title: Patient 249 Core Set (custom panel)


title: Patient 241 Core Set (custom panel)

status: Public on Jun 10 2008

type: RNA

city: Rochester

first: Robert

middle: B.

last: Jenkins

state: MN

address: 200 First Street SW

department: Laboratory Medicine and Pathology

country: USA

institute: Mayo Clinic

hyb_protocol: hybridization was performed in accordance with the manufacturer's instructions

scan_protocol: Arrays were scanned using Illumina's BeadArray Reader

data_processing: Illumina's Bead Studio Software using no normalization was used to process the image files. The raw data was then normalized using cyclic loess (fastlo). The normalized value for the probes was averaged to determine the expression level for the gene. The DASL method labels each sample with a mixture of CY3 and Cy5. Only a single sample is applied to each array.  The scanner measures fluorescence of both Cy3 and Cy5.  This data is contained in the red and grn files for each sample. The bead studio software averages the red and green signals to provide a single value for the expression of a particular probe.

label: cy3, cy5

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer

label_protocol: cy3, cy5 labeling was performed in accordance with the manufacturer's instructions

extract_protocol: Four freshly cut 10 micron sections of FFPE tissue were deparaffinized and the Gleason dominant cancer focus was macrodissected. RNA was extracted using the High Pure RNA Paraffin Kit from Roche (Indianapolis, IN).

tag: Case-Control Group

value: NED

tag: Training or Validation

value: trn

tag: Age (yrs) at RRP

tag: PSA (ng/ml) at RRP

tag: Revised Gleason Score

tag: Stage

tag: Ploidy

value: tetraploid

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA

tag: Second Rising PSA (ng/ml)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP

tag: patient's status

value: Alive

tag: Prostate cancer specific death

value: No


title: Patient 260 Core Set (cancer panel)

value: PSA

value: val


title: Patient 226 Core Set (custom panel)


title: Patient 266 Core Set (cancer panel)

value: TxN+


title: Patient 258 Core Set (cancer panel)

value: aneuploid


title: Patient 219 Core Set (custom panel)

value: Systemic


title: Patient 259 Core Set (cancer panel)

value: diploid


title: Patient 256 Core Set (cancer panel)


title: Patient 257 Core Set (cancer panel)


title: Patient 202 Core Set (custom panel)

value: Deceased


title: Patient 280 Core Set (custom panel)


title: Patient 254 Core Set (cancer panel)


title: Patient 255 Core Set (cancer panel)


title: Patient 272 Core Set (custom panel)


title: Patient 212 Core Set (custom panel)


title: Patient 234 Core Set (custom panel)


title: Patient 240 Core Set (custom panel)


title: Patient 251 Core Set (cancer panel)


title: Patient 249 Core Set (cancer panel)


title: Patient 288 Core Set (custom panel)


title: Patient 250 Core Set (cancer panel)

value: Yes


title: Patient 248 Core Set (custom panel)


title: Patient 264 Core Set (custom panel)


title: Patient 252 Core Set (cancer panel)


title: Patient 253 Core Set (cancer panel)


title: Patient 225 Core Set (custom panel)


title: Patient 200 Core Set (custom panel)


title: Patient 247 Core Set (cancer panel)


title: Patient 248 Core Set (cancer panel)


title: Patient 244 Core Set (cancer panel)


title: Patient 243 Core Set (cancer panel)


title: Patient 211 Core Set (custom panel)


title: Patient 218 Core Set (custom panel)


title: Patient 245 Core Set (cancer panel)


title: Patient 279 Core Set (custom panel)


title: Patient 233 Core Set (custom panel)


title: Patient 242 Core Set (cancer panel)


title: Patient 255 Core Set (custom panel)


title: Patient 263 Core Set (custom panel)


title: Patient 241 Core Set (cancer panel)


title: Patient 246 Core Set (cancer panel)


title: Patient 287 Core Set (custom panel)


title: Patient 240 Core Set (cancer panel)


title: Patient 271 Core Set (custom panel)


title: Patient 238 Core Set (cancer panel)


title: Patient 232 Core Set (custom panel)


title: Patient 247 Core Set (custom panel)


title: Patient 210 Core Set (custom panel)


title: Patient 239 Core Set (custom panel)


title: Patient 237 Core Set (cancer panel)


title: Patient 217 Core Set (custom panel)


title: Patient 224 Core Set (custom panel)


title: Patient 197 Core Set (custom panel)


title: Patient 235 Core Set (cancer panel)


title: Patient 234 Core Set (cancer panel)


title: Patient 262 Core Set (custom panel)


title: Patient 230 Core Set (cancer panel)


title: Patient 236 Core Set (cancer panel)


title: Patient 229 Core Set (cancer panel)


title: Patient 239 Core Set (cancer panel)


title: Patient 228 Core Set (cancer panel)


title: Patient 278 Core Set (custom panel)


title: Patient 238 Core Set (custom panel)


title: Patient 231 Core Set (custom panel)


title: Patient 231 Core Set (cancer panel)


title: Patient 254 Core Set (custom panel)


title: Patient 246 Core Set (custom panel)


title: Patient 233 Core Set (cancer panel)


title: Patient 226 Core Set (cancer panel)


title: Patient 224 Core Set (cancer panel)


title: Patient 232 Core Set (cancer panel)


title: Patient 222 Core Set (cancer panel)


title: Patient 220 Core Set (cancer panel)


title: Patient 209 Core Set (custom panel)


title: Patient 285 Core Set (custom panel)


title: Patient 277 Core Set (custom panel)


title: Patient 216 Core Set (custom panel)


title: Patient 219 Core Set (cancer panel)


title: Patient 269 Core Set (custom panel)


title: Patient 225 Core Set (cancer panel)


title: Patient 223 Core Set (cancer panel)


title: Patient 221 Core Set (cancer panel)


title: Patient 261 Core Set (custom panel)


title: Patient 253 Core Set (custom panel)


title: Patient 245 Core Set (custom panel)


title: Patient 216 Core Set (cancer panel)


title: Patient 218 Core Set (cancer panel)


title: Patient 217 Core Set (cancer panel)


title: Patient 230 Core Set (custom panel)


title: Patient 214 Core Set (cancer panel)


title: Patient 212 Core Set (cancer panel)


title: Patient 213 Core Set (cancer panel)


title: Patient 222 Core Set (custom panel)


title: Patient 210 Core Set (cancer panel)


title: Patient 211 Core Set (cancer panel)


title: Patient 208 Core Set (cancer panel)


title: Patient 209 Core Set (cancer panel)


title: Patient 208 Core Set (custom panel)


title: Patient 268 Core Set (custom panel)


title: Patient 276 Core Set (custom panel)


title: Patient 284 Core Set (custom panel)


title: Patient 206 Core Set (cancer panel)


title: Patient 252 Core Set (custom panel)


title: Patient 260 Core Set (custom panel)


title: Patient 205 Core Set (cancer panel)


title: Patient 244 Core Set (custom panel)


title: Patient 203 Core Set (cancer panel)


title: Patient 204 Core Set (cancer panel)


title: Patient 229 Core Set (custom panel)


title: Patient 221 Core Set (custom panel)


title: Patient 236 Core Set (custom panel)


title: Patient 201 Core Set (cancer panel)


title: Patient 202 Core Set (cancer panel)


title: Patient 172 Core Set (custom panel)


title: Patient 162 Core Set (custom panel)


title: Patient 153 Core Set (custom panel)


title: Patient 197 Core Set (cancer panel)


title: Patient 199 Core Set (cancer panel)


title: Patient 137 Core Set (custom panel)


title: Patient 145 Core Set (custom panel)


title: Patient 118 Core Set (custom panel)


title: Patient 195 Core Set (cancer panel)


title: Patient 214 Core Set (custom panel)


title: Patient 194 Core Set (cancer panel)


title: Patient 128 Core Set (custom panel)


title: Patient 192 Core Set (cancer panel)


title: Patient 200 Core Set (cancer panel)


title: Patient 198 Core Set (cancer panel)


title: Patient 191 Core Set (cancer panel)


title: Patient 194 Core Set (custom panel)


title: Patient 205 Core Set (custom panel)


title: Patient 190 Core Set (cancer panel)


title: Patient 189 Core Set (cancer panel)


title: Patient 193 Core Set (cancer panel)


title: Patient 180 Core Set (custom panel)


title: Patient 187 Core Set (custom panel)


title: Patient 170 Core Set (custom panel)


title: Patient 161 Core Set (custom panel)


title: Patient 188 Core Set (cancer panel)


title: Patient 187 Core Set (cancer panel)


title: Patient 185 Core Set (cancer panel)


title: Patient 144 Core Set (custom panel)


title: Patient 186 Core Set (cancer panel)


title: Patient 152 Core Set (custom panel)


title: Patient 184 Core Set (cancer panel)


title: Patient 183 Core Set (cancer panel)


title: Patient 136 Core Set (custom panel)


title: Patient 117 Core Set (custom panel)


title: Patient 108 Core Set (custom panel)


title: Patient 126 Core Set (custom panel)


title: Patient 204 Core Set (custom panel)


title: Patient 181 Core Set (cancer panel)


title: Patient 182 Core Set (cancer panel)


title: Patient 179 Core Set (cancer panel)


title: Patient 193 Core Set (custom panel)


title: Patient 180 Core Set (cancer panel)


title: Patient 186 Core Set (custom panel)


title: Patient 178 Core Set (cancer panel)


title: Patient 178 Core Set (custom panel)


title: Patient 177 Core Set (cancer panel)


title: Patient 176 Core Set (cancer panel)


title: Patient 151 Core Set (custom panel)


title: Patient 135 Core Set (custom panel)


title: Patient 143 Core Set (custom panel)


title: Patient 175 Core Set (cancer panel)


title: Patient 159 Core Set (custom panel)


title: Patient 174 Core Set (cancer panel)


title: Patient 173 Core Set (cancer panel)


title: Patient 116 Core Set (custom panel)


title: Patient 107 Core Set (custom panel)


title: Patient 203 Core Set (custom panel)


title: Patient 172 Core Set (cancer panel)


title: Patient 170 Core Set (cancer panel)


title: Patient 167 Core Set (cancer panel)


title: Patient 166 Core Set (cancer panel)


title: Patient 192 Core Set (custom panel)


title: Patient 177 Core Set (custom panel)


title: Patient 158 Core Set (custom panel)


title: Patient 150 Core Set (custom panel)


title: Patient 167 Core Set (custom panel)


title: Patient 165 Core Set (cancer panel)


title: Patient 164 Core Set (cancer panel)


title: Patient 134 Core Set (custom panel)


title: Patient 142 Core Set (custom panel)


title: Patient 162 Core Set (cancer panel)


title: Patient 163 Core Set (cancer panel)


title: Patient 159 Core Set (cancer panel)


title: Patient 161 Core Set (cancer panel)


title: Patient 158 Core Set (cancer panel)


