title: Normal  diet + 12h fasting, saline vs insulin 3

status: Public on Feb 26 2009

type: RNA

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

country: Sweden

institute: Karolinska institutet

description: Biological replicate 3 of 4.

hyb_protocol: Cy3- and Cy5 labelled samples were purifyed and mixed before addition of a hybridization buffer and added to respectively array for 18h of hybridization. After hybridization, the slides were washed multiple times, all according to the Pronto! Plus systems and the manufacturer´s instructions (Corning and Promega).

scan_protocol: Scanning was performed using a Genepix 4200A scanner (Axon). Images were quantified using Genepix 6.0 software (Axon).

data_processing: Background was subtracted using the in-house Easy Filter software. The data was normalized by the LOWESS method using the R language. The normalized data was finally statistically analyzed using SAM.

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver from male Sprague-Dawley rat

label_protocol: 5µg of total RNA was used for a first strand cDNA synthesis of each sample, labelled with either Cy3- or Cy5-dCTP. The microarray experiment was performed using the Pronto! Plus systems according to the manufacturer´s instructions (Corning and Promega).

extract_protocol: Total RNA was extracted from frozen livers using Trizol following manufacturer's instructions

treatment_protocol: Animal were treated with either saline or insulin after 4h or 12h of food deprivation

tag: Gender

value: male

tag: Fed standard rat chow

tag: 12h of food deprivation before treatment

tag: 40 minutes of saline treatment (i.p.)

tag: Age

value: 7 weeks

tag: Tissue

value: liver

tag: 40 minutes of insulin treatment (i.p.)


title: Normal  diet + 12h fasting, saline vs insulin 6

description: Biological replicate 2 of 4.

source_name: Liver from female Sprague-Dawley rat

value: female


title: Normal  diet + 12h fasting, saline vs insulin 4

description: Biological replicate 4 of 4.


title: Normal  diet + 4h fasting, saline vs insulin 5

description: Biological replicate 1 of 4.

tag: 4h of food deprivation before treatment


title: Normal  diet + 4h fasting, saline vs insulin 3

description: Biological replicate 3 of 4.


title: Normal  diet + 4h fasting, saline vs insulin 2

description: Biological replicate 2 of 4.


title: BRB + NMBA  treated, pool EP12 vs. reference pool

status: Public on Feb 23 2009

city: Columbus

first: Gary

middle: D

last: Stoner

state: OH

address: 2001 Polaris Pkwy

department: The Ohio State University

country: USA

institute: Department of Internal Medicine

description: Barcode: 251316210182

hyb_protocol: Agilent 60-mer Oligo Microarray Processing Protocol Version 4.1 using the Agilent In situ Hybridization Kit. In the hybridization reaction 0.75 ug of Cyanine 3 labeled cRNA and 0.75 ug of Cyanine 5 labeled cRNA were mixed together and allowed to co-hybridize on an Agilent Rat Whole Genome Oligo Microarray (44K) for 17 hours at 60°C. Slide was washed and dried according to Agilent's 60-mer Oligo microarray processing protocol for SSC wash.

scan_protocol: Slides were scanned with an Agilent dual laser scanner. PMT settings were set at 100% for both channels.

data_processing: Tiff images were analyzed using Agilent’s feature extraction software (version 7.5) to obtain fluorescent intensities for each spot on the array. Local background subtraction was performed. Linear&LOWESS normalization was performed on the intensity values.

label: Cyanine 3

source_name: Stratagene Rat reference RNA

label_protocol: Agilent Low Input Fluorescent Linear Amplification Kit, Protocol Version 2.0.

tag: Commercial reference RNA standard, Stratagene.

