title: f2#82 versus pool Mouse Adipose tissue


title: f2#87 versus pool Mouse Adipose tissue

status: Public on Jul 07 2006

type: RNA

city: Los Angeles

first: Leslie

last: Ingram-drake

state: CA

department: Medicine/MIMG/Human Genetics

country: USA

institute: UCLA

description: Adipose tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

data_processing: Arrays were quantified on the basis of spot intensity relative to background (Qhyb program, Rosetta), adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to an error model to determine significance (type I error).  Gene expression is reported as the ratio of the mean log10 intensity (mlratio) relative to the pool derived from 150 mice randomly selected from the F2 population. Normalized values are the reported as the ratio of the mlratio relative to the pool.

molecule: total RNA

organism: Mus musculus

tag: Strain:C57BL/6J and C3H/HeJ on ApoE null Age:24 weeks Gender:Female

source_name: pool

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


title: f2#81 versus pool Mouse Adipose tissue


title: f2#80 versus pool Mouse Adipose tissue


title: f2#79 versus pool Mouse Adipose tissue


title: f2#83 versus pool Mouse Adipose tissue


title: f2#72 versus pool Mouse Adipose tissue


title: f2#71 versus pool Mouse Adipose tissue


title: f2#75 versus pool Mouse Adipose tissue

tag: Strain:C57BL/6J and C3H/HeJ on ApoE null Age:24 weeks Gender:male


title: f2#73 versus pool Mouse Adipose tissue


title: f2#76 versus pool Mouse Adipose tissue


title: f2#78 versus pool Mouse Adipose tissue


title: f2#67 versus pool Mouse Adipose tissue


title: f2#77 versus pool Mouse Adipose tissue


title: f2#70 versus pool Mouse Adipose tissue


title: f2#63 versus pool Mouse Adipose tissue


title: f2#68 versus pool Mouse Adipose tissue


title: f2#64 versus pool Mouse Adipose tissue


title: f2#59 versus pool Mouse Adipose tissue


title: f2#51 versus pool Mouse Adipose tissue


title: f2#53 versus pool Mouse Adipose tissue


title: f2#54 versus pool Mouse Adipose tissue


title: f2#60 versus pool Mouse Adipose tissue


title: f2#55 versus pool Mouse Adipose tissue


title: f2#45 versus pool Mouse Adipose tissue


title: f2#40 versus pool Mouse Adipose tissue


title: f2#46 versus pool Mouse Adipose tissue


title: f2#43 versus pool Mouse Adipose tissue


title: f2#52 versus pool Mouse Adipose tissue


title: f2#49 versus pool Mouse Adipose tissue


title: f2#48 versus pool Mouse Adipose tissue


title: f2#56 versus pool Mouse Adipose tissue


title: f2#41 versus pool Mouse Adipose tissue


title: f2#50 versus pool Mouse Adipose tissue


title: f2#58 versus pool Mouse Adipose tissue


title: f2#62 versus pool Mouse Adipose tissue


title: f2#37 versus pool Mouse Adipose tissue


title: f2#61 versus pool Mouse Adipose tissue


title: f2#35 versus pool Mouse Adipose tissue


title: f2#36 versus pool Mouse Adipose tissue


title: f2#42 versus pool Mouse Adipose tissue


title: f2#34 versus pool Mouse Adipose tissue


title: f2#47 versus pool Mouse Adipose tissue


title: f2#39 versus pool Mouse Adipose tissue


title: f2#33 versus pool Mouse Adipose tissue


title: f2#38 versus pool Mouse Adipose tissue


title: f2#30 versus pool Mouse Adipose tissue


title: f2#31 versus pool Mouse Adipose tissue


title: f2#32 versus pool Mouse Adipose tissue


title: f2#28 versus pool Mouse Adipose tissue


title: f2#27 versus pool Mouse Adipose tissue


title: f2#20 versus pool Mouse Adipose tissue


title: f2#26 versus pool Mouse Adipose tissue


title: f2#25 versus pool Mouse Adipose tissue


title: f2#17 versus pool Mouse Adipose tissue


title: f2#23 versus pool Mouse Adipose tissue


title: f2#11 versus pool Mouse Adipose tissue


title: f2#9 versus pool Mouse Adipose tissue


title: f2#14 versus pool Mouse Adipose tissue


title: f2#24 versus pool Mouse Adipose tissue


title: f2#16 versus pool Mouse Adipose tissue


title: f2#19 versus pool Mouse Adipose tissue


title: f2#10 versus pool Mouse Adipose tissue


title: f2#22 versus pool Mouse Adipose tissue


title: f2#21 versus pool Mouse Adipose tissue


title: f2#8 versus pool Mouse Adipose tissue


title: f2#5 versus pool Mouse Adipose tissue


title: f2#15 versus pool Mouse Adipose tissue


title: f2#18 versus pool Mouse Adipose tissue


title: f2#7 versus pool Mouse Adipose tissue


title: f2#29 versus pool Mouse Adipose tissue


title: f2#13 versus pool Mouse Adipose tissue


title: f2#6 versus pool Mouse Adipose tissue


title: f2#4 versus pool Mouse Adipose tissue


title: f2#3 versus pool Mouse Adipose tissue


title: f2#2 versus pool Mouse Adipose tissue


title: f2#356 versus pool Mouse muscle tissue

description: Muscle tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#350 versus pool Mouse muscle tissue


