title: Acetaminophen  6hr  Rat  8918  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  2015  left_liver_lobe

status: Public on Sep 19 2007

type: RNA

city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

country: USA

institute: NIEHS

description: Liver Test (Blinded) Sample

data_processing: log base 2 ratio of Dye Normalized rProcessedSignal to gProcessedSignal

molecule: total RNA

organism: Rattus norvegicus

tag: Strain

value: F344/N Gender:male Age:10-12 weeks Tissue:Liver


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  1658  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  3420  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  1376  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  1277  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  1049  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  1045  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  6930  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  0504  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  1550  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  9632  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  0644  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  0186  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9100  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  0685  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  3942  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  7365  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 24hr Rat 1391 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1391 blood

value: F344/N Gender:male Age:10-12 weeks Tissue:blood


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  5396  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  8658  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  4678  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  5389  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 6hr Rat 5067 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 5067 blood


title: Acetaminophen 24hr Rat 6954 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 6954 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  0186  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  5407  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  4623  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  5339  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  7375  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 6hr Rat 0426 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0426 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0089 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0089 blood


title: Acetaminophen 3hr Rat 8511 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8511 blood


title: Acetaminophen 6hr Rat 9709 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 9709 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 9999 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 9999 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0766 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0766 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 4145 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4145 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2507 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2507 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 6954 blood

description: Blood Test (Blinded) Sample


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5027 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5027 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  2698  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1987 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1987 blood


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  9540  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 4258 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 4258 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 2222 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 2222 blood


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  1457  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  8897  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 6370 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6370 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  3426  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  1871  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 3565 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 3565 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 7270 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 7270 blood


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  2123  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8030 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8030 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0184 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0184 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  1009  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  5886  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9434 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 9434 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  0613  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 2789 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2789 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 8385 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 8385 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 6749 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 6749 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 7404 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7404 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0460 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0460 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5421 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5421 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0246 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0246 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2431 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2431 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5554 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5554 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5402 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5402 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0861 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0861 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 5143 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 5143 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 1286 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 1286 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 3046 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 3046 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0948 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0948 blood


title: Acetaminophen 3hr Rat 6622 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6622 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 3273 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 3273 blood


title: Acetaminophen 6hr Rat 2864 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2864 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 7532 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 7532 blood


title: Acetaminophen 3hr Rat 6370 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6370 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 7186 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7186 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 6034 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 6034 blood


title: Acetaminophen 24hr Rat 0572 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0572 blood


title: Acetaminophen 3hr Rat 5102 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5102 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 5067 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 5067 blood


title: Acetaminophen 6 hr Rat 8960 Blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6 hr Rat 8960 Blood


title: Acetaminophen 24hr Rat 5421 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5421 blood


title: Acetaminophen 3hr Rat 6219 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6219 blood


title: Acetaminophen 6hr Rat 3273 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample


title: Acetaminophen 24hr Rat 5480 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5480 blood


title: Acetaminophen 6hr Rat 0621 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0621 blood


title: Acetaminophen 6hr Rat 8597 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 8597 blood


title: Acetaminophen 6hr Rat 9434 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 9434 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2342 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2342 blood


title: Acetaminophen 6hr Rat 5143 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 5143 blood


title: Acetaminophen 3hr Rat 8846 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8846 blood


title: Acetaminophen 3hr Rat 0460 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0460 blood


title: Acetaminophen 6hr Rat 1578 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 1578 blood


title: Acetaminophen 24hr Rat 7404 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7404 blood


title: Acetaminophen 24hr Rat 1580 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1580 blood


title: Acetaminophen 24hr Rat 2486 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2486 blood


title: Acetaminophen 6hr Rat 4145 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4145 blood


title: Acetaminophen 3hr Rat 1286 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 1286 blood


title: Acetaminophen 6hr Rat 0089 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0089 blood


title: Acetaminophen 24hr Rat 9999 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 9999 blood


title: Acetaminophen 6hr Rat 2789 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2789 blood


title: Acetaminophen 6hr Rat 2927 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2927 blood


title: Acetaminophen 24hr Rat 5402 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5402 blood


title: Acetaminophen 24hr Rat 2344 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2344 blood


title: Acetaminophen 6hr Rat 6749 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 6749 blood


title: Acetaminophen 3hr Rat 0246 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0246 blood


title: Acetaminophen 24hr Rat 2342 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2342 blood


title: Acetaminophen 3hr Rat 2222 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 2222 blood


title: Acetaminophen 3hr Rat 5545 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5545 blood


title: Acetaminophen 3hr Rat 5554 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5554 blood


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  5557  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen 24hr Rat 2507 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2507 blood


title: Acetaminophen 24hr Rat 3565 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 3565 blood


title: Acetaminophen 6hr Rat 7270 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 7270 blood


title: Acetaminophen 6hr Rat 4178 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4178 blood


title: Acetaminophen 6hr Rat 8066 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 8066 blood


title: Acetaminophen 3hr Rat 3482 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 3482 blood


title: Acetaminophen 6hr Rat 3763 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 3763 blood


title: Acetaminophen 24hr Rat 8385 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 8385 blood


title: Acetaminophen 3hr Rat 7558 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 7558 blood


title: Acetaminophen 24hr Rat 3046 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 3046 blood


title: Acetaminophen 24hr Rat 0861 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0861 blood


title: Acetaminophen 3hr Rat 4258 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 4258 blood


title: Acetaminophen 3hr Rat 8282 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8282 blood


title: Acetaminophen 24hr Rat 6173 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 6173 blood


title: Acetaminophen 24hr Rat 8002 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 8002 blood


title: Acetaminophen 3hr Rat 4010 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 4010 blood


title: Acetaminophen 3hr Rat 7532 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 7532 blood


title: Acetaminophen 6hr Rat 4101 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4101 blood


title: Acetaminophen 6hr Rat 6034 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 6034 blood


title: Acetaminophen 24hr Rat 0184 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0184 blood


title: Acetaminophen 24hr Rat 7067 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7067 blood


title: Acetaminophen 3hr Rat 8030 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8030 blood


title: Acetaminophen 3hr Rat 2360 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 2360 blood


title: Acetaminophen 24hr Rat 1987 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1987 blood


title: Acetaminophen 3hr Rat 5027 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5027 blood


title: Acetaminophen 6hr Rat 0948 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0948 blood


title: Acetaminophen 3hr Rat 0766 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0766 blood


title: Acetaminophen 6hr Rat 9676 blood vs. Acetaminophen 6hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 9676 blood


title: Acetaminophen 3hr Rat 8691 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8691 blood


title: Acetaminophen 24hr Rat 2431 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2431 blood


title: Acetaminophen 24hr Rat 7186 blood vs. Acetaminophen 24hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7186 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 6622 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6622 blood


title: Acetaminophen 3hr Rat 0893 blood vs. Acetaminophen 3hr Rat Pooled Control blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 0893 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6 hr Rat 8960 Blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6 hr Rat 8960 Blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5545 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5545 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9676 blood

description: Blood Test (Blinded) Sample


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 0572 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 0572 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 5102 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 5102 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0426 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0426 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2486 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2486 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 4101 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4101 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 4010 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 4010 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 8066 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 8066 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8511 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8511 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 1578 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 1578 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 4178 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 4178 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 7067 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 7067 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8691 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8691 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 0893 blood

description: Blood Test (Blinded) Sample


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 2360 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 2360 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 2927 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2927 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 8002 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 8002 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 6173 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 6173 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 8597 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 8597 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8282 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8282 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 2344 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 2344 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 6219 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 6219 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 3482 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 3482 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 0621 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 0621 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 2864 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 2864 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1391 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1391 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 1580 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 1580 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 9709 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 9709 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 7558 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 7558 blood


title: Acetaminophen 6hr Rat Pooled Control blood vs. Acetaminophen 6hr Rat 3763 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 6hr Rat 3763 blood


title: Acetaminophen 3hr Rat Pooled Control blood vs. Acetaminophen 3hr Rat 8846 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 3hr Rat 8846 blood