title: Patient 124 Core Set (custom panel)


title: Patient 106 Core Set (custom panel)


title: Patient 115 Core Set (custom panel)


title: Patient 191 Core Set (custom panel)


title: Patient 156 Core Set (cancer panel)


title: Patient 157 Core Set (cancer panel)


title: Patient 155 Core Set (cancer panel)


title: Patient 201 Core Set (custom panel)


title: Patient 154 Core Set (cancer panel)


title: Patient 176 Core Set (custom panel)


title: Patient 166 Core Set (custom panel)


title: Patient 152 Core Set (cancer panel)


title: Patient 151 Core Set (cancer panel)


title: Patient 184 Core Set (custom panel)


title: Patient 157 Core Set (custom panel)


title: Patient 153 Core Set (cancer panel)


title: Patient 149 Core Set (cancer panel)


title: Patient 141 Core Set (custom panel)


title: Patient 149 Core Set (custom panel)


title: Patient 148 Core Set (cancer panel)


title: Patient 147 Core Set (cancer panel)


title: Patient 133 Core Set (custom panel)


title: Patient 114 Core Set (custom panel)


title: Patient 150 Core Set (cancer panel)


title: Patient 105 Core Set (custom panel)


title: Patient 199 Core Set (custom panel)


title: Patient 190 Core Set (custom panel)


title: Patient 123 Core Set (custom panel)


title: Patient 144 Core Set (cancer panel)


title: Patient 145 Core Set (cancer panel)


title: Patient 142 Core Set (cancer panel)


title: Patient 143 Core Set (cancer panel)


title: Patient 140 Core Set (cancer panel)


title: Patient 141 Core Set (cancer panel)


title: Patient 183 Core Set (custom panel)


title: Patient 146 Core Set (cancer panel)


title: Patient 165 Core Set (custom panel)


title: Patient 138 Core Set (cancer panel)


title: Patient 139 Core Set (cancer panel)


title: Patient 148 Core Set (custom panel)


title: Patient 136 Core Set (cancer panel)


title: Patient 137 Core Set (cancer panel)


title: Patient 175 Core Set (custom panel)


title: Patient 135 Core Set (cancer panel)


title: Patient 134 Core Set (cancer panel)


title: Patient 133 Core Set (cancer panel)


title: Patient 130 Core Set (cancer panel)


title: Patient 132 Core Set (cancer panel)


title: Patient 128 Core Set (cancer panel)


title: Patient 129 Core Set (cancer panel)


title: Patient 113 Core Set (custom panel)


title: Patient 125 Core Set (cancer panel)


title: Patient 126 Core Set (cancer panel)


title: Patient 124 Core Set (cancer panel)


title: Patient 147 Core Set (custom panel)


title: Patient 182 Core Set (custom panel)


title: Patient 155 Core Set (custom panel)


title: Patient 164 Core Set (custom panel)


title: Patient 140 Core Set (custom panel)


title: Patient 104 Core Set (custom panel)


title: Patient 174 Core Set (custom panel)


title: Patient 139 Core Set (custom panel)


title: Patient 122 Core Set (custom panel)


title: Patient 198 Core Set (custom panel)


title: Patient 132 Core Set (custom panel)


title: Patient 127 Core Set (cancer panel)


title: Patient 111 Core Set (custom panel)


title: Patient 122 Core Set (cancer panel)


title: Patient 130 Core Set (custom panel)


title: Patient 195 Core Set (custom panel)


title: Patient 121 Core Set (custom panel)


title: Patient 123 Core Set (cancer panel)


title: Patient 181 Core Set (custom panel)


title: Patient 188 Core Set (custom panel)


title: Patient 154 Core Set (custom panel)


title: Patient 121 Core Set (cancer panel)


title: Patient 112 Core Set (cancer panel)


title: Patient 116 Core Set (cancer panel)


title: Patient 113 Core Set (cancer panel)


title: Patient 173 Core Set (custom panel)


title: Patient 117 Core Set (cancer panel)


title: Patient 163 Core Set (custom panel)


title: Patient 146 Core Set (custom panel)


title: Patient 138 Core Set (custom panel)


title: Patient 114 Core Set (cancer panel)


title: Patient 103 Core Set (custom panel)


title: Patient 118 Core Set (cancer panel)


title: Patient 111 Core Set (cancer panel)


title: Patient 092 Core Set (custom panel)


title: Patient 115 Core Set (cancer panel)


title: Patient 084 Core Set (custom panel)


title: Patient 109 Core Set (cancer panel)


title: Patient 119 Core Set (cancer panel)


title: Patient 076 Core Set (custom panel)


title: Patient 107 Core Set (cancer panel)


title: Patient 104 Core Set (cancer panel)


title: Patient 106 Core Set (cancer panel)


title: Patient 015 Core Set (custom panel)


title: Patient 102 Core Set (custom panel)


title: Patient 023 Core Set (custom panel)


title: Patient 006 Core Set (custom panel)


title: Patient 031 Core Set (custom panel)


title: Patient 091 Core Set (custom panel)


title: Patient 057 Core Set (custom panel)


title: Patient 066 Core Set (custom panel)


title: Patient 083 Core Set (custom panel)


title: Patient 108 Core Set (cancer panel)


title: Patient 100 Core Set (cancer panel)


title: Patient 098 Core Set (cancer panel)


title: Patient 102 Core Set (cancer panel)


title: Patient 103 Core Set (cancer panel)


title: Patient 039 Core Set (custom panel)


title: Patient 105 Core Set (cancer panel)


title: Patient 101 Core Set (cancer panel)


title: Patient 097 Core Set (cancer panel)


title: Patient 074 Core Set (custom panel)


title: Patient 099 Core Set (cancer panel)


title: Patient 096 Core Set (cancer panel)


title: Patient 095 Core Set (cancer panel)


title: Patient 056 Core Set (custom panel)


title: Patient 047 Core Set (custom panel)


title: Patient 030 Core Set (custom panel)


title: Patient 091 Core Set (cancer panel)


title: Patient 094 Core Set (cancer panel)


title: Patient 022 Core Set (custom panel)


title: Patient 092 Core Set (cancer panel)


title: Patient 014 Core Set (custom panel)


title: Patient 089 Core Set (cancer panel)


title: Patient 065 Core Set (custom panel)


title: Patient 093 Core Set (cancer panel)


title: Patient 090 Core Set (cancer panel)


title: Patient 088 Core Set (cancer panel)


title: Patient 038 Core Set (custom panel)


title: Patient 005 Core Set (custom panel)


title: Patient 087 Core Set (cancer panel)


title: Patient 085 Core Set (cancer panel)


title: Patient 101 Core Set (custom panel)


title: Patient 084 Core Set (cancer panel)


title: Patient 086 Core Set (cancer panel)


title: Patient 083 Core Set (cancer panel)


title: Patient 082 Core Set (custom panel)


title: Patient 081 Core Set (cancer panel)


title: Patient 082 Core Set (cancer panel)


title: Patient 080 Core Set (cancer panel)


title: Patient 073 Core Set (custom panel)


title: Patient 064 Core Set (custom panel)


title: Patient 079 Core Set (cancer panel)


title: Patient 046 Core Set (custom panel)


title: Patient 077 Core Set (cancer panel)


title: Patient 076 Core Set (cancer panel)


title: Patient 078 Core Set (cancer panel)


title: Patient 075 Core Set (cancer panel)


title: Patient 074 Core Set (cancer panel)


title: Patient 055 Core Set (custom panel)


title: P.aeruginosaPlanktonic_Tb-treated_Sample2

city: Hanover

first: George

last: O'Toole

state: NH

address: 505 Vail Building

department: Department of Microbiology and Immunology

institute: Dartmouth Medical School

description: The is part of a study of the effects of tobramycin treatment on planktonic P. aeruginosa.

hyb_protocol: Biotinylated cDNA products were hybridized by Affymetrix GeneChip arrays for 16 h at 40°C in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix, Santa Clara, CA).  After hybridization, the arrays were washed and stained the Fluidics Station 450 (Affymetrix).

scan_protocol: The chip was scanned with the 7G AffymetrixGene Scanner (Affymetrix) according to the manufacturer's procedures.

data_processing: Data was analysed using Affymetrix Microarray Suite software.

label: biotin

organism: Pseudomonas aeruginosa

source_name: tobramycin-treated

label_protocol: Labeling was carried out according to the Affymetrix GeneChip Pseudomonas aeruginosa Genome Array Expression Analysis Protocol.

growth_protocol: P. aeruginosa was grown in 10 mL MEM/2% LB until mid to late exponential phase, diluted 1:4 into fresh MEM/2% LB, and grown for an additional 3-4 hours to reach mid-exponential phase.  Cultures were then treated for 30 minutes with 5 micrograms/mL tobramycin.

extract_protocol: RNA was extracted using the Bacteria Protocol of the RNeasy RNA Isolation kit from Qiagen (Qiagen, Valencia, CA).  cDNA synthesis and fragmentation was carried out according to the Affymetrix GeneChip Pseudomonas aeruginosa Genome Array Expression Analysis Protocol.

tag: Pseudomonas aeruginosa PA14

tag: grown to mid-exponential phase in MEM/2%LB


title: Patient 037 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation


title: Patient 073 Core Set (cancer panel)

tag: Age (yrs) at RRP

tag: PSA (ng/ml) at RRP


title: P.aeruginosaPlanktonic_Tb-treated_Sample1

treatment_protocol: 30 minutes with 5 micrograms/mL tobramycin


title: Patient 072 Core Set (cancer panel)

tag: Revised Gleason Score

tag: Stage


title: Patient 071 Core Set (cancer panel)

tag: Ploidy

tag: First Rising PSA (ng/ml)


title: Patient 029 Core Set (custom panel)

tag: Time (yrs) from RRP to first rising PSA

tag: Second Rising PSA (ng/ml)


title: Patient 021 Core Set (custom panel)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)


title: Patient 069 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP


title: P.aeruginosaPlanktonic_untreated_Sample2

source_name: untreated control

growth_protocol: P. aeruginosa was grown in 10 mL MEM/2% LB until mid to late exponential phase, diluted 1:4 into fresh MEM/2% LB, and grown for an additional 3-4 hours to reach mid-exponential phase.

treatment_protocol: untreated control


title: P.aeruginosaPlanktonic_untreated_Sample1


title: Patient 067 Core Set (cancer panel)

tag: patient's status

tag: Prostate cancer specific death


title: Patient 070 Core Set (cancer panel)


title: Patient 066 Core Set (cancer panel)


title: Patient 013 Core Set (custom panel)


title: Patient 065 Core Set (cancer panel)


title: Patient 063 Core Set (cancer panel)


title: Patient 064 Core Set (cancer panel)


title: Patient 098 Core Set (custom panel)


title: P.aeruginosaCFBEbiofilm_Tb-treated_Sample3

description: This is part of a study of the effects of tobramycin treatment on P. aeruginosa biofilms grown on human airway cells.

