title: f2#224 versus pool Mouse Liver tissue


title: f2#223 versus pool Mouse Liver tissue


title: f2#219 versus pool Mouse Liver tissue


title: f2#217 versus pool Mouse Liver tissue


title: f2#355 versus pool Mouse Liver tissue


title: f2#229 versus pool Mouse Liver tissue


title: f2#356 versus pool Mouse Liver tissue


title: f2#361 versus pool Mouse Liver tissue


title: f2#362 versus pool Mouse Liver tissue


title: f2#230 versus pool Mouse Liver tissue


title: f2#334 versus pool Mouse Liver tissue


title: f2#360 versus pool Mouse Liver tissue


title: f2#335 versus pool Mouse Liver tissue


title: f2#342 versus pool Mouse Liver tissue


title: f2#333 versus pool Mouse Liver tissue


title: f2#332 versus pool Mouse Liver tissue


title: f2#350 versus pool Mouse Liver tissue


title: f2#349 versus pool Mouse Liver tissue


title: f2#340 versus pool Mouse Liver tissue


title: f2#343 versus pool Mouse Liver tissue


title: f2#348 versus pool Mouse Liver tissue


title: f2#341 versus pool Mouse Liver tissue


title: f2#325 versus pool Mouse Liver tissue


title: f2#324 versus pool Mouse Liver tissue


title: f2#315 versus pool Mouse Liver tissue


title: f2#326 versus pool Mouse Liver tissue


title: f2#313 versus pool Mouse Liver tissue


title: f2#294 versus pool Mouse Liver tissue


title: f2#323 versus pool Mouse Liver tissue


title: f2#312 versus pool Mouse Liver tissue


title: f2#330 versus pool Mouse Liver tissue


title: f2#286 versus pool Mouse Liver tissue


title: f2#293 versus pool Mouse Liver tissue


title: f2#285 versus pool Mouse Liver tissue


title: f2#331 versus pool Mouse Liver tissue


title: f2#311 versus pool Mouse Liver tissue


title: f2#304 versus pool Mouse Liver tissue


title: f2#314 versus pool Mouse Liver tissue


title: f2#287 versus pool Mouse Liver tissue


title: f2#291 versus pool Mouse Liver tissue


title: f2#284 versus pool Mouse Liver tissue


title: f2#275 versus pool Mouse Liver tissue


title: f2#305 versus pool Mouse Liver tissue


title: f2#292 versus pool Mouse Liver tissue


title: f2#270 versus pool Mouse Liver tissue


title: f2#273 versus pool Mouse Liver tissue


title: f2#249 versus pool Mouse Liver tissue


title: f2#245 versus pool Mouse Liver tissue


title: f2#238 versus pool Mouse Liver tissue


title: f2#227 versus pool Mouse Liver tissue


title: f2#272 versus pool Mouse Liver tissue


title: f2#252 versus pool Mouse Liver tissue


title: f2#220 versus pool Mouse Liver tissue


title: f2#222 versus pool Mouse Liver tissue


title: f2#271 versus pool Mouse Liver tissue


title: f2#237 versus pool Mouse Liver tissue


title: f2#236 versus pool Mouse Liver tissue


title: f2#251 versus pool Mouse Liver tissue


title: f2#209 versus pool Mouse Liver tissue


title: f2#207 versus pool Mouse Liver tissue


title: f2#200 versus pool Mouse Liver tissue


title: f2#205 versus pool Mouse Liver tissue


title: f2#262 versus pool Mouse Liver tissue


title: f2#203 versus pool Mouse Liver tissue


title: f2#261 versus pool Mouse Liver tissue


title: f2#202 versus pool Mouse Liver tissue


title: f2#210 versus pool Mouse Liver tissue


title: f2#211 versus pool Mouse Liver tissue


title: f2#206 versus pool Mouse Liver tissue


title: f2#250 versus pool Mouse Liver tissue


title: f2#225 versus pool Mouse Liver tissue


title: f2#221 versus pool Mouse Liver tissue


title: f2#239 versus pool Mouse Liver tissue


title: f2#214 versus pool Mouse Liver tissue


title: f2#199 versus pool Mouse Liver tissue


title: f2#212 versus pool Mouse Liver tissue


title: f2#228 versus pool Mouse Liver tissue


title: f2#244 versus pool Mouse Liver tissue


title: f2#226 versus pool Mouse Liver tissue


title: f2#213 versus pool Mouse Liver tissue


title: f2#215 versus pool Mouse Liver tissue


title: f2#216 versus pool Mouse Liver tissue


title: f2#182 versus pool Mouse Liver tissue


title: f2#181 versus pool Mouse Liver tissue


title: f2#178 versus pool Mouse Liver tissue


title: f2#190 versus pool Mouse Liver tissue


title: f2#208 versus pool Mouse Liver tissue


title: f2#188 versus pool Mouse Liver tissue


title: f2#201 versus pool Mouse Liver tissue


title: f2#187 versus pool Mouse Liver tissue


title: f2#177 versus pool Mouse Liver tissue


title: f2#172 versus pool Mouse Liver tissue


title: f2#198 versus pool Mouse Liver tissue


title: f2#204 versus pool Mouse Liver tissue


title: f2#189 versus pool Mouse Liver tissue


title: f2#170 versus pool Mouse Liver tissue


title: f2#165 versus pool Mouse Liver tissue


title: f2#159 versus pool Mouse Liver tissue


title: f2#158 versus pool Mouse Liver tissue


title: f2#173 versus pool Mouse Liver tissue


title: f2#140 versus pool Mouse Liver tissue


title: f2#134 versus pool Mouse Liver tissue


title: f2#151 versus pool Mouse Liver tissue


title: f2#157 versus pool Mouse Liver tissue


title: f2#167 versus pool Mouse Liver tissue


title: f2#152 versus pool Mouse Liver tissue


title: f2#166 versus pool Mouse Liver tissue


title: f2#150 versus pool Mouse Liver tissue


title: f2#149 versus pool Mouse Liver tissue


title: f2#139 versus pool Mouse Liver tissue


title: f2#171 versus pool Mouse Liver tissue


title: f2#148 versus pool Mouse Liver tissue


title: f2#125 versus pool Mouse Liver tissue


title: f2#133 versus pool Mouse Liver tissue


title: f2#126 versus pool Mouse Liver tissue


title: f2#124 versus pool Mouse Liver tissue


title: f2#118 versus pool Mouse Liver tissue


title: f2#117 versus pool Mouse Liver tissue


title: f2#123 versus pool Mouse Liver tissue


title: f2#119 versus pool Mouse Liver tissue


title: f2#129 versus pool Mouse Liver tissue


title: f2#120 versus pool Mouse Liver tissue


title: f2#116 versus pool Mouse Liver tissue


title: f2#109 versus pool Mouse Liver tissue


title: f2#94 versus pool Mouse Liver tissue


title: f2#100 versus pool Mouse Liver tissue


title: f2#102 versus pool Mouse Liver tissue


title: f2#97 versus pool Mouse Liver tissue


title: f2#88 versus pool Mouse Liver tissue


title: f2#93 versus pool Mouse Liver tissue


title: f2#96 versus pool Mouse Liver tissue


title: f2#77 versus pool Mouse Liver tissue


title: f2#78 versus pool Mouse Liver tissue


title: f2#101 versus pool Mouse Liver tissue


title: f2#87 versus pool Mouse Liver tissue


title: f2#95 versus pool Mouse Liver tissue


title: f2#92 versus pool Mouse Liver tissue


title: f2#71 versus pool Mouse Liver tissue


title: f2#72 versus pool Mouse Liver tissue


title: f2#86 versus pool Mouse Liver tissue


title: f2#69 versus pool Mouse Liver tissue


title: f2#68 versus pool Mouse Liver tissue


title: f2#61 versus pool Mouse Liver tissue


title: f2#60 versus pool Mouse Liver tissue


title: f2#70 versus pool Mouse Liver tissue


title: f2#56 versus pool Mouse Liver tissue


title: f2#57 versus pool Mouse Liver tissue


title: f2#67 versus pool Mouse Liver tissue


title: f2#63 versus pool Mouse Liver tissue


title: f2#196 versus pool Mouse Liver tissue


title: f2#62 versus pool Mouse Liver tissue


title: f2#194 versus pool Mouse Liver tissue