title: Acetaminophen 24hr Rat Pooled Control blood vs. Acetaminophen 24hr Rat 5480 blood

description: Blood Test (Blinded) Sample

source_name: Acetaminophen 24hr Rat 5480 blood


title: 3616 PC 24Hr (pool) vs.1500mg/kg APAP 24Hr rat 3625 blood

description: 1500 mg/kg X 24 hr

source_name: 3616 PC 24Hr (pool)

source_name: 1500mg/kg APAP 24Hr rat 3625 blood


title: 150mg/kg APAP 12Hr rat 4127 blood vs. PC 12Hr rat 4126 blood

description: 150 mg/kg X 12 hr

source_name: 150mg/kg APAP 12Hr rat 4127 blood

source_name: PC 12Hr rat 4126 blood


title: 150mg/kg APAP 12Hr rat 4130 blood vs. PC 12Hr rat 4126 blood

description: 150 mg/kg X 12 hr

source_name: 150mg/kg APAP 12Hr rat 4130 blood


title: 3616 PC 24Hr (pool) vs. 1500mg/kg APAP 24Hr rat 3623 blood

description: 1500 mg/kg X 24 hr

source_name: 1500mg/kg APAP 24Hr rat 3623 blood


title: PC 12Hr rat 4126 blood vs. 150mg/kg APAP 12Hr rat 4127 blood

description: 150 mg/kg X 12 hr


title: PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4135 blood

description: 2500 mg/kg X 12 hr

source_name: 2500mg/kg APAP 12Hr rat 4135 blood


title: 150mg/kg APAP 12Hr rat 4128 blood vs. PC 12Hr rat 4126 blood

description: 150 mg/kg X 12 hr

source_name: 150mg/kg APAP 12Hr rat 4128 blood


title: PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4133 blood

description: 1500 mg/kg X 12 hr

source_name: 1500mg/kg APAP 12Hr rat 4133 blood


title: 1500mg/kg APAP 12Hr rat 4133 blood vs. PC 12Hr rat 4126 blood

description: 1500 mg/kg X 12 hr


title: 1500mg/kg APAP 12Hr rat 4132 blood vs. PC 12Hr rat 4126 blood

description: 1500 mg/kg X 12 hr

source_name: 1500mg/kg APAP 12Hr rat 4132 blood


title: 2500mg/kg APAP 12Hr rat 4135 blood vs. PC 12Hr rat 4126 blood

description: 2500 mg/kg X 12 hr


title: 1500mg/kg APAP 24Hr rat 3624 blood vs. 3616 PC 24Hr (pool)

description: 1500 mg/kg X 24 hr

source_name: 1500mg/kg APAP 24Hr rat 3624 blood


title: PC 12Hr rat 4126 blood vs. 150mg/kg APAP 12Hr rat 4130 blood

description: 150 mg/kg X 12 hr


title: 3616 PC 24Hr (pool) vs. 1500mg/kg APAP 24Hr rat 3624 blood

description: 1500 mg/kg X 24 hr


title: PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4134 blood

description: 1500 mg/kg X 12 hr

source_name: 1500mg/kg APAP 12Hr rat 4134 blood


title: 2500mg/kg APAP 12Hr rat 4138 blood vs. PC 12Hr rat 4126 blood

description: 2500 mg/kg X 12 hr

source_name: 2500mg/kg APAP 12Hr rat 4138 blood


title: PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4136 blood

description: 2500 mg/kg X 12 hr

source_name: 2500mg/kg APAP 12Hr rat 4136 blood


title: 1500mg/kg APAP 24Hr rat 3625 blood vs. 3616 PC 24Hr (pool)

description: 1500 mg/kg X 24 hr


title: 1500mg/kg APAP 12Hr rat 4134 blood vs. PC 12Hr rat 4126 blood

description: 1500 mg/kg X 12 hr


title: PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4137 blood

description: 2500 mg/kg X 12 hr

source_name: 2500mg/kg APAP 12Hr rat 4137 blood


title: 150mg/kg APAP 6Hr rat 3589 blood vs. PC 6Hr rat 3586 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3589 blood

source_name: PC 6Hr rat 3586 blood


title: 150mg/kg APAP 6Hr rat 3590 blood vs. PC 6Hr rat 3586 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3590 blood


title: 150mg/kg APAP 6Hr rat 3588 blood vs. PC 6Hr rat 3586 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3588 blood


title: PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3588 blood

description: 150 mg/kg X 6 hr


title: 2500mg/kg APAP 12Hr rat 4136 blood vs. PC 12Hr rat 4126 blood

description: 2500 mg/kg X 12 hr


title: 1500mg/kg APAP 24Hr rat 3623 blood vs. 3616 PC 24Hr (pool)

description: 1500 mg/kg X 24 hr

source_name: 3616 PC 24Hr (pool)


title: PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3590 blood

description: 150 mg/kg X 6 hr


title: 150mg/kg APAP 24Hr rat 3619 blood vs. 3616 PC 24Hr (pool)

description: 150 mg/kg X 24 hr

source_name: 150mg/kg APAP 24Hr rat 3619 blood


title: PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3587 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3587 blood


title: 2500mg/kg APAP 24Hr rat 3629 blood vs. 3616 PC 24Hr (pool)

description: 2500 mg/kg X 24 hr

source_name: 2500mg/kg APAP 24Hr rat 3629 blood


title: 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3619 blood

description: 150 mg/kg X 24 hr


title: 150mg/kg APAP 24Hr rat 3620 blood vs. 3616 PC 24Hr (pool)

description: 150 mg/kg X 24 hr

source_name: 150mg/kg APAP 24Hr rat 3620 blood


title: PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3595 blood

description: 2500 mg/kg X 6 hr

source_name: 2500mg/kg APAP 6Hr rat 3595 blood


title: 2500mg/kg APAP 12Hr rat 4137 blood vs. PC 12Hr rat 4126 blood

description: 2500 mg/kg X 12 hr

source_name: PC 12Hr rat 4126 blood


title: PC 12Hr rat 4126 blood vs. 2500mg/kg APAP 12Hr rat 4138 blood

description: 2500 mg/kg X 12 hr


title: 3616 PC 24Hr (pool) vs. 2500mg/kg APAP 24Hr rat 3631 blood

description: 2500 mg/kg X 24 hr

source_name: 2500mg/kg APAP 24Hr rat 3631 blood


title: PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3597 blood

description: 2500 mg/kg X 6 hr

source_name: 2500mg/kg APAP 6Hr rat 3597 blood


title: 3616 PC 24Hr (pool) vs. 1500mg/kg APAP 24Hr rat 3626 blood

description: 1500 mg/kg X 24 hr

source_name: 1500mg/kg APAP 24Hr rat 3626 blood


title: 3616 PC 24Hr (pool) vs. 2500mg/kg APAP 24Hr rat 3629 blood

description: 2500 mg/kg X 24 hr


title: 1500mg/kg APAP 24Hr rat 3626 blood vs. 3616 PC 24Hr (pool)

description: 1500 mg/kg X 24 hr


title: 3616 PC 24Hr (pool) vs. 2500mg/kg APAP 24Hr rat 3628 blood

description: 2500 mg/kg X 24 hr

source_name: 2500mg/kg APAP 24Hr rat 3628 blood


title: 1500mg/kg APAP 6Hr rat 3592 blood vs. PC 6Hr rat 3586 blood

description: 1500 mg/kg X 6 hr

source_name: 1500mg/kg APAP 6Hr rat 3592 blood


title: 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3620 blood

description: 150 mg/kg X 24 hr


title: 1500mg/kg APAP 6Hr rat 3594 blood vs. PC 6Hr rat 3586 blood

description: 1500 mg/kg X 6 hr

source_name: 1500mg/kg APAP 6Hr rat 3594 blood


title: 2500mg/kg APAP 6Hr rat 3595 blood vs. PC 6Hr rat 3586 blood

description: 2500 mg/kg X 6 hr


title: PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3598 blood

description: 2500 mg/kg X 6 hr

source_name: 2500mg/kg APAP 6Hr rat 3598 blood


title: PC 12Hr rat 4126 blood vs. 150mg/kg APAP 12Hr rat 4128 blood

description: 150 mg/kg X 12 hr

source_name: 150mg/kg APAP 12Hr rat 4128 blood


title: 1500mg/kg APAP 6Hr rat 3593 blood vs. PC 6Hr rat 3586 blood

description: 1500 mg/kg X 6 hr

source_name: 1500mg/kg APAP 6Hr rat 3593 blood

source_name: PC 6Hr rat 3586 blood


title: PC 6Hr rat 3586 blood vs. 150mg/kg APAP 6Hr rat 3589 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3589 blood