hyb_protocol: Biotinylated cDNA products were hybridized to Affymetrix GeneChip arrays for 16 h at 40°C in a Gene Chip Hybridization oven 640 using the manufacturer's hybridization buffer (Affymetrix, Santa Clara, CA).  After hybridization, the arrays were washed and stained the Fluidics Station 450 (Affymetrix).

scan_protocol: The chip was scanned with the 7G Affymetrix Gene Scanner (Affymetrix) according to manufacturer's procedures.

data_processing: Data was analyzed using Affymetrix Microarray Suite software.

growth_protocol: P. aeruginosa were grown as biofilms on CFBE41o- cells for 9 in MEM/0.4% arginine, then washed with PBS and incubated 30 minutes with 500 micrograms/mL tobramycin.

extract_protocol: Biofilms were washed 2-3 times with 2 mL PBS, and RNA was harvested using a modification of the protocol from the RNeasy RNA isolation kit (Qiagen, Valencia, CA).  Specifically, cells were incubated with 600 μL of 1 μg/mL lysozyme in TE buffer for 10 minutes at room temperature.  Then the cells were homogenized with 600 μL RLT lysis buffer from the Qiagen RNeasy kit, and the homogenate was vortexed for several seconds and drawn through a 20g needle 10 times.  600 μL of 100% ethanol was then added and the solution was applied to an RNeasy column.  From this point, we followed the manufacturer’s protocol for isolation of bacterial RNA.  Mammalian RNA was removed using the MICROBEnrichTM kit  (Ambion, Austin, TX) according to the manufacturer’s protocol.  cDNA synthesis and fragmentation was carried out according to the Affymetrix GeneChip Pseudomonas aeruginosa Genome Array Expression Analysis Protocol.

tag: Pseudomonas aeruginosa PA14

tag: Biofilms growing on CFBE41o- human aiway cells

tag: grown 9.5 hours


title: P.aeruginosaCFBEbiofilm_Tb-treated_Sample1

treatment_protocol: 30 minutes with 500 micrograms/mL tobramycin


title: Patient 089 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation

tag: Age (yrs) at RRP


title: Patient 061 Core Set (cancer panel)

tag: PSA (ng/ml) at RRP

tag: Revised Gleason Score

tag: Stage


title: Patient 062 Core Set (cancer panel)

tag: Ploidy

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA


title: P.aeruginosaCFBEbiofilm_Tb-treated_Sample2


title: Patient 081 Core Set (custom panel)

tag: Second Rising PSA (ng/ml)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)


title: P.aeruginosaCFBEbiofilm_untreated_Sample3

growth_protocol: P. aeruginosa were grown as biofilms on CFBE41o- cells for 9.5 hours in MEM/0.4% arginine.

treatment_protocol: Untreated control


title: Patient 060 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP

tag: patient's status


title: Patient 059 Core Set (cancer panel)

tag: Prostate cancer specific death


title: P.aeruginosaCFBEbiofilm_untreated_Sample1

tag: Pseudomonas aeruginosa PA14

tag: Biofilms growing on CFBE41o- human aiway cells

tag: grown 9.5 hours


title: Patient 057 Core Set (cancer panel)

tag: Case-Control Group

tag: Training or Validation

tag: Age (yrs) at RRP


title: Patient 055 Core Set (cancer panel)

tag: PSA (ng/ml) at RRP

tag: Revised Gleason Score

tag: Stage


title: Patient 072 Core Set (custom panel)

tag: Ploidy

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA


title: Patient 056 Core Set (cancer panel)

tag: Second Rising PSA (ng/ml)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)


title: Patient 058 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP

tag: patient's status


title: P.aeruginosaCFBEbiofilm_untreated_Sample2

tag: Pseudomonas aeruginosa PA14

tag: grown as biofilm on CFBE41o- airway cells in culture

tag: 9.5 hours in MEM/0.4% arginine


title: Patient 063 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation

tag: Prostate cancer specific death


title: Control Water_7

city: New Haven

first: Jun

last: Lu

state: CT

address: 10 Amistad St

department: Yale Stem Cell Center and Department of Genetics

institute: Yale University

description: A water only sample for control and background subtraction, for samples MEP_2, MEP5, MEP8, ERY2_3, ERY3_2, MEGA2_3, MEGA2_6.

hyb_protocol: Samples were hybridized at 50 degrees overnight in TMAC buffer

scan_protocol: Samples were washed with SAPE in 1xTMAC then detected on Luminex S100 machine at 45 degrees

data_processing: Median fluorescent intensity values (raw data) were used. Data went through background subtraction, post-control normalization and sample normalization.

label: biotin then strepavidin-phycoerythrin

source_name: Broad Institute

label_protocol: microRNAs were labeled by a new plate-capture method, through ligation-mediated amplification

extract_protocol: Total RNA extracted using TriZol

tag: purified by FACS from umbilical cord blood


title: Patient 054 Core Set (cancer panel)

tag: Age (yrs) at RRP

tag: PSA (ng/ml) at RRP

tag: Revised Gleason Score

tag: Stage


title: Patient 054 Core Set (custom panel)

tag: Ploidy

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA

tag: Second Rising PSA (ng/ml)


title: Control Water_8


title: Patient 045 Core Set (custom panel)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP


title: Control Water_6


title: Patient 027 Core Set (custom panel)

tag: patient's status


title: Patient 047 Core Set (cancer panel)

tag: Case-Control Group


title: Patient 050 Core Set (cancer panel)

tag: Training or Validation


title: Control Water_5

description: A water only sample for control and background subtraction, for samples MEP6, MEP7, ERY1_2, ERY2_1, MEGA1_1, MEGA1_2, MEGA1_3 and MEGA2_5.


title: Patient 051 Core Set (cancer panel)

tag: Prostate cancer specific death


title: Control Water_4

tag: purified by FACS from umbilical cord blood


title: Patient 045 Core Set (cancer panel)

tag: Age (yrs) at RRP


title: Control Water_3


title: Patient 020 Core Set (custom panel)

tag: PSA (ng/ml) at RRP


title: Patient 044 Core Set (cancer panel)

tag: Revised Gleason Score


title: Patient 012 Core Set (custom panel)

tag: Stage


title: Patient 043 Core Set (cancer panel)

tag: Ploidy


title: Patient 042 Core Set (cancer panel)

tag: First Rising PSA (ng/ml)


title: Patient 053 Core Set (cancer panel)

tag: Time (yrs) from RRP to first rising PSA


title: Patient 041 Core Set (cancer panel)

tag: Second Rising PSA (ng/ml)


title: Patient 046 Core Set (cancer panel)

tag: Time (yrs) from RRP to second rising PSA


title: Control Water_2

description: A water only sample for control and background subtraction, for samples MEP_1, MEP_3, MEP4, ERY1_1, ERY1_3, ERY1_4, ERY2_2, ERY3_1, MEGA1_4, MEGA2_1, MEGA2_2 and MEGA2_4.


title: Patient 003 Core Set (custom panel)

tag: PSA Slope (ng/ml/yr)


title: Control Water_1


title: Patient 040 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease


title: Patient 096 Core Set (custom panel)

tag: Years of Followup after RRP


title: Patient 039 Core Set (cancer panel)

tag: patient's status


title: Patient 038 Core Set (cancer panel)

tag: Case-Control Group


title: Patient 037 Core Set (cancer panel)

tag: Training or Validation


title: Megakaryocyte population 2 MEGA2_6

description: A sample purified from umbilical cord blood, among one of the following populations: MEP, MEGA1, MEGA2, ERY1, ERY2 and ERY3


title: Patient 034 Core Set (cancer panel)

tag: Prostate cancer specific death


title: Patient 035 Core Set (cancer panel)


title: Megakaryocyte population 2 MEGA2_5

tag: purified by FACS from umbilical cord blood


title: Patient 088 Core Set (custom panel)

tag: Age (yrs) at RRP


title: Megakaryocyte population 2 MEGA2_4


title: Patient 080 Core Set (custom panel)

tag: PSA (ng/ml) at RRP


title: Patient 030 Core Set (cancer panel)

tag: Revised Gleason Score


title: Patient 071 Core Set (custom panel)

tag: Stage


title: Patient 032 Core Set (cancer panel)

tag: Ploidy


title: Patient 031 Core Set (cancer panel)

tag: First Rising PSA (ng/ml)


title: Patient 033 Core Set (cancer panel)

tag: Time (yrs) from RRP to first rising PSA


title: Patient 028 Core Set (cancer panel)

tag: Second Rising PSA (ng/ml)


title: Patient 029 Core Set (cancer panel)

tag: Time (yrs) from RRP to second rising PSA


title: Patient 027 Core Set (cancer panel)

tag: PSA Slope (ng/ml/yr)


title: Megakaryocyte population 2 MEGA2_3


title: Patient 053 Core Set (custom panel)

tag: Time (yrs) from PSA recurrence to systemic disease


title: Patient 024 Core Set (cancer panel)

tag: Years of Followup after RRP


title: Patient 035 Core Set (custom panel)

tag: patient's status


title: Patient 025 Core Set (cancer panel)

tag: Case-Control Group


title: Patient 026 Core Set (cancer panel)

tag: Training or Validation


title: Megakaryocyte population 1 MEGA1_4


title: Patient 044 Core Set (custom panel)

tag: Prostate cancer specific death


title: Megakaryocyte population 2 MEGA2_1

tag: purified by FACS from umbilical cord blood


title: Patient 023 Core Set (cancer panel)

tag: Age (yrs) at RRP


title: Megakaryocyte population 1 MEGA1_3


title: Megakaryocyte population 2 MEGA2_2


title: Patient 021 Core Set (cancer panel)

tag: PSA (ng/ml) at RRP


title: Patient 022 Core Set (cancer panel)

tag: Revised Gleason Score


title: Patient 019 Core Set (custom panel)

tag: Stage


title: Megakaryocyte population 1 MEGA1_2


title: Patient 026 Core Set (custom panel)

tag: Ploidy


title: Patient 019 Core Set (cancer panel)

tag: First Rising PSA (ng/ml)


title: Patient 020 Core Set (cancer panel)

tag: Time (yrs) from RRP to first rising PSA


title: Patient 018 Core Set (cancer panel)

tag: Second Rising PSA (ng/ml)


title: Patient 011 Core Set (custom panel)

tag: Time (yrs) from RRP to second rising PSA


title: Patient 002 Core Set (custom panel)

tag: PSA Slope (ng/ml/yr)


title: Patient 017 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease


title: Patient 015 Core Set (cancer panel)

tag: Years of Followup after RRP


title: Erythrocyte population 3 ERY3_1


title: Megakaryocyte population 1 MEGA1_1


title: Patient 014 Core Set (cancer panel)

tag: patient's status


title: Patient 016 Core Set (cancer panel)

tag: Case-Control Group


title: Patient 095 Core Set (custom panel)