title: f2#358 versus pool Mouse muscle tissue


title: f2#348 versus pool Mouse muscle tissue


title: f2#357 versus pool Mouse muscle tissue


title: f2#345 versus pool Mouse muscle tissue


title: f2#342 versus pool Mouse muscle tissue


title: f2#399 versus pool Mouse muscle tissue


title: f2#355 versus pool Mouse muscle tissue


title: f2#352 versus pool Mouse muscle tissue


title: f2#359 versus pool Mouse muscle tissue


title: f2#347 versus pool Mouse muscle tissue


title: f2#353 versus pool Mouse muscle tissue


title: f2#341 versus pool Mouse muscle tissue


title: f2#354 versus pool Mouse muscle tissue


title: f2#12 versus pool Mouse Adipose tissue


title: f2#344 versus pool Mouse muscle tissue


title: f2#337 versus pool Mouse muscle tissue


title: f2#349 versus pool Mouse muscle tissue


title: f2#351 versus pool Mouse muscle tissue


title: f2#338 versus pool Mouse muscle tissue


title: f2#335 versus pool Mouse muscle tissue


title: f2#336 versus pool Mouse muscle tissue


title: f2#340 versus pool Mouse muscle tissue


title: f2#346 versus pool Mouse muscle tissue


title: f2#332 versus pool Mouse muscle tissue


title: f2#334 versus pool Mouse muscle tissue


title: f2#333 versus pool Mouse muscle tissue


title: f2#329 versus pool Mouse muscle tissue


title: f2#326 versus Mouse muscle tissue


title: f2#331 versus pool Mouse muscle tissue


title: f2#330 versus pool Mouse muscle tissue


title: f2#317 versus pool Mouse muscle tissue


title: f2#328 versus pool Mouse muscle tissue


title: f2#227 versus pool Mouse muscle tissue


title: f2#324 versus pool Mouse muscle tissue


title: f2#323 versus pool Mouse muscle tissue


title: f2#318 versus pool Mouse muscle tissue


title: f2#315 versus pool Mouse muscle tissue


title: f2#311 versus pool Mouse muscle tissue


title: f2#310 versus pool Mouse muscle tissue


title: f2#302 versus pool Mouse muscle tissue


title: f2#321 versus pool Mouse muscle tissue


title: f2#314 versus pool Mouse muscle tissue


title: f2#304 versus pool Mouse muscle tissue


title: f2#316 versus pool Mouse muscle tissue


title: f2#325 versus pool Mouse muscle tissue


title: f2#309 versus pool Mouse muscle tissue


title: f2#307 versus pool Mouse muscle tissue


title: f2#308 versus pool Mouse muscle tissue


title: f2#322 versus pool Mouse muscle tissue


title: f2#301 versus pool Mouse muscle tissue


title: f2#305 versus pool Mouse muscle tissue


title: f2#306 versus pool Mouse muscle tissue


title: f2#303 versus pool Mouse muscle tissue


title: f2#300 versus pool Mouse muscle tissue


title: f2#312 versus pool Mouse muscle tissue


title: f2#299 versus pool Mouse muscle tissue


title: f2#296 versus pool Mouse muscle tissue


title: f2#292 versus pool Mouse muscle tissue


title: f2#295 versus pool Mouse muscle tissue


title: f2#298 versus pool Mouse muscle tissue


title: f2#293 versus pool Mouse muscle tissue


title: f2#297 versus pool Mouse muscle tissue


title: f2#287 versus pool Mouse muscle tissue


title: f2#291 versus pool Mouse muscle tissue


title: f2#289 versus pool Mouse muscle tissue


title: f2#290 versus pool Mouse muscle tissue


title: f2#288 versus pool Mouse muscle tissue


title: f2#313 versus pool Mouse muscle tissue


title: f2#278 versus pool Mouse muscle tissue


title: f2#284 versus pool Mouse muscle tissue


title: f2#285 versus pool Mouse muscle tissue


title: f2#282 versus pool Mouse muscle tissue


title: f2#276 versus pool Mouse muscle tissue


title: f2#294 versus pool Mouse muscle tissue


title: f2#283 versus pool Mouse muscle tissue


title: f2#279 versus pool Mouse muscle tissue


title: f2#280 versus pool Mouse muscle tissue


title: f2#286 versus pool Mouse muscle tissue


title: f2#277 versus pool Mouse muscle tissue


title: f2#274 versus pool Mouse muscle tissue


title: f2#275 versus pool Mouse muscle tissue


title: f2#267 versus pool Mouse muscle tissue


title: f2#270 versus pool Mouse muscle tissue


title: f2#272 versus pool Mouse muscle tissue


title: f2#271 versus pool Mouse muscle tissue


title: f2#268 versus pool Mouse muscle tissue


title: f2#269 versus pool Mouse muscle tissue


title: f2#264 versus pool Mouse muscle tissue


title: f2#266 versus pool Mouse muscle tissue


title: f2#265 versus pool Mouse muscle tissue


title: f2#263 versus pool Mouse muscle tissue


title: f2#257 versus pool Mouse muscle tissue


title: f2#262 versus pool Mouse muscle tissue


title: f2#261 versus pool Mouse muscle tissue


title: f2#259 versus pool Mouse muscle tissue


title: f2#252 versus pool Mouse muscle tissue


title: f2#250 versus pool Mouse muscle tissue


title: f2#246 versus pool Mouse muscle tissue


title: f2#254 versus pool Mouse muscle tissue


title: f2#248 versus pool Mouse muscle tissue


title: f2#256 versus pool Mouse muscle tissue


title: f2#247 versus pool Mouse muscle tissue


title: f2#255 versus pool Mouse muscle tissue


title: f2#242 versus pool Mouse muscle tissue


title: f2#258 versus pool Mouse muscle tissue


title: f2#240 versus pool Mouse muscle tissue


title: f2#236 versus pool Mouse muscle tissue


title: f2#243 versus pool Mouse muscle tissue


title: f2#239 versus pool Mouse Muscle tissue


title: f2#234 versus pool Mouse muscle tissue


title: f2#253 versus pool Mouse muscle tissue


title: f2#249 versus pool Mouse muscle tissue


title: f2#235 versus pool Mouse muscle tissue


title: f2#244 versus pool Mouse muscle tissue


title: f2#232 versus pool Mouse muscle tissue


title: f2#241 versus pool Mouse muscle tissue


title: f2#237 versus pool Mouse muscle tissue


title: f2#260 versus pool Mouse muscle tissue


title: f2#231 versus pool Mouse muscle tissue


title: f2#230 versus pool Mouse muscle tissue


title: f2#245 versus pool Mouse muscle tissue


title: f2#229 versus pool Mouse muscle tissue


title: f2#228 versus pool Mouse muscle tissue


title: f2#233 versus pool Mouse muscle tissue


title: f2#227_2 versus pool Mouse Muscle tissue


title: f2#224 versus pool Mouse muscle tissue


title: f2#225 versus pool Mouse muscle tissue


title: f2#223 versus pool Mouse Muscle tissue


title: f2#220 versus pool Mouse muscle tissue


title: f2#219 versus pool Mouse muscle tissue


title: f2#203 versus pool Mouse Muscle tissue


title: f2#200 versus pool Mouse muscle tissue


title: f2#221 versus pool Mouse muscle tissue


title: f2#209 versus pool Mouse muscle tissue


title: f2#218 versus pool Mouse muscle tissue


title: f2#222 versus pool Mouse muscle tissue


title: f2#216 versus pool Mouse muscle tissue


title: f2#207 versus pool Mouse muscle tissue


title: f2#201 versus pool Mouse muscle tissue


title: f2#199 versus pool Mouse muscle tissue


title: f2#202 versus pool Mouse muscle tissue


title: f2#281 versus pool Mouse muscle tissue


title: f2#196 versus pool Mouse muscle tissue


title: f2#211 versus pool Mouse muscle tissue


title: f2#214 versus pool Mouse muscle tissue


title: f2#208 versus pool Mouse muscle tissue


title: f2#213 versus pool Mouse muscle tissue


title: f2#198 versus pool Mouse muscle tissue


title: f2#217 versus pool Mouse muscle tissue


title: f2#210 versus pool Mouse muscle tissue


title: f2#197 versus pool Mouse muscle tissue


title: f2#212 versus pool Mouse muscle tissue


title: f2#215 versus pool Mouse muscle tissue


title: f2#187 versus pool Mouse muscle tissue


title: f2#192 versus pool Mouse muscle tissue


title: f2#194 versus pool Mouse muscle tissue


title: f2#190 versus pool Mouse muscle tissue


title: f2#193 versus pool Mouse muscle tissue


title: f2#186 versus pool Mouse muscle tissue


title: f2#189 versus pool Mouse Muscle tissue


title: f2#183 versus pool Mouse muscle tissue


title: f2#184 versus pool Mouse muscle tissue


title: f2#182 versus pool Mouse muscle tissue


title: f2#191 versus pool Mouse muscle tissue


title: f2#177 versus pool Mouse muscle tissue


title: f2#188 versus pool Mouse muscle tissue


title: f2#185 versus pool Mouse muscle tissue


title: f2#178 versus pool Mouse muscle tissue


title: f2#181 versus pool Mouse muscle tissue


title: f2#180 versus pool Mouse muscle tissue


title: f2#179 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.20) (3)