title: f2#55 versus pool Mouse Liver tissue


title: f2#191 versus pool Mouse Liver tissue


title: f2#195 versus pool Mouse Liver tissue


title: f2#197 versus pool Mouse Liver tissue


title: f2#179 versus pool Mouse Liver tissue


title: f2#193 versus pool Mouse Liver tissue


title: f2#185 versus pool Mouse Liver tissue


title: f2#183 versus pool Mouse Liver tissue


title: f2#54 versus pool Mouse Liver tissue


title: f2#176 versus pool Mouse Liver tissue


title: f2#180 versus pool Mouse Liver tissue


title: f2#184 versus pool Mouse Liver tissue


title: f2#162 versus pool Mouse Liver tissue


title: f2#174 versus pool Mouse Liver tissue


title: f2#169 versus pool Mouse Liver tissue


title: f2#175 versus pool Mouse Liver tissue


title: f2#164 versus pool Mouse Liver tissue


title: f2#168 versus pool Mouse Liver tissue


title: f2#163 versus pool Mouse Liver tissue


title: f2#161 versus pool Mouse Liver tissue


title: f2#153 versus pool Mouse Liver tissue


title: f2#155 versus pool Mouse Liver tissue


title: f2#160 versus pool Mouse Liver tissue


title: f2#156 versus pool Mouse Liver tissue


title: f2#154 versus pool Mouse Liver tissue


title: f2#146 versus pool Mouse Liver tissue


title: f2#142 versus pool Mouse Liver tissue


title: f2#131 versus pool Mouse Liver tissue


title: f2#147 versus pool Mouse Liver tissue


title: f2#132 versus pool Mouse Liver tissue


title: f2#137 versus pool Mouse Liver tissue


title: f2#128 versus pool Mouse Liver tissue


title: f2#130 versus pool Mouse Liver tissue


title: f2#138 versus pool Mouse Liver tissue


title: f2#136 versus pool Mouse Liver tissue


title: f2#141 versus pool Mouse Liver tissue


title: f2#145 versus pool Mouse Liver tissue


title: f2#127 versus pool Mouse Liver tissue


title: f2#144 versus pool Mouse Liver tissue


title: f2#135 versus pool Mouse Liver tissue


title: f2#121 versus pool Mouse Liver tissue


title: f2#122 versus pool Mouse Liver tissue


title: f2#113 versus pool Mouse Liver tissue


title: f2#107 versus pool Mouse Liver tissue


title: f2#106 versus pool Mouse Liver tissue


title: f2#110 versus pool Mouse Liver tissue


title: f2#99 versus pool Mouse Liver tissue


title: f2#108 versus pool Mouse Liver tissue


title: f2#104 versus pool Mouse Liver tissue


title: f2#186 versus pool Mouse Liver tissue


title: f2#112 versus pool Mouse Liver tissue


title: f2#90 versus pool Mouse Liver tissue


title: f2#85 versus pool Mouse Liver tissue


title: f2#105 versus pool Mouse Liver tissue


title: f2#82 versus pool Mouse Liver tissue


title: f2#80 versus pool Mouse Liver tissue


title: f2#83 versus pool Mouse Liver tissue


title: f2#91 versus pool Mouse Liver tissue


title: f2#111 versus pool Mouse Liver tissue


title: f2#84 versus pool Mouse Liver tissue


title: f2#81 versus pool Mouse Liver tissue


title: f2#89 versus pool Mouse Liver tissue


title: f2#114 versus pool Mouse Liver tissue


title: f2#98 versus pool Mouse Liver tissue


title: f2#79 versus pool Mouse Liver tissue


title: f2#115 versus pool Mouse Liver tissue


title: f2#76 versus pool Mouse Liver tissue


title: f2#73 versus pool Mouse Liver tissue


title: f2#75 versus pool Mouse Liver tissue


title: f2#64 versus pool Mouse Liver tissue


title: f2#74 versus pool Mouse Liver tissue


title: f2#53 versus pool Mouse Liver tissue


title: f2#51 versus pool Mouse Liver tissue


title: f2#52 versus pool Mouse Liver tissue


title: f2#65 versus pool Mouse Liver tissue


title: f2#359 versus pool Mouse Adipose tissue (2008)

description: Adipose tissue from 295 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Adipose tissue were dissected and flash frozen in LN2 and stored at -80°C.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#66 versus pool Mouse Liver tissue


title: f2#352 versus pool Mouse Adipose tissue (2008)


title: f2#357 versus pool Mouse Adipose tissue (2008)


title: f2#347 versus pool Mouse Adipose tissue (2008)


title: f2#353 versus pool Mouse Adipose tissue (2008)


title: f2#358 versus pool Mouse Adipose tissue (2008)


title: f2#345 versus pool Mouse Adipose tissue (2008)


title: f2#351 versus pool Mouse Adipose tissue (2008)


title: f2#59 versus pool Mouse Liver tissue


title: f2#58 versus pool Mouse Liver tissue


title: f2#338 versus pool Mouse Adipose tissue (2008)


title: f2#346 versus pool Mouse Adipose tissue (2008)


title: f2#321 versus pool Mouse Adipose tissue (2008)


title: f2#344 versus pool Mouse Adipose tissue (2008)


title: f2#327 versus pool Mouse Adipose tissue (2008)


title: f2#320 versus pool Mouse Adipose tissue (2008)


title: f2#318 versus pool Mouse Adipose tissue (2008)


title: f2#317 versus pool Mouse Adipose tissue (2008)


title: f2#329 versus pool Mouse Adipose tissue (2008)


title: f2#337 versus pool Mouse Adipose tissue (2008)


title: f2#303 versus pool Mouse Adipose tissue (2008)


title: f2#328 versus pool Mouse Adipose tissue (2008)


title: f2#302 versus pool Mouse Adipose tissue (2008)


title: f2#322 versus pool Mouse Adipose tissue (2008)


title: f2#299 versus pool Mouse Adipose tissue (2008)


title: f2#297 versus pool Mouse Adipose tissue (2008)


title: f2#319 versus pool Mouse Adipose tissue (2008)


title: f2#306 versus pool Mouse Adipose tissue (2008)


title: f2#336 versus pool Mouse Adipose tissue (2008)


title: f2#354 versus pool Mouse Adipose tissue (2008)


title: f2#301 versus pool Mouse Adipose tissue (2008)


title: f2#298 versus pool Mouse Adipose tissue (2008)


title: f2#307 versus pool Mouse Adipose tissue (2008)


title: f2#316 versus pool Mouse Adipose tissue (2008)


title: f2#309 versus pool Mouse Adipose tissue (2008)


title: f2#277 versus pool Mouse Adipose tissue (2008)


title: f2#269 versus pool Mouse Adipose tissue (2008)


title: f2#278 versus pool Mouse Adipose tissue (2008)


title: f2#290 versus pool Mouse Adipose tissue (2008)


title: f2#295 versus pool Mouse Adipose tissue (2008)


title: f2#289 versus pool Mouse Adipose tissue (2008)


title: f2#279 versus pool Mouse Adipose tissue (2008)


title: f2#288 versus pool Mouse Adipose tissue (2008)


title: f2#257 versus pool Mouse Adipose tissue (2008)


title: f2#259 versus pool Mouse Adipose tissue (2008)


title: f2#265 versus pool Mouse Adipose tissue (2008)


title: f2#267 versus pool Mouse Adipose tissue (2008)


title: f2#296 versus pool Mouse Adipose tissue (2008)


title: f2#281 versus pool Mouse Adipose tissue (2008)


title: f2#258 versus pool Mouse Adipose tissue (2008)


title: f2#263 versus pool Mouse Adipose tissue (2008)


title: f2#266 versus pool Mouse Adipose tissue (2008)


title: f2#268 versus pool Mouse Adipose tissue (2008)


title: f2#248 versus pool Mouse Adipose tissue 2 (2008)


title: f2#254 versus pool Mouse Adipose tissue (2008)


title: f2#264 versus pool Mouse Adipose tissue (2008)


title: f2#255 versus pool Mouse Adipose tissue (2008)


title: f2#247 versus pool Mouse Adipose tissue (2008)


title: f2#243 versus pool Mouse Adipose tissue (2008)


title: f2#246 versus pool Mouse Adipose tissue (2008)


title: f2#241 versus pool Mouse Adipose tissue (2008)