tag: Training or Validation


title: Patient 062 Core Set (custom panel)

tag: Prostate cancer specific death


title: Patient 013 Core Set (cancer panel)


title: Erythrocyte population 2 ERY2_3

tag: purified by FACS from umbilical cord blood


title: Patient 012 Core Set (cancer panel)

tag: Age (yrs) at RRP


title: Patient 087 Core Set (custom panel)

tag: PSA (ng/ml) at RRP


title: Erythrocyte population 3 ERY3_2


title: Patient 009 Core Set (cancer panel)

tag: Revised Gleason Score


title: Patient 011 Core Set (cancer panel)

tag: Stage


title: Patient 008 Core Set (cancer panel)

tag: Ploidy


title: Erythrocyte population 2 ERY2_2


title: Erythrocyte population 2 ERY2_1


title: Erythrocyte population 1 ERY1_4


title: Patient 061 Core Set (custom panel)

tag: First Rising PSA (ng/ml)


title: Patient 002 Core Set (cancer panel)

tag: Time (yrs) from RRP to first rising PSA


title: Patient 070 Core Set (custom panel)

tag: Second Rising PSA (ng/ml)


title: Patient 001 Core Set (cancer panel)

tag: Time (yrs) from RRP to second rising PSA


title: Patient 003 Core Set (cancer panel)

tag: PSA Slope (ng/ml/yr)


title: Patient 006 Core Set (cancer panel)

tag: Time (yrs) from PSA recurrence to systemic disease


title: Erythrocyte population 1 ERY1_3


title: Megakaryocyte-erythrocyte precursors MEP_8


title: Erythrocyte population 1 ERY1_2


title: Erythrocyte population 1 ERY1_1


title: Patient 033 Core Set (custom panel)

tag: Years of Followup after RRP


title: Patient 005 Core Set (cancer panel)

tag: patient's status


title: Megakaryocyte-erythrocyte precursors MEP_7


title: Patient 025 Core Set (custom panel)

tag: Case-Control Group


title: Megakaryocyte-erythrocyte precursors MEP_6


title: Patient 007 Core Set (cancer panel)

tag: Training or Validation


title: Patient 009 Core Set (custom panel)

tag: Prostate cancer specific death


title: Patient 018 Core Set (custom panel)


title: Patient 001 Core Set (custom panel)


title: Patient 051 Core Set (custom panel)


title: Megakaryocyte-erythrocyte precursors MEP_4

tag: purified by FACS from umbilical cord blood


title: Megakaryocyte-erythrocyte precursors MEP_5


title: Patient 094 Core Set (custom panel)

tag: Age (yrs) at RRP


title: Patient 086 Core Set (custom panel)

tag: PSA (ng/ml) at RRP


title: Patient 069 Core Set (custom panel)

tag: Revised Gleason Score


title: Patient 059 Core Set (custom panel)

tag: Stage


title: Patient 050 Core Set (custom panel)

tag: Ploidy


title: Megakaryocyte-erythrocyte precursors MEP_1


title: Megakaryocyte-erythrocyte precursors MEP_2


title: rufipogon_VS_indica_A

city: NEW HAVEN

first: zhiyu

last: peng

address: 165 Prospect

department: Molecular, Cellular & Developmental Biology

description: comparing the expression pattern of heading-stage panicle in six rice lineages.

hyb_protocol: 42C 50% formamide

scan_protocol: Axon GenePix 4000B

data_processing: The raw signal intensities were normalized by lowess normalization followed with quantile normalization.

organism: Oryza sativa

source_name: rufipogon

label_protocol: amino-allyl and monofunctional dye

extract_protocol: Trizol/RNeasy

tag: O. rufipogon (IRRI Accession no. 106161, Laos)

source_name: indica

tag: Oryza sativa ssp. indica (9311, China)


title: Patient 043 Core Set (custom panel)

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA

tag: Second Rising PSA (ng/ml)


title: Megakaryocyte-erythrocyte precursors MEP_3


title: rufipogon_VS_japonica_A

source_name: japonica

tag: O. sativa ssp. japonica (Nipponbare, Japan)


title: Patient 078 Core Set (custom panel)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP


title: glaberrima_VS_nivara_A

source_name: glaberrima

tag: O. glaberrima (Macina, Mali)

source_name: nivara

tag: O. nivara (IRRI Accession no. 106061, India)


title: nivara_VS_indica_A


title: nivara_VS_rufipogon_A


title: Patient 042 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation

tag: Age (yrs) at RRP

tag: patient's status

tag: Prostate cancer specific death


title: rufipogon_VS_japonica_B

tag: O. rufipogon (IRRI Accession no. 106161, Laos)


title: javanica_VS_glaberrima_A

source_name: javanica

tag: O. sativa ssp. javanica (Sipak, Indonesia)


title: japonica_VS_javanica_A


title: glaberrima_VS_rufipogon_A


title: javanica_VS_nivara_A


title: japonica_VS_glaberrima_A


title: indica_VS_javanica_A

tag: Oryza sativa ssp. indica (9311, China)


title: rufipogon_VS_indica_B


title: Patient 085 Core Set (custom panel)

tag: PSA (ng/ml) at RRP

tag: Revised Gleason Score

tag: Stage

tag: Ploidy

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA


title: indica_VS_japonica_slideA

tag: O. sativa ssp. japonica (Nipponbare, Japan)


title: Patient 017 Core Set (custom panel)

tag: Second Rising PSA (ng/ml)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP


title: Patient 077 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation

tag: Age (yrs) at RRP

tag: patient's status


title: Patient 024 Core Set (custom panel)

tag: Prostate cancer specific death


title: Patient 058 Core Set (custom panel)

tag: PSA (ng/ml) at RRP


title: Patient 032 Core Set (custom panel)

tag: Revised Gleason Score


title: nivara_VS_rufipogon_B

tag: O. nivara (IRRI Accession no. 106061, India)

tag: O. rufipogon (IRRI Accession no. 106161, Laos)


title: nivara_VS_indica_B

tag: Oryza sativa ssp. indica (9311, China)


title: Patient 041 Core Set (custom panel)

tag: Stage

tag: Ploidy

tag: First Rising PSA (ng/ml)

tag: Time (yrs) from RRP to first rising PSA


title: glaberrima_VS_rufipogon_B

tag: O. glaberrima (Macina, Mali)


title: japonica_VS_glaberrima_B

tag: O. sativa ssp. japonica (Nipponbare, Japan)


title: japonica_VS_javanica_B

tag: O. sativa ssp. javanica (Sipak, Indonesia)


title: glaberrima_VS_nivara_B


title: javanica_VS_glaberrima_B


title: MDCK LIB 2nd Inf Sel

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: MDCK cells transduced with mouse testis retroviral library (2nd Infection) and selected by growth on polyhema

hyb_protocol: Hybridization of MDCK-derived cRNAs was carried out on Illumina Mouse-6_V1 arrays (Cat. N. BD-26-101), using 1.5 µg of T7-pFB-derived cRNA. These arrays contain all the RefSeq probes present in the Mouse_Ref_8_V1 arrays, plus additional 24k probes exploring less characterized transcripts, additional Unigene clusters and singletones, to allow a more complete coverage of the transcriptome. Array washing was performed using Illumina High-stringency wash buffer for 30 min at 55°C, and followed by staining and scanning with Illumina Bead Array Reader.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Illumina Bead Studio 1.5.1.3 was used to summarize BeadChip Signals; data were not normalized. Further analysis were performed on custom XAS, Xenoarray Analysis Studio (www.sourceforge.net/projects/xas)

organism: Canis lupus familiaris

label_protocol: RNA was extracted using the TRIzol reagent (Invitrogen), according to the manufacturer’s protocoll, and then further purified using the RNeasy Mini kit  from Qiagen.. The quantification and quality analysis of RNA was performed on a Bioanalyzer 2100 (Agilent). Synthesis of cDNA and biotinylated cRNA was performed using the Illumina TotalPrep RNA Amplification Kit (Ambion Cat. n. IL1791), according to the manufacturer’s protocol, with the following variations to optimize xenoarray analysis: (i) standard cDNA synthesis with the T7-dT(24) primer: 1 µg of total RNA was used, with the doubling of the reaction volume and of all reagents; (ii) library-specific cDNA synthesis: 20 µg of total RNA were used with 4 pm of a pFB-specific primer (T7-pFB, sequence: GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGCGAACCCCAGAGTCCCGCTCA, HPLC-purified from Sigma) with standard reaction conditions. The T7-pFB primer contains the T7 promoter (for cRNA synthesis) followed by a vector-specific sequence, which is present in the 3’ region of all transcripts derived from the library. Quality assessment and quantification of cRNAs were performed on Bioanalyzer 2100.

growth_protocol: Standard culture conditions

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

tag: Madin-Darby Canine Kidney (MDCK) cells

tag: oligo pFB retrotranscription


title: MDCK LIB 2nd Inf Uns

description: MDCK cells transduced with mouse testis retroviral library (2nd Infection)


title: MDCK LIB 1st Inf Sel B

description: MDCK cells transduced with mouse testis retroviral library (1st Infection), replicate selection by growth on polyhema


title: javanica_VS_nivara_B


title: MDCK LIB 1st Inf Uns B

description: MDCK cells transduced with mouse testis retroviral library (1st Infection), replicate B


title: Patient 067 Core Set (custom panel)

tag: Case-Control Group

tag: Training or Validation

tag: Age (yrs) at RRP

tag: Second Rising PSA (ng/ml)

tag: Time (yrs) from RRP to second rising PSA

tag: PSA Slope (ng/ml/yr)

tag: Time (yrs) from PSA recurrence to systemic disease

tag: Years of Followup after RRP


title: indica_VS_javanica_B

tag: Oryza sativa ssp. indica (9311, China)


title: indica_VS_japonica_B


title: 22RV1 spink1 sirna dye rep2

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

department: Pathology

institute: University of Michigan

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. Over and under-expressed signatures were generated by filtering to include only features with significant differential expression (PValueLogRatio < 0.01) in all hybridizations and Cy5/Cy3 ratios > or < 1 (non-logged) in all hybridizations after dye flip correction

label_protocol: One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

growth_protocol: 22RV1 cells transfected with non-targeting siRNA or siRNA targeting SPINK1 were maintained in 10% RPMI media

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions

treatment_protocol: Cells were not treated prior to RNA extraction

tag: 22RV1 prostate cancer cell lines transiently transfected with siRNA targeting SPINK1

tag: 22RV1 prostate cancer cell lines transiently transfected with non targeting siRNA


title: 22RV1 spink1 sirna dye rep1


title: ovary CR  6 month (AMC113)(251411710036)

status: Public on Jun 09 2008

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Female Mouse (6 Month) Ovary on Caloric Restriction

hyb_protocol: Agilent 60-mer oligo microarray processing protocol (SSC Wash/SureHyb Chamber set-up) V4.1, April 2004.  Agilent Publication Number:  G4140-90030 V4.1 APRIL 2004.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2505-64120 at 100% PMT in both channels, with a scan resolution of 10um.  A scan window of 61 x 21.6 mm was used, then images were cropped to size and saved in a modified two-color TIFF format.  Images were examined visually for evidence of foreign debris or major failures. Agilent Microarray Scanner User Manual (6.3) http://www.chem.agilent.com/scripts/literaturePDF.asp?iWHID=33696

data_processing: Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.