title: 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3618 blood

description: 150 mg/kg X 24 hr

source_name: 3616 PC 24Hr (pool)

source_name: 150mg/kg APAP 24Hr rat 3618 blood


title: 2500mg/kg APAP 24Hr rat 3628 blood vs. 3616 PC 24Hr (pool)

description: 2500 mg/kg X 24 hr


title: PC 6Hr rat 3586 blood vs. 2500mg/kg APAP 6Hr rat 3596 blood

description: 2500 mg/kg X 6 hr

source_name: 2500mg/kg APAP 6Hr rat 3596 blood


title: 150mg/kg APAP 6Hr rat 3587 blood vs. PC 6Hr rat 3586 blood

description: 150 mg/kg X 6 hr

source_name: 150mg/kg APAP 6Hr rat 3587 blood


title: PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3593 blood

description: 1500 mg/kg X 6 hr


title: 3616 PC 24Hr (pool) vs. 150mg/kg APAP 24Hr rat 3617 blood

description: 150 mg/kg X 24 hr

source_name: 150mg/kg APAP 24Hr rat 3617 blood


title: 150mg/kg APAP 24Hr rat 3618 blood vs. 3616 PC 24Hr (pool)

description: 150 mg/kg X 24 hr


title: PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3592 blood

description: 1500 mg/kg X 6 hr


title: PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3594 blood

description: 1500 mg/kg X 6 hr


title: 2500mg/kg APAP 24Hr rat 3631 blood vs. 3616 PC 24Hr (pool)

description: 2500 mg/kg X 24 hr


title: 2500mg/kg APAP 24Hr rat 3630 blood vs. 3616 PC 24Hr (pool)

description: 2500 mg/kg X 24 hr

source_name: 2500mg/kg APAP 24Hr rat 3630 blood


title: PC 12Hr rat 4126 blood vs. 1500mg/kg APAP 12Hr rat 4132 blood

description: 1500 mg/kg X 12 hr

source_name: PC 12Hr rat 4126 blood

source_name: 1500mg/kg APAP 12Hr rat 4132 blood


title: 2500mg/kg APAP 6Hr rat 3598 blood vs. PC 6Hr rat 3586 blood

description: 2500 mg/kg X 6 hr


title: TSA (Trichostatin A) Treated LNCaP Cells at 24h - biological rep 1

status: Public on Sep 15 2007

city: Notre Dame

first: Randy

last: Jeffrey

state: IN

address: Rm 232, Galvin Life Sciences Bldg

department: Biological Sciences

institute: University of Notre Dame

description: Gene expression data from LNCaP prostate cancer cells treated with 5uM TSA for 24h

hyb_protocol: Refer to Nimblegen Systems Inc

scan_protocol: Refer to Nimblegen Systems Inc

data_processing: RMA normalized data sets provided by Nimblegen Systems Inc were analyzed using GeneSpring (Agilent)

label: Refer to Nimblegen Systems Inc

organism: Homo sapiens

source_name: TSA (5uM) treated LNCaP cells harvested after 24h of incubation

label_protocol: Refer to Nimblegen Systems Inc

growth_protocol: LNCaP prostate cancer cells were plated at a density of five million cells per 150cm2 dish in 25mL of RPMI-1640 medium supplemented with 10% FBS and PenStrep and incubated for 24h prior to treatment

extract_protocol: Qiagen RNeasy extraction protocol according to manufacturer's instuctions.

treatment_protocol: 150cm2 dishes containing LNCaP cells were treated with 5uM TSA (DMSO - Carrier) following a 24h incubation period after initial plating

tag: LNCaP prostate cancer cells


title: CG-1521 (HDAC Inhibitor) Treated LNCaP cells at 24h - biological rep 1

description: Gene expression data from LNCaP prostate cancer cells treated with 7.5uM CG-1521 for 24h

source_name: CG-1521 (7.5uM) treated LNCaP cells harvested after 24h of incubation

treatment_protocol: 150cm2 dishes containing LNCaP cells were treated with 7.5uM CG-1521 (DMSO - Carrier) following a 24h incubation period after initial plating


title: 150mg/kg APAP 24Hr rat 3617 blood vs. 3616 PC 24Hr (pool)

description: 150 mg/kg X 24 hr


title: 3616 PC 24Hr (pool) vs. 2500mg/kg APAP 24Hr rat 3630 blood

description: 2500 mg/kg X 24 hr


title: TSA (Trichostatin A) Treated LNCaP Cells at 24h - biological rep 3


title: 2500mg/kg APAP 6Hr rat 3596 blood vs. PC 6Hr rat 3586 blood

description: 2500 mg/kg X 6 hr


title: 1500mg/kg APAP 6Hr rat 3591 blood vs. PC 6Hr rat 3586 blood

description: 1500 mg/kg X 6 hr

source_name: 1500mg/kg APAP 6Hr rat 3591 blood


title: LNCaP Control Cells at 24h - biological rep 7

description: Gene expression data from LNCaP prostate cancer cells treated with vehicle control for 24h

source_name: Vehicle treated LNCaP cells harvested after 24h of incubation

treatment_protocol: 150cm2 dishes containing LNCaP cells were treated with vehicle control (DMSO - Carrier) following a 24h incubation period after initial plating


title: CG-1521 (HDAC Inhibitor) Treated LNCaP cells at 24h - biological rep 4


title: LNCaP Control Cells at 24h - biological rep 4


title: PC 6Hr rat 3586 blood vs. 1500mg/kg APAP 6Hr rat 3591 blood

description: 1500 mg/kg X 6 hr


title: LNCaP Control Cells at 48h - biological rep 3

description: Gene expression data from LNCaP prostate cancer cells treated with vehicle control for 48h

source_name: Vehicle treated LNCaP cells harvested after 48h of incubation

growth_protocol: LNCaP prostate cancer cells were plated at a density of one million cells per 150cm2 dish in 25mL of RPMI-1640 medium supplemented with 10% FBS and PenStrep and incubated for 24h prior to treatment

extract_protocol: Qiagen Rneasy extraction protocol according to manufacturer's instuctions.

treatment_protocol: 150cm2 dishes containing LNCaP cells were treated with vehicle control (75% EtOH and 25%DMSO - Carrier) following a 24h incubation period after initial plating


title: CG-1521 (HDAC Inhibitor) Treated LNCaP cells at 24h - biological rep 2


title: 2500mg/kg APAP 6Hr rat 3597 blood vs. PC 6Hr rat 3586 blood

description: 2500 mg/kg X 6 hr

source_name: 2500mg/kg APAP 6Hr rat 3597 blood


title: LNCaP Control Cells at 24h - biological rep 5


title: PC-346C Control Cells at 48h - biological rep 1

description: Gene expression data from PC-346C prostate cancer cells treated with vehicle control for 48h

source_name: Vehicle treated PC-346C cells harvested after 48h of incubation

growth_protocol: PC-346C prostate cancer cells were plated at a density of three million cells per 150cm2 dish in 25mL of DMEM/F-12 medium supplemented with 2% Charcoal Stripped Serum, ITS-G, testosterone, EGF, Hydrocortisone, T3, phosphoethanolamine, Fibronectin, Fetuin, cholera toxin and PenStrep and incubated for 36h prior to treatment

treatment_protocol: 150cm2 dishes containing PC-346C cells were treated with vehicle control (75% EtOH and 25%DMSO - Carrier) following a 24h incubation period after initial plating