title: f2#233 versus pool Mouse Adipose tissue (2008)


title: f2#253 versus pool Mouse Adipose tissue (2008)


title: f2#230 versus pool Mouse Adipose tissue (2008)


title: f2#224 versus pool Mouse Adipose tissue (2008)


title: f2#232 versus pool Mouse Adipose tissue (2008)


title: f2#242 versus pool Mouse Adipose tissue (2008)


title: f2#218 versus pool Mouse Adipose tissue (2008)


title: f2#217 versus pool Mouse Adipose tissue (2008)


title: f2#235 versus pool Mouse Adipose tissue (2008)


title: f2#349 versus pool Mouse Adipose tissue (2008)


title: f2#219 versus pool Mouse Adipose tissue (2008)


title: f2#231 versus pool Mouse Adipose tissue (2008)


title: f2#356 versus pool Mouse Adipose tissue (2008)


title: f2#248 versus pool Mouse Adipose tissue (2008)


title: f2#342 versus pool Mouse Adipose tissue (2008)


title: f2#360 versus pool Mouse Adipose tissue (2008)


title: f2#223 versus pool Mouse Adipose tissue (2008)


title: f2#234 versus pool Mouse Adipose tissue (2008)


title: f2#362 versus pool Mouse Adipose tissue (2008)


title: f2#361 versus pool Mouse Adipose tissue (2008)


title: f2#229 versus pool Mouse Adipose tissue (2008)


title: f2#343 versus pool Mouse Adipose tissue (2008)


title: f2#240 versus pool Mouse Adipose tissue (2008)


title: f2#341 versus pool Mouse Adipose tissue (2008)


title: f2#334 versus pool Mouse Adipose tissue (2008)


title: f2#350 versus pool Mouse Adipose tissue (2008)


title: f2#333 versus pool Mouse Adipose tissue (2008)


title: f2#326 versus pool Mouse Adipose tissue (2008)


title: f2#331 versus pool Mouse Adipose tissue (2008)


title: f2#323 versus pool Mouse Adipose tissue (2008)


title: f2#324 versus pool Mouse Adipose tissue (2008)


title: f2#330 versus pool Mouse Adipose tissue (2008)


title: f2#313 versus pool Mouse Adipose tissue (2008)


title: f2#312 versus pool Mouse Adipose tissue (2008)


title: f2#335 versus pool Mouse Adipose tissue (2008)


title: f2#311 versus pool Mouse Adipose tissue (2008)


title: f2#305 versus pool Mouse Adipose tissue (2008)


title: f2#314 versus pool Mouse Adipose tissue (2008)


title: f2#310 versus pool Mouse Adipose tissue (2008)


title: f2#304 versus pool Mouse Adipose tissue (2008)


title: f2#291 versus pool Mouse Adipose tissue (2008)


title: f2#287 versus pool Mouse Adipose tissue (2008)


title: f2#286versus pool Mouse Adipose tissue (2008)


title: f2#294 versus pool Mouse Adipose tissue (2008)


title: f2#285 versus pool Mouse Adipose tissue (2008)


title: f2#292 versus pool Mouse Adipose tissue (2008)


title: f2#315 versus pool Mouse Adipose tissue (2008)


title: f2#293 versus pool Mouse Adipose tissue (2008)


title: f2#275 versus pool Mouse Adipose tissue (2008)


title: f2#273 versus pool Mouse Adipose tissue (2008)


title: f2#284 versus pool Mouse Adipose tissue (2008)


title: f2#272 versus pool Mouse Adipose tissue (2008)


title: f2#262 versus pool Mouse Adipose tissue (2008)


title: f2#271 versus pool Mouse Adipose tissue (2008)


title: f2#256 versus pool Mouse Adipose tissue (2008)


title: f2#261 versus pool Mouse Adipose tissue (2008)


title: f2#252 versus pool Mouse Adipose tissue (2008)


title: f2#250 versus pool Mouse Adipose tissue (2008)


title: f2#270 versus pool Mouse Adipose tissue (2008)


title: f2#251 versus pool Mouse Adipose tissue (2008)


title: f2#236 versus pool Mouse Adipose tissue (2008)


title: f2#237 versus pool Mouse Adipose tissue (2008)


title: f2#249 versus pool Mouse Adipose tissue (2008)


title: f2#226 versus pool Mouse Adipose tissue (2008)


title: f2#227 versus pool Mouse Adipose tissue (2008)


title: f2#222 versus pool Mouse Adipose tissue (2008)


title: f2#220 versus pool Mouse Adipose tissue (2008)


title: f2#221 versus pool Mouse Adipose tissue (2008)


title: f2#238 versus pool Mouse Adipose tissue (2008)


title: f2#244 versus pool Mouse Adipose tissue (2008)


title: f2#239 versus pool Mouse Adipose tissue (2008)


title: f2#213 versus pool Mouse Adipose tissue (2008)


title: f2#215 versus pool Mouse Adipose tissue (2008)


title: f2#245 versus pool Mouse Adipose tissue (2008)


title: f2#228 versus pool Mouse Adipose tissue (2008)


title: f2#214 versus pool Mouse Adipose tissue (2008)


title: f2#212 versus pool Mouse Adipose tissue (2008)


title: f2#208 versus pool Mouse Adipose tissue (2008)


title: f2#210 versus pool Mouse Adipose tissue (2008)


title: f2#216 versus pool Mouse Adipose tissue (2008)


title: f2#206 versus pool Mouse Adipose tissue (2008)


title: f2#209 versus pool Mouse Adipose tissue (2008)


title: f2#205 versus pool Mouse Adipose tissue (2008)


title: f2#204 versus pool Mouse Adipose tissue (2008)


title: f2#207 versus pool Mouse Adipose tissue (2008)


title: f2#201 versus pool Mouse Adipose tissue (2008)


title: f2#198 versus pool Mouse Adipose tissue (2008)


title: f2#203 versus pool Mouse Adipose tissue (2008)


title: f2#189 versus pool Mouse Adipose tissue (2008)


title: f2#190 versus pool Mouse Adipose tissue (2008)


title: f2#211 versus pool Mouse Adipose tissue (2008)


title: f2#202 versus pool Mouse Adipose tissue (2008)


title: f2#178 versus pool Mouse Adipose tissue (2008)


title: f2#182 versus pool Mouse Adipose tissue (2008)


title: f2#200 versus pool Mouse Adipose tissue (2008)


title: f2#181 versus pool Mouse Adipose tissue (2008)


title: f2#187 versus pool Mouse Adipose tissue (2008)


title: f2#199 versus pool Mouse Adipose tissue (2008)


title: f2#188 versus pool Mouse Adipose tissue (2008)


title: f2#172 versus pool Mouse Adipose tissue (2008)


title: f2#332 versus pool Mouse Adipose tissue (2008)


title: f2#166 versus pool Mouse Adipose tissue (2008)


title: f2#177 versus pool Mouse Adipose tissue (2008)


title: f2#325 versus pool Mouse Adipose tissue (2008)


title: f2#165 versus pool Mouse Adipose tissue (2008)


title: f2#167 versus pool Mouse Adipose tissue (2008)


title: f2#151 versus pool Mouse Adipose tissue (2008)


title: f2#170 versus pool Mouse Adipose tissue (2008)


title: f2#157 versus pool Mouse Adipose tissue (2008)


title: f2#148 versus pool Mouse Adipose tissue (2008)


title: f2#158 versus pool Mouse Adipose tissue (2008)


title: f2#171 versus pool Mouse Adipose tissue (2008)


title: f2#126 versus pool Mouse Adipose tissue (2008)


title: f2#159 versus pool Mouse Adipose tissue (2008)


title: f2#125 versus pool Mouse Adipose tissue (2008)


title: f2#152 versus pool Mouse Adipose tissue (2008)


title: f2#134 versus pool Mouse Adipose tissue (2008)


title: f2#173 versus pool Mouse Adipose tissue (2008)


title: f2#123 versus pool Mouse Adipose tissue (2008)


title: f2#150 versus pool Mouse Adipose tissue (2008)


title: f2#124 versus pool Mouse Adipose tissue (2008)


title: f2#149 versus pool Mouse Adipose tissue (2008)


title: f2#133 versus pool Mouse Adipose tissue (2008)


title: f2#140 versus pool Mouse Adipose tissue (2008)


