title: AR-CO-24-3-571

description: Pre-frontal cortex of male c57Bl/6 mice

source_name: prefrontal cortex (collagen)

treatment_protocol: Eight week old C57Bl/6 male mice were injected i.d. with 100 ul type II Collagen in 100 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Type II collagen in Complete Freunds adjuvant

treatment_protocol: Eight week old C57Bl/6 male mice were injected i.d. with 200 ul of Complete Freunds ajuvant at day 24 were injected with LPS and sacrifice by decapitation at day 31 h

tag: Pre-frontal cortex from male C57Bl/6 mice 31 d after i.d. injection of Complete Freunds adjuvant


title: AR-CO-24-2-549

status: Public on May 02 2007

type: RNA

city: Ciudad de Buenos Aires

first: Mariano

middle: Cesar

last: Salibe

address: Av. Patricias Argentinas 435

country: Argentina

institute: Gentron LLC

description: Pre-frontal cortex of male c57Bl/6 mice

hyb_protocol: Slides were prehybridised at 42°C in 2X SSC, 0.1% SDS, 1% BSA. Labeled probes were mixed with hybridization buffer containing 30% formamide and hybridized overnight at 42°C

scan_protocol: Images were obtained with a VersArray ChipReader system (BioRad) at 10 um resolution and 16bit depth. Each slide was scanned three times, each time with a 5% increment in the sensitivity of the scanner. The data integration for multipole scanning were calculated by M = log2(cy3 / cy2) and A = 0.5 * log2(cy2 * cy3) values for all the possible combinations between channels among the three scannings. Quality score for each couple of channels was calculated as QS = min(QScy2, QScy3). The resulting 9 sets of A and M values were averaged using the QS as weights to obtain the integrated A and M sets.

data_processing: Data was log2 transformed and normalizaed with an intensity- and location-dependent loess fit

molecule: total RNA

organism: Mus musculus

label_protocol: RNA was reversed transcribed using Superscript II RT (Invitrogen) with oligo dT primers and random primers, both in the presence of aa-dUTP (Sigma). The cDNA was labeled with Cy3 or Cy5 dyes (Amersham), resuspended in DMSO, and incubated for 1 hr at room temperature in the dark. The probes were purified using the SNAP Gel Purification Kit (Invitrogen) following manufacturer instructions with the following modification: at the initial step, 500 ul of loading buffer (2.25 M guanidinium HCl in 70% isopropanol) were added to the sample, placed in a SNAP column and incubated for 4 min before the first centrifugation

growth_protocol: Mice were housed in HEPA filtered air racks (Tecniplast, Italy) with food and water ad libitum

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen)

source_name: prefrontal cortex (control)


title: P-HT-72-2-187

description: hypothalamus of male c57Bl/6 mice

molecule: polyA RNA

source_name: hypothalamus (control)

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). Poly A+ RNA was obtained from total RNA using the MicroPoly(A) Pure kit (Ambion)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus from male C57Bl/6 mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-HT-72-1-182

description: hypothalamus of male c57Bl/6 mice


title: M-HT-72-1-143

description: hypothalamus of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of 4T-1 mammary cancer cell)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: P-HT-18-2-175

description: hypothalamus of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Hypothalamus from male C57Bl/6 mice 18 h after s.c. injection of PBS

source_name: hypothalamus (18 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Hypothalamus form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: AR-CO-24-3-570

description: Pre-frontal cortex of male c57Bl/6 mice


title: P-CO-192-5-525

description: Pre-frontal cortex of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Pre-frontal cortex form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: AR-CO-24-1-541

description: Pre-frontal cortex of male c57Bl/6 mice


title: M-MB-192-1-396

description: Mid Brain of female balb/c mice

source_name: midbrain (control)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of PBS

source_name: midbrain (192 h after injection of 4T-1 mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 192 h

tag: Mid Brain from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: M-HT-72-1-149

description: hypothalamus of female balb/c mice


title: P-HT-18-1-176

description: hypothalamus of male c57Bl/6 mice


title: P-HT-18-2-177

description: hypothalamus of male c57Bl/6 mice


title: P-MB-18-2-393

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (18 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: AR-CO-24-2-548

description: Pre-frontal cortex of male c57Bl/6 mice


title: P-HT-18-1-168

description: hypothalamus of male c57Bl/6 mice


title: AR-CO-24-1-542

description: Pre-frontal cortex of male c57Bl/6 mice


title: P-HT-72-2-142

description: hypothalamus of male c57Bl/6 mice


title: C-MB-18-2-397

description: midbrain of male balb/c mice

source_name: midbrain (18 h after injection of CT26 colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Midbrain form male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Midbrain from male Balb/c mice 18 h after s.c. injection of PBS


title: P-HT-72-2-148

description: hypothalamus of male c57Bl/6 mice


title: C-HT-72-2-153

description: hypothalamus of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus from male Balb/c mice 72 h after s.c. injection of PBS

source_name: hypothalamus (72 h after injection of colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Hypothalamus form male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells


title: P-HT-72-1-147

description: hypothalamus of male c57Bl/6 mice


title: P-MB-18-1-392

description: Mid Brain of male c57Bl/6 mice

tag: Mid Brain  from male C57Bl/6 mice 18 h after s.c. injection of PBS

tag: Mid Brain from male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-MB-192-2-391

description: Mid Brain of male C57Bl/6 mice

source_name: midbrain (192 h after injection of LL/2(LLC1) lung cancer cell)

tag: Mid Brain from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Mid Brain from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: M-HT-192-3-415

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of PBS

source_name: hypothalamus (192 h after injection of 4T-1 mammary cancer cell)

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: M-HT-192-3-416

description: hypothalamus of female balb/c mice

tag: Hypothalamus form female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: P-HT-72-1-141

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus from male C57Bl/6 mice 72 h after s.c. injection of PBS

tag: Hypothalamus form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: C-HT-72-1-190

description: hypothalamus of male balb/c mice


title: C-HT-72-2-146

description: hypothalamus of male balb/c mice


title: M-HT-72-1-394

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of PBS

tag: Hypothalamus from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: C-HT-72-1-152

description: hypothalamus of male balb/c mice


title: P-HT-192-4-424

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus from male C57Bl/6 mice 192 h after s.c. injection of PBS

source_name: hypothalamus (192 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Hypothalamus form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: C-HT-72-1-145

description: hypothalamus of male balb/c mice


title: P-HT-192-3-408

description: hypothalamus of male c57Bl/6 mice


title: C-CO-72-2-132

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of CT26 colon carcinoma cells)

tag: Pre-frontal cortex from male Balb/c mice 72 h after s.c. injection of CT26 colon carcinoma cells


title: P-HT-192-3-409

description: hypothalamus of male C57Bl/6 mice

tag: Hypothalamus form male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: P-HT-72-3-404

description: hypothalamus of male c57Bl/6 mice


title: P-HT-72-3-405

description: hypothalamus of male C57Bl/6 mice

tag: Hypothalamus form male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: P-HT-192-4-425

description: hypothalamus of male C57Bl/6 mice


title: M-CO-18-2-172

description: Pre-frontal cortex of female balb/c mice

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 100 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from female Balb/c mice 18 h after s.c. injection of PBS

source_name: prefrontal cortex (18 h after injection of mammary cancer cells)

treatment_protocol: Eight week old Balb/c female mice were injected s.c. with 1E5 4T-1 cells in 100 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from female Balb/c mice 18 h after s.c. injection of 4T-1 mammary cancer cells


title: P-HT-18-3-401

description: hypothalamus of male C57Bl/6 mice

tag: Hypothalamus form male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Hypothalamus from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: C-MB-18-2-361

description: midbrain of male balb/c mice

tag: Midbrain form male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells

tag: Midbrain from male Balb/c mice 18 h after s.c. injection of PBS


title: C-CO-72-1-123

description: Pre-frontal cortex of male balb/c mice


title: C-CO-72-2-192

description: Pre-frontal cortex of male balb/c mice


title: C-MB-18-2-369

description: midbrain of male balb/c mice


title: C-CO-72-1-139

description: Pre-frontal cortex of male balb/c mice


title: M-CO-18-2-160


title: C-MB-18-1-349

description: midbrain of male balb/c mice


title: C-CO-72-2-140

description: Pre-frontal cortex of male balb/c mice


title: P-HT-18-3-400

description: hypothalamus of male c57Bl/6 mice

tag: Hypothalamus form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-CO-18-1-166


title: M-CO-18-1-159


title: M-CO-72-2-124

tag: Pre-frontal cortex from female Balb/c mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of mammary cancer cells)

tag: Pre-frontal cortex from female Balb/c mice 72 h after s.c. injection of 4T-1 mammary cancer cells


title: M-CO-72-1-106

source_name: prefrontal cortex (control)


title: C-HT-192-3-421

description: hypothalamus of male balb/c mice

source_name: hypothalamus (192 h after injection of colon carcinoma cells)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Hypothalamus form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells

source_name: hypothalamus (control)