tag: PC-346C prostate cancer cells


title: LNCaP Control Cells at 24h - biological rep 1


title: PC-346C Control Cells at 48h - biological rep 3


title: LNCaP Casodex Treated Cells at 48h - biological rep 3

description: Gene expression data from LNCaP prostate cancer cells treated with 50uM Casodex for 48h

source_name: Casodex (50uM) treated LNCaP cells harvested after 48h of incubation

treatment_protocol: 150cm2 dishes containing LNCaP cells were treated with 50uM Casodex (75% EtOH and 25%DMSO - Carrier) following a 24h incubation period after initial plating


title: LNCaP Casodex Treated Cells at 48h - biological rep 1


title: PC-346C Casodex Treated Cells at 48h - biological rep 2

source_name: Casodex (50uM) treated PC-346C cells harvested after 48h of incubation

treatment_protocol: 150cm2 dishes containing PC-346C cells were treated with 50uM Casodex (75% EtOH and 25%DMSO - Carrier) following a 24h incubation period after initial plating


title: LNCaP Control Cells at 24h - biological rep 2


title: TSA (Trichostatin A) Treated LNCaP Cells at 24h - biological rep 2


title: MPSS-SIS-17bp

status: Public on Sep 14 2007

type: MPSS

city: Manchester

first: Junfeng

last: Chen

address: Kilburn Building, Oxford Road

department: School of Computer Science

country: United Kingdom

institute: University of Manchester

description: RNA extraction and MPSS experiment in Meyers Lab (http://mpss.udel.edu/)

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the SIS library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

organism: Arabidopsis thaliana

source_name: Silique - 24 to 48 hr post-fertilization, signature MPSS

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Siliques were harvested ~24-48 hours after fertilization, when petals have begun to detach (Stage 16-17). Tissue was harvested ~2 hours after dark. Length of siliques was 5-10 mm. Total RNA was isolated using TRIzol reagent.


title: fibroblast, MFS subject GDO1051 rep 4

city: Seattle

first: Walter

middle: L.

last: Ruzzo

state: WA

department: CSE

institute: University of Washington

description: Individual GF211 filters were stripped and reused several times; `Filter Number/Use Number' characteristic columns show which filter/which reuse corresponds to each hybridization.  Each hyb was exposed on the phosphoimager multiple times with varying durations; each exposure was scanned once; the `Exposures' characteristic shows how many exposures were combined to produce normalized intensity estimates.  This information is also encoded in the `Sample name'.  Un-normalized values from all exposures/scans of all hybridizations are provided in one of the two attached data files (one for normal fibroblast samples, one for MFS samples).  These two files do *not* use the GEO-defined gene ID's for platform GPL538; instead, correlate via GenBank Accession.

hyb_protocol: Each sample was analyzed twice on duplicate arrays. The Research Genetics GF211 arrays were hybridized with 30-60 million cpm of probe/array for 18h then washed extensively at 50 degrees C in 0.5X SSC +0.1% SDS.

scan_protocol: Multiple exposures were collected on a Storm phosphorimager. Images were imported using Research Genetics Pathways 3 software.

data_processing: See Yao et al., `A Marfan syndrome gene expression phenotype in cultured skin fibroblasts', submitted.  In outline, we do the following.  The median of log10-transformed expression values for each gene across all exposures of all arrays is calculated, and serves as a common baseline for comparison between experiments. Then, for each exposure, we compute a smooth `local' (loess) regression line between its log intensities and the median levels.  The resulting regression function transforms the expression values of each exposure to the scale of the common baseline while capturing nonlinear effects. Finally, we combine data from multiple exposures of an array by taking their medians. This technique builds on earlier work [Dozmorov I, Galecki A, Chang Y, Krzesicki R, Vergara M, Miller RA: Gene expression profile of long-lived snell dwarf mice. J Gerontol A Biol Sci Med Sci 2002, 57: B99-108], [Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J et al.: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30: e15.] and more details are reported in [Mulvihill ER, Jaeger J, Sengupta R, Ruzzo WL, Reimer C, Lukito S et al.: Atherosclerotic plaque smooth muscle cells have a distinct phenotype. Arterioscler Thromb Vasc Biol 2004, 24: 1283-1289].   One innovation introduced here is the following:  to reduce the impact of outliers and differentially expressed genes on the inferred levels of other genes, the loess regression is based on only a `stable' subset of genes uniformly chosen across all intensity levels.  Specifically, for each gene we calculate the rank of its measured intensity in each exposure, and the median absolute deviation (MAD) of its rank across exposures.  We sort all n genes by increasing median intensity and partition them into n/5 groups of consecutive genes.  From each group of 5, the gene with the minimum MAD statistic is chosen. This selection of n/5 genes comprises the stable subset of genes on which our regression is based.  Other approaches to normalization based on stable genes have been proposed [Kepler TB, Crosby L, Morgan KT: Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol 2002, 3: RESEARCH0037.], [Schadt EE, Li C, Ellis B, Wong WH: Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl 2001, Suppl 37: 120-125.] but those techniques seem more complex, and choose stable genes in ways that potentially yield sparse coverage of some regions of the intensity spectrum, consequently increasing the influence of anomalous or differentially expressed genes on the normalization in those regions.  As intensity-dependent non-linearity is a key concern in our normalization, uniform representation of intensities in the stable subset is valuable.

source_name: cultured skin fibroblasts from Marfan subjects

label_protocol: For hybridization to individual arrays, 1 µg of total RNA was used to synthesize 33P-dCTP labeled first strand cDNA with Invitrogen Superscript II.

growth_protocol: Study participants were recruited under an institutional review board approved protocol and informed consent. A skin punch biopsy was used to establish a fibroblast cell culture. Unaffected control subjects were selected from patients visiting dermatology clinics. All of the cell strains (in the array group, between passage 2 and 6 and in the New Subject group, passage 2) were grown to confluence in SmGM2 +10% FBS + bullet kit containing recombinant EGF, FGF and insulin (BioWhittaker). After reaching confluence, the medium was modified to include ascorbic acid at 50-µg/ml [Jain MK, Layne MD, Watanabe M, Chin MT, Feinberg MW, Sibinga NE et al.: In vitro system for differentiating pluripotent neural crest cells into smooth muscle cells. J Biol Chem 1998, 273: 5993-5996]. Fresh medium was added after 24 hours.

extract_protocol: At 48h, total RNA was isolated using a guanidinium iso-thiocyanate-phenol-chloroform extraction protocol [Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987, 162: 156-159].   Each sample was analyzed for quality and quantity by UV spectroscopy and gel electrophoresis.

tag: age

tag: sex

value: F

tag: disease status

value: Marfan subject

tag: Filter number

tag: Usage number

tag: Exposures


title: fibroblast, MFS subject 60FR rep 3

value: M


title: fibroblast, MFS subject 60FR rep 4


title: LNCaP Control Cells at 48h - biological rep 2


title: MPSS-SAP-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the SAP library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: sup/ap1 infloresence - mixed stage, immature buds, signature MPSS

tag: Plants were grown in soil in growth chamber with 16 hours of light for 5 weeks. Immature inflorescence was harvested ~2 hours after dark. Tissue included inflorescence meristem and early stage floral buds (up to Stage 11/12). Total RNA was isolated using TRIzol reagent.


title: fibroblast, MFS subject GDO21 rep 4


title: MPSS-AP3-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the AP3 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: ap3-6 infloresence - mixed stage, immature buds, signature MPSS

extract_protocol: Total RNA was isolated using TRIzol reagent


title: MPSS-LES-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the LES library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Leaves - 21 day, untreated,  signature MPSS

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark. Equal amounts of leaf tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.


title: fibroblast, MFS subject GDO21 rep 3


title: Melanocyte UV irradiated

city: Zürich

first: Keith

middle: S

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: No further information

hyb_protocol: Standard 16h hybridization protocol, followed by standard wash protocol

scan_protocol: The microarray scanning was performed with confocal laser microscopy and computerized image analysis.