label: Cyanine 5

source_name: Rat Esophagus, BRB + NMBA  treated, EP12

extract_protocol: RNA extraction. Total cellular RNA was isolated from frozen tissue using TRIzol reagent (Life Technologies, Gaithersburg, MD), according to the manufacture’s instructions, and cleaned using RNeasy Mini kit (Qiagen, Valencia, CA). The integrity of the RNA samples was checked by resolving the total RNA on an agarose gel and visualizing the 18S and 28S ribosomal bands after staining the gel with ethidium bromide. Samples were aliquoted and frozen at -80C. Further quality control check of total RNA from each biological sample was made using an Agilent 2100 Bioanalyzer and the 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA), and analyzed for purity using a spectrophotometer; a 260/280 ratio in the range of 1.9-2.2 was considered acceptable. Samples having apparent degradation were excluded from the study.

treatment_protocol: Rats were randomized into four experimental groups of nine animals each.  Rats in Groups 1 and 3 were placed on control AIN-76A diet and those in Groups 2 and 4 were given AIN-76A+5% BRB diet.  After two weeks Group 1 (vehicle-control) and Group 2 (BRB-control) rats received three s.c. injections of 20% DMSO/water, while Group 3 (NMBA-control) and Group 4 (BRB+NMBA) rats received three s.c. injections of NMBA (0.5 mg/kg body weight).  All rats were sacrificed 24h after the last NMBA treatment.  Their excised esophagi were opened longitudinally and sectioned into two parts.  One part was stripped of the submucosal and muscularis layers and immersed in 1 ml of TRIZOL® Reagent (Life Technologies, Gaithersburg, MD) for RNA extraction.

tag: 4-5 week old male Fischer-344 rats (F344)


title: BRB + NMBA  treated, pool EP10 vs. reference pool

description: Barcode: 251316210207

source_name: Rat Esophagus, BRB + NMBA  treated, EP10


title: BRB + NMBA  treated, pool EP11 vs. reference pool

description: Barcode: 251316210181

tag: Commercial reference RNA standard, Stratagene

source_name: Rat Esophagus, BRB + NMBA  treated, EP11


title: BRB treated, pool EP7 vs. reference pool

description: Barcode: 251316210191

source_name: Rat Esophagus, BRB treated, pool EP7


title: MA_0296; location: Charleston Harbor, SC

status: Public on Feb 21 2009

city: Charleston

first: Marine

last: Genomics

state: SC

address: 331 Ft. Johnson Road

institute: Medical University South Carolina

description: Total RNA (1-2 ug) was used to produce Cy3-labeled aminoallyl RNA (Cy3-aaRNA) probe using the Amino Allyl MessageAmpTM Kit (Ambion Inc, Austin, TX), according to the manufacturers instructions and 10 mg of the subsequently produced Cy3-aaRNA was used to probe a custom dolphin peripheral blood leukocyte cDNA microarray as previously described (Mancia et al., 2007).

hyb_protocol: the solution: 33% formamide, 2.6X SSPE, 2.4% SDS, 1.7X Denhardts; blocking agent:poly dA (1 mg/ml), mouse cot-1 DNA (1 mg/ml); wash procedure:2XSSC-0.1% SDS (5 min, 1X), 0.2XSSC-0.1% SDS (5 min, 2X), 0.2XSSC (5 min, 2X), 0.1XSSC (5 min, 1X), water (10 sec, 1X); quantity of labelled target used: 10 micrograms; time, concentration, volume, temperature:18 hours, 0.11 mg/ml, 90 microliters, 50 C; description of the hybridization instruments:SlideOut oven model 241000, Boekel

scan_protocol: scanning hardware: ScanArray Express; scanning software: ScanArray Express

data_processing: The data were handled on the R/BioConductor environment using functions from the packages "limma" and "vsn".  The data background was corrected using the "normexp" method.  The corrected data was normalized using the "loess" method to adjust for print-order effects that could have been generated by differences in the cDNA batches printed onto the microarrays.  After the normalization, the genes in which both replicates did not present expression levels three times higher than the average expression level of the non-dolphin genes present in the arrays (e.g. Duck IgY Heavy Chain and *Karenia brevis* photolyase) on at least 10% of the slides were discarded from the analyzes.  Next, the remaining data were transformed using the variance stabilization normalization (vsn) method.