city: Ithaca

first: Dr Zhijun

last: Wang

email: zw37@cornell.edu, zjwang@shmu.edu.cn

state: NY

address: Uptown road

department: Department of Population Medicine and Diagnostic Sciences

institute: Cornell University

description: BL21/pOri2 (mu=0.20)

hyb_protocol: 10 microgram of cDNA were hybridized for 16 hr at 45C on GeneChip E. coli Antisense Genome Array (Affymetrix, USA) chips

scan_protocol: GeneChips were scanned  with DNA Microarray Scanner BA (Agilent Technologies, Inc, CA)

data_processing: Expression data were analyzed with the Microarray Analysis Suite, version 5.0  (Affymetrix). Global scaling was performed to compare genes between chips. Each chip was normalized to a target intensity value of 2,500. Expression analysis files created by Microarray Suite, version 5.0, were exported to Microsoft Excel for data formatting.

label: biotin

organism: Escherichia coli

source_name: Escherichia coli BL21/pOri2 (mu=0.20)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: All cultures were carried out in a 5 l fermentor BIOSTAT B-DCU (Sartorius BBI Systems Inc. Melsungen) at controlled temperature 37°C, pH 7.0, and dissolved oxygen tension 30%. The culture volume was 2 l. All reagents were purchased from Sigma-Aldrich, Inc. The synthetic culture medium had the following composition (g l-1): 8, glucose; 14.6, K2HPO4; 3.6, NaH2PO4·H2O; 2.68, (NH4)2SO4; 2, Na2SO4; 1, MgSO4; 1, Na-citrate; 0.5, NH4Cl; 2 ml of 10 mg l-1 of thiamine; 3 ml of trace element solution (g l-1 20.0, Na-EDTA; 15.0, FeCl3·6H2O; 0.5, CaCl2·2H2O; 0.2, ZnSO4·7H2O; 0.2, CoCl2·6H2O; 0.2, CuSO4·5H2O; 0.2, MnSO4·4H2O). The chemostat culture was performed with adding feed medium

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: E. coli samples for RNA extraction were taken during fermentation. Cells were harvested by centrifugation at the cultivation temperature (37°C, 10,000 g, 1 min), separated from the supernatant, and rapidly frozen in dry ice. The samples were stored at -70°C until analysis

tag: Genotype

value: F- ompT hsdSB(rB-mB-) gal dcm (DE3)


title: BL21/pOri2 (mu=0.20) (2)

description: BL21/pOri2 (mu=0.20)


title: BL21/pOri2 (mu=0.20) (4)

description: BL21/pOri2 (mu=0.20)


title: f2#176 versus pool Mouse muscle tissue


title: f2#226 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.20) (1)

description: BL21/pOri2 (mu=0.20)


title: f2#173 versus pool Mouse muscle tissue


title: BL21/pOri1 (mu=0.20) (4)

description: BL21/pOri1 (mu=0.20)

source_name: Escherichia coli BL21/pOri1 (mu=0.20)


title: f2#273 versus pool Mouse muscle tissue


title: BL21/pOri1 (mu=0.20) (3)

description: BL21/pOri1 (mu=0.20)


title: f2#174 versus pool Mouse muscle tissue


title: f2#175 versus pool Mouse muscle tissue


title: BL21 (mu=0.20) (4)

description: BL21 (mu=0.20)

source_name: Escherichia coli BL21 (mu=0.20)


title: BL21 (mu=0.20) (2)

description: BL21 (mu=0.20)


title: f2#172 versus pool Mouse muscle tissue


title: BL21 (mu=0.20) (3)

description: BL21 (mu=0.20)


title: f2#171 versus pool Mouse muscle tissue


title: f2#170 versus pool Mouse muscle tissue


title: BL21 (mu=0.20) (1)

description: BL21 (mu=0.20)


title: BL21/pOri1 (mu=0.20) (1)

description: BL21/pOri1 (mu=0.20)


title: f2#195 versus pool Mouse muscle tissue


title: BL21/pOri1 (mu=0.20) (2)

description: BL21/pOri1 (mu=0.20)


title: f2#168 versus pool Mouse muscle tissue


title: f2#167 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.29) (3)

description: BL21/pOri2 (mu=0.29)

source_name: Escherichia coli BL21/pOri2 (mu=0.29)


title: f2#164 versus pool Mouse muscle tissue


title: f2#166 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.29) (4)

description: BL21/pOri2 (mu=0.29)


title: f2#169 versus pool Mouse muscle tissue


title: f2#163 versus pool Mouse muscle tissue


title: f2#162 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.29) (2)

description: BL21/pOri2 (mu=0.29)


title: f2#161 versus pool Mouse muscle tissue


title: f2#159 versus pool Mouse muscle tissue


title: BL21/pOri2 (mu=0.29) (1)

description: BL21/pOri2 (mu=0.29)


title: BL21/pOri1 (mu=0.39) (4)

description: BL21/pOri1 (mu=0.39)

source_name: Escherichia coli BL21/pOri1 (mu=0.39)


title: f2#158 versus pool Mouse muscle tissue


title: BL21/pOri1 (mu=0.39) (3)

description: BL21/pOri1 (mu=0.39)


title: BL21(mu=0.46) (4)

source_name: Escherichia coli BL21 (mu=0.46)


title: BL21(mu=0.46) (2)


title: BL21/pOri1 (mu=0.39) (1)

description: BL21/pOri1 (mu=0.39)


title: BL21(mu=0.46) (3)


title: f2#160 versus pool Mouse muscle tissue


title: BL21/pOri1 (mu=0.39) (2)

description: BL21/pOri1 (mu=0.39)


title: BL21(mu=0.46) (1)