data_processing: see Valery et al. 2001

source_name: melanocyte

label_protocol: reverse transcription to incorporate Cy3-labelled nucleotides

extract_protocol: Trizol

tag: infant foreskin derived melanocyte culture, untreated

label_protocol: reverse transcription to incorporate Cy5-labelled nucleotides

tag: infant foreskin derived melanocyte culture, irradiated with 100 mJ per square cm


title: MPSS-CAS-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the CAS library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Callus - actively growing, signature MPSS

tag: Callus was initiated from Col-0 seeds grown on media containing 1/2X MS salts, 3% sucrose in presence of 2,4D (0.5 mg/l), IAA (2 mg/l) and kinetin (0.1mg/l). Tissue was grown ~3 months in dark at 22C and transfered to fresh plates every ~10-14 days. Total RNA was isolated using TRIzol reagent.


title: MPSS-ROS-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the ROS library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Root - 21 day, untreated

tag: Plants were grown in 16 hours of light for 21 days, grown under sterile conditions in vermiculite or perlite. Tissue was harvested ~2 hours after dark, and roots were rinsed in water and frozen immediately. Equal amounts of root tissue from each growth condition were mixed and RNA was isolated using TRIzol reagent.


title: fibroblast, MFS subject GDO1051 rep 3


title: MPSS-S04-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the S04 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Leaves, 4 hr after salicylic acid treatment, signature MPSS

tag: Plants were grown in soil in a growth chamber at 20 degrees C with 8 hours of light for 54 days. Half-strength Hoagland's solution was used to bottom-water the plants. Plants were sprayed to run-off with 0.3 mM SA in 0.02% silwet in the light. Four hours post-treatment, rosettes were cut above the soil line and harvested (in the light), quick-frozen in liquid nitrogen, then stored at -80 degrees C. Total RNA was later extracted using TRIzol reagent.


title: fibroblast, MFS subject GDO32 rep 1


title: fibroblast, MFS subject 60FR rep 2


title: fibroblast, MFS subject GDO32 rep 2


title: fibroblast, MFS subject 60FR rep 1


title: MPSS-AGM-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the AGM library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: agamous infloresence - mixed stage, immature buds, signature MPSS


title: fibroblast, MFS subject FB992 rep 2


title: LNCaP Control Cells at 24h - biological rep 6


title: MPSS-INS-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the INS library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Infloresence - mixed stage, immature buds, signature MPSS


title: MPSS-S52-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the S52 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: Leaves, 52 hr after salicylic acid treatment, signature MPSS

tag: Plants were grown in soil in a growth chamber at 20 degrees C with 8 hours of light for 46 days. Half-strength Hoagland's solution was used to bottom-water the plants. Plants were sprayed to run-off with 0.3 mM SA in 0.02% silwet in the light. Fifty-two hours post-treatment, rosettes were cut above the soil line and harvested (in the light), quick-frozen in liquid nitrogen, then stored at -80 degrees C. Total RNA was later extracted using TRIzol reagent.


title: fibroblast, MFS subject GDO1051 rep 2


title: fibroblast, MFS subject GDO1051 rep 1


title: PC-346C Casodex Treated Cells at 48h - biological rep 3


title: fibroblast, MFS subject GDO21 rep 2


title: fibroblast, MFS subject FB992 rep 1


title: fibroblast, MFS subject FB1040 rep 1


title: fibroblast, MFS subject FB1040 rep 2


title: CG-1521 (HDAC Inhibitor) Treated LNCaP cells at 24h - biological rep 3

source_name: CG-1521 (7.5uM) treated LNCaP cells harvested after 24h of incubation

tag: LNCaP prostate cancer cells


title: LNCaP Control Cells at 24h - biological rep 3

source_name: Vehicle treated LNCaP cells harvested after 24h of incubation


title: PC-346C Control Cells at 48h - biological rep 2

source_name: Vehicle treated PC-346C cells harvested after 48h of incubation

tag: PC-346C prostate cancer cells


title: fibroblast, MFS subject FB837 rep 4


title: fibroblast, MFS subject FB881 rep 4


title: fibroblast, MFS subject FB1627 rep 4


title: fibroblast, MFS subject FB890 rep 5


title: fibroblast, MFS subject FB969 rep 4


title: fibroblast, MFS subject FB783 rep 3


title: fibroblast, MFS subject FB969 rep 5


title: fibroblast, MFS subject FB1211 rep 2


title: fibroblast, MFS subject FB881 rep 3


title: fibroblast, MFS subject FB783 rep 4


title: fibroblast, MFS subject FB890 rep 4


title: LNCaP Control Cells at 48h - biological rep 1

source_name: Vehicle treated LNCaP cells harvested after 48h of incubation


title: fibroblast, MFS subject FB1286 rep 4


title: fibroblast, MFS subject GDO21 rep 1


title: MPSS-AP1-17bp

data_processing: For each of these samples, we determined the normalized abundance value for each signature in the library in "transcripts per million" or TPM. More details on this process are available in Meyers et al. (2004, Genome Research 14:1641). The numbers in the VALUE column represent the expression level of the corresponding signatures for the AP1 library. More details about the samples, library replicates and individual signatures are available at http://mpss.udel.edu/at.

source_name: ap1-10 infloresence - mixed stage, immature buds, signature MPSS


title: LNCaP Casodex Treated Cells at 48h - biological rep 2

source_name: Casodex (50uM) treated LNCaP cells harvested after 48h of incubation


title: fibroblast, MFS subject FB1211 rep 1

source_name: cultured skin fibroblasts from Marfan subjects


title: fibroblast, MFS subject FB1286 rep 3


title: fibroblast, MFS subject FB837 rep 3


title: fibroblast, MFS subject FB1234 rep 4


title: fibroblast, MFS subject FB1234 rep 3


title: fibroblast, MFS subject FB1627 rep 3


title: fibroblast, MFS subject FB969 rep 2


title: fibroblast, MFS subject FB773 rep 4


title: fibroblast, MFS subject FB837 rep 2


title: fibroblast, MFS subject FB773 rep 3


title: fibroblast, MFS subject FB836 rep 2


title: fibroblast, MFS subject FB969 rep 1


title: fibroblast, MFS subject FB881 rep 2


title: fibroblast, MFS subject FB890 rep 1


title: fibroblast, MFS subject FB890 rep 2


title: fibroblast, MFS subject FB890 rep 3


title: fibroblast, MFS subject FB881 rep 1


title: fibroblast, MFS subject FB969 rep 3


title: fibroblast, MFS subject FB837 rep 1


title: fibroblast, MFS subject FB836 rep 1


title: fibroblast, MFS subject FB1627 rep 2


title: fibroblast, MFS subject FB1627 rep 1


title: fibroblast, MFS subject FB773 rep 2


title: fibroblast, MFS subject FB1286 rep 2


title: fibroblast, MFS subject FB783 rep 1


title: fibroblast, MFS subject FB783 rep 2


title: fibroblast, MFS subject FB1234 rep 1


title: fibroblast, MFS subject FB1286 rep 1


title: fibroblast, control subject NF10 rep 3

source_name: cultured skin fibroblasts from control subjects

value: control subject


title: fibroblast, control subject NM4 rep 1


title: fibroblast, control subject NF3 rep 2


title: fibroblast, MFS subject FB773 rep 1


title: fibroblast, MFS subject FB1234 rep 2


title: fibroblast, control subject NF5 rep 1


title: fibroblast, control subject NM4 rep 2


title: fibroblast, control subject NM3 rep 2


title: fibroblast, control subject NF3 rep 1


title: fibroblast, control subject NF5 rep 2


title: fibroblast, control subject NM5 rep 2


title: fibroblast, control subject NM3 rep 1


title: fibroblast, control subject NF6 rep 4


title: KO_A9/21_vs_control_A9/21

city: Cologne

first: Bernhard

last: Gerstmayer

address: Stockheimer Weg 1

country: Germany

institute: Miltenyi Biotec GmbH

description: 1 µg of total RNA was used for linear T7-amplification.

hyb_protocol: The fluorescent labeled probes were subsequently combined and hybridized on topic-defined PIQORTM Immunology Microarrays Mouse Antisense.