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Hypothalamus from male Balb/c mice 192 h after s.c. injection of PBS


title: M-CO-72-1-135


title: C-MB-192-2-317

description: midbrain of male balb/c mice

source_name: midbrain (192 h after injection of CT26 colon carcinoma cells)

tag: Midbrain form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells

tag: Midbrain from male Balb/c mice 192 h after s.c. injection of PBS


title: C-MB-192-1-313

description: midbrain of male balb/c mice

tag: Midbrain from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: C-HT-192-3-420

description: hypothalamus of male balb/c mice


title: P-CO-18-1-173

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex from male C57Bl/6 mice 18 h after s.c. injection of PBS

source_name: prefrontal cortex (18 h after injection of LL/2(LLC1) lung cancer cell)

tag: Pre-frontal cortex form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-CO-18-2-174

description: Pre-frontal cortex of male c57Bl/6 mice


title: RU486+F4.Cy3 Vs REF4.Cy5

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

country: USA

institute: Woods Hole Oceanographic Institution

description: Post-processing: After hybridization, the cover slip was removed by immersion in a low stringency wash buffer (1X SSC, 0.2% SDS). The slide was then washed for 10 min in low stringency wash buffer, 5 min in high stringency wash buffer (0.1x SSC, 0.2% SDS, and MilliQ water), and twice for 2.5 min in 0.1X SSC. Low stringency washing was carried out at 48oC, whereas the remaining washing steps were at room temperature with shaking. Finally, the slides were quickly dipped in MilliQ water and centrifuged at 1,000 g for 2 min in a 50 ml Falcon tube at room temperature for drying.

hyb_protocol: Before hybridization, the Cy3 and Cy5 labeled samples were combined and dried in a speed vac. To the dried sample 26 l of hybridization buffer and 2 µl each of calf thymus DNA (10 mg/ml) and yeast tRNA (10 mg/ml) were added. The samples were denatured for 2 min at 95°C, snap cooled on ice for 1 min, and centrifuged for 1 min at maximum speed. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization was carried out overnight in a water bath at 37°C.

scan_protocol: Image analysis was carried out using Versarray chipreader software Version 3.1 (BioRad, Canada). For each microarray slide, two images were produced by illuminating the array at 635 nm (excitation of Cy5) and 532 nm (Cy3). For both illuminations, photomultiplier tube (gain and light amplification) settings were at 900 and laser power was set at 90%. All images were captured in TIFF format. Spot finding and quantification was carried out with ImaGene 3.0 microarray image analysis software (BioDiscovery; Los Angeles, CA). Briefly, a grid was created taking into account the number of spots, the printing pattern, and the size of the spots. Spot finding was performed using a semiautomatic method in which each spot is checked for proper alignment within the grid manually. Finally, spot quantification was performed to obtain the expression level of each gene on the array.

data_processing: The data analysis was carried out using microarray data analysis system (MIDAS) (Saeed et al.,2003). Poor or negative control spots were flagged as unreliable and were excluded from the analysis. For each spot, signal/noise (SN) threshold was calculated using the following formula: [I(A or B) + Bkg (A or B)]/ Bkg(A or B), where I(A) and I (B) denotes background corrected signal intensity for channel A and B;  Bkg(A) and Bkg(B) denotes background intensity for channel A and B respectively. The SN ratios for each channel was compared to the set threshold value of 2.0 and any spots which are less than or equal to 2.0 were marked as bad and excluded from downstream analysis. The data were then LOWESS normalized before calculating the gene expression ratios. The data for each treatment (fold change relative to the reference standard) was calculated as a ratio of normalized gene intensity for the sample to that of the reference RNA on each slide.

organism: Oncorhynchus mykiss

source_name: RU486+Cortisol 4

label_protocol: Thirty micrograms of intact total RNA (either treatment sample or reference RNA) were indirectly labeled with Cy5 and Cy3 following the TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) (Amersham Biosciences, Piscataway, NJ).  In brief, cDNA was synthesized by incorporating aminoallyl dUTP (AA-dUTP) at 42°C for 3 h. RNA was hydrolyzed with 10 µl of 1 M NaOH and 10 µl of 0.5 M EDTA for 15 min at 70°C and neutralized by adding 10 µl of 1 M HCl. To remove unincorporated AA-dUTP and free amines, the reactions were purified with Qiagen columns using phosphate wash buffer and phosphate elution buffer. The purified sample was dried in a speed vac and AA-cDNA was resuspended in 0.1 M sodium bicarbonate buffer, and coupling to the Cyanine dye ester was performed for 90 min in the dark at room temperature. The removal of uncoupled dye was performed using the Qiagen PCR Purification Kit.

extract_protocol: Total RNA was extracted from trout hepatocytes using the RNeasy extraction kit (Qiagen,ON). The quality of the total RNA obtained was checked by gel electrophoresis on a 1% agarose gel containing ethidium bromide and the concentration was determined spectrophotometrically at 260/280 nm using Cary 50 UV-Vis spectrophotometer (Varian Inc, ON).

treatment_protocol: Primary culture of trout hepatocytes were exposed to 1000 ng/ml of RU486 and 100 ng/ml of cortisol for 24 hours and sampled. RU486 was added 30 min prior to the addition of cortisol.

tag: RU486+Cortisol treated sample was labelled with Cy3

source_name: Reference 4

treatment_protocol: Total RNA was isolated from untreated trout hepatocytes and used as Reference standard.

tag: Reference RNA was labelled with Cy5


title: M-HT-192-1-329

description: hypothalamus of female balb/c mice

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of PBS

tag: Hypothalamus from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: C-CO-192-3-417

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of CT26 colon carcinoma cells)

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: C-MB-192-2-309

description: midbrain of male balb/c mice

source_name: midbrain (control)


title: RU486+F1.Cy5 Vs REF1.Cy3

source_name: Reference 1

tag: Reference RNA was labelled with Cy3

tag: RU486+Cortisol treated sample was labelled with Cy5


title: RU486+F3.Cy5 Vs REF3.Cy3

source_name: Reference 3

source_name: RU486+Cortisol 3


title: RU486+F2.Cy3 Vs REF2.Cy5

source_name: RU486+Cortisol 2

source_name: Reference 2


title: RU486-4.Cy3 Vs REF4.Cy5

treatment_protocol: Primary culture of trout hepatocytes were exposed to 1000 ng/ml of RU486 for 24 hours and sampled.

tag: RU486 treated sample was labelled with Cy3


title: P-CO-72-1-137

description: Pre-frontal cortex of male c57Bl/6 mice

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 72 h

tag: Pre-frontal cortex from male C57Bl/6 mice 72 h after s.c. injection of PBS

source_name: prefrontal cortex (72 h after injection of LL/2(LLC1) lung cancer cell)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 72 h

tag: Pre-frontal cortex form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: M-CO-192-3-413

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of mammary cancer cells)

tag: Pre-frontal cortex from female Balb/c mice 192 h after s.c. injection of 4T-1 mammary cancer cells


title: RU486-3.Cy5 Vs REF3.Cy3

tag: RU486 treated sample was labelled with Cy5


title: RU486-1.Cy5 Vs REF1.Cy3


title: P-CO-192-4-423

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (192 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex from male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 192 h

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: RU486-2.Cy3 Vs REF2.Cy5


title: C-CO-192-3-419

description: Pre-frontal cortex of male balb/c mice

source_name: prefrontal cortex (control)

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of PBS


title: M-CO-192-3-414


title: C-HT-18-1-348

description: hypothalamus of male balb/c mice

tag: Hypothalamus from male Balb/c mice 18 h after s.c. injection of PBS

source_name: hypothalamus (18 h after injection of colon carcinoma cells)

tag: Hypothalamus form male Balb/c mice 18 h after s.c. injection of CT26 colon carcinoma cells


title: C-HT-18-2-360

description: hypothalamus of male balb/c mice

source_name: hypothalamus (control)


title: P-HT-192-2-328

description: hypothalamus of male C57Bl/6 mice

source_name: hypothalamus (192 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 192 h

tag: Hypothalamus form male C57BL/6 mice 192 h after s.c. injection of  LL/2(LLC1) lung tumor cells

tag: Hypothalamus from male C57Bl/6 mice 192 h after s.c. injection of PBS


title: CON2.Cy5 Vs REF.Cy3

source_name: Control 2

treatment_protocol: Primary culture of trout hepatocytes were exposed to 0.01% ethanol (vehicle control) for 24 hours and sampled.