title: f2#129 versus pool Mouse Adipose tissue (2008)


title: f2#95 versus pool Mouse Adipose tissue (2008)


title: f2#109 versus pool Mouse Adipose tissue (2008)


title: f2#119 versus pool Mouse Adipose tissue (2008)


title: f2#120 versus pool Mouse Adipose tissue (2008)


title: f2#117 versus pool Mouse Adipose tissue (2008)


title: f2#101 versus pool Mouse Adipose tissue (2008)


title: f2#93 versus pool Mouse Adipose tissue (2008)


title: f2#118 versus pool Mouse Adipose tissue (2008)


title: f2#94 versus pool Mouse Adipose tissue (2008)


title: f2#100 versus pool Mouse Adipose tissue (2008)


title: f2#116 versus pool Mouse Adipose tissue (2008)


title: f2#87 versus pool Mouse Adipose tissue (2008)


title: f2#88 versus pool Mouse Adipose tissue (2008)


title: f2#72 versus pool Mouse Adipose tissue (2008)


title: f2#78 versus pool Mouse Adipose tissue (2008)


title: f2#71 versus pool Mouse Adipose tissue (2008)


title: f2#102 versus pool Mouse Adipose tissue (2008)


title: f2#77 versus pool Mouse Adipose tissue (2008)


title: f2#97 versus pool Mouse Adipose tissue (2008)


title: f2#62 versus pool Mouse Adipose tissue (2008)


title: f2#70 versus pool Mouse Adipose tissue (2008)


title: f2#86 versus pool Mouse Adipose tissue (2008)


title: f2#69 versus pool Mouse Adipose tissue (2008)


title: f2#63 versus pool Mouse Adipose tissue (2008)


title: f2#68 versus pool Mouse Adipose tissue (2008)


title: f2#92 versus pool Mouse Adipose tissue (2008)


title: f2#61 versus pool Mouse Adipose tissue (2008)


title: f2#55 versus pool Mouse Adipose tissue (2008)


title: f2#183 versus pool Mouse Adipose tissue (2008)


title: f2#194 versus pool Mouse Adipose tissue (2008)


title: f2#54 versus pool Mouse Adipose tissue (2008)


title: f2#197 versus pool Mouse Adipose tissue (2008)


title: f2#59 versus pool Mouse Adipose tissue (2008)


title: f2#57 versus pool Mouse Adipose tissue (2008)


title: f2#56 versus pool Mouse Adipose tissue (2008)


title: f2#180 versus pool Mouse Adipose tissue (2008)


title: f2#176 versus pool Mouse Adipose tissue (2008)


title: f2#192 versus pool Mouse Adipose tissue (2008)


title: f2#195 versus pool Mouse Adipose tissue (2008)


title: f2#193 versus pool Mouse Adipose tissue (2008)


title: f2#60 versus pool Mouse Adipose tissue (2008)


title: f2#179 versus pool Mouse Adipose tissue (2008)


title: f2#184 versus pool Mouse Adipose tissue (2008)


title: f2#186 versus pool Mouse Adipose tissue (2008)


title: f2#196 versus pool Mouse Adipose tissue (2008)


title: f2#185 versus pool Mouse Adipose tissue (2008)


title: f2#175 versus pool Mouse Adipose tissue (2008)


title: f2#169 versus pool Mouse Adipose tissue (2008)


title: f2#191 versus pool Mouse Adipose tissue (2008)


title: f2#174 versus pool Mouse Adipose tissue (2008)


title: f2#164 versus pool Mouse Adipose tissue (2008)


title: f2#168 versus pool Mouse Adipose tissue (2008)


title: f2#163 versus pool Mouse Adipose tissue (2008)


title: f2#155 versus pool Mouse Adipose tissue (2008)


title: f2#146 versus pool Mouse Adipose tissue (2008)


title: f2#162 versus pool Mouse Adipose tissue (2008)


title: f2#130 versus pool Mouse Adipose tissue (2008)


title: f2#142 versus pool Mouse Adipose tissue (2008)


title: f2#160 versus pool Mouse Adipose tissue (2008)


title: f2#154 versus pool Mouse Adipose tissue (2008)


title: f2#161 versus pool Mouse Adipose tissue (2008)


title: f2#156 versus pool Mouse Adipose tissue (2008)


title: f2#153 versus pool Mouse Adipose tissue (2008)


title: f2#144 versus pool Mouse Adipose tissue (2008)


title: f2#138 versus pool Mouse Adipose tissue (2008)


title: f2#131 versus pool Mouse Adipose tissue (2008)


title: f2#128 versus pool Mouse Adipose tissue (2008)


title: f2#141 versus pool Mouse Adipose tissue (2008)


title: f2#143 versus pool Mouse Adipose tissue (2008)


title: f2#132 versus pool Mouse Adipose tissue (2008)


title: f2#135 versus pool Mouse Adipose tissue (2008)


title: f2#145 versus pool Mouse Adipose tissue (2008)


title: f2#137 versus pool Mouse Adipose tissue (2008)


title: f2#115 versus pool Mouse Adipose tissue (2008)


title: f2#121 versus pool Mouse Adipose tissue (2008)


title: f2#127 versus pool Mouse Adipose tissue (2008)


title: f2#136 versus pool Mouse Adipose tissue (2008)


title: f2#122 versus pool Mouse Adipose tissue (2008)


title: f2#114 versus pool Mouse Adipose tissue (2008)


title: f2#111 versus pool Mouse Adipose tissue (2008)


title: f2#105 versus pool Mouse Adipose tissue (2008)


title: f2#108 versus pool Mouse Adipose tissue (2008)


title: f2#112 versus pool Mouse Adipose tissue (2008)


title: f2#106 versus pool Mouse Adipose tissue (2008)


title: f2#104 versus pool Mouse Adipose tissue (2008)


title: f2#110 versus pool Mouse Adipose tissue (2008)


title: f2#98 versus pool Mouse Adipose tissue (2008)


title: f2#113 versus pool Mouse Adipose tissue (2008)


title: f2#90 versus pool Mouse Adipose tissue (2008)


title: f2#99 versus pool Mouse Adipose tissue (2008)


title: f2#91 versus pool Mouse Adipose tissue (2008)


title: f2#82 versus pool Mouse Adipose tissue (2008)


title: f2#107 versus pool Mouse Adipose tissue (2008)


title: f2#83 versus pool Mouse Adipose tissue (2008)


title: f2#85 versus pool Mouse Adipose tissue (2008)


title: f2#84 versus pool Mouse Adipose tissue (2008)


title: f2#80 versus pool Mouse Adipose tissue (2008)


title: f2#89 versus pool Mouse Adipose tissue (2008)


title: f2#75 versus pool Mouse Adipose tissue (2008)


title: f2#81 versus pool Mouse Adipose tissue (2008)


title: f2#79 versus pool Mouse Adipose tissue (2008)


title: f2#76 versus pool Mouse Adipose tissue (2008)


title: f2#74 versus pool Mouse Adipose tissue (2008)


title: f2#73 versus pool Mouse Adipose tissue (2008)


title: f2#66 versus pool Mouse Adipose tissue (2008)


title: f2#53 versus pool Mouse Adipose tissue (2008)


title: f2#64 versus pool Mouse Adipose tissue (2008)


title: f2#51 versus pool Mouse Adipose tissue (2008)


title: f2#58 versus pool Mouse Adipose tissue (2008)


title: f2#52 versus pool Mouse Adipose tissue (2008)


title: ME0055

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

description: Small molecule inhibitors have recently been shown to down regulate trascription of TTS in enterohaemorrhagic E. coli (EHEC). E. coli O157 strain TUV93-0 has been shown to induce Type III secretion (TTS) in MEM-HEPES media. Transcriptional profiling of E.coli TUV93-0 was carried out in MEM-HEPES in the prescence and absence of small molecule inhibitors to establish the global effects of these inhibitors in EHEC.