scan_protocol: Image capture and signal quantification were done with the ScanArray Lite (PerkinElmer Life and Analytical Sciences, Boston, USA) and ImaGene software (BioDiscovery Inc., El Segundo, USA)

data_processing: PubmedID

organism: Mus musculus

source_name: thymocytes from RAG2° mice, control_A9/21

label_protocol: After quantification and checking for integrity, 1 µg of RNA was subjected to linear amplification. The resulting aRNA was labeled by reverse transcription via Cy5-dCTP incorporation and Cy3-dCTP incorporation.

extract_protocol:
Total RNA was isolated using TRIzol according to manufacturer's instructions (Invitrogen).
Thymocyte single cell suspensions were generated using 100 µm nylon mesh (PGC Scientifics). DP thymocytes were isolated from RAG2° control or PS1/2° 5CC7 TCR H2bb mice by magnetic bead separation on anti-CD4 coated microbeads (Miltenyi Biotec.).

tag: control_A9/21, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-

source_name: thymocytes from PS1/2° 5CC7 TCR H2bb mice, KO_A9/21

tag: KO_A9/21, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-, CD4Cre+/-


title: fibroblast, control subject NM2 rep 2

tag: age

tag: sex


title: KO7/29_vs_control7/29

source_name: thymocytes from RAG2° mice, control_7/29

tag: control_7/29, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-

source_name: thymocytes from PS1/2° 5CC7 TCR H2bb mice, KO_7/29

tag: KO_7/29, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-, CD4Cre+/-


title: fibroblast, control subject NF4 rep 1

tag: disease status

tag: Filter number

tag: Usage number

tag: Exposures


title: fibroblast, control subject NM5 rep 1


title: fibroblast, control subject NM2 rep 1


title: fibroblast, control subject NF6 rep 3


title: KO_B9/21_vs_control_B9/21

source_name: thymocytes from RAG2° mice, control_B9/21

tag: control_B9/21, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-

source_name: thymocytes from PS1/2° 5CC7 TCR H2bb mice, KO_B9/21

tag: KO_B9/21, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-, CD4Cre+/-


title: KO8/9_vs_control8/9

source_name: thymocytes from RAG2° mice, control_8/9

tag: control_8/9, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-

source_name: thymocytes from PS1/2° 5CC7 TCR H2bb mice, KO_8/9

tag: KO_8/9, 5CC7 TCR TG, RAG2-/-, H-2b, Presenilin1flox/flox, Presenilin2-/-, CD4Cre+/-


title: control8/9_vs_control7/29

source_name: thymocytes from RAG2° mice,  control_8/9


title: fibroblast, control subject NM9 rep 1


title: fibroblast, control subject NF4 rep 2


title: fibroblast, control subject NF9 rep 2


title: fibroblast, control subject NM8 rep 2


title: fibroblast, control subject NF9 rep 1


title: fibroblast, control subject NM9 rep 2


title: fibroblast, control subject NM8 rep 1


title: fibroblast, control subject NF6 rep 1


title: fibroblast, control subject NF6 rep 2


title: fibroblast, control subject NM7 rep 2


title: fibroblast, control subject NM7 rep 1


title: fibroblast, control subject NF10 rep 1


title: fibroblast, control subject NM10 rep 1


title: fibroblast, control subject NM10 rep 2


title: fibroblast, control subject NF12 rep 1


title: fibroblast, control subject NF8 rep 2


title: fibroblast, control subject NF11 rep 2


title: fibroblast, control subject NF10 rep 2


title: fibroblast, control subject NM6 rep 2


title: fibroblast, control subject NF7 rep 1


title: fibroblast, control subject NF11 rep 1


title: fibroblast, control subject NF12 rep 2


title: fibroblast, control subject NF7 rep 2


title: fibroblast, control subject NF8 rep 1


title: fibroblast, control subject NM6 rep 1


title: KO8/9_vs_KO7/29


title: RA LUMC-48 LC14n103 vs LCR syn tis

status: Public on Sep 13 2007

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10521.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: RA mRNA

label_protocol: not provided

extract_protocol: not provided

tag: RA mRNA

source_name: LCR

tag: LCR


title: RA LB-12 LC14n034 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11482.gif


title: RA LB-25 LC14n039 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Osteoarthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11237.gif


title: RA LUMC -12 LC14n038 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11236.gif


title: RA LUMC-42 LC14n106 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10526.gif


title: RA LUMC-19 LC14n065 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10668.gif


title: RA  LUMC-27 LC14n115 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11487.gif

source_name: RA LUMC-5 mRNA

tag: RA LUMC-5 mRNA


title: RA LUMC-57 LC14n061 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10666.gif


title: RA LUMC-8 LC14n040 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10905.gif


title: RA LUMC-7 LC14n105 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10637.gif


title: RA LUMC-53 LC14n060 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10574.gif


title: RA LUMC-21 LC14n036 vs LCR syn tis

description:
Simple annotation: Diseased tissue, Rheumatoid arthritis
Image: http://smd.stanford.edu/MicroArray/gifs/2000-11/11485.gif


title: MM649

status: Public on Sep 12 2007

type: genomic

city: Brisbane

first: Mitchell

last: Stark

address: 300 Herston Rd Herston

country: Australia

institute: QIMR

description: The 76 melanoma cell lines used in this study were derived from primary cutaneous melanomas or melanoma metastases.

hyb_protocol: The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.

scan_protocol: After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Beadstudio 2.0 (Illumina). All genomic positions were based upon hg17 from the UCSC Genome Browser.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Melanoma Cell Line

label_protocol: The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.

extract_protocol: As per manufacturers protocol using QIAGEN QIamp DNA Blood Maxi Kit

tag: Cell line was derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: A12


title: MM628

tag: Cell line was derived from a secondary melanoma tumor with the primary being occult.


title: RPMI7932

tag: UNKNOWN


title: D64


title: D49


title: MM636


title: D54


title: WW

tag: Cell Line was derived from a secondary melanoma tumor with primary site being occult


title: SKMEL5

tag: Cell Line was derived from a secondary melanoma tumor with primary site being occult.


title: MW


title: A07


title: SKMEL28


title: MM647


title: MM648


title: MM485


title: MM548


title: MM622

tag: Cell line was derived from a primary melanoma tumor located in a non-CSD body site.


title: MM472

tag: Cell line was derived from a secondary melanoma tumor with the primary being in a CSD body site.


title: C57BL/10J-T43H/+, spermatids, biological rep1

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

description: Gene expression data from mouse spermatids

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Bioconductor 1.9 and R statistics (version 2.3) using the gcRMA method with default settings and custom chip description file (probes were annotated to Entrez identifiers - NCBI build 36) mm430mmentrezg8, from the Bioconductor repository.

label: biotin

source_name: Mouse spermatids

label_protocol: Between 15 to 40 ng of total RNA were used to prepare biotinylated cRNA according to the standard Affymetrix Two-Cycle protocol (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: Mouse lines used in the experiment were C57BL/10J, C57BL/10J-T43H/T43H and C57BL/10J-T43H/+. All the male mice used in the experiment were two months old.  Mice were euthanized by cervical dislocation and single cell suspension from testicular tubules was prepared.

extract_protocol: Total RNA was isolated from individual populations using RNeasy micro kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Specific spermatogenic cell populations of pre-pachytene spermatocytes, pachytene spermatocytes and spermatids were isolated using fluorescence activated cell sorting of testicular single cell suspension according to ref. (Bastos et al. 2005) with minor modifications.

tag: Genotype

value: C57BL/10J-T43H/+, Gender:male, Age:2 months, Tissue:testes


title: C57BL/10J-T43H/+, spermatids, biological rep2


title: MM595


title: MM540


title: MM426


title: C57BL/10J-T43H/+, pachytene spermatocytes, biological rep2

description: Gene expression data from mouse pachytene spermatocytes

source_name: Mouse pachytene spermatocytes


title: MM604


title: MM473


title: MM418

tag: Cell line was derived from a primary melanoma tumor being located in a non-CSD body site.