tag: Control RNA was labelled with Cy5


title: P-CO-72-1-117

description: Pre-frontal cortex of male c57Bl/6 mice


title: P-CO-72-2-138

description: Pre-frontal cortex of male c57Bl/6 mice


title: C-HT-192-2-316

description: hypothalamus of male balb/c mice

source_name: hypothalamus (192 h after injection of colon carcinoma cells)

tag: Hypothalamus form male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells

tag: Hypothalamus from male Balb/c mice 192 h after s.c. injection of PBS


title: F5.Cy5 Vs REF.Cy3

source_name: Reference 5

treatment_protocol: Untreated trout hepatocytes were used as Reference Standard.

tag: Reference RNA was labelled with Cy3

source_name: Cortisol 5

treatment_protocol: Primary culture of trout hepatocytes were exposed to 100 ng/ml cortisol and sampled after 24 hours.

tag: Cortisol treated sample was labelled with Cy5


title: C-HT-192-1-312

description: hypothalamus of male balb/c mice


title: P-CO-72-2-116

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex from male C57Bl/6 mice 72 h after s.c. injection of PBS


title: F3.Cy5 Vs REF.Cy3

source_name: Cortisol 3

tag: Cortisol treated sample was treated with Cy5


title: P-CO-192-4-422

description: Pre-frontal cortex of male c57Bl/6 mice

tag: Pre-frontal cortex form male C57Bl/6 mice 192 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-CO-192-3-411

description: Pre-frontal cortex of male C57Bl/6 mice


title: C-HT-192-2-308

description: hypothalamus of male balb/c mice


title: F2.Cy5 Vs REF.Cy3

source_name: Cortisol 2

tag: Cortisol treated hepatocytes were treated with Cy5


title: F1.Cy3 Vs Ref.Cy5

source_name: Cortisol 1

treatment_protocol: Primary culture of trout hepatocytes were exposed to 100 ng/ml cortisol and sampled after 24 hours .

tag: Cortisol treated hepatocytes were labelled with Cy3

source_name: Reference 1

tag: Reference RNA was labelled with Cy5


title: CON4.Cy3 Vs REF.Cy5

source_name: CONTROL 4

tag: Control RNA was labelled with Cy3

source_name: REFERENCE 4


title: F4.Cy3 Vs REF.Cy5

source_name: Cortisol 4

source_name: Reference 4


title: CON3.Cy5 Vs REF.Cy3

source_name: REFERENCE 3

treatment_protocol: Untreated trout hepatocytes were used as Reference Standard

tag: Reference RNA labelled with Cy3

source_name: CONTROL 3

tag: Control RNA labelled with Cy5


title: P-CO-192-3-410

description: Pre-frontal cortex of male c57Bl/6 mice

source_name: prefrontal cortex (control)

tag: Pre-frontal cortex from male C57Bl/6 mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of  LL/2(LLC1) lung tumor cells)


title: C-CO-192-1-310

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal Cortex from male Balb/c mice 192 h after s.c. injection of PBS

source_name: prefrontal cortex (192 h after injection of CT26 colon carcinoma cells)

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of CT26 colon carcinoma cells


title: CON1.Cy3 Vs REF.Cy5

source_name: Control. Cy3

tag: Control RNA labelled with Cy3

source_name: Reference. Cy5

tag: Reference RNA labelled with Cy5


title: P-CO-72-3-406

description: Pre-frontal cortex of male c57Bl/6 mice

source_name: prefrontal cortex (72 h after injection of  LL/2(LLC1) lung tumor cells)

tag: Pre-frontal cortex form male C57Bl/6 mice 72 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: P-CO-72-3-407

description: Pre-frontal cortex of male C57Bl/6 mice

tag: Pre-frontal cortex from male C57BL/6 mice 72 h after s.c. injection of  LL/2(LLC1) lung tumor cells


title: P-CO-18-3-403

description: Pre-frontal cortex of male C57Bl/6 mice

source_name: prefrontal cortex (18 h after injection of  LL/2(LLC1) lung tumor cells)

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 1E6 LL/2(LLC1) lung tumor cells in 300 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from male C57BL/6 mice 18 h after s.c. injection of  LL/2(LLC1) lung tumor cells

treatment_protocol: Eight week old C57Bl/6 male mice were injected s.c. with 300 ul PBS and sacrifice by decapitation after 18 h

tag: Pre-frontal cortex from male C57Bl/6 mice 18 h after s.c. injection of PBS


title: C-CO-192-2-306

description: Pre-frontal cortex of male balb/c mice

tag: Pre-frontal cortex from male Balb/c mice 192 h after s.c. injection of PBS


title: 7wkC

status: Public on May 01 2007

city: Dublin

first: Finian

last: Martin

address: Conway Institute, Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: University College Dublin

description: Recommended Affymetrix protocols were followed.

hyb_protocol: Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.

data_processing: Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.

label: biotin

source_name: mammary gland, 7wk

label_protocol: 5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.

growth_protocol: All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.

extract_protocol: Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.

treatment_protocol: No treatment

tag: Strain

tag: Gender

value: female

tag: Age

value: 7 weeks

tag: Tissue

value: mammary gland


title: 7wkB


title: C-CO-192-2-314

description: Pre-frontal cortex of male balb/c mice

treatment_protocol: Eight week old Balb/c male mice were injected s.c. with 1E6 CT-26.WT cells in 300 ul PBS and sacrifice by decapitation after 192 h


title: 6wkC

source_name: mammary gland, 6wk

value: 6 weeks


title: 5wkB

source_name: mammary gland, 5wk

value: 5 weeks


title: P-CO-18-3-402

description: Pre-frontal cortex of male c57Bl/6 mice

source_name: prefrontal cortex (18 h after injection of LL/2(LLC1) lung cancer cell)

tag: Pre-frontal cortex form male C57Bl/6 mice 18 h after s.c. injection of LL/2(LLC1) lung cancer cell


title: 6wkA


title: 5wkA


title: 7wkA


title: 6wkB


title: P-CO-18-1-161

description: Pre-frontal cortex of male c57Bl/6 mice


title: KT2440(pCAR1deltaORF70)_succinate_rep1

city: Sendai

first: Masatoshi

last: Miyakoshi

state: Miyagi

address: Aoba-ku, Katahira, 2-1-1

department: Department of Environmental Life Sciences

country: Japan

institute: Tohoku University

description: Exponential phase

hyb_protocol: Hybridization was performed by Nimblegen Systems, Inc. www.nimblegen.com

scan_protocol: Scan was performed by Nimblegen Systems, Inc. www.nimblegen.com

data_processing: Microarray data analysis was performed using the robust multi-array average (RMA) method (Irizarry et al., 2003) based on log2 values of absolute signal intensities for PM probes only.

organism: Pseudomonas putida

label_protocol:
Samples were labeled by Nimblegen Systems, Inc.
www.nimblegen.com

growth_protocol: 100 ml of Nitrogen-plus Mineral Medium-4 supplemented with 1.0 mg ml-1 sodium succinate was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer. Total RNA was extracted using the RNeasy Midi kit (Qiagen). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 1 h. After the inactivation of the DNase by the addition of the stop reagent, and subsequent incubation at 65˚C for 15 min, RNA samples were again purified with the RNeasy Mini column according to the manufacturer’s clean-up protocol (Qiagen).


title: KT2440_succinate_rep1

description: Exponential phase

tag: Pseudomonas putida KT2440


title: 4wkB

source_name: mammary gland, 4wk

value: 4 weeks


title: KT2440(pCAR1)_succinate_rep2

description: Exponential phase

tag: Pseudomonas putida KT2440(pCAR1)


title: LONFvs3.31859_slide40

city: PARIS

first: Emilie

last: Aït Yahya Graison

address: 2 place jussieu

department: UFR BIOCHIMIE

country: France

institute: UNIVERSITE PARIS 7

description: Normalized data from each slide were then filtered using two criteria: i) for each oligonucleotide, at least two values among the four replicates had to be available, and ii) standard deviation of A values corresponding to the geometric mean in log2 of Cy3 and Cy5 signal intensities had to be below 1.

hyb_protocol: Hybridizations of samples pairs on HSA21 oligoarrays (one DS and one control) according to the experimental design were carried out in hybridization buffer (formamide 50%, SSC 4X, SDS 0.1%, Denhart 5X) at 42°C over night.