hyb_protocol: Prior to hybridization, the slides were treated with the background-reducing Pronto! Pre-Soak System (Corning Life Sciences). The slides were incubated for 20 min in prewarmed Universal Pre-Soak solution at 42 °C and washed twice in 0.1_SSC, 0.1% SDS for 30 s at room temperature. Slides were immediately transferred into prewarmed prehybridization solution (5_ SSC, 0.1% SDS, and 0.1% bovine serum albumin) and incubated for 2–4 h at 42 °C. The microarray slides were finally washed at room temperature once in 0.1_ SSC, 0.1% SDS for 1 min and twice in 0.1_ SSC for 30 s, briefly dipped in water and then ethanol, and dried by centrifugation for 5 min at 800_g. For each experiment, equal quantities (80 pmol) of each Cy5- and Cy3-labeled cDNA were added to a final volume of 80 _l of hybridization solution containing 25% formamide, 10 mg of bovine serum albumin (fraction V) per ml, 5_ SSC (1_ SSC is 0.15 M NaCl, 0.015 M sodium citrate), 0.1% SDS, 8 _g of poly(A), and 1_Denhardt’s solution. The cDNA probes were denatured at 95 °C for 3 min and hybridized for 16 h at 42 °C. After hybridization was complete, the slides were washed in 2_SSC, 0.1% SDS at 42 °C for 2 min in 0.1_SSC, 0.1% SDS for 2 min at room temperature, and finally twice in 0.1_ SSC for 2 min at room temperature. The microarray slides were dried by centrifugation for 5 min at 800g.

scan_protocol: Slide was scanned at 532 and 630 nm by using a Genepix 4000A scanner (Axon Instruments, Union City, CA).

data_processing: LOWESS normalised data that represents the average of the three replicate experiments

organism: Escherichia coli

source_name: Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0055 (in DMSO)

label_protocol:
20 ug total RNA was converted to Cy3-labelled cDNA
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy3 NHS-dye esters to the amino-allyl-labelled
cDNAs.

growth_protocol: Escherichia coli O157 TUV93-0 was grown at 37 degrees C to OD 0.7 in MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2.

extract_protocol: An RNeasy minikit was used to prepare total RNA according to the manufacturer’s instructions (QIAGEN Ltd.). Any contaminating DNA was removed using a DNAase column kit (QIAGEN Ltd).

treatment_protocol: Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0055

value: O157:H7 EHEC TUV93-0

tag: od

tag: media

tag: inhibitor

source_name: Escherichia coli O157 TUV93-0 MEM-HEPES + DMSO

growth_protocol: Escherichia coli O157 TUV93-0 was grown at 37 degrees C to OD 0.7 in MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2 and and equivalent volume of DMSO.

treatment_protocol: Escherichia coli O157 TUV93-0 was grown in the presence of DMSO

tag: no inhibitor

value: equivalent volume of DMSO added


title: f2#65 versus pool Mouse Adipose tissue (2008)


title: ME0053

source_name: Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0053 (in DMSO)

treatment_protocol: Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0053

value: MEM-HEPES supplemented with 0.1% Glucose and 250nM Fe(NO3)2

label_protocol:
using the CyScribe Post-Labelling Kit (Amersham Biosciences/GE
Healthcare) according to manufacturer’s instructions. Amino-allyllabelled
nucleotides were incorporated into the cDNA by reverse
transcription of the total RNA, followed by a direct chemical coupling
of Cy3 NHS-dye esters to the amino-allyl-labelled
cDNAs.


title: ME0054

source_name: Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0054 (in DMSO)

treatment_protocol: Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0054


title: C57BL6 IL4 18h rep 2

city: Regensburg

first: Carol

last: El Chartouni

address: Franz-Josef-Strauß Allee 11

department: Hematology and oncology

country: Germany

institute: University Hospital Regensburg

description: Gene expression after 18h IL-4 stimulation

hyb_protocol: Labelled cRNA was then purified using Qiagen’s RNease mini spin columns (Qiagen) and 1.65 µg from each sample were fragmented for 30 min and mixed with a 2xGExHybridization Buffer HI-RPM according to the manufacturer’s instructions (Agilent Technologies). The resulting mixture was applied to a Whole Mouse Genome (4x44k) Oligo Microarray (Agilent Technologies Inc.) and the hybridization followed at 65°C for 17 h.

scan_protocol: Arrays were then washed and scanned according to Agilent protocols with the Agilent Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb 97 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Extracted data were further processed with GeneSpring GX 7.3.1. Data Values below 10.0 were set to 10.0. Each measurement was divided by the 50th percentile of all measurements in that sample. The percentile was calculated using only genes marked present. Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 0 then each measurement for that gene was divided by 0 if the numerator was above 0, otherwise the measurement was thrown out. Median polishing was done, where each chip was normalized to its median and each gene was normalized to its median. These normalizations were repeated until the medians converged. Prior to median polishing, raw values below 10 were replaced with 10. All genes except those marked absent were used in this calculation. Specific samples were normalized to one another: sample(s) 1-12 were normalized against the median of the control sample(s) 7, 10. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples.

source_name: Bone Marrow Macrophages

label_protocol: Agilent’s Low RNA Input Linear Amplification One-Color kit (Agilent Technologies, Inc. Wimmington, DE, USA) was used to label the target RNA for hybridization following the manufacturer instructions. Briefly, 1 µg total RNA was reverse transcribed using a T7 promoter Primer. The resulting cDNAs were then in vitro transcribed followed by reverse transcription in the presence of Cyanin 3-CTP.

growth_protocol: To generate bone marrow-derived macrophages (BMM), bone marrow cells were flushed from femurs and tibias of 8 to 12 weeks old mice using cold PBS. Cells from several animals were pooled and plated on bacteriological 100 mm square plastic plates (Bibby Sterilin, Staffordshire, UK Ltd) at 0.5 Mio cells/ml in 20 ml endotoxin-free RPMI 1640 medium (Biochrom KG, Berlin, Germany) supplemented with glutamine, vitamins, pyruvate, nonessential amino acids, β-mercaptoethanol (all purchased from Invitrogen, Germany), 10% FCS (PAA Laboratories GmbH, Austria), and 200 ng/ml human rCSF1 (Cetus) per plate for 5 days. Complete medium was replaced on day 5, cells were harvested on day 6 and seeded with rCSF1 at a density of 10 Mio cells/10 ml medium on 10 cm tissue culture dishes (Falcon).

extract_protocol: Cells were collected, pelleted and used for total RNA preparation with the RNeasy midi kit (Qiagen).

treatment_protocol: On day 7, cells were incubated for 18 h with or without IL4 (10 ng/ml). In the last 4 h of incubation, cells were incubated or not with LPS (10 ng/ml) for 4, 8 or 24 h (in the absence or presence of IL4).

tag: il4 stimulation

tag: age

value: 8 to 12 weeks

tag: sex

value: 2 males and 1 female

tag: tissue

value: Bone marrow


title: C57BL6 IL4 4h rep 2

description: Gene expression after 4h IL-4 stimulation


title: C57BL6 Mock rep 2

description: Gene expression in the absence of IL-4


title: ME0052

description: Recent small molecule inhibitors have been shown to down regulate trascription of TTS in enterohaemorrhagic E. coli (EHEC). E. coli O157 strain TUV93-0 has been shown to induce Type III secretion (TTS) in MEM-HEPES media. Transcriptional profiling of E.coli TUV93-0 was carried out in MEM-HEPES the prescence and absence of small molecule inhibitors to establish the global effects of these inhibitors in EHEC.

source_name: Escherichia coli O157 TUV93-0 MEM-HEPES + 20uM ME0052 (in DMSO)

treatment_protocol: Escherichia coli O157 TUV93-0 was grown in the presence of 20uM ME0052


title: C57BL6 IL4 18h rep 1


title: C57BL6 IL4 4h rep 1


title: C57BL6 Mock rep 1

description: Gene expression in the absence of IL-4


title: Balbc IL4 18h rep 2

value: Balb/cAnNCrl


title: T-ALL 37B

type: genomic

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: gDNA from Affymetrix 250K arrays using the standard protocol

hyb_protocol: Affymetrix 250K protocol

scan_protocol: Affymetrix 250K protocol

data_processing: Standard Affymetrix data generation protocol: CEL, CHP files. CHP files were generated by Dynamic Model 3.0 algorithm.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA from T-cell lymphoblastic leukemia at diagnosis

label_protocol: Affymetrix 250K protocol

extract_protocol: Lysis with detergents follwed by salt and ethanol precipitation

tag: cell type

value: T-cell lymphoblastic leukemia

tag: status

value: at diagnosis


title: T-ALL 40C

source_name: Genomic DNA from T-cell lymphoblastic leukemia at relapse

value: at relapse


title: T-ALL 37C


title: T-ALL 37A

source_name: Normal (remission) DNA from T-cell lymphoblastic leukemia

value: Normal (remission)


title: T-ALL 35C


title: T-ALL 39A


title: T-ALL 33B

source_name: Genomic DNA from T-cell acute lymphoblastic leukemia at diagnosis

value: T-cell acute lymphoblastic leukemia

value: Normal (remission) at diagnosis


title: T-ALL 33C

source_name: Genomic DNA from T-cell acute lymphoblastic leukemia at relapse


title: Balbc IL4 4h rep 2


title: T-ALL 30C


title: T-ALL 35B


title: T-ALL 33A

source_name: Normal (remission) DNA from T-cell acute lymphoblastic leukemia at relapse

value: Normal (remission) at relapse


title: T-ALL 30B


title: T-ALL 27C


title: T-ALL 39C


title: T-ALL 39B


title: T-ALL 40B


title: Balbc Mock rep 2

description: Gene expression in the absence of IL-4


title: Balbc IL4 18h rep 1


title: Aorta proximal versus distal to coarctation 10-1 P(Cy3) vs 10-1D(Cy5)

city: College Station

first: Natasa

last: Popovic

state: TX

address: 355 Reynolds Medical Bldg.