organism: Mus musculus

source_name: Female Mouse Ovary on Caloric Restriction (AMC113, 6 months)

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

growth_protocol: The UMRR is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the UMRR for use as follows: 1.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  2.Carefully remove the supernatant. 3.Wash the pellet in 70% ethanol. 4.Centrifuge the tube at 12,000 x g for 15 minutes at 4C.  5.Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol. 6.Resuspend the pellet in RNase-free water to the desired concentration.

extract_protocol: RNEasy protocol

treatment_protocol: RNA was prepared from entire ovary. The tissue was processed using a Bead Beater (Bio-Spec, Bartlesville, OK) follewed by RNA purification using the RNEasy Mini Kit (Qiagen, Valencia, CA)

tag: ovary

tag: Strain

tag: Gender

value: female

tag: Age

value: 6 months

tag: Development stage

value: adult

tag: Genetic modification

value: the animal was in Caloric Restriction

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts

tag: Universale Mouse Reference


title: 22RV1 spink1 sirna rep1


title: MDCK LIB 1st Inf Sel

description: MDCK cells transduced with mouse testis retroviral library (1st Infection) and selected by growth on polyhema

tag: Madin-Darby Canine Kidney (MDCK) cells

tag: oligo pFB retrotranscription


title: ovary AL 24 month (AMC174)(251411710035)

description: Female Mouse (24 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC174, 1 year 11months 9 days)

value: 23 months

value: the animal was Ad Libitum


title: testis CR 24 month (AMC207)(251411710028)

description: Male Mouse (24 Month) Testis on on Caloric Restriction

source_name: Male Mouse Testis on on Caloric Restriction (AMC207, 1 year 10 months)

treatment_protocol: RNA was prepared from entire testis. The tissue was processed using a Bead Beater (Bio-Spec, Bartlesville, OK) follewed by RNA purification using the RNEasy Mini Kit (Qiagen, Valencia, CA)

tag: testis

value: male

value: 22 months


title: ovary AL  6 month (AMC137)(251411710031)

description: Female Mouse (6 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC137, 6 months)

value: 6 month


title: ovary AL 16 month (AMC131)(251411710034)

description: Female Mouse (16 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC131, 1 year 3 months)

value: 15 months


title: MDCK LIB 1st Inf Uns

description: MDCK cells transduced with mouse testis retroviral library (1st Infection)


title: testis CR 16 month (AMC57)(251411710027)

description: Male Mouse (16 Month) Testis on on Caloric Restriction

source_name: Male Mouse Testis on on Caloric Restriction (AMC57, 1 year 3 months)

value: 16 months


title: ovary CR 24 month (AMC25)(251411710033)

description: Female Mouse (24 Month) Ovary on Caloric Restriction

source_name: Female Mouse Ovary on Caloric Restriction (AMC25, 2 years 13 days)

value: 24 months


title: ovary CR 16 month (AMC152)(251411710032)

description: Female Mouse (16 Month) Ovary on Caloric Restriction

source_name: Female Mouse Ovary on Caloric Restriction (AMC152, 1 year 4 months)

value: 16 month


title: MDCK GFP

description: MDCK cells transduced with pFB-GFP retroviral vector


title: 22RV1 spink1 sirna rep2


title: testis CR 16 month (AMC58)(251411710026)

source_name: Male Mouse Testis on on Caloric Restriction (AMC58, 1 year 3 months)


title: testis CR  6 month (AMC7)(251411710025)

description: Male Mouse (6 Month) Testis on on Caloric Restriction

source_name: Male Mouse Testis on on Caloric Restriction (AMC7, 6 month 6 days)


title: testis CR  6 month (AMC217)(251411710023)

source_name: Male Mouse Testis on on Caloric Restriction (AMC217, 5 months 27 days )


title: testis CR 24 month (AMC208)(251411710029)

source_name: Male Mouse Testis on on Caloric Restriction (AMC208, 1 year 10 months)


title: testis AL 16 month (AMC125)(251411710020)

description: Male Mouse (16 Month) Testis on ad Libitum

source_name: Male Mouse Testis on ad Libitum (AMC125, 1 year 3 months)


title: testis AL 24 month (AMC163)(251411710022)

description: Male Mouse (24 Month) Testis on ad Libitum

source_name: Male Mouse Testis on ad Libitum (AMC163, 2 years 3 days)


title: testis AL  6 month (AMC133)(251411710018)

description: Male Mouse (6 Month) Testis on ad Libitum

source_name: Male Mouse Testis on ad Libitum (AMC133, 6 months)


title: testis AL 24 month (AMC119)(251411710021)

source_name: Male Mouse Testis on ad Libitum (AMC119, 2 years)


title: NOEC Zn exposure exp 2 rep 1

city: Boston

first: Helen

middle: C

last: Poynton

state: MA

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: biological rep 2, technical rep 1

hyb_protocol: The labeled cDNA pools from the unexposed and exposed D. magna were mixed and hybridized to the Daphnia microarray (for protocols, see mguide at the Stanford Brown Lab website).

scan_protocol: Scanning and quantification was performed using an arrayWoRx Biochip Reader (Applied Precision, Issaquah, WA) and GenePix software version 3.01 (Axon Instruments, Union City, CA).

data_processing: Technical replicates were normalized to remove possible non-linearity, if any, and checked for homogeneity using boxplots.  As an alternative to between-slide normalization we applied an approach based on sequential single-slide data analysis and utilized the α-outlier-generating model and outlier regions approach to identify differentially expressed cDNAs.  Details of the method can be found in: Loguinov, A. V., Mian, I. S. & Vulpe, C. D. (2004) Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome Biol. 5, R18.

organism: Daphnia magna

source_name: whole organism not exposed

label_protocol: cDNA was synthesized using Superscript III Reverse Transcriptase (Invitrogen, Carlsbad, CA) from total RNA in the presence of aminoallyl labeled dUTP. Fluorescence labeling proceeded by incubating the aminoallyl labeled cDNA with Cy5 or Cy3 fluorescent dyes (Amersham Biosciences, Piscataway, NJ). The dyes were switched for each technical replicate so that the control cDNA was labeled with Cy3 in one hybridization and Cy5 in the other.

growth_protocol: Genetically homogeneous Daphnia magna, purchased from Aquatic Research Organisms (Hampton, NH), were cultured in COMBO modified for water hardness (the constituents of COMBO media are described by Kilham et al. (Kilham et al., 1998)) and maintained at 23.50 C in a Percival environmental chamber according to standard protocols (Weber, 1993; Lewis et al., 1994).  Kilham, S. S., Kreeger, D. A., Lynn, S. G., Goulden, C. E. & Herrera, L. (1998) COMBO: a defined freshwater culture medium for algae and zooplankton. Hydrobiologia. 377, 147-159.; Weber, C. I. (1993) Methods for Measuring the Acute Toxicity of Effluent and Receiving Waters to Freshwater and Marine Organisms. U.S. Environmental Protection Agency: EPA/600/4-90/027F; Lewis, P. A., Klemm, D. J., Lazorchak, J. M., Norberg-King, T. J., Peltier, W. H. & Heber, M. A. (1994) Short-term Methods for Estimating the Chronic Toxicity of Effluents and Receiving Waters to Freshwater Organisms. US Environmental Protection Agency: EPA/600/4-91/002

extract_protocol: Whole daphnids (10-15 pooled for each exposure) were frozen in liquid nitrogen and ground with a morter and pestle. RNA was isolated using Trizol according to standard methods (Invitrogen, Carlsbad, CA).

treatment_protocol: All exposures to the metal concentrations were conducted on adult female daphnids 14-16 days old and occurred in a Percival environmental chamber maintained at 23.50 C for 24 hours

tag: no metals present

source_name: whole organsim exposed to NOEC Zn

tag: 1000 micrograms/L Zn


title: testis AL  6 month (AMC135)(251411710017)

source_name: Male Mouse Testis on ad Libitum (AMC135, 5 month 24 days)

source_name: Universal Mouse Reference Cell Line Pool


title: NOEC Zn exposure exp 3 rep 2

description: biological rep 3, technical rep 2


title: testis AL  1 month (AMC239)(251411710015)

description: Male Mouse (1 Month) Testis on ad Libitum

source_name: Male Mouse Testis on ad Libitum (AMC239, 1 month 10 days)

value: 1 month


title: testis AL 16 month (AMC80)(251411710019)

source_name: Male Mouse Testis on ad Libitum (AMC80, 1 year 3 months)


title: NOEC Zn exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: testis AL  1 month (AMC186)(251411710016)

source_name: Male Mouse Testis on ad Libitum (AMC186, 1 month 14 days)


title: NOEC Zn exposure exp 3 rep 1

description: biological rep 3, technical rep 1


title: NOEC Zn exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_nrs1_50_3d_2)

city: Chiba

first: Kazunori

last: Nojiri

address: 4-9-1, Anagawa, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: 3 days after gamma irradiation at 50 Gy

hyb_protocol: CodeLink Gene Expression System: Single-Assay Bioarray Hybridization and Detection

scan_protocol: Scanning CodeLink Bioarrays on Agilent G2565 microarray scanner

data_processing: global median normalization

source_name: Murine tumor

label_protocol: CodeLink Gene Expression System: Manual Labelled cRNA Target Preparation

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_nrs1_50_1d_3)

description: 1 day after gamma irradiation at 50 Gy


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_nrs1_50_1d_4)

description: 1 day after gamma irradiation at 50 Gy


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_nrs1_50_3d_1)

description: 3 days after gamma irradiation at 50 Gy


title: NOEC Zn exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_nrs1_50_6h_2)


title: NOEC Cd exposure exp 3 rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to NOEC Cd

tag: 100 micrograms/L Cd


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_nrs1_50_6h_1)


title: NOEC Cd exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: NOEC Cd exposure exp 3 rep 1

description: biological rep 3, technical rep 1


title: NOEC Cd exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: NOEC Cd exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: NOEC Cd exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_nrs1_30_1d_3)

description: 1 day after gamma irradiation at 30 Gy


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30 Gy (g_nrs1_30_3d_1)

description: 3 days after gamma irradiation at 30 Gy


title: NOEC Cu exposure exp 3 rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to NOEC Cu

tag: 30 micrograms/L Cu


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30Gy (g_nrs1_30_3d_2)

description: 3 days after gamma irradiation at 30Gy


title: NOEC Cu exposure exp 3 rep 1

description: biological rep 3, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_nrs1_30_1d_4)

description: 1 day after gamma irradiation at 30 Gy


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_nrs1_30_6h_2)