scan_protocol: Data were acquired with GenePix® 4000B scanner and using the GenePix® Pro 6.0 software (Axon™). For each array, the raw data comprised the median feature pixel intensity at wavelength 635 and 532nm for Cy5 and Cy3 labeling respectively. After subtraction of the background signal, LOWESS normalization [43] of the M values corresponding to Cy5/Cy3 signals ratios in log2 was applied to all oligonucleotides representing non HSA21 genes and used to calculate a correction factor applied to M values for HSA21 probes.

data_processing: Arithmetic means of normalized and filtered M and A values were calculated for each oligonucleotide

organism: Homo sapiens

source_name: lymphoblastoid cell line,euploid, n°12

label_protocol: Two µg of polyA RNA were converted into Cy5 labeled cDNA by incorporation of fluorescent dUTP (Amersham™) using the Reverse-iT™ RTase Blend kit (ABGene™).

growth_protocol: Culture media consisted of Opti-MEM® with GlutaMax® supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin (10000 unities/ml). Cell lines were grown at 37°C in humidified incubators, in an atmosphere of 5% CO2.

extract_protocol: polyA RNAs were extracted from frozen individual cell samples using Fast Track® 2.0 mRNA Isolation kit (Invitrogen™) according to the manufacturer’s instructions. To eliminate DNA contamination, the appended DNase protocol of RNeasy® mini kit (Qiagen™) was used according to manufacturer’s protocol.

treatment_protocol: Cell line has been obtained after immortalization by Epstein-Barr virus (EBV) of B lymphocytes collected from blood samples of a control patient.

tag: status

value: euploid

value: Male

source_name: lymphoblastoid cell line, trisomic, n°5

label_protocol: Two µg of polyA RNA were converted into Cy3 labeled cDNA by incorporation of fluorescent dUTP (Amersham™) using the Reverse-iT™ RTase Blend kit (ABGene™).

treatment_protocol: Cell line has been obtained after immortalization by Epstein-Barr virus (EBV) of B lymphocytes collected from blood samples of a DS patient.

tag: Status

value: trisomic


title: KT2440(pCAR1)_carbazole_rep2

description: Exponential phase


title: 3wkA

source_name: mammary gland, 3wk

value: 3 weeks


title: P-CO-18-2-162

description: Pre-frontal cortex of male c57Bl/6 mice


title: KT2440(pCAR1)_carbazole_rep1

description: Exponential phase


title: 3wkB


title: 3.31963vsCC232/2_slide39

source_name: lymphoblastoid cell line, trisomic, n°2

source_name: lymphoblastoid cell line,euploid, n°

treatment_protocol: Cell line has been obtained after immortalization by Epstein-Barr virus (EBV) of B lymphocytes collected from blood samples of a control individual.


title: 3wkC


title: KT2440(pCAR1)_succinate_rep1

description: Exponential phase

growth_protocol: 100 ml of Nitrogen-plus Mineral Medium-4 supplemented with 1.0 mg ml-1 sodium succinate was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05.  Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: A total of 1 × 10^9 cells were mixed with RNA Protect Bacteria reagent (Qiagen, Valencia, CA) as recommended by the manufacturer.  Total RNA was extracted using the RNeasy Midi kit (Qiagen).  The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 1 h.  After the inactivation of the DNase by the addition of the stop reagent, and subsequent incubation at 65˚C for 15 min, RNA samples were again purified with the RNeasy Mini column according to the manufacturer’s clean-up protocol (Qiagen).


title: YCOvs3.32006_slide38

source_name: lymphoblastoid cell line, euploid, n°11

source_name: lymphoblastoid cell line, trisomic, n°1


title: 3.31964vsEE5/5_slide36

source_name: lymphoblastoid cell line, trisomic, n°8

value: Female

source_name: lymphoblastoid cell line,euploid, n°17


title: 4wkA


title: 3.31965vsRBR_slide37

source_name: lymphoblastoid cell line, trisomic, n°7

source_name: lymphoblastoid cell line,euploid, n°21


title: 4wkC


title: KT2440(pCAR1deltaORF70)_succinate_rep2

description: Exponential phase


title: KT2440_succinate_rep2

description: Exponential phase


title: LONFvsVAL_slide35

source_name: lymphoblastoid cell line, trisomic, n°10


title: VALvsRBR_slide33


title: 3.32061vsYCO_slide34

source_name: lymphoblastoid cell line, trisomic, n°6

source_name: lymphoblastoid cell line,euploid, n°11


title: AA676/1vs3.32061_slide30

source_name: lymphoblastoid cell line,euploid, n°13


title: 3.31859vsEE5/5_slide32


title: VALvsMR22/7_slide31

source_name: lymphoblastoid cell line,euploid, n°14


title: YCOvs3.32064_slide28

source_name: lymphoblastoid cell line, trisomic, n°9


title: MR22/7vs3.32064_slide29


title: MR22/7vs3.31964_slide22


title: EE5/5vs3.31965_slide21

source_name: lymphoblastoid cell line,trisomic, n°7


title: AA676/1vsVAL_slide16


title: AA676/1vs3.31963_slide20

source_name: lymphoblastoid cell line, trisomic, n° 2


title: 3.31859vsMR22/7_slide25

source_name: lymphoblastoid cell line, trisomic, n°5


title: BB78/2vs3.31963_slide24

source_name: lymphoblastoid cell line,euploid, n°20


title: RBRvs3.32064_slide19

source_name: ymphoblastoid cell line,euploid, n°21


title: PME_LONF_slide11

source_name: lymphoblastoid cell line, trisomic, n°4

source_name: lymphoblastoid cell line,euploid, n°12


title: 3.32061vsCCH_slide26

source_name: lymphoblastoid cell line,euploid, n°18


title: 3.31964vsAA676/1_slide27

source_name: lymphoblastoid cell line, trisomic, n°8


title: CCH_3.31858_slide10

source_name: lymphoblastoid cell line, trisomic, n°3


title: 3.31858vsAA676/1_slide15


title: VALvsYCO_slide14


title: 3.32064vsAA676/1_slide17

source_name: lymphoblastoid cell line,trisomic, n°9


title: RBRvs3.32061_slide18

source_name: lymphoblastoid cell line,euploid, n°21


title: 3.31963_YCO_slide6


title: 3.32064_BB78/2_slide8


title: CCHvs3.31964_slide4

source_name: lymphoblastoid cell line, trisomic, n° 8


title: PCH_3.32064_slide9

source_name: lymphoblastoid cell line,euploid, n°19


title: 3.32064_CCH_slide5

source_name: lymphoblastoid cell line, trisomic, n° 9


title: EE5/5vsVAL_slide3

source_name: lymphoblastoid cell line,euploid, n°17

source_name: lymphoblastoid cell line, trisomic, n°10


title: 3.32064vsSME_slide2

source_name: lymphoblastoid cell line,euploid, n°16


title: Expression of CfMNPV select ORFs, mock-infected, Expt. 2

type: mixed

city: Guelph

first: Dan-Hui

last: Yang

state: Ontario

address: 488 Gordon Street

department: Dept. of Molecular and Cellular Biology

country: Canada

institute: University of Guelph

description: Oligonucleotide-based two-channel DNA microarray was used for characterization of temporal gene expression profiles of select CfMNPV genes representing all four temporal classes. We adapted the DNA normalization protocol using CfMNPV vgDNA as a reference with microarray chips containing oligonucleotide probes for 23 select CfMNPV ORFs and their complements.

data_processing: GenePix Pro 3.0, Excel

molecule: genomic DNA

organism: Choristoneura fumiferana multiple nucleopolyhedrovirus

source_name: Cy5-labeled viral genomic DNA

tag: Fluorescence signals measured at 635 nm of Cy5-labeled viral genomic DNA co-hybridized with Cy3-cDNA to the chip.

organism: Choristoneura fumiferana

source_name: Cy3-labeled cDNA

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from mock-infected insect Cf203 cells at 48 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: 3.31964vsLONF_slide13


title: 3.32006_PCH_slide7

source_name: lymphoblastoid cell line, trisomic, n°1


title: Expression of CfMNPV select ORFs, 48hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 48 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: Expression of CfMNPV select ORFs, 6 hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 6 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: Expression of CfMNPV select ORFs, 48hpi, Expt. 1


title: Expression of CfMNPV select ORFs, 24hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 24 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: Expression of CfMNPV select ORFs, 12 hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 12 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: Expression of CfMNPV select ORFs, 3 hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 3 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: CC232/2vs3.31964_slide1

source_name: lymphoblastoid cell line,euploid, n°15

treatment_protocol: Cell line has been obtained after immortalization by Epstein-Barr virus (EBV) of B lymphocytes collected from blood samples of a Down syndrome patient.