title: C57BL/10J-T43H/+, pachytene spermatocytes, biological rep1


title: C57BL/10J-T43H/+, pre-pachytene spermatocytes, biological rep2

description: Gene expression data from mouse pre-pachytene spermatocytes

source_name: Mouse pre-pachytene spermatocytes


title: MM409


title: C57BL/10J-T43H/T43H, spermatids, biological rep2

value: C57BL/10J-T43H/T43H, Gender:male, Age:2 months, Tissue:testes


title: C57BL/10J-T43H/+, pre-pachytene spermatocytes, biological rep1


title: MM384

tag: Cell line was derived from a secondary melanoma tumor with the primary tumor being occult.


title: C57BL/10J-T43H/T43H, spermatids, biological rep1


title: C57BL/10J-T43H/T43H, pachytene spermatocytes, biological rep2


title: MM266

source_name: Melanoma Cell line


title: C57BL/10J-T43H/T43H, pachytene spermatocytes, biological rep1


title: MM396


title: MM488

tag: Cell line was derived from a primary tumour from a non-CSD body site.


title: MM127


title: C57BL/10J, pachytene spermatocytes, biological rep2

value: C57BL/10J, Gender:male, Age:2 months, Tissue:testes


title: MM370

tag: Cell line was derived from a secondary melanoma tumor with the primary tumor being in a non-CSD body site.


title: MM138


title: C57BL/10J, spermatids, biological rep2


title: MM229


title: D40


title: C57BL/10J-T43H/T43H, pre-pachytene spermatocytes, biological rep1


title: MM537


title: D38

source_name: Melanoma cell Line

tag: Cell line was derived from a secondary melanoma tumour with the primary tumor being occult.


title: MM200

tag: Cell line was derived form a primary melanoma tumor located in a non-CSD body site.


title: D36

tag: Cell line was was derived from a secondary melanoma tumor with the primary being in a non-CSD body site.


title: C57BL/10J, spermatids, biological rep1


title: HT144

tag: Cell line was derived from asecondary melanoma tumor with the primary being occult.


title: C57BL/10J-T43H/T43H, pre-pachytene spermatocytes, biological rep2


title: MM369


title: C57BL/10J, pre-pachytene spermatocytes, biological rep1


title: C57BL/10J, pre-pachytene spermatocytes, biological rep2


title: BMDM WT4

city: Cape Town

first: Anita

middle: R

last: Schwegmann

state: Western Cape

address: Institute for Infectious Diseases and Molecular Medicine, UCT medical School, Anzio Rd, Observatory

department: Division of Infectious Immunology

country: South Africa

institute: Institute for Infectious Diseases and Molecular Medicine, University of Cape Town

description:
Slide barcode: 12301856
Image Used: 12301856_1
635nm PMT (volts): 650
PMT (volts): 590
Number of times scanned: 1
Scan date:04/10/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages BioConductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and BioConductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

hyb_protocol: Coverslips (Erie Scientific Company, Portsmouth, NH, USA) were washed in 100% acetone for 1 hour, in 0.2 % SDS for 10 minutes, then twice in double distilled water for 10 minutes for each wash. All wash steps were done at room temperature with gentle agitation. The coverslips were dried in an oven at 42°C for 10 minutes. The MEEBO (Illumina, San Diego, CA, USA) spotted microarrays were printed at the capar Microarray Facility (University of Cape Town, South Africa). The MEEBO array was placed in a hybridisation chamber (ArrayIt, Sunnyvale, CA ,USA) and 200μl pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) added between the array and the coverslip. The Hybridization chamber was sealed and submerged in a plastic container containing water preheated to 42°C. The plastic container was placed in a hybridisation preheated to 42°C and the slides were pre-hybridized for 30 minutes. The slides were washed 5 times in double distilled water. Each wash was done at room temperature for 30-60 seconds. The slides were then dipped in 100% isopropanol and dried by centrifugation in swinging bucket rotor for 5 minutes at 1000 rpm at room temperature. The dried slides were placed in a hybridization chamber and the cleaned hybridization coverslip carefully placed over the array. The microarray slides were used immediately for hybridization. 28μl of the 2 X hybridization buffer pre-heated to 42°C was mixed with the 30μl of the amplified RNA (aRNA) probe mixture. The aRNA probe mixture contained 4ug each of "LM + IFN-y" and untreated aRNA labelled samples. The probe was then heat denatured at 90°C for 3 minutes and then cooled to 42°C. The denatured probe was added very carefully to the pre-hybridized microarray slide at the bottom end of coverslip. Any air bubbles were worked toward the edge by gently tapping the coverslip surface. The hybridization chamber was sealed wrapped in foil to keep out light. The chamber was then submerged in a plastic container containing water tub preheated to 42°C. The hybridization reactions were incubated at 42°C in a hybridization oven for 16-20 hours. The plastic container was also wrapped with foil to retain humidity and block out light. The MEEBO array slide was then washed as follows: the low stringency wash buffer (2 X SSC, 0.1% SDS), medium-stringency wash buffer (1.0X SSC) and high-stringency wash buffer (0.02X SSC) were made fresh. All staining dishes were covered with foil to make them light tight and the laboratory lights were turned off, in order to minimize the exposure of the microarray slides to light. The hybridization chamber was unsealed, the microarray slide gently removed from the chamber. The microarray slide was submerged into a dish containing low stringency wash buffer (2 X SSC, 0.1% SDS) and gently agitated at to remove the coverslip. The microarray slide was washed in the low stringency wash buffer for 4 minutes at room temperature with gentle agitation. The microarray slide was then washed twice in medium stringency wash buffer (1.0X SSC) at room temperature for 4 minutes. The microarray was washed in high-stringency wash buffer (0.02X SSC) slide for each wash. The slides were then dipped 5 times in 100% isopropanol and dried by centrifugation in swinging bucket rotor for 5 minutes at 1000 rpm at room temperature. The slides were kept in a light-tight container and scanned immediately.

scan_protocol: The microarray slides were scanned using an Axon GenePix 4000A (Axon Instruments/Molecular Devices Corporation, Sunnyvale, CA, U.S.A) scanner and GenePix Pro 5.1.0.19 software running on a Windows XP operating system. The scan power was set to 100100, the resolution to 10um and the pixel size to 10. The internal scanner temperature averaged between 37°C to 38°C. The number of lines averaged during the scanning process was set to 2. The microarray slides were scanned at 635nm and 532nm wavelengths and the gene/spot ratios were set for 635nm/532nm. No normalization or background subtraction was done at this stage. The MEEBO microarray slide was initially scanned in the “Preview Mode” to optimise the photo-multiplier (PMT) settings so that the overall fluorescence in the red and green channels were balanced. The channels were considered balanced when the ratio of overall fluorescence in the green and read channels were equal to 1. The microarray slide was then scanned at the optimized PMT settings and the image saved as tiff file. The MEEBO microarray slide was scanned no more than 3 times to avoid damaging the dye molecules resulting in subsequent loss of quantitative florescence data. The array list and grid was loaded over the tiff images using the GenePix 5.1.0.19 software. Individual spots were aligned using the single irregular and /or regular feature tool. Each spot was individually checked for quality and to see if it was aligned to the grid. Spots were flagged as bad if they were (1) printed on top of each other, (2) dilated, (3) looked like doughnuts, (4) were irregular in morphology, (5) had a comet tail or (6) contained particles or scratches. Once the grids were aligned, the settings were saved and the quantitative gene expression data exported as a “GenePix Results” (.gpr) file.

data_processing: Background correction method: probabilistic; Normalization method: print-tip LOWESS and slide scale; the M values in derived from the GenePix results file (.gpr) represent the Cy5/Cy3 intensity ratio. The M values in this sample file represent the treated/untreated sample ratios.

source_name: BMDM, WT (NF-IL6+/+) mouse, LM + IFN-y, 4h

label_protocol: RNA was amplified and labelled as per the manufacturer’s instructions using the Amino Allyl MessageAmp II - Cy3/Cy5 aRNA Amplification Kit from Ambion (Cat #1797).