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_nrs1_0_0h_1)

description: no irradiation


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_scc7_50_3d_2)

description: 3 days after gamma irradiation at 50 Gy

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA


title: NOEC Cu exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: NOEC Cu exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_scc7_50_6h_1)


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_scc7_50_1d_4)

description: 1 day after gamma irradiation at 50 Gy


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_nrs1_30_6h_1)


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_scc7_50_3d_1)

description: 3 days after gamma irradiation at 50 Gy


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_nrs1_0_0h_2)

description: no irradiation


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_scc7_50_6h_2)


title: tenth EC50 Zn exposure exp 3 rep 1

description: biological rep 3, technical rep 1

source_name: whole organism exposed to 10th EC50 Zn

tag: 12 micrograms/L Zn


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30 Gy (g_scc7_30_3d_1)

description: 3 days after gamma irradiation at 30 Gy


title: NOEC Cu exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: tenth EC50 Zn exposure exp 3 rep 2

description: biological rep 3, technical rep 2


title: tenth EC50 Zn exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: NOEC Cu exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30 Gy (g_scc7_30_3d_2)

description: 3 days after gamma irradiation at 30 Gy


title: tenth EC50 Zn exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_scc7_30_1d_4)

description: 1 day after gamma irradiation at 30 Gy


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_scc7_30_1d_3)

description: 1 day after gamma irradiation at 30 Gy


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_scc7_0_0h_2)

description: no irradiation


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_scc7_30_6h_1)


title: SCC induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_scc7_30_6h_2)


title: tenth EC50 Zn exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, no irradiation (g_scc7_0_0h_1)

description: no irradiation


title: tenth EC50 Zn exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: tenth EC50 Cd exposure exp 3 rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to 10th EC50 Cd

tag: 0.06 microgram/L Cd


title: tenth EC50 Cd exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: tenth EC50 Cd exposure exp 3 rep 1

description: biological rep 3, technical rep 1


title: tenth EC50 Cd exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: tenth EC50 Cd exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: tenth EC50 Cu exposure exp 3 rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to 10th EC50 Cu

tag: 2.4 micrograms/L Cu


title: tenth EC50 Cd exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after gamma irradiation at 50 Gy (g_8520_50_3d_1)

description: 3 days after gamma irradiation at 50 Gy

tag: Radiation induced C3H mouse Fibrosarcoma eatablished by National Institute of Radiological Science, Chiba, Japan


title: tenth EC50 Cu exposure exp 3 rep 1

description: biological rep 3, technical rep 1


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after gamma irradiation at 50 Gy (g_8520_50_3d_2)

description: 3 days after gamma irradiation at 50 Gy


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after gamma irradiation at 30 Gy (g_8520_30_3d_2)

description: 3 days after gamma irradiation at 30 Gy


title: Radiation induced C3H mouse Fibrosarcoma, 6 hours after gamma irradiation at 50 Gy (g_8520_50_6h_1)


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 50 Gy (g_8520_50_1d_3)

description: 1 day after gamma irradiation at 50 Gy


title: Radiation induced C3H mouse Fibrosarcoma, 6 hours after gamma irradiation at 50 Gy (g_8520_50_6h_2)


title: tenth EC50 Cu exposure exp 1 rep 2

description: biological rep 1, technical rep 2


title: tenth EC50 Cu exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 50 Gy (g_8520_50_1d_4)

description: 1 day after gamma irradiation at 50 Gy


title: tenth EC50 Cu exposure exp 2 rep 2

description: biological rep 2, technical rep 2


title: 20th EC50 Cu exposure exp 4 rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to 20th EC50 Cu

tag: 1 microgram/L Cu


title: tenth EC50 Cu exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: 20th EC50 Cu exposure exp 3 rep 2

description: biological rep 2, technical rep 2


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 30 Gy (g_8520_30_1d_3)

description: 1 day after gamma irradiation at 30 Gy


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after gamma irradiation at 30 Gy (g_8520_30_1d_4)

description: 1 day after gamma irradiation at 30 Gy


title: SCC induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_scc7_50_1d_3)

description: 1 day after gamma irradiation at 50 Gy


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 038

city: Ames

first: Qijing

last: Zhang

state: IA

address: 1600 S 16th Street

department: VMPM

institute: Iowa State University

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts (120 pmol of label) of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 3 min. The hybridization mixture was loaded onto a microarray slide (OciChipTM, Ocimum Biosolutions, Indianapolis, IN) and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as per the manufacture’s recommendations and dried by centrifugation. Briefly, the slides the slides were washed three times in wash buffer 1 (2X SSC + 0.1% SDS) for 5 minutes at 32 C. They were then washed three times in wash buffer 2 (1X SSC) at 32 C ofr 5 minutes and finally three times in wash buffer 3 (0.1X SSC) for 5 minutes at 32 C. The slides were dried in a conical bottom tube centrifuges at 400g for 3 minutes.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength and the spot-specific background median of each spot. Using the R statistical package (Version 2.0.1, The R Foundation for Statistical Computing) a background-subtracted value for each spot of each of the three scans was obtained by subtracting the spot-specific background median from the spot-specific signal mean. The natural log of each value was obtained and each of the same array by dye combinations was median centered to a common median by addition of a constant. Following median centering the median of the three adjusted-log-background subtracted spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni

label_protocol: cDNA was synthesized using aminoallyl-dNTP with the ChipShotTM indirect cDNA Labeling System (Promega) according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with CyTMDye Post-labeling Reactive Pack (Amersham Bioscience, Piscataway, NJ).

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: the bacterial cells were treated with 0.06µg/ml（0.5X MIC）ciprofloxacin for 1.5 hours


title: 20th EC50 Cu exposure exp 4 rep 1

description: biological rep 3, technical rep 1


title: 20th EC50 Cu exposure exp 2 rep 1

description: biological rep 2, technical rep 1


title: 20th EC50 Cu exposure exp 2 rep 2

description: biological rep 1, technical rep 2


title: 20th EC50 Cu exposure exp 1 rep 1

description: biological rep 1, technical rep 1


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_nfsa_50_3d_2)

description: 3 days after gamma irradiation at 50 Gy

tag: Fibrosarcoma developed spontaneously in C3H/He mouse etablished by Dr. L. Milas from the University of Texas, M. D. Anderson Cancer Center, Huston, USA


title: Radiation induced C3H mouse Fibrosarcoma, 6 hours after gamma irradiation at 30 Gy (g_8520_30_6h_2)


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (g_8520_0_0h_1)

description: no irradiation


title: Radiation induced C3H mouse Fibrosarcoma, 6 hours after gamma irradiation at 30 Gy (g_8520_30_6h_1)


title: untreated campylobacter (1.5 hour) slide 038

tag: untreated control


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (g_8520_0_0h_2)

description: no irradiation


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after gamma irradiation at 30 Gy (g_8520_30_3d_1)

description: 3 days after gamma irradiation at 30 Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_nfsa_50_1d_4)

description: 1 day after gamma irradiation at 50 Gy


title: untreated campylobacter (1.5 hour) slide 037


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 50 Gy (g_nfsa_50_3d_1)

description: 3 days after gamma irradiation at 50 Gy


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 035


title: untreated campylobacter (1.5 hour) slide 035


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 037


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 034


title: untreated campylobacter (1.5 hour) slide 034


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_nfsa_50_6h_2)


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 033


title: untreated campylobacter (1.5 hour) slide 033


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30 Gy (g_nfsa_30_3d_2)

description: 3 days after gamma irradiation at 30 Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_nfsa_30_1d_4)

description: 1 day after gamma irradiation at 30 Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 50 Gy (g_nfsa_50_1d_3)

description: 1 day after gamma irradiation at 50 Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 50 Gy (g_nfsa_50_6h_1)


title: 0.06 µg/ml ciprofloxacin-treated campylobacter (1.5 hour) slide 032


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after gamma irradiation at 30 Gy (g_nfsa_30_1d_3)

description: 1 day after gamma irradiation at 30 Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_nfsa_30_6h_2)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after gamma irradiation at 30 Gy (g_nfsa_30_3d_1)

description: 3 days after gamma irradiation at 30 Gy


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 049

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts (120 pmol of label) of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 3 min. The hybridization mixture was loaded onto a microarray slide (OciChipTM, Ocimum Biosolutions, Indianapolis, IN) and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as per the manufacture’s recommendations and dried by centrifugation. Briefly, the slides the slides were washed three times in wash buffer 1 (2X SSC + 0.1% SDS) for 5 minutes at 32 C. They were then washed three times in wash buffer 2 (1X SSC) at 32 C for 5 minutes and finally three times in wash buffer 3 (0.1X SSC) for 5 minutes at 32 C. The slides were dried in a conical bottom tube centrifuges at 400g for 3 minutes.

tag: the bacterial cells were treated with 10X MIC ciprofloxacin for 0.5 hours


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6 hours after gamma irradiation at 30 Gy (g_nfsa_30_6h_1)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d3_2)

description: 3days after carbon-ion irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_nfsa_30_d1_2)

description: 1day after carbon-ion irradiation at 30Gy


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (g_nfsa_0_0h_1)

description: no irradiation


title: untreated campylobacter (0.5 hour) slide 049


title: untreated campylobacter (0.5 hour) slide 048


title: untreated campylobacter (1.5 hour) slide 032


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 045


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 048

tag: he bacterial cells were treated with 10X MIC ciprofloxacin for 0.5 hours


title: untreated campylobacter (0.5 hour) slide 045


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_nfsa_30_6h_2)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (g_nfsa_0_0h_2)

description: no irradiation


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_nfsa_30_d3_1)


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_nfsa_30_d1_1)


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 044


title: untreated campylobacter (0.5 hour) slide 044


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 042


title: untreated campylobacter (0.5 hour) slide 042


title: 1.2 µg/ml ciprofloxacin-treated campylobacter (0.5 hour) slide 024


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (c_nfsa_30_0h_2)

description: no irradiation


title: Fibrosarcoma induced spontaneously in C3H/He mouse, no irradiation (c_nfsa_30_0h_1)

description: no irradiation


title: Fibrosarcoma induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_nfsa_30_6h_1)