title: Expression of CfMNPV select ORFs, 24hpi, Expt. 1


title: Expression of CfMNPV select ORFs, 6 hpi, Expt. 1


title: Expression of CfMNPV select ORFs, 0 hpi, Expt. 2

tag: Fluorescence signals measured at 532 nm of Cy3-labeled cDNA from total RNA isolated from CfMNPV-infected insect Cf203 cells at 0 hpi, co-hybridized with Cy5-vgDNA to the chip.


title: Expression of CfMNPV select ORFs, 3 hpi, Expt. 1


title: Expression of CfMNPV select ORFs, mock-infected, Expt. 1


title: Expression of CfMNPV select ORFs, 12 hpi, Expt. 1


title: Wilcox lake cutthroat trout-5 liver RNA

description: A custom-made cDNA microarray consisting of 147 rainbow trout genes with known function was employed to screen for transcriptional responses in the liver of these fish. The trout array cross-hybridized with 100% efficiency with the cutthroat trout samples and, therefore, pooled liver RNA from hatchery reared trout was used as the reference sample for each slide. Briefly, each microarray slide was hybridized with RNA from liver samples from a single sample and the reference RNA pool (obtained from rainbow trout) for a total of 8 slides (5 Wilcox Lake and 3 Skymo Lake).

hyb_protocol: Before hybridization the Cy3 and Cy5 labeled samples were combined and dried in a speed vac. To the dried sample 26 µL of hybridization buffer and 2 µL each of calf thymus DNA (10 mg/ml) and yeast tRNA (10 mg/ml) were added. The samples were denatured for 2 min at 95°C, snap cooled on ice for 1 min, and centrifuged for 1 min at maximum speed. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization was done overnight in a water bath at 37°C.

scan_protocol: Image analysis was carried out using Versarray chipreader software Version 3.1 (BioRad, Hercules, CA). For each microarray slide, two images were produced by illuminating the array at 635 nm (excitation of Cy5) and 532 nm (Cy3). For both illuminations, photomultiplier tube (gain and light amplification) settings were at 900 and laser power was set at 90%. All images were captured in TIFF format. Spot finding and quantification was carried out with ImaGene 3.0 microarray image analysis software (BioDiscovery; Los Angeles, CA). Briefly, a grid was created taking into account the number of spots, the printing pattern, and the size of the spots. Spot finding was performed using a semiautomatic method in which each spot is checked for proper alignment within the grid manually. Finally, spot quantification was performed to obtain the expression level of each gene on the array.

data_processing: For each data set, the background was subtracted (data transformation), and poor or negative control spots were flagged as unreliable and were excluded from the analysis. The data set was LOWESS (Locally Weighted Regression and Smoothing Scatterplots) tested and the ratio of Cy3 to Cy5 was calculated. The data for each fish (fold change relative to the reference pool) was then calculated as a ratio of normalized gene intensity for the sample to that of the reference RNA on each slide. The average fold-change data set obtained for Wilcox Lake (5 independent samples) and Skymo Lake (3 independent samples) was compared for statistical differences using an unpaired Student’s t-test. A P-value of <0.05 was considered statistically significant.

organism: Oncorhynchus clarkii

source_name: Wilcox lake cutthroat trout liver RNA

label_protocol: Fifty micrograms of intact total RNA (either lake sample or reference RNA) were indirectly labeled following the Institute for Genomic Research TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) with cyanine 3 (Cy3) (Amersham Biosciences, Piscataway, NJ).

extract_protocol: Total RNA was extracted from livers using the RNAeasy extraction kit (Qiagen, ON). The quality of the total RNA obtained was checked by gel electrophoresis on a 1% agarose gel containing ethidium bromide, and the concentration was determined spectrophotometrically at 260/280 nm using Cary 50 UV-Vis spectrophotometer (Varian Inc, ON).

treatment_protocol: Livers were obtained from Wilcox lake, Washington State, USA by angling

tag: Liver total RNA was obtained from Cutthroat trout from Wilcox lake, Washington State, USA.

source_name: Reference RNA

label_protocol: Fifty micrograms of intact total RNA (either lake sample or reference RNA) were indirectly labeled following the Institute for Genomic Research TIGR protocol (http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml) with cyanine 5 (Cy5) (Amersham Biosciences, Piscataway, NJ).

treatment_protocol: Rainbow trout were untreated before sampling livers to isolate total RNA and used as Reference RNA in this experiment.

tag: Liver total RNA was obtained from untreated juvenile rainbow trout.


title: Wilcox lake cutthroat trout-4 liver RNA

source_name: Wilcox lake Cutthroat trout liver RNA


title: Wilcox lake cutthroat trout-2 liver RNA


title: Wilcox lake cutthroat trout-1 liver RNA


title: Expression of CfMNPV select ORFs, 0 hpi, Expt. 1


title: Skymo lake cutthroat trout-2 liver RNA

data_processing: For each data set, the background was subtracted (data transformation), and poor or negative control spots were flagged as unreliable and were excluded from the analysis. The data set was LOWESS (Locally Weighted Regression and Smoothing Scatterplots) tested (26) and the ratio of Cy3 to Cy5 was calculated. The data for each fish (fold change relative to the reference pool) was then calculated as a ratio of normalized gene intensity for the sample to that of the reference RNA on each slide. The average fold-change data set obtained for Wilcox Lake (5 independent samples) and Skymo Lake (3 independent samples) was compared for statistical differences using an unpaired Student’s t-test. A P-value of <0.05 was considered statistically significant.

source_name: Skymo lake cutthroat trout liver RNA

treatment_protocol: Livers were obtained from Skymo lake, Washington State, USA by angling

tag: Liver total RNA was obtained from Cutthroat trout from Skymo lake, Washington State, USA.


title: Skymo lake cutthroat trout liver RNA


title: Skymo lake cutthroat-3 trout liver RNA


title: Ecoli_argR_8uM_DeaNO_Sample2_TechRep1

status: Public on Apr 26 2007

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: Cells were grown in MOPS media/0.5% glucose and aerobic conditions.

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual.  Slides were blocked and washed as specified in the Corning UltraGAPS manual.

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files.  The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

organism: Escherichia coli

source_name: Ecoli with argR deleted grown in MOPS prior to DeaNO treatment

label_protocol: Samples were directly labeled by direct incorporation of labeled dCTP.

growth_protocol: Cells grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.

extract_protocol: RNA extracted by hot phenol choloroform folled by Qiagen RNA Midi column.

tag: Strain

source_name: Ecoli with argR deleted grown in MOPS 5 minutes after DeaNO (8 microM ) treatment

growth_protocol: Cells aerobically grown to mid-log phase in MOPS/0.5% glucose at 37C and ~250 RPM.

treatment_protocol: Treated with DeaNO [8 micromolar] for 5 minutes prior to harvesting.


title: Wilcox lake cutthroat trout-3 liver RNA


title: Ecoli_argR_8uM_DeaNO_Sample2_TechRep2


title: Ecoli_argR_8uM_DeaNO_Sample1_TechRep2


title: Ecoli_argR_8uM_DeaNO_Sample1_TechRep1


title: MCF7 + DTX 100 nM 24h B

status: Public on Feb 14 2007

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

description:
Spotted cDNA microarrays.
The CNIO Oncochip contains about 11,500 cDNA clones representing 9,300 genes (UniGene clusters) plus several hundred not included in UniGene.

hyb_protocol: Hybridization was performed in 4× standard saline citrate, 1× bovine serum albumin, 2 g/ml DNAs and 0.1% sodium dodecyl sulphate at 42°C for 15 hr.

scan_protocol: Slides were washed, dried and then scanned in a Scanarray 5000 XL scanner (GSI Lumonics Kanata, Ontario, Canada) at wavelengths of 635 and 532 nm for Cy5 and Cy3 dyes, respectively.

data_processing:
10-um resolution images were quantified using the GenePix Pro 6.0 program (Axon Instruments, Union City, CA).