title: f2#155 versus pool Mouse muscle tissue


title: f2#154 versus pool Mouse muscle tissue


title: f2#157 versus pool Mouse muscle tissue


title: f2#152 versus pool Mouse muscle tissue


title: f2#156 versus pool Mouse muscle tissue


title: f2#148 versus pool Mouse muscle tissue


title: f2#143 versus pool Mouse muscle tissue


title: f2#141 versus pool Mouse muscle tissue


title: f2#127 versus pool Mouse muscle tissue


title: f2#151 versus pool Mouse muscle tissue


title: f2#128 versus pool Mouse muscle tissue


title: f2#117 versus pool Mouse muscle tissue


title: f2#142 versus pool Mouse muscle tissue


title: f2#116 versus pool Mouse muscle tissue


title: f2#144 versus pool Mouse muscle tissue


title: f2#115 versus pool Mouse muscle tissue


title: f2#123 versus pool Mouse muscle tissue


title: f2#120 versus pool Mouse muscle tissue


title: f2#149 versus pool Mouse muscle tissue


title: f2#126 versus pool Mouse muscle tissue


title: f2#145 versus pool Mouse muscle tissue


title: f2#119 versus pool Mouse muscle tissue


title: f2#122 versus pool Mouse muscle tissue


title: f2#121 versus pool Mouse muscle tissue


title: f2#114 versus pool Mouse muscle tissue


title: f2#153 versus pool Mouse muscle tissue


title: f2#124 versus pool Mouse muscle tissue


title: f2#113 versus pool Mouse muscle tissue


title: f2#111 versus pool Mouse Muscle tissue


title: f2#107 versus pool Mouse muscle tissue


title: f2#110 versus pool Mouse muscle tissue


title: f2#125 versus pool Mouse muscle tissue


title: f2#147 versus pool Mouse muscle tissue


title: f2#118 versus pool Mouse muscle tissue


title: f2#109 versus pool Mouse muscle tissue


title: f2#94 versus pool Mouse muscle tissue


title: f2#146 versus pool Mouse muscle tissue


title: f2#91 versus pool Mouse muscle tissue


title: f2#105 versus pool Mouse muscle tissue


title: f2#86 versus pool Mouse muscle tissue


title: f2#87 versus pool Mouse muscle tissue


title: f2#80 versus pool Mouse muscle tissue


title: f2#85 versus pool Mouse muscle tissue


title: f2#104 versus pool Mouse muscle tissue


title: f2#112 versus pool Mouse muscle tissue


title: f2#83 versus pool Mouse muscle tissue


title: f2#93 versus pool Mouse muscle tissue


title: f2#78 versus pool Mouse muscle tissue


title: f2#79 versus pool Mouse muscle tissue


title: f2#95 versus pool Mouse muscle tissue


title: f2#81 versus pool Mouse muscle tissue


title: f2#77 versus pool Mouse muscle tissue


title: f2#88 versus pool Mouse muscle tissue


title: f2#82 versus pool Mouse muscle tissue


title: f2#92 versus pool Mouse muscle tissue


title: f2#76 versus pool Mouse muscle tissue


title: f2#73 versus pool Mouse muscle tissue


title: f2#72 versus pool Mouse muscle tissue


title: f2#74 versus pool Mouse muscle tissue


title: f2#70 versus pool Mouse muscle tissue


title: f2#75 versus pool Mouse muscle tissue


title: f2#67 versus pool Mouse muscle tissue


title: f2#71 versus pool Mouse muscle tissue


title: f2#69 versus pool Mouse muscle tissue


title: f2#56 versus pool Mouse muscle tissue


title: f2#58 versus pool Mouse muscle tissue


title: f2#66 versus pool Mouse muscle tissue


title: f2#55 versus pool Mouse muscle tissue


title: f2#61 versus pool Mouse muscle tissue


title: f2#63 versus pool Mouse muscle tissue


title: f2#64 versus pool Mouse muscle tissue


title: f2#57 versus pool Mouse muscle tissue


title: f2#60 versus pool Mouse muscle tissue


title: f2#54 versus pool Mouse muscle tissue


title: f2#50 versus pool Mouse muscle tissue


title: f2#51 versus pool Mouse muscle tissue


title: f2#52 versus pool Mouse muscle tissue


title: f2#59 versus pool Mouse muscle tissue


title: f2#48 versus pool Mouse muscle tissue


title: f2#46 versus pool Mouse muscle tissue


title: f2#47 versus pool Mouse muscle tissue


title: f2#44 versus pool Mouse muscle tissue


title: f2#41 versus pool Mouse muscle tissue


title: f2#53 versus pool Mouse muscle tissue


title: f2#42 versus pool Mouse muscle tissue


title: f2#39 versus pool Mouse muscle tissue


title: f2#43 versus pool Mouse muscle tissue


title: f2#45 versus pool Mouse muscle tissue


title: f2#68 versus pool Mouse muscle tissue


title: f2#89 versus pool Mouse muscle tissue


title: f2#40 versus pool Mouse muscle tissue


title: f2#36 versus pool Mouse muscle tissue


title: f2#31 versus pool Mouse Muscle tissue


title: f2#30 versus pool Mouse muscle tissue


title: f2#32 versus pool Mouse Muscle tissue


title: f2#34 versus pool Mouse muscle tissue


title: f2#28 versus pool Mouse muscle tissue


title: f2#27 versus pool Mouse muscle tissue


title: f2#26 versus pool Mouse Muscle tissue


title: f2#24 versus pool Mouse muscle tissue


title: f2#29 versus pool Mouse muscle tissue


title: f2#35 versus pool Mouse muscle tissue


title: f2#23 versus pool Mouse muscle tissue


title: f2#21 versus pool Mouse muscle tissue


title: f2#18 versus pool Mouse muscle tissue


title: f2#17 versus pool Mouse muscle tissue


title: f2#19 versus pool Mouse muscle tissue


title: f2#9 versus pool Mouse muscle tissue


title: f2#25 versus pool Mouse muscle tissue


title: f2#3 versus pool Mouse muscle tissue


title: f2#16 versus pool Mouse muscle tissue


title: f2#20 versus pool Mouse muscle tissue


title: f2#22 versus pool Mouse muscle tissue


title: f2#14 versus pool Mouse muscle tissue


title: f2#4 versus pool Mouse muscle tissue


title: f2#11 versus pool Mouse muscle tissue


title: f2#8 versus pool Mouse muscle tissue


title: f2#15 versus pool Mouse muscle tissue


title: f2#355 versus pool Mouse Brain tissue

description: Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.


title: f2#38 versus pool Mouse muscle tissue


title: f2#2 versus pool Mouse muscle tissue


title: f2#358 versus pool Mouse Brain tissue


title: f2#6 versus pool Mouse muscle tissue


title: f2#1 versus pool Mouse muscle tissue


title: f2#357 versus pool Mouse Brain tissue


title: Canine_Temporal lobe_Gpaez_rep3

status: Public on Jul 06 2006

city: Philadelphia

first: Gerardo

middle: L.

last: Paez

state: PA

address: 3900 Delancey Street

department: Clinical Studies Philadelphia

institute: University of Pennsylvania

description: Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA) and further purified by Rneasy mini kit (Qiagen, Valencia, CA). Purity and RNA quality were evaluated by absorbance at 260 nm and by denaturing formaldehyde agarose gel electrophoresis. High quality RNAs with A260/280 ratio over 1.8 and intact 28S and 18S RNA bands were used for microarray analysis. To generate an RNA reference sample for microarray hybridizations, we pooled equal amounts of total RNA from the occipital, temporal, and frontal brain regions collected from three 16-week-old beagles to achieve a homogeneous pool of transcripts. The pooled RNA was divided into aliquots (2μg/μl) and stored at -80 ?C until use. For the purpose of this work, four tissue groups have been established, containing five biological replicates for normal retina and three for each respective brain region. After initial validation of reproducibility, only one microarray experiment was used for each sample.