growth_protocol:
BMDM growth protocol:
After harvesting, the BMDMs were plated at a density of 5 x 10e5 BMDMs/ml in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) and incubated overnight at 37°C under 5% CO2.
Bacteria growth protocol:
Virulent Listeria monocytogenes (EGD strain) were grown at 37°C in tryptose-soy broth (Difco, Detroit, MI, USA) until early to mid log-phase of growth (OD600=0.2). DMSO was added to a final concentration of 10% and aliquots made and stored at –80°C until use. The titre of the stock was determined checked by plating 100μl of 10-fold serial dilutions of the thawed L. monocytogenes stock on tryptose-soy agar plates. The plates were incubated overnight at 37°C and the next day the number of colonies was counted and the colony forming units (CFU)/ml calculated. Before each infection experiment, a vial was thawed and vortexed (mixed) thoroughly to disperse clumps.

extract_protocol: At 4 hours post-infection the culture supernatant was removed from the BMDM cultures, aliquoted and stored at -80°C. The BMDMs were directly lysed in the culture dish using 1ml TriReagent (Molecular Research Company, Cincinnati, USA) for every 5 x 10e5 BMDMs. Total RNA was extracted from the BMDM lysate using the TriReagent protocol as per the manufacturer’s instructions. The RNA was DNAseI treated and “cleaned up” using the RNeasy RNA Extraction Kit (Qiagen) according to manufacturer’s instructions. This “clean up” step helped remove contaminating genomic DNA, proteins, residual phenol and salts. The elimination of contaminating genomic DNA was confirmed by RT-PCR using primers that bound to genomic DNA. The quality and quantity of the RNA was checked by spectroscopy and denaturing gel electrophoresis. The A260/A280 ratio was measured and an aliquot was run on a 1% agarose gel containing 2.2M formaldehyde. The RNA was stored at –80°C until used.

treatment_protocol:
“LM + IFN-y" refers to BMDMs simultaneously activated with IFN-gamma and infected with L. monocytogenes.
Treatment Protocol:
Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The BMDM monolayers were then simultaneously stimulated with 100U/ml IFN-gamma (BD Pharmigen, BD Biosciences, San Jose, CA, USA) and infected with L. monocytogenes at a multiplicity of infection (MOI) of 10:1 (10 bacilli : 1 macrophage). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml to kill extracellular bacteria.

tag: Bone marrow derived macrophages (BMDMs) were generated in vitro from NF-IL6 KO mouse:

tag: University of Cape Town Mouse ID number

tag: Mouse date of birth

tag: Mouse Sex

value: male

tag: Protocol:

tag: Mice were sacrificed by cervical dislocation and the femur and tibia bones collected. The bone marrow cells were flushed from the bones using DMEM (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) containing 10% FCS, 100U/ml penicillin G and 100μg/ml streptomycin. The cells were washed and concentrated by centrifuging at 1200 rpm at 4°C for 10 minutes. The bone marrow cells were added at a final concentration of 1 x 10e6 cells/ml in PLUTZNIK media (DMEM containing 10% FCS, 5% horse serum, 2mM L-glutamine, 1mM Na-pyruvate, 0.1mM 2-beta-Mercaptoethanol, 30% L929 cell-conditioned medium, 100U/ml penicillin G, 100μg/ml streptomycin) and transferred into a special gas-permeable 15cm x 6cm Teflon coated-bag (Max Planck Institute for Immunobiology, Max Planck, Freiberg, Germany). The L929 conditioned medium contained GM-CSF, which stimulated the differentiation and growth of bone marrow stem cells into macrophages. The open end of the bag was heat-sealed and bone marrow stem cells incubated at 37°C under 5% CO2 for 10 days. The supernatant was discarded and the adherent cells were massaged from the Teflon-coated bags into DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin. The BMDMs were washed twice in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin to get rid of residual GM-CSF from the L929 conditioned medium. The BMDMs were plated at a density of 5 x 10e5 BMDMs/ml and incubated overnight at 37°C under 5% CO2.

source_name: BMDM, WT (NF-IL6+/+) mouse, untreated, 4h

treatment_protocol:
“Untreated” refers to BMDMs that were left untreated (mock control)
Treatment Protocol: Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The "untreated"BMDM monolayers were left untreated and represent mock controls (i.e. they were NOT activated or infected). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml.


title: D28

tag: Cell line was derived from a secondary melanoma tumor with the primary being occult.


title: BMDM WT2

description:
Slide barcode: 12301862
Image Used: 12301862_1
635nm PMT (volts): 670
PMT (volts): 610
Number of times scanned: 1
Scan date: 17/08/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

source_name: BMDM, WT (NF-IL6+/+) mouse, "LM + IFN-y", 4h

treatment_protocol:
"LM + IFN-y" refers to BMDMs simultaneously activated with IFN-gamma and infected with L. monocytogenes.
Treatment Protocol:
Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The BMDM monolayers were then simultaneously stimulated with 100U/ml IFN-gamma (BD Pharmigen, BD Biosciences, San Jose, CA, USA) and infected with L. monocytogenes at a multiplicity of infection (MOI) of 10:1 (10 bacilli : 1 macrophage). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml to kill extracellular bacteria.

growth_protocol:
BMDM growth protocol:
After harvesting, the BMDMs were plated at a density of 5 x 10e5 BMDMs/ml in DMEM containing 10% FCS, 100U/ml penicillin G, 100μg/ml streptomycin (Gibco, Invitrogen Corporation, Carlsbad, CA, USA) and incubated overnight at 37°C under 5% CO2.


title: BMDM NF-IL6 KO4

description:
Slide barcode: 12301882
Image Used: 12301882_1
635nm PMT (volts): 650
PMT (volts): 590
Number of times scanned: 1
Scan date:04/10/2005
All image and data analysis was conducted in the R environment for statistical computing and programming using packages Bi°Conductor, Limma  and Smida. R version 2.2.0. was downloaded from CRAN and Bi°Conductor, LIMMA and SMIDA from bioconductor project website. R was run on a Windows XP operating system. The gpr. Files were parsed into limma and genes that were flagged as “bad” were given a weighting 0.1, which meant that the “bad” spots would not be excluded from further analyses, but only 10% of their values would be used. The layout of the array was composed of 4 x 8 grids, where each grid was composed of 35 rows x 35 columns. This layout was parsed into Limma which was then used for subsequent image plots. The background for each array was corrected using a “probabilistic” method rather than subtraction. The variation in background, foreground and log-ratios (treated vs. untreated; also called M-values) for each array was assessed using image plots. The balance of the densities of the red and green channels was evaluated by density plots. Systematic bias and print-tip artifacts were identified by whole array and print-group Ratio-Intensity plots (also called MA-plots) before normalization. Evaluation of these plots helped decide which normalization method would be best to use. The data within each array was normalized using print-group LOWESS. The effectiveness of normalization in removing the systematic and printing biases was assessed by image plots of the spatially normalized M values and MA plots and box plots for each array and its print-tip groups. The data between arrays were normalized using the slide-scale normalization method and the effectiveness of the normalization was assessed by density plots and box plots. The duplicate spots in the normalized data were merged and averaged, taking into account gene weights for bad spots.

source_name: BMDM, NF-IL6-deficient (KO) mouse, "LM + IFN-y", 4h

treatment_protocol:
“LM + IFN-y” refers to BMDMs simultaneously activated with IFN-gamma and infected with L. monocytogenes.
Treatment Protocol:
Before each infection experiment, the BMDM cultures were washed three times in DMEM containing 10% FCS but without antibiotics. These washing steps ensured that any residual antibiotics were washed away. The BMDM monolayers were then simultaneously stimulated with 100U/ml IFN-gamma (BD Pharmigen, BD Biosciences, San Jose, CA, USA) and infected with L. monocytogenes at a multiplicity of infection (MOI) of 10:1 (10 bacilli : 1 macrophage). After 1 hour, gentamycin (Sigma-Aldrich, Munich, Germany) was added at 50μg/ml to kill extracellular bacteria.

value: female

source_name: BMDM, NF-IL6-deficient (KO) mouse, untreated, 4h