DNMAD Normalization

Layout information:
Main grid (12 rows X 4 columns)
Sub-grid  (24 rows X 24 columns)

Layout normalization options:
Use negative flags
Return negative flagged points as NA
Use background correction

source_name: MCF7 + DTX 100 nM 24h

label_protocol: Cy5-dUTP fluorochrome (Amersham, Uppsala, Sweden)

extract_protocol: Total RNA and T7-(deoxythymidine)24 oligo primer were used to amplify the double-strand cDNA by the Superscript Choice System (Life Technologies, Gaithersburg, MD). In vitro transcription was carried out with MegascriptTM T7 (Ambion, Austin, TX).

tag: MCF7 cells after 24 hours of exposure to 100 nM docetaxel

source_name: Reference

label_protocol: Cy3-dUTP fluorochrome (Amersham, Uppsala, Sweden)

tag: Universal Human Reference RNA


title: MCF7 + DTX 4 nM 24h B

source_name: MCF7 + DTX 4 nM 24h

tag: MCF7 cells after 24 hours of exposure to 4 nM docetaxel


title: MCF7 + DTX 100 nM 48h B

source_name: MCF7 + DTX 100 nM 48h

tag: MCF7 cells after 48 hours of exposure to 100 nM docetaxel


title: MCF7 Control B

status: Public on Feb 09 2007

source_name: MCF7 Control 0h

tag: MCF7 human breast carcinoma cell line.

tag: No treatment.


title: MCF7 + DTX 100 nM 8h B

source_name: MCF7 + DTX 100nM 8h

tag: MCF7 cells after 8 hours of exposure to 100 nM docetaxel


title: MCF7 Control G


title: MCF7 + DTX 4 nM 8h A

source_name: MCF7 + DTX 4 nM 8h

tag: MCF7 cells after 8hours of exposure to 4 nM docetaxel


title: MCF7 + DTX 100 nM 8h A

description:
Spotted cDNA microarrays.
CNIO Oncochip contains about 11,500 cDNA clones representing 9,300 genes (UniGene clusters) plus several hundred not included in UniGene.


title: MCF7 Control F


title: MCF7 + DTX 4 nM 48h A

source_name: MCF7 + DTX 4 nM 48h

tag: MCF7 cells after 48 hours of exposure to 4 nM docetaxel


title: MCF7 Control C


title: MCF7 + DTX 100 nM 48h A

description: 10-m resolution images were quantified using the GenePix Pro 4.0 program (Axon Instruments, Union City, CA).


title: MCF7 + DTX 4 nM 8h B

tag: MCF7 cells after 8 hours of exposure to 4 nM docetaxel


title: MCF7 + DTX 4 nM 24h A

tag: MCF7 cells after 24 hours exposure to 4 nM docetaxel


title: MCF7 Control A


title: MCF7 Control D


title: MCF7 Control E


title: MCF7 + DTX 4 nM 48h B


title: YCOvsPME_slide23

source_name: lymphoblastoid cell line,euploid, n°11

tag: status

tag: Gender

source_name: lymphoblastoid cell line, trisomic, n°4


title: MCF7 + DTX 100 nM 24h A

tag: MCF7 cells after 24h exposure to 100 nM docetaxel


title: SME_3.31859_slide12

source_name: lymphoblastoid cell line,euploid, n°16

source_name: lymphoblastoid cell line, trisomic, n°5


title: C. elegans, Gene By Temperature, T=24C,Array78

status: Public on Nov 29 2006

city: Haren(GN)

first: Yang

last: Li

address: Kerklaan 30

country: Netherlands

institute: Groningen Bioinformatics Center

description: C. elegans RIL

scan_protocol: ScanArray Express HT (PerkinElmer Inc) Software: Easy Quant with Adaptive circle

data_processing: after background correction, normalization within  and between array using LIMMA (R Package), log base 2 expression ratios

organism: Caenorhabditis elegans

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN5

growth_protocol: . Culturing. All nematodes were reared on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Populations were started with only non-mated hermaphrodites and screened regularly to remove any occurring males.Synchronization. Experiments were carried out with nematodes belonging to the L3 life stage. In order to determine the entry into this stage at 16° C and 24° C, the size of the gonads and vulva were monitored. At 72 hours of age, nematodes kept at 16° C were at the L3 stage, whereas 40 hours of age determined this life stage at 24° C. Populations of each of the RILs were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each RIL were kept in each of the two temperatures until L3 was reached. The nematodes were then collected and frozen in liquid nitrogen.

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN25


title: C. elegans, Gene By Temperature, T=24C,Array75

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN19

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN55

growth_protocol: Culturing. All nematodes were reared on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Populations were started with only non-mated hermaphrodites and screened regularly to remove any occurring males.Synchronization. Experiments were carried out with nematodes belonging to the L3 life stage. In order to determine the entry into this stage at 16° C and 24° C, the size of the gonads and vulva were monitored. At 72 hours of age, nematodes kept at 16° C were at the L3 stage, whereas 40 hours of age determined this life stage at 24° C. Populations of each of the RILs were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each RIL were kept in each of the two temperatures until L3 was reached. The nematodes were then collected and frozen in liquid nitrogen.