institute: Texas A&M University

description: Tissue samples isolated from the same animal from the area proximally and distally to the occluder were paired on the same microarray slide.

hyb_protocol: Preparation of microarray slides for hybridization: Microarray slides were incubated at 48˚C for 45 min in pre-warmed prehybridization buffer (5X SSC , 0.1% SDS AND 0.2% BSA). After that, they were washed with nuclease free water 2 times 5 minutes, following with isopropanol washes 2 times 5 minutes at room temperature. The slides were spun-dried and used within 1hr. Preparation of the probes for hybridization:100ul of Dye Coupled aRNA were vacuum-dried to the volume needed for the Fragmentation assay using Ambion's Fragmentation Reagents ( Ambion  Cat # 8740 ). After the Fragmentation assay the volume was brought to final volume of 35ul with the Slidehyb Glass  Hybridization buffer (Ambion Cat # 8861 ). The hybridization mix was incubated at 95°C for 5 minutes, then gently vortexed and briefly microfuged. The hybridization mix was added to a pre-warmed slide and a glass cover slip was applied to the array. Slides were incubated for 17-20 hr at the 48°C. Posthybridization washes: The microarray slides were removed from the hybridization chamber. The care was taken not to disturb the coverslip. Each slide was placed in a dish containing  1X  SSC and 0.1%SDS preheated at 48 °C.  The coverslips were removed by gentle agitation while the slides were in solution.  The slides were further agitated for 6 minutes, transferred to a dish containing 1 X SSC and 0.1% SDS at room temperature and agitated for 6 min. The slides were then transferred to a dish containing 0.1 X SSC at room temperature and agitated for 2 times 6 min. Slides were spun dried and scanned immediately.

scan_protocol: The microarray slides were scanned at a 532 nm wavelength and at a 635 nm wavelength with a 10 µm resolution by using GenePix 4000A Microarray Scanner.  The two individual wavelength scans were processed with GenePix Pro 6.0 software. They were integrated and superimposed into a false color ratio image (we normally choose Red vs. Green). From these images, the data was then acquired from both wavelengths, that was to say that fluorescence data was collected at 635 nm and 532 nm from every 10 µm square area within the entire array area scanned.  Then a grid of feature indicators was overlaid on the scan to identify the spots and delineate background from signal for each spot.  All data was then acquired in tabular form and exported to GeneSpring GX 7.3.1 bioinformatics software for normalization and analysis.

data_processing:
Normalizations were preformed in GeneSpring GX 7.3.1 sofware:
1) Data transformation: dye swap (switched Cy3 and Cy5 measurements);
2) Cy5 measurements less than 1 were set to 1;
3) Intensity dependent Lowess normalization (percent of the data used for smoothing 20%; set Cy3 measurement less than 1 to 1).

molecule: polyA RNA

organism: Sus scrofa

source_name: Aortic tissue excised 3cm distally to the surgically introduced occluder

label_protocol: Poly A RNA was amplified, and amino allyl modified by incorporation of UTP molecules into amplified RNA (Amino Allyl  MessageAmp aRNA, Ambion, Ausitn,TX). Two and a half ug of amplified RNA was subsequently coupled with Cy5 dye (Amersham Biosciences).

extract_protocol: Total RNA was isolated by using Totally RNA kit (Ambion, Austin TX). DNAse treatment was used to remove any possible DNA contamination (DNA-free, Ambion, Ausitn,TX). RNA quantity, purity and integrity were assessed by Agilent 2100 bioanalyzer and spectrophotometry.

treatment_protocol: Pig aortic coarctation was used as an animal model of hypertension. The occluder was surgiaclly introduced arround suprarenal aorta proxiamlly to diaphragm. The pigs were allowed to recover form surgery for one week. After that the occluder was gradually inflated over the period of two weeks, until the mean blood pressure was >150 mmHg. This point was considered as the experimental day one. After 2 weeks of hypertension (14 experimental days) the pigs were terminated and aortic tissue 3 cm distally form the occluder was excised, cleaned from adventitia and snap frozen in liquid nitrogen.

tag: Eight to eleven months old male Yucatan Micro Minipigs were used in the study.

source_name: Aortic tissue excised 3cm proximally to the surgically introduced occluder

label_protocol: Poly A RNA was amplified, and amino allyl modified by incorporation of UTP molecules into amplified RNA (Amino Allyl  MessageAmp aRNA, Ambion, Ausitn,TX). Two and a half ug of amplified RNA was subsequently coupled with Cy3 dye (Amersham Biosciences).

treatment_protocol: Pig aortic coarctation was used as an animal model of hypertension. The occluder was surgiaclly introduced arround suprarenal aorta proxiamlly to diaphragm. The pigs were allowed to recover form surgery for one week. After that the occluder was gradually inflated over the period of two weeks, until the mean blood pressure was >150 mmHg. This point was considered as the experimental day one. After 2 weeks of hypertension (14 experimental days) the pigs were terminated and aortic tissue 3 cm proximally form the occluder was excised, cleaned from adventitia and snap frozen in liquid nitrogen.


title: T-ALL 27B


title: T-ALL 40A


title: Aorta proximal versus distal to coarctation 10-1 P(Cy5) vs 10-1D(Cy3)

data_processing:
Normalizations were preformed in GeneSpring GX 7.3.1 sofware:
1) Cy5 measurements less than 1 were set to 1;
2) Intensity dependent Lowess normalization (percent of the data used for smoothing 20%; set Cy3 measurement less than 1 to 1).


title: T-ALL 30A

value: Normal (remission) at relapase


title: Balbc IL4 4h rep 1


title: T-ALL 35A

source_name: Normal (remission) DNA from T-cell acute lymphoblastic leukemia


title: Aorta proximal versus distal to coarctation 6-25P(Cy5) vs 6-25D(Cy3)


title: Balbc Mock rep 1

description: Gene expression in the absence of IL-4


title: Aorta proximal versus distal to coarctation 6-25P(Cy3) vs 6-25D(Cy5)


title: Aorta proximal versus distal to coarctation 5-5P(Cy3) vs 5-5D(Cy5)

hyb_protocol: Preparation of microarray slides for hybridization: Microarray slides were incubated at 48˚C for 45 min in pre-warmed prehybridization buffer (5X SSC , 0.1% SDS AND 0.2% BSA). After that, they were washed with nuclease free water 2 times 5 minutes, following with isopropanol washes 2 times 5 minutes at room temperature. The slides were spun-dried and used within 1hr. Preparation of the probes for hybridization:100ul of Dye Coupled aRNA were vacuum-dried to the volume needed for the Fragmentation assay using Ambion's Fragmentation Reagents ( Ambion  Cat # 8740 ). After the Fragmentation assay the volume was brought to final volume of 35ul with the Slidehyb Glass  Hybridization buffer (Ambion Cat # 8861 ). The hybridization mix was incubated at 95°C for 5 minutes, then gently vortexed and briefly microfuged. The hybridization mix was added to a pre-warmed slide and a glass cover slip was applied to the array. Slides were incubated for 17-20 hr at the 48°C. Posthybridization washes: The microarray slides were removed from the hybridization chamber. The care was taken not to disturb the coverslip. Each slide was placed in a dish containing  1X  SSC and 0.1%SDS preheated at 48 °C.  The coverslips were removed by gentle agitation while the slides were in solution.  The slides were further agitated for 6 minutes, transferred to a dish containing 1 X SSC and 0.1% SDS at room temperature and agitated for 6 min. The slides were then transferred to a dish containing 0.1 X SSC at room temperature and agitated for 2 times 6 min. Slides were spun dried and scanned immediately.