data_processing: loess subgrid normalization

organism: Canis lupus familiaris

source_name: Temporal brain tissue

tag: RNA extracted from Temporal brain tissue

source_name: Brain pool

tag: Brain pooled RNA made by adding equal amonts of Frontal, Occipital and Temporal Brain cortices


title: Rickettsia conorii experiment_2

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Evaluation of Rickettsia conorii gene expression in nutrient-limited medium

hyb_protocol: Hybridization was performed for 18 hours at 42�C. Slides were washed in 2X SSC with 0.2% SDS for 10 min then in 2X SSC for 10 min, and in 0.2X SSC for 10 min with gentle agitation.

scan_protocol: Slides were scanned using a ScanArray�Express (Perkin Elmer, Boston, MA, USA) with default parameters. Fluorescent signals extraction was performed using GenePix.

data_processing: GeneSpring 7.0

label: Cyanine 3

organism: Rickettsia conorii

source_name: Rickettsia conorii_complete medium

label_protocol: cDNA was synthesized from purified RNA (50 ng � 100 ng) and with reverse transcriptase (Superscript II). After RNaseH treatment cDNA was collected by ethanol precipitation. Twenty nanograms of cDNA were then amplified using the GenomiPhi DNA amplication kit (Amersham). Fluorescently labeled cDNA was prepared using BioPrime DNA labeling System (Invitrogen).

growth_protocol: Rickettsia conorii were grown in confluent monolayers of African green monkey kidney cells (Vero cell, ATCC C1587) with Eagle�s minimum essential medium (MEM) supplemented with 4% fetal calf serum and 2 mM L-glutamine for 48 hours at 32�C.

extract_protocol: Pellets of R. conorii-infected Vero cells were lyzed in TE buffer (10 mM Tris/HCl, 1mM EDTA pH7.0) containing lysozyme (10 mg/ml) for 10 minutes at room temperature. RNA was extracted and purified using RNeasy-Midi columns. RNA samples were treated with RNase-free DNase for 30 min. Eukaryotic RNA was removed from the mixture by using MICROBEnrich kit (Ambion, Austin, USA), based on oligonucleotide-derivatized magnetic beads that hybridize to 18S rRNA, 28S rRNA and to the polyadenylated 3' ends of eukaryotic mRNAs.

treatment_protocol: 48 hours after inoculation of Vero cell, the supernatant was removed and cells incubated for 6 additional hours in fresh medium before cell lysis and extraction.

tag: Rickettsia conorii Malish 7 (ATCC, VR613) grown in Vero cells

label: Cyanine 5

source_name: Rickettsia conorii_PBS

treatment_protocol: 48 hours after inoculation of Vero cell, the supernatant was removed and cells incubated for 6 additional hours in PBS before cell lysis and extraction.


title: f2#5 versus pool Mouse muscle tissue


title: Canine_Temporal lobe_Gpaez_rep2

tag: total RNA extracted from temporal brain tissue from dogs

tag: Brain pool sample made by adding equal amounts of RNA of Frontal, Temporal and Occipital Brain cortices.


title: Rickettsia conorii experiment_3

extract_protocol: 48 hours after inoculation of Vero cell, the supernatant was removed and cells incubated for 6 additional hours in fresh medium before cell lysis and extraction.

tag: Rickettsia conorii Malish 7 (ATCC, VR613)


title: Rickettsia conorii experiment_1

hyb_protocol: Hybridization was performed for 18 hours at 42°C. Slides were washed in 2X SSC with 0.2% SDS for 10 min then in 2X SSC for 10 min, and in 0.2X SSC for 10 min with gentle agitation.

scan_protocol: Slides were scanned using a ScanArray®Express (Perkin Elmer, Boston, MA, USA) with default parameters. Fluorescent signals extraction was performed using GenePix.

label_protocol: cDNA was synthesized from purified RNA (50 ng – 100 ng) and with reverse transcriptase (Superscript II). After RNaseH treatment cDNA was collected by ethanol precipitation. Twenty nanograms of cDNA were then amplified using the GenomiPhi DNA amplication kit (Amersham). Fluorescently labeled cDNA was prepared using BioPrime DNA labeling System (Invitrogen).

growth_protocol: Rickettsia conorii were grown in confluent monolayers of African green monkey kidney cells (Vero cell, ATCC C1587) with Eagle’s minimum essential medium (MEM) supplemented with 4% fetal calf serum and 2 mM L-glutamine for 48 hours at 32°C.


title: f2#354 versus pool Mouse Brain tissue


title: f2#108 versus pool Mouse muscle tissue


title: Normal retina vs.Brain pool

description:
the labeling system provides a more predictable and consistent signal than direct or
indirect dye incorporation for two reasons. First, since the fluorescent dye is part of the 3DNA reagent, it does not have
to be incorporated during the cDNA preparation. This avoids the inefficient hybridization of the cDNA to the array that
results from the incorporation of fluorescent dye nucleotide conjugates into the reverse transcript. Second, because
each 3DNA molecule contains an average of about 45 fluorescent dyes and each bound cDNA will be detected by a
single 3DNA molecule, the signal generated from each message will be largely independent of base composition or
length of the transcript. In contrast, the signal generated from each message labeled through dye incorporation will
vary depending on the base composition or length of the message.

source_name: Retina

tag: Retinas extracted from beagles aged at 16 weeks

tag: Brain pool reference tissue mada by adding equal amounts of Frontal, Occipital and Temporal brain cortices


title: Frontal lobe_Gpaez_rep3

description:
The labeling system provides a more predictable and consistent signal than direct or
indirect dye incorporation for two reasons. First, since the fluorescent dye is part of the 3DNA reagent, it does not have
to be incorporated during the cDNA preparation. This avoids the inefficient hybridization of the cDNA to the array that
results from the incorporation of fluorescent dye nucleotide conjugates into the reverse transcript. Second, because
each 3DNA molecule contains an average of about 45 fluorescent dyes and each bound cDNA will be detected by a
single 3DNA molecule, the signal generated from each message will be largely independent of base composition or
length of the transcript. In contrast, the signal generated from each message labeled through dye incorporation will
vary depending on the base composition or length of the message.

source_name: Frontal Lobe

tag: beagles aged at 16 weeks

source_name: brain pool

tag: reference tisuue created by adding equal amounts of frontal, occipital and temporal lobe RNA


title: Occipital lobe_Gpaez_rep1

description: For microarray production, 3,931

source_name: Occipital lobe

tag: RNA extracted from occipital brain lobe tissue from dogs aged at 16 weeks

tag: Brain pool made by adding equal amounts of F.O. and T regions


title: f2#359 versus pool Mouse Brain tissue


title: Frontal lobe_Gpaez_rep2

source_name: RNA extracted from frontal lobe

tag: Frontal tissue extracted form normal beagles aged at 16 weeks

tag: Reference tissue  created by adding equal amounts of frontal, occipital and temporal total RNA.


title: Occipital lobe_Gpaez_rep2

description: For microarray production, 3,931

tag: RNA extracted from Occipital brain tussue

tag: RNA pooled consistitng in equal amounts of F,T,O brain regions


title: Schizosaccharomyces Pombe wild type strain KCl treatment 15min, replicate 2 (slide18)

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 15min compared to non-treated sample at 25C.