title: C. elegans, Gene By Temperature, T=24C,Array79

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN3

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN22


title: C. elegans, Gene By Temperature, T=24C,Array76

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN61

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN39


title: C. elegans, Gene By Temperature, T=24C,Array80

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN60

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN77


title: C. elegans, Gene By Temperature, T=24C,Array77

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN14

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN65


title: C. elegans, Gene By Temperature, T=24C,Array72

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN71

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN79


title: C. elegans, Gene By Temperature, T=24C,Array71

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN50

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN28


title: C. elegans, Gene By Temperature, T=24C,Array70

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN4

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN73


title: C. elegans, Gene By Temperature, T=24C,Array64

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN15

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN35


title: C. elegans, Gene By Temperature, T=24C,Array58

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN80

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN7


title: C. elegans, Gene By Temperature, T=24C,Array73

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN20

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN53


title: C. elegans, Gene By Temperature, T=24C,Array69

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN31

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN44


title: C. elegans, Gene By Temperature, T=24C,Array67

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN51

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN74


title: C. elegans, Gene By Temperature, T=24C,Array61

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN17

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN33


title: C. elegans, Gene By Temperature, T=24C,Array63

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN67

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN26


title: C. elegans, Gene By Temperature, T=24C,Array65

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN65

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN30


title: C. elegans, Gene By Temperature, T=24C,Array57

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN24

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN49


title: C. elegans, Gene By Temperature, T=24C,Array68

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN76

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN59


title: C. elegans, Gene By Temperature, T=24C,Array60

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN54

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN6


title: C. elegans, Gene By Temperature, T=24C,Array54

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN43

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN40


title: C. elegans, Gene By Temperature, T=24C,Array53

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN38

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN47


title: C. elegans, Gene By Temperature, T=24C,Array55

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN2

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN52


title: C. elegans, Gene By Temperature, T=24C,Array62

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN64

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN63


title: C. elegans, Gene By Temperature, T=24C,Array50

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN9

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN62


title: C. elegans, Gene By Temperature, T=24C,Array51

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN1

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN80


title: C. elegans, Gene By Temperature, T=24C,Array74

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN57

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN32


title: C. elegans, Gene By Temperature, T=24C,Array49

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN46

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN69


title: C. elegans, Gene By Temperature, T=24C,Array48

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN8

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN41


title: C. elegans, Gene By Temperature, T=24C,Array52

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN36

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN72


title: C. elegans, Gene By Temperature, T=24C,Array47

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN27

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN56


title: C. elegans, Gene By Temperature, T=24C,Array59

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN45

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN12


title: C. elegans, Gene By Temperature, T=24C,Array46

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN58

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN38


title: C. elegans, Gene By Temperature, T=24C,Array56

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN16

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN34


title: C. elegans, Gene By Temperature, T=24C,Array44

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN75

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN66


title: C. elegans, Gene By Temperature, T=24C,Array45

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN42

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN11


title: C. elegans, Gene By Temperature, T=16C,Array38

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN50

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN28


title: C. elegans, Gene By Temperature, T=16C,Array30

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN5

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN25


title: C. elegans, Gene By Temperature, T=16C,Array33

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN4

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN73


title: C. elegans, Gene By Temperature, T=16C,Array31

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN17

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN33


title: C. elegans, Gene By Temperature, T=16C,Array32

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN27

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN56


title: C. elegans, Gene By Temperature, T=16C,Array40

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN46

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN69


title: C. elegans, Gene By Temperature, T=16C,Array34

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN29

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN78


title: C. elegans, Gene By Temperature, T=16C,Array37

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN61

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN39


title: C. elegans, Gene By Temperature, T=24C,Array42

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN70

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN48


title: C. elegans, Gene By Temperature, T=16C,Array39

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN9

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN62


title: C. elegans, Gene By Temperature, T=24C,Array41

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN68

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN37


title: C. elegans, Gene By Temperature, T=16C,Array36

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN19

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN55


title: C. elegans, Gene By Temperature, T=16C,Array28

description: C. elegans RIL


title: C. elegans, Gene By Temperature, T=24C,Array43

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN13

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN21


title: C. elegans, Gene By Temperature, T=16C,Array25

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN51

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN74


title: C. elegans, Gene By Temperature, T=16C,Array21

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN38

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN47


title: C. elegans, Gene By Temperature, T=16C,Array26

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN71

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN79


title: C. elegans, Gene By Temperature, T=16C,Array22

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN36

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN72


title: C. elegans, Gene By Temperature, T=16C,Array19

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN64

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN63


title: C. elegans, Gene By Temperature, T=16C,Array23

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN8

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN41


title: C. elegans, Gene By Temperature, T=16C,Array18

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN43

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN40


title: C. elegans, Gene By Temperature, T=16C,Array29

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN3

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN22


title: C. elegans, Gene By Temperature, T=16C,Array24

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN76

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN59


title: C. elegans, Gene By Temperature, T=16C,Array20

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN54

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN6


title: C. elegans, Gene By Temperature, T=16C,Array27

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN45

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN12


title: C. elegans, Gene By Temperature, T=16C,Array17

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN31

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN44


title: C. elegans, Gene By Temperature, T=16C,Array11

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN75

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN66


title: C. elegans, Gene By Temperature, T=16C,Array16

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN67

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN26


title: C. elegans, Gene By Temperature, T=16C,Array9

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN15

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN35


title: C. elegans, Gene By Temperature, T=16C,Array15

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN16

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN34


title: C. elegans, Gene By Temperature, T=16C,Array4

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN1

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN80


title: C. elegans, Gene By Temperature, T=16C,Array14

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN14

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN18


title: C. elegans, Gene By Temperature, T=16C,Array10

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN58

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN38


title: C. elegans, Gene By Temperature, T=16C,Array7

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN60

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN77


title: C. elegans, Gene By Temperature, T=16C,Array13

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN24

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN49


title: C. elegans, Gene By Temperature, T=16C,Array5

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN57

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN32


title: C. elegans, Gene By Temperature, T=16C,Array6

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN42

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN11


title: C. elegans, Gene By Temperature, T=24C,Array66

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN29

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN78


title: PRB3701 (MG-U74A)

status: Public on Sep 27 2006

city: South San Francisco

first: Zemin

last: Zhang

state: CA

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech Inc.

description: C14: 14 days after castration

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: C14: Prostate; 14 days after castration

label_protocol: 2 to 5 ug of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: Qiagen RNeasy Mini Kit

tag: Prostate tissue from castrated mouse (C57/B6)


title: PRB3710 (MG-U74A)

description: C14+T3: 3 days after testosterone treatment of C14

source_name: C14+T3: Prostate; 3 days after testosterone treatment of C14


title: C. elegans, Gene By Temperature, T=16C,Array1

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN68

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN37


title: PRB3702 (MG-U74A)

description: C14: 14 days after castration


title: PRB3711 (MG-U74A)


title: PRB3712 (MG-U74A)


title: PRB3708 (MG-U74A)


title: C. elegans, Gene By Temperature, T=16C,Array2

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN13

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN21


title: PRB3709 (MG-U74A)


title: PRB3698 (MG-U74A)

description: C14: 14 days after castration


title: C. elegans, Gene By Temperature, T=16C,Array8

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN80

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN7


title: C. elegans, Gene By Temperature, T=16C,Array3

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN2

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN52


title: C. elegans, Gene By Temperature, T=16C,Array35

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN20

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN53


title: C. elegans, Gene By Temperature, T=16C,Array12

description: C. elegans RIL

source_name: C.elegans, Recombination Inbred Lines, Cy3, WN65

source_name: C.elegans, Recombination Inbred Lines, Cy5, WN30


title: PRB3699 (MG-U74A)

description: C14: 14 days after castration


title: PRB3669 (MG-U74A)

description: C3: 3 days after castration

source_name: C3: Prostate; 3 days after castration


title: PRB3700 (MG-U74A)

description: C14: 14 days after castration


title: PRB3664 (MG-U74A)

description: N3: Prostate from sham-treated mouse (C57/B6)


title: PRB3667 (MG-U74A)

description: C3: 3 days after castration


title: PRB3668 (MG-U74A)

description: C3: 3 days after castration


title: PRB3666 (MG-U74A)

description: C3: 3 days after castration


title: PRB3665 (MG-U74A)

description: C3: 3 days after castration


title: PRB3663 (MG-U74A)

source_name: N3: Prostate from sham-treated mouse (C57/B6)


title: Fbx15-null ES (rep1)

status: Public on Aug 21 2006

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Fbx15 is specifically espressed in ES cells, but Fbx15-null ES cells do not show obvious phenotypes.

hyb_protocol: Manufature's prtocol

scan_protocol: Manufature's prtocol

data_processing: gProcessedSiganl value calculated by Agilent Microarray Scanner Feature Extraction Software

source_name: FBX15-null ES cells grown on STO cells

label_protocol: Manufature's protocol

extract_protocol: Trizao

tag: 129/SVJae, undifferentiated, grown on STO feeder cells


title: PRB3662 (MG-U74A)


title: Fbx15-null MEF (rep1)

description: These MEF cells were used to induce pluripotent-like cells

source_name: MEF derived from Fbx15-null E13.5 embryos

tag: G418 sensitive


title: wt 70hrs DD B

status: Public on Aug 08 2006

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

country: Germany

institute: University of Lübeck

description: sample is part of a series (of 12 time points) to identify circadian clock regulated genes in the murine adrenal

data_processing: expression data were normalized and modelled (PM/MM model) using Dchip 1.3

source_name: adult mouse whole adrenal 70hrs after lights off

extract_protocol: RNeasy Micro Kit (QIAGEN)

treatment_protocol: 2 weeks entrainment to LD 12:12

tag: Strain

value: male

tag: Age

value: 3 months

tag: Tissue

value: whole adrenal


title: FBX15-iPS MEF4-7 (rep1)

description: Retroviral vectors for the four factors were transfected into Fbx15 bgeo-KI MEF. Cells were cultured with ES cell condition and selected with G418 for 16 days.

source_name: iPS cells from Fbx15-KI MEF

tag: G418 resistant

tag: ES cell-like phenotypes


title: PRB3660 (MG-U74A)


title: wt 78hrs DD B

source_name: adult mouse whole adrenal 78hrs after lights off


title: PRB3661 (MG-U74A)


title: wt 46hrs DD B

source_name: adult mouse whole adrenal 46hrs after lights off


title: wt 82hrs DD B

source_name: adult mouse whole adrenal 82hrs after lights off


title: wt 82hrs DD

value: C57B/6J Gender:male Age:3 months Tissue:whole adrenal


title: wt 74hrs DD B

source_name: adult mouse whole adrenal 74hrs after lights off

extract_protocol: RNeasy Micor Kit (QIAGEN)


title: wt 54hrs DD

source_name: adult mouse whole adrenal 54hrs after lights off


title: wt 66hrs DD B

source_name: adult mouse whole adrenal 66hrs after lights off


title: wt 62hrs DD

source_name: adult mouse whole adrenal 62hrs after lights off


title: wt 66hrs DD


title: wt 54hrs DD B

extract_protocol: RNeasy Micro Kit (QUAGEN)


title: wt 50hrs DD B

source_name: adult mouse whole adrenal 50hrs after lights off


title: wt 58hrs DD

source_name: adult mouse whole adrenal 58hrs after lights off


title: wt 38hrs DD B

source_name: adult mouse whole adrenal 38hrs after lights off

treatment_protocol:
2 weeks entrainment to LD 12:12
killed in DD at 38hrs after "lights off"


title: wt 70hrs DD


title: wt 42hrs DD B

source_name: adult mouse whole adrenal 42hrs after lights off


title: wt 62hrs DD B


title: wt 50hrs DD


title: wt 78hrs DD


title: wt 74hrs DD


title: wt 46hrs DD


title: wt 42hrs DD


title: wt 58hrs DD B


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8375

status: Public on May 31 2006

city: Seattle

first: Marc

last: Facciotti

state: WA

address: 1441 North 34th Street

institute: Institute for Systems Biology

description: Halobacterium NRC-1 perturbed with 0.015 mM Zinc Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-56

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding.  see http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details

label: Alexa 647

organism: Halobacterium salinarum NRC-1

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.015mM Zinc Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.015mM Zinc Sulfate for 5 hours and harvested by centrifugation.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions havested 5 hours post 0.015mM Zinc Sulfate stress.

label: Alexa 546

source_name: Standard mid-log Halobacterium NRC-1 reference sample.