label: NSH ester Cy3 (Ambion)

organism: Tursiops truncatus

source_name: Blood cells (PBL)

label_protocol: amount of nucleic acids labeled: 10 micrograms; label used:NSH ester Cy3 (Ambion); label incorporation method: chemical conjugation

extract_protocol: extraction method:PAXgene Blood RNA kit; sample molecule:total RNA; amplification:cDNA tagged with T7 promoter followed by linear amplification of antisense RNA in the presence of amino allyl UTP (MessageAmp II, Ambion)

tag: sex

tag: gowth conditions

value: wild

tag: location

value: Charleston Harbor, SC

tag: organism part(tissue)

value: blood


title: Normal  diet + 4h fasting, saline vs insulin 7

description: Biological replicate 3 of 4.


title: Normal  diet + 12h fasting, saline vs insulin 5

description: Biological replicate 1 of 4.


title: MA_0284; location: Charleston Harbor, SC


title: MA_0281; location: Charleston Harbor, SC


title: Normal  diet + 12h fasting, saline vs insulin 7

description: Biological replicate 3 of 4.


title: Normal  diet + 12h fasting, saline vs insulin 8

description: Biological replicate 4 of 4.


title: MA_0273; location: Charleston Harbor, SC


title: MA_0272; location: Charleston Harbor, SC


title: Normal  diet + 12h fasting, saline vs insulin 2

description: Biological replicate 2 of 4.


title: Normal  diet + 12h fasting, saline vs insulin 1

description: Biological replicate 1 of 4.


title: MA_0266; location: Charleston Harbor, SC


title: Normal  diet + 4h fasting, saline vs insulin 8

description: Biological replicate 4 of 4.


title: MA_0264; location: Charleston Harbor, SC


title: Normal  diet + 4h fasting, saline vs insulin 6

description: Biological replicate 2 of 4.


title: Normal  diet + 4h fasting, saline vs insulin 4

description: Biological replicate 4 of 4.


title: MA_0245; location: Charleston Harbor, SC


title: MA_0247; location: Indian River Lagoon, FL

value: Indian River Lagoon, FL


title: MA_0251; location: Indian River Lagoon, FL


title: MA_0244; location: Charleston Harbor, SC


title: Normal  diet + 4h fasting, saline vs insulin 1

description: Biological replicate 1 of 4.