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Scan Express laser scanner

data_processing: Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 15min.

growth_protocol: Strain grow on YEA medium at 25C to log phase then treated with 1M KCl for 15min.

tag: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 15min at 25C.

growth_protocol: Strain grow on YEA medium at 25C to log phase in rich medium.

treatment_protocol: Schizosaccharomyces Pombe wild type strain Fy368 grow in rich medium at 25C.

tag: Schizosaccharomyces Pombe wild type strain Fy368 grow in rich medium at 25C as control.


title: Occipital lobe_Gpaez_rep3

description: For microarray production, 3,931

tag: RNA extracted from occipital brain region tissue.

tag: Brain pool made by addiing equal amounts of RNA from F,O, and T lobe


title: Lbeta T2_1hr Control

status: Public on Jul 05 2006

city: Evanston

first: Ying

last: Peng

state: IL

address: 2205 Tech Drive

institute: Northwestern University

description: Gene expression data from Lbeta T2 cells treated with human activin A.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse genechip 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Agilent Genearray Scanner 3000.

data_processing: The data were analyzed with Affymetrix Genechip Operating System version 1.4 (GCOS 1.4) and dCHIP using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Lbeta T2 cell, a mature pituitary cell line.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Cells were plated in cell culture flasks coated with matrigen (BD Biosciences, Bedford, MA) and maintained in F12:DMEM (Invitrogen) supplemented with 5% fetal bovine serum (FBS, Hyclone), 0.45% glucose and 100U of penicillin, and 100ug of streptomycin at 37C in 5% CO2.

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen, MD) according to the manufacturer's instructions.

treatment_protocol: Recombinant human activin A was produced in our laboratory and formulated in a buffer of 0.15M NaCl and 0.05M Tris (Ph 7.5). Subconfluent cells were seeded in cell culture flasks for 16 hours in phenol-free, serum-free F12:DMEM medium, and then treated with buffer as control.

tag: A cell line developed by utilizing LHß promoter for targeted expression of SV40 T-antigen in transgenic mice

tag: Expresses GnRH receptor, LHß and FSHß subunits, and secretes FSH upon activin stimulation


title: Lbeta T2_2hr Control


title: Lbeta T2_2hr Activin

treatment_protocol: Recombinant human activin A was produced in our laboratory and formulated in a buffer of 0.15M NaCl and 0.05M Tris (Ph 7.5). Subconfluent cells were seeded in cell culture flasks for 16 hours in phenol-free, serum-free F12:DMEM medium, and then treated with activin at 30ng/ml.


title: Retina vs. Brain Pool

tag: Brain pool tissue made by adding equal amounts of RNA from frontal, occipital and temporal cortices

tag: Normal retina extracted from dog beagles aged at 16 weeks.


title: Frontal lobe_ Gpaez_rep1

source_name: Frontal tissue extracted from beagles aged at 16 weeks

tag: Normal dogs (beagles) aged at 16 weeks

source_name: Reference tissue

tag: Brain pool maed by adding equal amounts of frontal, temporal and occipital RNA.


title: Lbeta T2_6hr Control


title: 11 day rats intermittent unloading pool 1

status: Public on Jul 04 2006

city: Columbia

first: Theodore

last: Zderic

state: MO

address: E102 Vet. Med. Bldg. / 1600 E. Rollins Rd.

department: Biomedical Sciences

institute: University of Missouri

description: Gene expression data from soleus of rats hindlimb unloaded for 10 hrs/day for 11 continuous days.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat U34A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Rattus norvegicus

source_name: Rat soleus after 11 days intermittent inactivity

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Gender

value: Female


title: Schizosaccharomyces Pombe wild type strain KCl treatment 15min, replicate 1 (slide16)

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Strain grow on YEA medium at 25C to log phase then treated with 1M KCl for 15min.

source_name: Schizosaccharomyces Pombe wild type strain Fy368


title: Lbeta T2_6hr Activin


title: 2 hrs treadmill walking after 12 hrs unloading (30 min walk, 30 min cage activity for 4 total hours) pool 2

description: Gene expression data from soleus of rats hindlimb unloaded for 12 hrs immediately followed by 2 hrs intermittent walking

source_name: Rat soleus after 2 hrs treadmill walking


title: 12 hrs of hindlimb unloading rats pool 3

description: Gene expression data from soleus of rats hindlimb unloaded for 12 hrs

source_name: Rat soleus after 12 hrs hindlimb unloading


title: 11 day spontaneous activity control rats pool 1

description: Gene expression data from soleus of normally caged rats.

source_name: Rat soleus control


title: 11 day rats intermittent unloading pool 2


title: 12 hrs of hindlimb unloading rats pool 2


title: Lbeta T2_1hr Activin


title: 2 hrs treadmill walking after 12 hrs unloading (30 min walk, 30 min cage activity for 4 total hours) pool 1


title: 11 day spontaneous activity control rats pool 2


title: 12 hrs spontaneous activity control rats pool 2


title: 12 hrs of hindlimb unloading rats pool 1


title: 12 hrs spontaneous activity control rats pool 3


title: 12 hrs spontaneous activity control rats pool 1


title: viremic HIV patient H

city: Frederick

first: Richard

middle: A

last: Lempicki

state: MD

address: PO Box B

department: Clinical Services Program

institute: Leidos Biomedical Research, Inc.

description: Monocytes isolated from an aviremic HIV infected patient; aviremia due to successful suppression of HIV by HAART.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on the Human U133A GeneChip. The GeneChips was washed and stained using the Affymetrix Fluidics Station 400 following Manufacturer's recommended protocol..