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium NRC-1 reference sample.

tag: Halobacterium NRC-1 standard reference grown in standard growth media to mid-log phase (OD600 0.5-0.6).


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8374

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-55


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8373

description: Halobacterium NRC-1 perturbed with 0.010 mM Zinc Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-54

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.010mM Zinc Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.010mM Zinc Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions havested 5 hours post 0.010mM Zinc Sulfate stress.


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8372

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-53


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7442

description: Halobacterium NRC-1 perturbed with 0.3 mM Cobalt Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-48

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.3mM Cobalt Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.3mM Cobalt Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditionsperturbed with 0.3 mM Cobalt Sulfate and harvested 5 hours post metal stress

label: Alexa 532


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7359

description: Halobacterium NRC-1 perturbed with 0.5 mM Cobalt Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-49

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.5mM Cobalt Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.5mM Cobalt Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditionsperturbed with 0.5 mM Cobalt Sulfate and harvested 5 hours post metal stress


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8369

description: Halobacterium NRC-1 perturbed with 0.005 mM Zinc Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-52

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.005mM Zinc Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.005mM Zinc Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions havested 5 hours post 0.005mM Zinc Sulfate stress.


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7358

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-47


title: Halobacterium Zinc Sulfate stress exposure experiment, Array 8368

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-51


title: wt 38hrs DD


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7443

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-50


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7440

description: No Cobalt control sample grown in standard conditions  versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-44

source_name: Mid-log phase Halobacterium NRC1, no Cobalt control harvested 5 hours post induction of metal stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 5 hours in the absence of Cobalt Sulfate then harvested by centrifugation.

tag: No Cobalt control sample grown in standard conditions and sampled 5 hours post induction of stress.


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7441

description: Halobacterium NRC-1 perturbed with 0.2 mM Cobalt Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-46

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.2mM Cobalt Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.2mM Cobalt Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditionsperturbed with 0.2 mM Cobalt Sulfate and harvested 5 hours post metal stress


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7439

description: Halobacterium NRC-1 perturbed with 1.5 mM Nickel Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-42

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 1.5mM Nickel Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 1.5mM Nickel Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions perturbed with 1.5 mM Nickel Sulfate and harvested 5 hours post metal stress.


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7355

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-41


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7438

description: Halobacterium NRC-1 perturbed with 0.75 mM Nickel Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-40

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.75mM Nickel Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.75mM Nickel Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions perturbed with 0.75 mM Nickel Sulfate and harvested 5 hours post metal stress.


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7356

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-43


title: Halobacterium Cobalt Sulfate stress exposure experiment, Array 7357

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-45


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7352

description: No Nickel control sample grown in standard conditions  versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

source_name: Mid-log phase Halobacterium NRC1, no Nickel control harvested 5 hours post induction of metal stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media,(OD600 0.5-0.6), incubated 5 hours in the absence of Nickel Sulfate then harvested by centrifugation.

tag: No Nickel control sample grown in standard conditions and sampled 5 hours post induction of stress.


title: RA_z

status: Public on Nov 04 2004

city: Berlin

first: Ute

last: Ungethuem

department: Core Center for Functional Genome Research

institute: Charité University Hospital

description: individual sample, rheumatoid arthritis z, synovial tissue

hyb_protocol: Fifteen micrograms of each cRNA sample was hybridized for 16 hours at 45°C to human expression Affymetrix HG U95Av2 GeneChip arrays. Following the hybridization arrays were washed and stained with streptavidin-phycoerythrin using a fluidics station in accordance with the Affymetrix protocol.

scan_protocol: Affymetrix GeneChip System confocal scanner 2500

data_processing: Affymetrix Microarray Suite MAS 5.0

label: biotin labeled

source_name: rheumatoid arthritis

label_protocol: The amplification and labeling of the RNA samples were carried out according to the manufacturer's instructions (Affymetrix, Santa Clara, CA). Briefly, total RNA was quantified by UV-spectroscopy and its quality evaluated by analysis on a LabChip (BioAnalyzer, AGILENT Technologies, Santa Clara, CA). In the presence of an oligo(dT)24 primer containing a T7 RNA polymerase promoter (Operon Biotechnology, Huntsville, AL, USA) five micrograms of total RNA were used for double-stranded cDNA synthesis (SuperScript transcriptase, Life Technologies, Inc., Carlsbad, CA). Labeled complementary RNA (cRNA) was prepared from double-stranded cDNA by in vitro transcription using the bioarray high yield RNA transcription kit (Enzo Diagnostics, Farmindale, N.Y., USA). After cleanup (Qiagen, Hilden, Germany), the biotin-labeled cRNA was fragmented by alkaline treatment (40 mM Tris-acetate (pH 8.2), 100 mM potassium acetate, and 50 mM magnesium acetate) at 94°C for 35 minutes.

growth_protocol: synovectomy

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen).

treatment_protocol: disease modifying antirheumatic drugs (DMARD), non-steroidal anti-inflammatory drugs (NSAID), steroids

tag: age

tag: gender


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7354

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-39


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7437

description: Halobacterium NRC-1 perturbed with 0.5 mM Nickel Sulfate versus standard reference.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-38

source_name: Mid-log phase Halobacterium NRC1,  havested 5 hours post 0.5mM Nickel Sulfate stress.

growth_protocol: Halobacterium NRC-1 cells grown to mid-log phase in complex media, (OD600 0.5-0.6), perturbed with 0.5mM Nickel Sulfate for 5 hours and harvested by centrifugation.

tag: Halobacterium NRC-1 grown to mid-log phase under standard conditions perturbed with 0.5 mM Nickel Sulfate and harvested 5 hours post metal stress.


title: RA_B

description: pool rheumatoid arthritis B, synovial tissue

treatment_protocol:
sample 1:
non-steroidal anti-inflammatory drugs (NSAID)
sample 2:
non-steroidal anti-inflammatory drugs (NSAID)
sample 3:
non-steroidal anti-inflammatory drugs (NSAID)

tag: sample 1:

tag: sample 2

tag: sample 3:


title: RA_y

description: individual sample, rheumatoid arthritis y, synovial tissue

treatment_protocol: disease modifying antirheumatic drugs (DMARD)


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7353

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-37


title: Halobacterium Nickel Sulfate stress exposure experiment, Array 7436

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-36


title: Control, Array 08395

first: Michael

middle: Hiroshi

last: Johnson

department: Computational Biology

description: Control vs. control

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35[optional]

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See the Microarray facility website at ISB for for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. see the Microarray pipeline data management website at ISB for more details

source_name: Halobacterium NRC-1, control

growth_protocol: Mid-log phase (OD600-0.5 - 0.6) Halobacterium NRC-1

tag: Halobacterium NRC-1 grown in standard growth media

source_name: Halobacterium NRC-1 Control culture


title: OA_B

description: pool osteoarthritis B, synovial tissue

source_name: osteoarthritis

treatment_protocol:
sample 1:
non-steroidal anti-inflammatory drugs (NSAID)
sample 2:
non-steroidal anti-inflammatory drugs (NSAID)


title: RA_A

description: pool rheumatoid arthritis A, synovial tissue


title: OA_y

description: individual sample, osteoarthritis y, synovial tissue

treatment_protocol: non-steroidal anti-inflammatory drugs (NSAID)


title: OA_A

description: pool osteoarthritis A, synovial tissue


title: OA_x

description: individual sample, osteoarthritis x, synovial tissue


title: ND_5

description: pool normal donor 5, synovial tissue

source_name: normal donor

treatment_protocol: no treatment

value: unknown


title: ND_3

description: pool normal donor 3, synovial tissue

tag: sample 3


title: ND_4

description: pool normal donor 4, synovial tissue


title: Germ free  Rectum 2

status: Public on Jun 24 2004

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

country: Switzerland

institute: Nestle Research Center

description:
Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later  and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum.
Keywords = gastrointestinal tract, microbiota, germ-free, microarray, gene ontology

source_name: Rectum


title: Germ free  Rectum 3


title: Germ free  Jejenum 2

source_name: Jejenum


title: Germ free  Rectum 1


title: ND_2

description: pool normal donor 2, synovial tissue

tag: sample 4


title: Germ free  Corpus 3

source_name: Corpus


title: ND_1

description: pool normal donor 1, synovial tissue

tag: sample 2:

tag: sample 4:


title: Germ free  Jejenum 1


title: Germ free  Jejenum 3


title: OA_z

description: individual sample, osteoarthritis z, synovial tissue


title: Germ free  Descending colon 3

source_name: Descending colon


title: Conventional  Rectum 3


title: Germ free  Descending colon 1


title: Germ free  Corpus 2


title: Conventional  Rectum 2