title: MA_0298; location: Charleston Harbor, SC


title: BRB treated, pool EP9 vs. reference pool

description: Barcode: 251316210206

source_name: Rat Esophagus, BRB treated, pool EP9


title: BRB treated, pool EP8 vs. reference pool

description: Barcode: 251316210192

source_name: Rat Esophagus, BRB treated, pool EP8


title: MA_0294; location: Charleston Harbor, SC


title: MA_0291; location: Charleston Harbor, SC


title: MA_0288; location: Charleston Harbor, SC


title: MA_0290; location: Charleston Harbor, SC


title: MA_0285; location: Charleston Harbor, SC


title: MA_0224; location: Indian River Lagoon, FL


title: MA_0223; location: Charleston Harbor, SC


title: MA_0231; location: Indian River Lagoon, FL


title: MA_0225; location: Indian River Lagoon, FL


title: MA_0279; location: Charleston Harbor, SC


title: MA_0220; location: Charleston Harbor, SC


title: MA_0216; location: Charleston Harbor, SC


title: MA_0214; location: Charleston Harbor, SC


title: MA_0269; location: Charleston Harbor, SC


title: MA_0275; location: Charleston Harbor, SC


title: MA_0262; location: Charleston Harbor, SC


title: MA_0210; location: Charleston Harbor, SC


title: MA_0196; location: Charleston Harbor, SC


title: MA_0255; location: Indian River Lagoon, FL


title: MA_0256; location: Indian River Lagoon, FL


title: MA_0258; location: Charleston Harbor, SC


title: MA_0261; location: Charleston Harbor, SC


title: MA_0195; location: Charleston Harbor, SC


title: MA_0189; location: Charleston Harbor, SC


title: MA_0186; location: Charleston Harbor, SC


title: MA_0182; location: Charleston Harbor, SC


title: MA_0254; location: Indian River Lagoon, FL


title: MA_0253; location: Indian River Lagoon, FL


title: MA_0249; location: Indian River Lagoon, FL


title: MA_0178; location: Indian River Lagoon, FL


title: MA_0179; location: Indian River Lagoon, FL


title: MA_0171; location: Indian River Lagoon, FL


title: MA_0176; location: Indian River Lagoon, FL


title: MA_0243; location: Charleston Harbor, SC


title: MA_0241; location: Charleston Harbor, SC


title: MA_0239; location: Charleston Harbor, SC


title: MA_0194; location: Charleston Harbor, SC


title: MA_0235; location: Indian River Lagoon, FL


title: MA_0201; location: Charleston Harbor, SC


title: MA_0152; location: Saint Josephs Bay, FL

value: Saint Josephs Bay, FL


title: MA_0234; location: Indian River Lagoon, FL


title: MA_0232; location: Indian River Lagoon, FL


title: MA_0150; location: Saint Josephs Bay, FL


title: MA_0149; location: Saint Josephs Bay, FL


title: MA_0147; location: Saint Josephs Bay, FL


title: MA_0222; location: Charleston Harbor, SC


title: MA_0145; location: Saint Josephs Bay, FL


title: MA_0146; location: Saint Josephs Bay, FL


title: MA_0141; location: Saint Josephs Bay, FL


title: MA_0143; location: Saint Josephs Bay, FL


title: MA_0140; location: Saint Josephs Bay, FL


title: MA_0218; location: Charleston Harbor, SC


title: MA_0203; location: Charleston Harbor, SC


title: MA_0211; location: Charleston Harbor, SC


title: MA_0138; location: Saint Josephs Bay, FL


title: MA_0208; location: Charleston Harbor, SC


title: MA_0205; location: Charleston Harbor, SC


title: MA_0133; location: Saint Josephs Bay, FL


title: MA_0192; location: Charleston Harbor, SC


title: MA_0136; location: Saint Josephs Bay, FL


title: MA_0190; location: Charleston Harbor, SC


title: MA_0135; location: Saint Josephs Bay, FL


title: MA_0181; location: Indian River Lagoon, FL


title: MA_0130; location: Sarasota, FL

value: Sarasota, FL


title: MA_0155; location: Saint Josephs Bay, FL


title: MA_0173; location: Indian River Lagoon, FL


title: MA_0156; location: Saint Josephs Bay, FL


title: MA_0154; location: Saint Josephs Bay, FL


title: MA_0157; location: Saint Josephs Bay, FL


title: MA_0200; location: Charleston Harbor, SC


title: MA_0151; location: Saint Josephs Bay, FL


title: MA_0153; location: Saint Josephs Bay, FL


title: MA_0148; location: Saint Josephs Bay, FL


title: MA_0119; location: Sarasota, FL


title: MA_0118; location: Sarasota, FL


title: MA_0142; location: Saint Josephs Bay, FL


title: MA_0125; location: Sarasota, FL


title: MA_0139; location: Saint Josephs Bay, FL


title: MA_0105; location: Sarasota, FL


title: MA_0103; location: Sarasota, FL


title: MA_0107; location: Sarasota, FL


title: MA_0112; location: Sarasota, FL


title: MA_0137; location: Saint Josephs Bay, FL


title: MA_0134; location: Saint Josephs Bay, FL


title: MA_0132; location: Sarasota, FL


title: MA_0093; location: Sarasota, FL