label_protocol: Poly A RNA was amplified, and amino allyl modified by incorporation of UTP into amplified RNA (Amino Allyl  MessageAmp aRNA, Ambion, Ausitn,TX). Two and a half ug of amplified RNA was subsequently coupled with Cy3 dye (Amersham Biosciences).

treatment_protocol: Pig aortic coarctation was used as an animal model of hypertension. The occluder was surgiaclly introduced arround suprarenal aorta proxiamlly to diaphragm. The pigs were allowed to recover form surgery for one week. After that the occluder was gradually inflated over the period of two weeks, until the mean blood pressure was >150 mmHg. This point was considered as the experimental day one. After 2 weeks of hypertension (14 experimental days) the pigs were terminated and aortic tissue 3 cm proximally form the occluder was excised, claned from adventitia and sanap frozen in liquid nitrogen.


title: T-ALL 27A


title: Aorta proximal versus distal to coarctation 5-5P(Cy5) vs 5-5D(Cy3)


title: T-ALL 17A

source_name: Normal (remission) genomic DNA from T-cell acute lymphoblastic leukemia


title: III_2182_c

status: Public on Aug 08 2009

city: Houston

first: Hon-chiu

middle: Eastwood

last: Leung

address: 1102 Bates Street  Room C1030.09

department: Pediatrics

institute: Baylor College of Medicine

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation

source_name: Xenograft passage III

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep kit for Illumina arrays

growth_protocol: tumor tissues were obtained from the cryostat laboratory and quickly transferred, in DMEM growth medium supplemented with 10% FBS on ice, to the tissue culture room, where they were washed and mechanically dispersed. After the cell suspension was passed through a 35 μ cell strainer, the live tumor cells as single cells and small clumps (~5-10 cells) were counted with trypan blue staining and resuspended in growth medium (1 x 108/ml), followed by surgical transplantation of tumor cells into mouse cerebrum.

extract_protocol: RNA was extracted with Trizol reagent

tag: type

value: mouse xenograft

value: 9 years old

value: right cerebrum


title: III_2467_c

description: replicate 3


title: III_2467_a

description: replicate 1


title: NC_2_c

description: replicate 3

source_name: Pooled normal sample

value: normal brain total RNA bought from Clontech


title: NC_2_b

description: replicate 2


title: T-ALL 17C


title: III_2467_b

description: replicate 2


title: hypomethylated pools Replicate 2

first: Elmar

last: Schilling

address: Franz-Josef-Strauss Allee 11

description: Biological replicate 2 of 2. Corresponding hypermethylated genome pools were utilized for hyper-rep2

hyb_protocol: Samples were hybridized using a stringent protocol. The differentially labelled genomic pools (ether hypo or hyper) were combined and supplemented with 50 µg mouse Cot-1 DNA (Invitrogen), 52 µl of Agilent blocking agent (10-fold) (Agilent), 15% Deionized formamide (Sigma) and 250 µl Agilent hybridization buffer (2-fold) as supplied in the Agilent oligo aCGH Hybridization kit. The samples are heated to 95° for 3 min, mixed and subsequently incubated at 37°C for 30 min. Hybridization was then carried out 67°C for 40 h using an SureHyb chamber and an Agilent hybridization oven. Slides were washed in Wash I (6xSSPE, 0.005% N-lauroylsarcosine) at room temperature for 5 min and in prewarmed Wash II (37°C, 0.06xSSPE) for an additional 5 min. Afterwards slides were dried using acetonitrile within an ozone free facility.

scan_protocol: Scanned on an Agilent scanner at 5 µm resolution. Images were quantified using Agilent Feature Extraction Software (version 9.5.1).

data_processing: Linear normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used. Processed signal intensities were further normalized using GC-dependent regression and imported into Microsoft Office Excel 2007 for further analysis.

label: Alexa Fluor 5

source_name: gDNA from BMM; MCIp treated, hypomethylated pool

label_protocol: MCIp treated genomic DNA pools were labeled using the BioPrime Total Genomic Labeling System (Invitrogen; Version A, 12 February 2007) according to the manufacturer's intruction.

growth_protocol: Bone marrow progenitor cells were flushed from femur and tibia of C57BL/6 & BALB/c mice with TBS using 27 gauge needle attached to a 5 ml syringe from both directions, centrifuged at 300 g, for 8 min at 4°C counted and seeded at a concentration of 5*10E5 cells/ml culture medium (90 % 1640 RPMI, 10 % fetal calf serum (FCS) supplied with 1 mM sodium pyruvate (Gibco), 2 mM L-Glutamine (Biochrome), 2 ml MEM Non-essential amino acids (Gibco), MEM Vitamines (Gibco), 50 U/ml Penicillin/Streptomycin (Gibco), 50 µM 2-Mercaptoethanol (Gibco)and 200 ng/ml rCSF (Cetus)) in bacteriological square plates in an humified incubator at 37°C and 5 % CO2.  After 5 days the medium was changed and cells were harvested on day 6 and replated at a density of 10*10E6 cells/10 ml media in 10 cm tissue culture dish. Cells were harvested on day 7.

extract_protocol: Genomic DNA was extracted from BMM's using Qiagen Blood & Cell Culture DNA Kit and Genomic-tip 100/G according to the manufacturer's instructions.

tag: gender

value: male

tag: Age

value: 8-12 weeks

tag: Tissue

value: bonemarrow

label: Alexa Fluor 3

tag: Strain

value: BALB/c


title: hypermethylated pools Replicate 1

description: Biological replicate 1 of 2. Corresponding hypomethylated genome pools were utilized for hypo-rep1

source_name: gDNA from BMM; MCIp treated, hypermethylated pool

tag: strain


title: T-ALL 17B


title: I_1490_c

description: replicate 3

source_name: Xenograft passage I


title: hypermethylated pools Replicate 2

description: Biological replicate 2 of 2. Corresponding hypomethylated genome pools were utilized for hypo-rep2


title: III_2182_a

description: replicate 1


title: NC_2_a

description: replicate 1


title: III_2182_b

description: replicate 2


title: T-ALL  13C

source_name: Genomic DNA from T-cell acute lymphoblastic leukemia at Relapse

value: at Relapse


title: hypomethylated pools Replicate 1

description: Biological replicate 1 of 2. Corresponding hypermethylated genome pools were utilized for hyper-rep1


title: I_1489_c

description: replicate 3


title: I_1489_b

description: replicate 2


title: shTop1

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

hyb_protocol: DNA was hybridised to Affymetrix GeneChip Human Tiling 2.0R A Array Set (Chromosome 1, 6), using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G.

data_processing: Enrichment was calculated with the Tiling Analysis Software v1.1 (Affymetrix) and profiles were generated with the Affymetrix Integrated Genome Browser (v5.01). Data from two biological replicates were combined and loci enriched in gamma-H2AX with a P-value lower than 0.01 were scored.

source_name: Gamma-H2AX ChIP DNA from shTop1 HCT116 cells

label_protocol: 7 µg of amplified DNA was fragmented and labelled using the GeneChip WT Double-Stranded DNA Terminal Labelling kit (Affymetrix, PN 900812) following manufacturer’s recommendations.

extract_protocol: Asynchronous cultures of HCT116 cells were harvested with Trypsin, washed with PBS, and fixed with 1% formaldehyde in PBS during 10 minutes at room temperature. The ChIP experiments were performed as previously described (PMID: 16307919) with the following modifications. Briefly, 5 µg of anti gamma-H2AX antibody (Abcam ab2893) was first bound to 20 µL of Dynabeads Protein A (Dynal, Invitrogen) then added to 200 µL of lysate, normalised to 2.10^6 cells. After purification, the immunoprecipitated DNA was amplified using the WGA2 GenomePlex Complete Whole Genome Amplification kit (SIGMA) with addition of 0.1 mM dUTP.