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after carbon-ion irradiation at 30Gy (c_8520_30_d3_2)


title: Radiation induced C3H mouse Fibrosarcoma, 3 days after carbon-ion irradiation at 30Gy (c_8520_30_d3_1)


title: untreated campylobacter (0.5 hour) slide 024


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after carbon-ion irradiation at 30Gy (c_8520_30_d1_1)


title: Radiation induced C3H mouse Fibrosarcoma, 1 day after carbon-ion irradiation at 30Gy (c_8520_30_d1_2)


title: Radiation induced C3H mouse Fibrosarcoma, 6hours after carbon-ion irradiation at 30Gy (c_8520_30_6h_2)


title: Radiation induced C3H mouse Fibrosarcoma, 6hours after carbon-ion irradiation at 30Gy (c_8520_30_6h_1)


title: Greenhorn mine downstream 2 exp 2, rep 2

description: biological rep 2, technical rep 2

treatment_protocol: Greenhorn Mine field samples were collected on Aug. 25, 2006. All exposures to the field samples were conducted on adult female daphnids 14-16 days old and occurred in the laboratory in a Percival environmental chamber maintained at 23.50 C for 24 hours

tag: < 2.0 micrograms/L Cu

source_name: whole organism exposed to Greenhorn Mine downstream 2 sample

tag: 67 micrograms/L Cu


title: Greenhorn mine downstream 2 exp 1, rep 2

description: biological rep 1, technical rep 2


title: Greenhorn mine downstream 2 exp 3, rep 1

description: biological rep 3, technical rep 1


title: Greenhorn mine downstream 2 exp 3, rep 2

description: biological rep 3, technical rep 2


title: Greenhorn mine downstream 2 exp 2, rep 1

description: biological rep 2, technical rep 1


title: Greenhorn mine downstream 2 exp 1, rep 1

description: biological rep 1, technical rep 1


title: Greenhorn Mine downstream 1 exp 3, rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to Greenhorn Mine downstream 1 sample

tag: 74 micrograms/L Cu


title: SCC induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_scc7_30_d3_2)


title: SCC induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_scc7_30_d1_1)


title: SCC induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_scc7_30_d1_2)


title: SCC induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_scc7_30_d3_1)


title: Greenhorn Mine downstream 1 exp 3, rep 1

description: biological rep 3, technical rep 1


title: Greenhorn Mine downstream 1 exp 1, rep 1

description: biological rep 1, technical rep 1


title: Greenhorn Mine mine drainage entry site 3, rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to Greenhorn mine drainage entry site sample

tag: 117 micrograms/L Cu


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (c_8520_30_0h_1)

description: no irradiation


title: Greenhorn Mine downstream 1 exp 1, rep 2

description: biological rep 1, technical rep 2

source_name: whole organism not exposed


title: SCC induced spontaneously in C3H/He mouse, no irradiation (c_scc7_30_0h_2)

description: no irradiation


title: Radiation induced C3H mouse Fibrosarcoma, no irradiation (c_8520_30_0h_2)

description: no irradiation


title: Greenhorn Mine downstream 1 exp 2, rep 2

description: biological rep 2, technical rep 2


title: SCC induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_scc7_30_6h_2)


title: SCC induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_scc7_30_6h_1)


title: SCC induced spontaneously in C3H/He mouse, no irradiation (c_scc7_30_0h_1)

description: no irradiation


title: SCC induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_nrs1_30_d1_1)

tag: Squamous cell carcinoma developed spontaneously in C3H/He mouse etablished by National Institute of Radiological Science, Chiba, Japan


title: Greenhorn Mine mine drainage entry site 3, rep 1

description: biological rep 3, technical rep 1


title: Greenhorn Mine mine drainage entry site exp 2, rep 1

description: biological rep 2, technical rep 1


title: SCC induced spontaneously in C3H/He mouse, 1 day after carbon-ion irradiation at 30Gy (c_nrs1_30_d1_2)


title: SCC induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d3_1)


title: SCC induced spontaneously in C3H/He mouse, no irradiation (c_nrs1_30_0h_2)

description: no irradiation


title: Greenhorn Mine mine drainage entry site 2, rep 2

description: biological rep 2, technical rep 2


title: Gibson_1-14_ferm-102hr_Rep3_Yeast2.0

city: Loughborough

first: Katherine

middle: A

last: Smart

state: Leicestershire

address: Sutton Bonington Campus

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

description:
Yeast sampling: Triplicate samples of the lager yeast strain CB11 were sampled from a 140 hL (14,000 L) propagation vessel immediately after inoculation and at intervals throughout a 30-hour propagation period. The yeast batch had been incubated aerobically in an 8 hL propagation vessel prior to incubation in this principal (140 hL) vessel.  Propagation wort (85% malt and 15% sugar adjunct) contained 0.5 mg L-1 Zn2+ (added as zinc sulphate heptahydrate) and was oxygenated with a ramped supply of molecular oxygen (5-100 L min-1) to give a consistent dissolved oxygen concentration of 7-8 mg L-1. Temperature of the wort was maintained throughout at 20°C. Specific gravity of the wort was 17º Plato. Triplicate samples of the same yeast strain were also collected from a fourth-generation 3275hL wort fermentation, i.e. the yeast batch had been used in four fermentations previously. The cylindroconical fermentation vessel was filled in stages, with six successive batches of oxygenated wort (each between 520 and 570 hL) added. The wort used for fermentation was the same as that used for the propagation (85% malt and 15% sugar adjunct), contained 0.2 mg L-1 zinc sulphate and was oxygenated in line prior to vessel filling to achieve a dissolved oxygen concentration of 25 mg L-1. An in line oxygen meter (Orbisphere), upstream of yeast pitching, was used to measure dissolved oxygen. Yeast was pitched with the 2nd and 4th batches of wort. The first sample for analysis was taken 8 hours after all of the yeast had been pitched (and 5 hours after the last batch of oxygenated wort had been added to the fermentation vessel). The fermentation vessel's sample point was located on the vertical side of the vessel, 1 metre above the cone. The sample valves were hygienic needle-type valves. Samples were taken at intervals for up to 102 hours after pitching and were transported between the process vessels and the laboratory at 4ºC and in under 5 minutes. Cells and wort were separated by centrifugation at 4ºC. Cell pellets for RNA extraction were flash-frozen in liquid nitrogen and stored at -80°C until required.
Cell density and budding index: Cell suspensions were diluted to an appropriate volume and density was measured using an Improved Neubauer counting chamber (Weber Scientific International Ltd, Middlesex, UK) and standard light microscope (Zeiss, Oberkocken, Germany) at 200x magnification. To determine budding index, a minimum of 500 cells were scored microscopically and the number of budded cells was calculated as a percentage of the total.
HPLC analysis of fermentable sugars in wort samples: Wort samples (2 mL) were passed through C18 Plus solid phase extraction cartridges (Waters, Milford, USA) previously conditioned with 5 mL methanol and equilibrated with 5 mL water. The first 1 mL of sample to pass through the cartridge was discarded; the second 1 mL of sample was collected for analysis. An aliquot of the sample (20 µL), was injected onto an amino column (250 x 4.6mm ID, 5µm particle size, Spherisorb NH2, Waters) and the sugars eluted using acetonitrile:water (80:20, v/v) at a flow rate of 3 mL min-1. Detection was achieved using a Wyatt Refractive Index (RI) Detector (Optilab 903, Wyatt Technology Corporation, Santa Barbara, USA). Peak heights were recorded for each compound and concentrations determined by reference to standards of known concentration. The retention times [s] of the sugars were as follows; fructose [185]; glucose [214]; sucrose [338]; maltose [414] and maltotriose [820].

hyb_protocol: = Yeast Genome 2.0 GeneChip® arrays (Affymetrix) were hybridized with 15 micrograms of fragmented, labelled cRNA for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual. GeneChip® arrays were stained with streptavidin-phycoerythrin solution.

scan_protocol: Samples were scanned using a G2500A GeneArray Scanner (Affymetrix). Following scanning, non-scaled RNA signal intensity (CEL) files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). Non-scaled RNA CEL files contain the raw signal intensity values for each probe on the array, generated from the scanned image of the GeneChip® array. The RNA CEL file contains signal intensity values for the 11 perfect match probes and 11 mismatch probes within each probe set; more than 100,000 signal intensity values for the Yeast Genome 2.0 GeneChip® array.

data_processing: Five time points from the fermentation (8, 30, 60, 80 and 102 hours after pitching) were chosen for microarray analysis. All analyses were carried out in triplicate (except for the 30 hour sample from which only duplicate samples were used for analysis), with each replicate processed separately. In total, therefore, 14 samples were used in this investigation. Non-scaled RNA signal intensity (CEL) files were generated using the GeneChip® operating system (GCOS version 5.0; Affymetrix). Non-scaled RNA CEL files contain the raw signal intensity values for each probe on the array, generated from the scanned image of the GeneChip® array. The RNA CEL file contains signal intensity values for the 11 perfect match probes and 11 mismatch probes within each probe set; more than 100,000 signal intensity values for the Yeast Genome 2.0 GeneChip® array.

organism: Saccharomyces cerevisiae

label_protocol: Approximately 5 micrograms of total RNA was reverse-transcribed at 42°C for one hour to generate first-strand cDNA using 100 pmol oligo dT primer containing a 5'-T7 RNA polymerase promoter sequence, 1X Affymetrix First-Strand Master Mix, 10 mM dithiothreitol (DTT), 10 mM dNTPs and 200 units of SuperScript II reverse transcriptase (Invitrogen). Following first-strand synthesis, second-strand cDNA was synthesized using ten units of Escherichia coli polymerase I, ten units of E. coli DNA ligase and two units of RNase H in a reaction containing 1X Affymetrix Second-Strand Master Mix and 10 mM dNTPs. The second-strand synthesis reaction proceeded at 16°C for two hours before ten units of T4 DNA polymerase were added and the reaction allowed to continue for a further five minutes. The reaction was terminated by adding 0.5 M EDTA. Double-stranded cDNA products were purified using the GeneChip® Sample Cleanup Module (Affymetrix). The synthesized cDNAs were in vitro transcribed by T7 RNA polymerase (Enzo BioArray High Yield RNA Transcript Labelling Kit; Enzo Life Sciences Inc., Farmingdale, NY, USA) using biotinylated nucleotides to generate biotinylated complementary RNAs (cRNAs). The cRNAs were purified using the GeneChip® Sample Cleanup Module (Affymetrix). The cRNAs were then randomly fragmented at 94°C for 35 minutes in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to generate molecules of approx. 35-200 bp.

extract_protocol: RNA extraction was carried out following the method of Lyne et al. (Lyne, et al., 2003). Cell samples (1x108 cells) were washed with DEPC-treated water, pelleted by centrifugation (13,000 g; 5 minutes) and re-suspended in 750 uL TES. 750 uL of chilled (4°C) acidic phenol:chloroform (5:1; pH 4.7) (Sigma) was added and the samples were incubated on a heating block at 65°C for one hour with agitation of the sample by vortexing every ten minutes for 15 seconds. Samples were then cooled on ice and centrifuged (13,000 g; 4°C; five minutes). The upper phase was transferred to a 2.0 mL Eppendorf Phase Lock GelTM tube (Eppendorf AG, Hamburg, Germany), mixed by inversion and centrifuged (13,000 g; 4°C; five minutes). The upper phase was again removed and transferred to a fresh 2.0 mL Eppendorf Phase Lock GelTM tube containing 700 uL of chloroform:isoamyl alcohol (24:1; Sigma). The samples were mixed by inversion and centrifuged (13,000 g; 4°C; five minutes). The upper phase was transferred to an Eppendorf tube containing 1.5 mL ethanol (-20°C) and 50 uL 3 M sodium acetate pH 5 and agitated briefly by vortexing. RNA was precipitated from the sample by incubation at -70°C for one hour. The sample was then centrifuged (13,000 g; room temperature; five minutes). Supernatant was discarded and the RNA was washed with 70% ethanol (4°C). Ethanol was removed by aspiration and the RNA sample was allowed to dry. 100 uL of DEPC-treated water was added and the RNA sample incubated for ten minutes at room temperature.