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Homo sapiens

source_name: Monocytes from viremic (OFF HAART) HIV patient H

label_protocol: One half to two micrograms of total RNA was isolated from 1-2 million CD14+ sorted cells.  Target RNA was labeled (as biotinylated cRNA) as described in the Affymetrix 2003 Technical Note “GeneChip Eukaryotic Small Sample Target Labeling Assay Version II”.

growth_protocol: Cells were not cultured i.e. total RNA isolated following cell sorting.

extract_protocol: Qiagen RNAEasy extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PBMCs were isolated using Ficoll and stored in Liquid N2. Cells were thawed and peripheral blood CD14+ cells were isolated by fluorescence-activated cell sorting, using a FACSVantage SE FACSDiVa flow cytometer (BD Immunocytometry Systems, San Jose, CA).  Frozen peripheral blood mononuclear cells were thawed and lymphocytes were stained according to the manufacturer’s instructions with the monoclonal antibodies CD3 FITC (BD Immunocytometry Systems San Jose, CA), CD4 PC5 (Beckman Coulter, Miami, FL), and CD14 PE (Becton Dickenson). Sorting for CD14+ monocytes was performed using a quadrant gate on CD3 FITC-CD14 PE+.  CD14+ monocyte purity was determined by flow cytometry to be >95%.


title: viremic HIV patient D

source_name: Monocytes from viremic (OFF HAART) HIV patient D

tag: Monocytes isolated from an aviremic HIV infected patient; aviremia due to successful suppression of HIV by HAART.


title: viremic HIV patient G

source_name: Monocytes from viremic (OFF HAART) HIV patient G


title: viremic HIV patient F

source_name: Monocytes from viremic (OFF HAART) HIV patient F


title: viremic HIV patient B

source_name: Monocytes from viremic (OFF HAART) HIV patient B


title: aviremic HIV patient G

source_name: Monocytes from  aviremic (ON HAART) HIV patient G


title: aviremic HIV patient E

source_name: Monocytes from  aviremic (ON HAART) HIV patient E


title: aviremic HIV patient F

source_name: Monocytes from  aviremic (ON HAART) HIV patient F


title: viremic HIV patient A

source_name: Monocytes from viremic (OFF HAART) HIV patient A


title: viremic HIV patient E

source_name: Monocytes from viremic (OFF HAART) HIV patient E


title: Su(Ste) tiling, wt (Cy3) vs. spn-E (Cy5)

status: Public on Jul 03 2006

type: other

city: Worcester

first: Hervé

last: Seitz

state: MA

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: University of Massachusetts Medical School

description: Short RNAs (< 200 nt) were gel-purified, labeled and hybridized by LC Sciences (Houston, TX, USA). See http://www.lcsciences.com/ for additional details.

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Background, defined as the average of values from the "BKG0" spots (which were spotted with chemical linker, but no probe), was subtracted from each value. Cy5 values were then normalized by dividing each of them by the geometric average of the (Cy5-bkg)/(Cy3-bkg) ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...).

molecule: other

organism: Drosophila melanogaster

source_name: wt testes

extract_protocol: Short RNAs were extracted using miRVana kit (Ambion), then gel-purified (size cutoff: 200 nt) by LC Sciences (Houston, TX, USA).

tag: Testes from wt (Oregon-R) Drosophila melanogaster were hand-dissected.

source_name: spindle-E mutant testes

tag: Testes from spindle-E homozygotes from the w;;spnE100.37/TM3 Sb strain were hand-dissected.


title: aviremic HIV patient H

source_name: Monocytes from  aviremic (ON HAART) HIV patient H


title: aviremic HIV patient D

source_name: Monocytes from  aviremic (ON HAART) HIV patient D


title: viremic HIV patient C

source_name: Monocytes from viremic (OFF HAART) HIV patient C


title: White tiling, wt (Cy3) vs. dcr-2 (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Background, defined as the average of values from the "BKG0" spots (which were spotted with chemical linker, but no probe), was subtracted from each value. Cy5 values were then normalized by dividing each of them by the geometric average of the (Cy5-bkg)/(Cy3-bkg) ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...). Replicates for ANTIwhiteAfter3 tiling probes were then averaged.

source_name: wt heads

source_name: dicer-2 mutant heads

tag: Testes from dicer-2 homozygotes from the FRT42D dcr-2L811fsX/CyO;P[w-IR]/P[w-IR] strain were hand-dissected.


title: aviremic HIV patient B

source_name: Monocytes from  aviremic (ON HAART) HIV patient B;


title: Su(Ste) tiling, wt (Cy3) vs. armi (Cy5)

source_name: armitage mutant testes

tag: Testes from armitage homozygotes from the armi72.1/TM3 Sb P[hs-hid] strain were hand-dissected.


title: aviremic HIV patient C

source_name: Monocytes from  aviremic (ON HAART) HIV patient C


title: Su(Ste) tiling, cry (Cy3) vs. wt (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Cy3 values were normalized by dividing each of them by the geometric average of the Cy3/Cy5 ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...).

source_name: crystal mutant testes

tag: Testes from crystal (cry1Y) Drosophila melanogaster were hand-dissected.


title: roo tiling, wt (Cy3) vs. wt (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Background, defined as the average of values from the "BKG0" spots (which were spotted with chemical linker, but no probe), was subtracted from each value. Cy5 values were then normalized by dividing each of them by the slope of the linear regression of (Cy3-bkg) (x-axis) vs. (Cy5-bkg) (y-axis) for significantly detected, non-saturated, spiked-in synthetic siRNAs (for each of those siRNAs, the same amount was spiked in each of the two "total RNA" samples before gel-purification and labeling).

source_name: wt ovaries

tag: Ovaries from wt (Oregon-R) Drosophila melanogaster were hand-dissected.


title: 12Mm.191

status: Public on May 22 2006

city: Indianapolis

first: Hosein

last: Kouros-Mehr

state: IN

address: 533 Merrill St.

department: Oncology

institute: Eli Lilly

description: Total RNA from microdissected ducts compared to epithelium-free distal stroma of 5 week old mammary gland

data_processing: Lowess print-tip normalization (Acuity 4.0)

source_name: Ducts

tag: Ducts

source_name: Distal Stroma

tag: Distal Stroma


title: 12Mm.203

description: Total RNA from microdissected terminal end buds compared to epithelium-free distal stroma of 5 week old mammary gland

source_name: Terminal end buds

tag: Terminal end buds


title: Su(Ste) tiling, armi (Cy3) vs. wt (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Background, defined as the average of values from the "BKG0" spots (which were spotted with chemical linker, but no probe), was subtracted from each value. Cy3 values were then normalized by dividing each of them by the geometric average of the (Cy3-bkg)/(Cy5-bkg) ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...).


title: 12Mm.202


title: 12Mm.200


title: 12Mm.192


title: 12Mm.199


title: 12Mm.193


title: roo tiling, armi heterozygotes (Cy3) vs. armi homozygotes (Cy5)

source_name: armi heterozygotes ovaries

tag: Ovaries from armitage heterozygotes from the armi72.1/TM3 Sb P[hs-hid] strain were hand-dissected.

source_name: armi homozygotes ovaries

tag: Ovaries from armitage homozygotes from the armi72.1/TM3 Sb P[hs-hid] strain were hand-dissected.


title: aviremic HIV patient A

source_name: Monocytes from aviremic (ON HAART) HIV patient A


title: 12Mm.196


title: 12Mm.201


title: Su(Ste) tiling, wt (Cy3) vs. piwi (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Background, defined as the average of values from the "BKG0" spots (which were spotted with chemical linker, but no probe), was subtracted from each value. Cy5 values were then normalized by dividing each of them by the geometric average of the (Cy5-bkg)/(Cy3-bkg) ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...). Replicates of ANTIHoppel tiling probes were then averaged.