tag: antibody

value: gamma-H2AX antibody

source_name: Genomic DNA from shTop1 HCT116 cells

tag: cell line


title: shCtrl

source_name: Gamma-H2AX ChIP DNA from shCtrl HCT116 cells

source_name: Genomic DNA from shCtrl HCT116 cells


title: I_1489_a

description: replicate 1


title: 1425_pt_b

description: replicate 2

source_name: Right cerebrum of a  male patient


title: 1425_pt_a

description: replicate 1


title: I_1490_a

description: replicate 1


title: T-ALL 13A

source_name: Normal (Remission) DNA sample from T-cell lymphoblastic leukemia

value: T-cell lymphoblastic leukemia


title: 1425_pt_c

description: replicate 3


title: I_1490_b

description: replicate 2


title: NR.100nMT3.replicate2

city: Davis

first: Michael

middle: L

last: Goodson

address: One Shields Ave

institute: University of California Davis

description: Empty plasmid control stably transformed cells treated with T3 for 6h

hyb_protocol: Affymetrix GeneChip(r) Human Gene 1.0 ST arrays were hybridized to 2 ug of labeled, amplified single-stranded cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G

data_processing: The raw microarray data was normalized by the Robust Multichip Array (RMA) method using R 2.7.1 software and the affylmGUI 1.14.0 Bioconductor package.

label_protocol: 200ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol (version 4)

growth_protocol: HepG2 transformants expressing ectopic TRa1, ectopic TRb1, or an empty plasmid control were generated as described in Chan IH et. al. (Oncogene. 2006 Jun 15;25(25):3576-88) using a G418 co-selection methodology.  Cell clones arising from individual transformation events were propagated and screened for integration and expression of the expression plasmid by PCR/reverse-transcriptase PCR.  Six, twelve, and eleven independent cell clones, scored as positive for the presence/expression of the introduced construct were pooled for the TRa1, TRb1, and empty plasmid control cell populations, respectively and used in the expression analysis.  HepG2 cells were maintained at 37°C in Dulbecco's Modified Eagle's Medium (DME) supplemented with 10% fetal bovine serum using bicarbonate buffer and a 5% CO2 atmosphere.

extract_protocol: The cells were harvested and the RNA was isolated using an RNeasy kit (Qiagen, Valencia CA).

treatment_protocol: The HepG2 transformant pools expressing ectopic TRa1, ectopic TRb1, or the empty plasmid control were treated with 100 nM T3 or with ethanol carrier alone for 6h in DMEM containing 10% hormone-stripped fetal bovine serum.


title: NR.vehicle.replicate2

description: Empty plasmid control stably transformed cells treated with ethanol for 6h


title: NR.100nMT3.replicate1

source_name: Empty plasmid control stably transformed cells treated with T3 for 6h


title: NR.vehicle.replicate3

source_name: Empty plasmid control stably transformed cells treated with ethanol for 6h


title: NR.100nMT3.replicate3


title: T-ALL 13B

source_name: Genomic DNA from T-cell acute lymphoblastic leukemia at diagnosis

value: at diagnosis


title: p0 v. p3 rep3

city: East Lansing

first: Linda

middle: S.

last: Mansfield

state: MI

address: 181 Food Safety Bldg.

department: Microbiology and Molecular Genetics

institute: Michigan State University

hyb_protocol: Dyed samples to be compared were combined and resuspended in 196µl Ambion SlideHyb buffer 1.  Samples were added to Agilent gasket slides, sandwiched with a UV-crosslinked, blocked microarray slide and sealed inside an Agilent hybridization chamber.  This was rotated at 54 degrees celsius for 18 hours to allow hybridization to the array before washing and scanning.

scan_protocol: Slides were scanned using a GenePix scanner and GenePix Pro 4.1 software.  PMT values were adjusted to obtain approximately equal levels of signal from both wavelength channels.

data_processing: Done using R/LIMMA.  Signal ratios were normalized using a global loess procedure.  A least squares linear model was fit, and using false-discovery rate adjustment, P-values less than 0.05 were considered differentially expressed.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Unpassaged Camylobacter jejuni 11168 RNA

label_protocol: 6µg RNA was reverse transcribed with random hexamer primers and an aminoallyl-dUTP/dNTP mix using Invitrogen SuperScriptIII  CyDyes 3 or 5 from New England Biolabs were used to dye aminoallyl-cDNA samples.  Reactions were cleaned at each step using a QIAGEN QIAquick kit.

growth_protocol: C. jejuni strains were grown in jars with atmospheric gas exchanged for a 10% CO2, 10% H2, 80% N2 in Bolton broth in 25cm2 tissue culture flasks.  Jars were shaken at 80 rpm, 37 degrees Celsius for 18 hours, at which point the bacteria has reached mid-stationary phase growth.

extract_protocol: Contents of C. jejuni broth cultures were poured into 15ml tubes containing 0.1 volume of cold RNA “stop solution” consisting of 1:10 volumes of saturated phenol:ethanol.  This was centrifuged at 5000rpm, 4 degrees Celsius for 20 minutes to pellet cells.  RNA was extracted by lysing C. jejuni with 200µl 1mg/ml lysozyme solution supplemented with 20µl Proteinase K, followed by RNA isolation with QIAGEN RNeasy kit (following manufacturer's instructions).  On column DNase digestion was done twice.  Total RNA was ethanol precipitated overnight before determining RNA quality and concentration using the NanoDrop, PCR for DNA detection, and the Agilent 2100 BioAnalyzer.

tag: adaptation status

value: Unadapted (unpassaged in C57 BL/6 IL-10-/- mice)

source_name: Passaged Camylobacter jejuni 11168 RNA

value: Adapted:3 passages in C57 BL/6 IL-10-/- mice


title: Transition phase sample 3

city: Tampa

first: James

middle: Timothy

last: Riordan

state: FL

address: 4202 E Fowler Ave BSF 218

department: CMMB

institute: University of South Florida

description: There are probes on the array that target three different E. coli genomes. Those that were specific for genomes other than Sakai were excluded from the analysis.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5× SSC, and 1 mg/mL BSA at 42°C for 1 hour. After blocking, arrays were washed 2× 5 min in 0.1× SSC and 2× 30 s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95°C for 5 min and then mixed with 40 uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47°C for 16–18 h. After hybridization, arrays were washed in 2× SSC, 0.5% SDS 37C for 5 min, followed by 2× 5 min in 0.1× SSC, 0.1% SDS 37°C, and then 2 × 2.5 min in room temperature 0.1× SSC. Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain and growth phase as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (wild type or mutant) + growth phase (exponential or stationary) + strain*growth phase + sample (biological replicate) + error. Significant differences in expression due to strain, growth phase and strain*growth phase were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 500 random permutations to estimate the p-values. The q-value package in R was used for determining the false discovery rate (FDR).

organism: Escherichia coli O157:H7 str. Sakai

source_name: rpoN mutant grown to transition phase

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM amino-allyl dUTP. 30uL C. cDNA was purified using PCRreactions were incubated overnight at 42 cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

growth_protocol: EcJR-8 grown to OD600 = 1.8 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM).

extract_protocol: 5mL of culture was mixed with 5mL of hot acid phenol:chloroform. Samples were held at 65ºC with periodic shaking for at least 10 minutes before centrifuging at 4000 rpm for 20 min. Supernatant was extracted again with acid-phenol:chloroform and then with chloroform:isoamyl alcohol (24.1). RNA was precipitated overnight at –80ºC in 2.5V 100% ethanol and 1/10V 3M sodium acetate pH 5.2. RNA samples were purified and treated with DNase using the Rneasy kit (Qiagen).

tag: genotype

value: rpoN mutant (EcJR-8)

tag: growth protocol

value: transition phase in DMEM-MOPS

source_name: wild type grown to transition phase

growth_protocol: Sakai grown to OD600 = 1.8 in DMEM-MOPS 0.4% glucose at a 10:1 flask-to-media volume in a rotary shaker (180 RPM).

value: wild type


title: p0 v. p3 rep2


title: Transition phase sample 4

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).


title: p0 v. p3 rep1


title: Transition phase sample 2


title: bWT.100nMT3.replicate2

description: TRb1 stably transformed cells treated with T3 for 6h


title: bWT.100nMT3.replicate3

source_name: TRb1 stably transformed cells treated with T3 for 6h