tag: Fermentation time point

tag: Strain

value: Lager Yeast Strain CB11


title: Gibson_1-13_ferm-102hr_Rep2_Yeast2.0


title: Gibson_1-11_ferm-80hr_Rep3_Yeast2.0


title: Gibson_1-12_ferm-102hr_Rep1_Yeast2.0


title: Greenhorn Mine upstream exp 3, rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to Greenhorn Mine upstream sample


title: Greenhorn Mine mine drainage entry site exp 1, rep 2

description: biological rep 1, technical rep 2


title: Greenhorn Mine mine drainage entry site exp 1, rep 1

description: biological rep 1, technical rep 1


title: Greenhorn Mine upstream exp 3, rep 1

description: biological rep 3, technical rep 1


title: GreenhornMine upstream exp 2, rep 2

description: biological rep 2, technical rep 2


title: Gibson_1-10_ferm-80hr_Rep2_Yeast2.0


title: SCC induced spontaneously in C3H/He mouse, 3 days after carbon-ion irradiation at 30Gy (c_nrs1_30_d3_2)


title: SCC induced spontaneously in C3H/He mouse, no irradiation (c_nrs1_30_0h_1)

description: no irradiation


title: Greenhorn Mine upstream exp 1, rep 2

description: biological rep 1, technical rep 2


title: Greenhorn Mine upstream exp 2, rep 1

description: biological rep 2, technical rep 1


title: Gibson_1-9_ferm-80hr_Rep1_Yeast2.0


title: Greenhorn Mine upstream exp 1, rep 1

description: biological rep 1, technical rep 1


title: Gibson_1-8_ferm-60hr_Rep3_Yeast2.0


title: Gibson_1-7_ferm-60hr_Rep2_Yeast2.0


title: Gibson_1-6_ferm-60hr_Rep1_Yeast2.0


title: Walker Mine little grizzly creek exp 3, rep 2

description: biological rep 3, technical rep 2

treatment_protocol: Walker Mine field samples were collected on Aug. 24, 2006. All exposures to the field samples were conducted on adult female daphnids 14-16 days old and occurred in the laboratory in a Percival environmental chamber maintained at 23.50 C for 24 hours

source_name: whole organism exposed to Walker Mine Little Grizzly sample

tag: 51 micrograms/L Cu

tag: GPS


title: SCC induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_nrs1_30_6h_1)


title: Walker Mine little grizzly creek exp 2, rep 1

description: biological rep 2, technical rep 1


title: Walker Mine little grizzly creek exp 2, rep 2

description: biological rep 2, technical rep 2


title: Gibson_1-5_ferm-30hr_Rep2_Yeast2.0


title: Walker Mine little grizzly creek exp 1, rep 1

description: biological rep 1, technical rep 1


title: Gibson_1-2_ferm-8hr_Rep2_Yeast2.0


title: Walker Mine little grizzly creek exp 1, rep 2

description: biological rep 1, technical rep 2


title: Walker Mine little grizzly creek exp 3, rep 1

description: biological rep 3, technical rep 1


title: Gibson_1-1_ferm-8hr_Rep1_Yeast2.0


title: Gibson_1-3_ferm-8hr_Rep3_Yeast2.0


title: Gibson_1-4_ferm-30hr_Rep1_Yeast2.0


title: Walker Mine downstream tailings exp 2, rep 2

description: biological rep 2, technical rep 2

source_name: whole organism exposed to Walker Mine downstream mine tailings sample

tag: 113 micrograms/L Cu


title: SCC induced spontaneously in C3H/He mouse, 6hours after carbon-ion irradiation at 30Gy (c_nrs1_30_6h_2)


title: Walker Mine downstream tailings exp 3, rep 2

description: biological rep 3, technical rep 2


title: Walker Mine downstream mine portal 3, rep 2

description: biological rep 3, technical rep 2

source_name: whole organism exposed to Walker Mine downstream mine portal sample

tag: 4.8 micrograms/L Cu


title: Walker Mine downstream tailings exp 1, rep 1

description: biological rep 1, technical rep 1


title: Walker Mine downstream tailings exp 1, rep 2

description: biological rep 1, technical rep 2


title: Walker Mine downstream tailings exp 2, rep 1

description: biological rep 2, technical rep 1


title: Walker Mine downstream tailings exp 3, rep 1

description: biological rep 3, technical rep 1


title: Walker Mine downstream mine portal 2, rep 2

description: biological rep 2, technical rep 2


title: Walker Mine downstream mine portal 3, rep 1

description: biological rep 3, technical rep 1


title: Walker Mine downstream mine portal exp 2, rep 1

description: biological rep 2, technical rep 1


title: Walker Mine downstream mine portal exp 1, rep 2

description: biological rep 1, technical rep 2


title: ovary AL 24 month (AMC167)(251279910195)

source_name: Female Mouse Ovary ad Libitum (AMC167, 2 years)

tag: ovary

tag: Gender

tag: Age

value: 2 years

tag: Development stage

tag: Genetic modification

tag: Individual Identifier

source_name: Universal Mouse Reference Cell Line Pool

tag: Universale Mouse Reference


title: Greenhorn Mine downstream 1 exp 2, rep 1

description: biological rep 2, technical rep 1

tag: < 2.0 micrograms/L Cu


title: ovary AL 16 month (AMC48)(251279910194)

source_name: Female Mouse Ovary ad Libitum (AMC48, 1 year)


title: Walker Mine downstream mine portal exp 1, rep 1

description: biological rep 1, technical rep 1


title: ovary AL  1 month (AMC244)(251279910196)

description: Female Mouse (1 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC244, 1 month)


title: Walker Mine upstream exp 2, rep 1

description: biological rep 2, technical rep 1

source_name: whole organism exposed to Walker Mine upstream sample


title: Walker Mine upstream exp 3, rep 1

description: biological rep 3, technical rep 1


title: ovary CR 16 month (AMC27)(251279910193)

source_name: Female Mouse Ovary on Caloric Restriction (AMC27, 1 year)


title: Walker Mine upstream exp 3, rep 2

description: biological rep 3, technical rep 2


title: ovary CR  6 month (AMC34)(251279910191)

description: Female Mouse (6 Month) Ovary on Caloric Restriction

source_name: Female Mouse Ovary on Caloric Restriction (AMC34, 6 months)


title: Walker Mine upstream exp 2, rep 2

description: biological rep 2, technical rep 2


title: ovary AL  6 month (AMC52)(251279910192)

description: Female Mouse (6 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC52, 6 months)

value: 6 moth

value: the animal ad Libitum


title: ovary AL  1 month (AMC196)(251279910189)

description: Female Mouse (1 Month) Ovary ad Libitum

source_name: Female Mouse Ovary ad Libitum (AMC196, 17 days)

value: female

value: 17 days

value: the animal was ad Libitum


title: ovary CR 24 month (AMC1)(251279910190)

source_name: Female Mouse Ovary on Caloric Restriction (AMC1, 2 years)

value: adult

value: the animal was in Caloric Restriction


title: Walker Mine upstream exp 1, rep 1

description: biological rep 1, technical rep 1


title: Walker Mine upstream exp 1, rep 2

description: biological rep 1, technical rep 2


title: PBMC_WY_personF

status: Public on Jun 06 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Arrays were hybridized on an Affymetrix 450 fluidics stations according to the protocol Midi_euk2v3_450, as described by Affymetrix

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G, according to the standard protocols of Affymetrix

data_processing: Expression estimates were calculated using RMA

source_name: Peripheral blood mononuclear cells, WY14,643 treated for 12 hours

label_protocol: Total RNA from PBMCs (5µg) was labeled using the Affymetrix One-cycle Target Labeling Assay

extract_protocol: PBMCs were lysed in Qiagen RLT buffer and homogenized using seringes with 0.4 mm needles, whereafter purified total RNA was isolated using Qiagen RNEasy columns

treatment_protocol: PBMCs were incubated in RPMI1640 medium with 2 mmol/L L-glutamine, 10% fetal bovine serum and antibiotics (penicillin and streptomycin) in the presence of 5% CO2 at 37°C. at 1e6 cells per ml with either WY14,643 (50 μM) or vehicle (DMSO, 0.1%) for 12 hours.

tag: Male, aged between 30-48


title: PBMC_WY_personE


title: PBMC_DMSO_personF

source_name: Peripheral blood mononuclear cells, DMSO treated for 12 hours


title: PBMC_DMSO_personE


title: PBMC_WY_personB


title: PBMC_DMSO_personB


title: PBMC_WY_personD


title: PBMC_DMSO_personC


title: PBMC_DMSO_personD


title: PBMC_WY_personC


title: PBMC_DMSO_personA


title: PBMC_WY_personA


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M06_Louisiana_06

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Adult workers were randomly collected from the foraging area and frozen individually. RNA from 7-10 workers of the same genotype were pooled.

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization (marray, Bioconductor)

organism: Solenopsis invicta

source_name: Reference RNA batch 2006

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's instructions

tag: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: Adult workers homozygote BB Gp9 monogyne

tag: Genotype

value: homozygote BB

tag: Colony form

value: monogyne

tag: Source population

value: Louisiana


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P05_Louisiana_06

source_name: Adult workers heterozygote Bb Gp9 polygyne

value: heterozygote Bb

value: polygyne


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M09_Georgia_04

source_name: Reference RNA batch 2004

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Pooled 25% of the amplified RNA from each experimental sample

value: Georgia


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P06_Georgia_04

source_name: Adult workers homozygote BB Gp9 polygyne


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P05_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P05_Louisiana_06


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P07_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P06_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P05_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P07_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P03_Georgia_04


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P07_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P07_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M29_Georgia_06


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P05_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P05_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M35_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P04_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M07_Louisiana_06


title: Adult_workers_heterozygote_Bb_Gp9_polygyne_colony_P04_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P03_Georgia_04


title: Adult_workers_little_bb_Gp9_polygyne_multiple_colonies_Georgia_04

source_name: Adult workers little bb Gp9 polygyne

value: little bb


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M34_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P08_Georgia_06


title: Adult_workers_homozygote_BB_Gp9_monogyne_colony_M05_Louisiana_06


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P01_Georgia_04


title: Adult_workers_homozygote_BB_Gp9_polygyne_colony_P02_Georgia_04