source_name: wt testes

source_name: piwi mutant testes

tag: Testes from piwi homozygotes from the w;piwi2/CyO strain were hand-dissected.


title: Su(Ste) tiling, wt (Cy3) vs. aub (Cy5)

source_name: aubergine mutant testes

tag: Testes from aubergine trans-heterozygotes from  strains aubHN2 cn bw/CyO and aubQC42 cn bw/CyO were hand-dissected.


title: 12Mm.197


title: 12Mm.198


title: Abundance of piRNAs in rat testes

city: Waltham

first: Nelson

middle: C

last: Lau

address: 415 South St MS029

department: Biology

institute: Brandeis University

description: Abundance levels are represented by the number of reads of that sequence within a sequencing run of the cDNA library.

data_processing: See Supplemental Online Materials from Lau et al. Science. 2006 Jun 15; [Epub ahead of print] PMID: 16778019 for detailed protocol on data processing.

source_name: Q column eluate fractions from rat testes extract

extract_protocol: See Supplemental Online Materials from Lau et al. Science. 2006 Jun 15; [Epub ahead of print] PMID: 16778019 for detailed protocol on testes extract production, chromatography and cDNA construction.

tag: testis tissue from Sprague-Dawley male rats, 7-8 weeks old


title: Su(Ste) tiling, wt (Cy3) vs. cry (Cy5)

data_processing: Signal was defined as the mean of pixel intensities on the ~50 pixels corresponding to each spot. Cy5 values were normalized by dividing each of them by the geometric average of the Cy5/Cy3 ratios for every significant (intensity>exp(5); this cutoff was determined by applying the method described in Lu et al. (2005), Nature 435:834-838 to similar experiments, identically processed, in which probes were spotted as replicates) and non-saturated (intensity<30000; this cutoff was determined in similar experiments, identically processed, where various quantities of synthetic siRNAs were spiked in the samples) control RNAs (i.e.: non-microRNAs and non-rasiRNAs: ribosomal RNAs, tRNAs, ...).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen), then short RNAs were gel-purified (size cutoff: 200 nt) by LC Sciences (Houston, TX, USA).


title: 12Mm.190


title: Abundance of piRNAs in mouse testes

source_name: Q column eluate fractions of mouse testes extract

tag: testes tissue from Swiss Webster male mice, 8-10 weeks old


title: f2#10 versus pool Mouse muscle tissue

description: Muscle tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  All sample were compared to a common pool created from equal portions of RNA from each of the samples.

data_processing: Arrays were quantified on the basis of spot intensity relative to background (Qhyb program, Rosetta), adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to an error model to determine significance (type I error).  Gene expression is reported as the ratio of the mean log10 intensity (mlratio) relative to the pool derived from 150 mice randomly selected from the F2 population. Normalized values are the reported as the ratio of the mlratio relative to the pool.

tag: Strain:C57BL/6J and C3H/HeJ on ApoE null Age:24 weeks Gender:male

source_name: pool

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


title: M-CSF macrophage without stimulation/CD14 PMNC slide A, second trial

status: Public on Oct 05 2005

city: Fukuoka

first: Vahid

last: Khajoee

state: Fukuoka

address: 3-1-1 Maidashi, higashi-ku

department: Pediatrics

country: Japan

institute: Kyuhsu University

description: RNA amplified before cDNA synthesis.

data_processing: Lowess normalization (GeneSpring software)

source_name: M-CSF macrophage without stimulation

tag: Culture of CD14 cells with M-CSF for 7 days.

source_name: CD14 PMNC

tag: CD14 cells were seperated from PBMN by magnetic sorting.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide A, second trial

description: RNA amplified before cDNA synthesis.

source_name: GM-CSF macrophage without stimulation

tag: Culture of CD14 cells with GM-CSF for 7 days.


title: M-CSF macrophage with BCG stimulation/CD14 PMNC slide A first trial

description: RNA amplified before cDNA synthesis.

source_name: M-CSF macrophage with BCG stimulation

tag: Culture of CD14 cells with M-CSF for 7 days and 24 hours stimulation with BCG.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide A, second trial

description: RNA amplified before cDNA synthesis.

source_name: GM-CSF macrophage with BCG stimulation

tag: Culture of CD14 cells with GM-CSF for 7 days and 24 hours stimulation with BCG.


title: M-CSF macrophage without stimulation/CD14 PMNC slide A first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide A first trial

description: RNA amplified before cDNA synthesis.

tag: CD14 were cells seperated from PBMN by magnetic sorting.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide C, second trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide A first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide B, second trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage with BCG stimulation/CD14 PMNC slide C, first trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage without stimulation/CD14 PMNC slide B, second trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide B, first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide C, first trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage with BCG stimulation/CD14 PMNC slide B, first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage without stimulation/CD14 PMNC slide C, first trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage without stimulation/CD14 PMNC slide C, second trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide B, second trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage without stimulation/CD14 PMNC slide B, first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide B, first trial

description: RNA amplified before cDNA synthesis.


title: GM-CSF macrophage with BCG stimulation/CD14 PMNC slide C, second trial

description: RNA amplified before cDNA synthesis.


title: M-CSF macrophage without stimulation/CD14 PMNC slide C, first trial

description: RNA amplified before cDNA synthesis.


title: 48h_post-AMI_IVS tissue, biological rep2, Av2

status: Public on Jul 14 2006

city: Laramie

first: Mark

last: Stayton

state: WY

address: Dept. 3944, 1000 E. University Ave.

department: Molecular Biology

institute: University of Wyoming

description: Gene expression data from different regions of the mouse heart

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Robust Multi-array Averaging (RMA; www.bioconductor.org) and global scaling (across 192 chips)as normalization method.

source_name: C57/BL6 heart tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared from individual frozen tissue samples using an SDS/phenol isolation protocol after which equal weights of RNA from 4-10 mice were pooled for each dissected tissue type.

treatment_protocol:
Permanent occlusion of the Left Anterior Descending coronary artery was performed on adult male (8 to 10 wk old) C57BL/6J mice. To exclude surgical effects on gene expression, sham surgeries were conducted by passing suture under the artery without ligation. Animals were sacrificed at time t=0 (naïve control) and at each time point post-AMI (0.25, 1, 4, 12, 24 and 48 h)
At each time point 4-10 animals were sacrificed and hearts harvested, regionally dissected and immediately frozen in liquid N2.

tag: Weight of mouse

tag: Age

value: 8-10 wk old


title: f2#324 versus pool Mouse Brain tissue

description: Brain tissue from 330 F2 female and male mice (animals fed a high fat "Western" diet from 8-24 weeks of age.) C57BL/J6 and C3H/HeJ on ApoE null backgrounds.  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 on ApoE null Age:24 weeks Gender:Female