title: MA_0095; location: Sarasota, FL


title: MA_0083; location: Sarasota, FL


title: MA_0087; location: Sarasota, FL


title: MA_0128; location: Sarasota, FL


title: MA_0127; location: Sarasota, FL


title: MA_0063; location: Indian River Lagoon, FL


title: MA_0124; location: Sarasota, FL


title: MA_0081; location: Sarasota, FL


title: MA_0126; location: Sarasota, FL


title: MA_0055; location: Indian River Lagoon, FL


title: MA_0051; location: Indian River Lagoon, FL


title: MA_0059; location: Indian River Lagoon, FL


title: MA_0049; location: Indian River Lagoon, FL


title: MA_0123; location: Sarasota, FL


title: MA_0120; location: Sarasota, FL


title: MA_0121; location: Sarasota, FL


title: MA_0045; location: Indian River Lagoon, FL


title: MA_0129; location: Sarasota, FL


title: MA_0144; location: Saint Josephs Bay, FL


title: MA_0116; location: Sarasota, FL


title: MA_0104; location: Sarasota, FL


title: MA_0110; location: Sarasota, FL


title: MA_0097; location: Sarasota, FL


title: MA_0099; location: Sarasota, FL


title: MA_0033; location: Charleston Harbor, SC


title: MA_0031; location: Charleston Harbor, SC


title: MA_0114; location: Sarasota, FL


title: MA_0015; location: Charleston Harbor, SC


title: MA_0027; location: Charleston Harbor, SC


title: MA_0053; location: Indian River Lagoon, FL


title: MA_0061; location: Indian River Lagoon, FL


title: MA_0003; location: Charleston Harbor, SC


title: MA_0122; location: Sarasota, FL


title: MA_0043; location: Indian River Lagoon, FL


title: MA_0041; location: Indian River Lagoon, FL


title: MA_0039; location: Indian River Lagoon, FL


title: MA_0037; location: Indian River Lagoon, FL


title: 5GR_B

status: Public on Feb 18 2009

city: Rockville

first: Jia

last: Liu

state: MD

address: 9712 Medical Center Drive

institute: Plant Genomics

description: Study Description   All plants used in this study were derived from the IBM 94 (Lee, Sharopova et al. 2002) mapping population and names used in the MIAME information correspond to Stapleton laboratory names.  A conversion table identifying the official IBM names is presented below. Maize IBM94 seed was supplied by the Maize Coop and increased at the field nursery in Clayton, NC.  For sowing, twelve seeds were placed in six-pack pots filled with sterilized vermiculite.  Flats filled with 36 pots were placed in the greenhouse at the University of North Carolina Wilmington with solar illumination and daily watering until the majority of the plants were at the three-leaf stage (8 days).  These growth conditions are similar to those used for previous inbred comparisons (Blum, Casati et al. 2004).  Glass does not transmit UV-B, therefore, the plants received none of this radiation unless treated as part of the experimental design. For treatment, one set of flats with a six-pot of each line was moved onto irradiation benches with UV313 bulbs (Q-Panel Lab Products, Cleveland, OH USA) mounted 30 cm above the bench and covered with cellulose diacetate (US Plastics, Lima OH, USA).  These plants received UV-B at a rate of 0.024 Wm-2, as previously described (Blum et al., 2004) for two hours (11 AM to 1PM) in August 2004.  Control plants were placed under UV313 bulbs that were covered with plastic (MylarD, US Plastics, Lima, OH, USA) to block all UV-B radiation.  Immediately following irradiation plants were removed from irradiation benches, and both control and experimental groups were allowed to recover for 3 h in the greenhouse.  Three hours of recovery allows time for post-transcriptional regulation (such as RNA processing and small RNA cleavage) so that we are measuring the steady-state level of mRNA for each gene.  Plants were irradiated centered on solar noon to maximize the amount of sunlight reaching the plants.  Following recovery, the second and third seedling leaves of each of the control and experimental plants were harvested and immediately frozen in liquid nitrogen.  The second and third replicate sets of plants were irradiated and harvested on succeeding days. Plant tissue batches used for RNA preparation were later used to verify genotypes. Genomic DNA was prepared from crushed tissue samples and PCR products from eleven SSR primers were scored by comparison to parental B73 and Mo17 PCR product sizes.  The eleven SSR primers were chosen using and algorithm designed by T. Hudson, Dept. of Computer Science, UNCW; the algorithm allows rapid selection of a minimal combination of markers that will distinguish each IBM94 genotype.   Total RNA was extracted from frozen tissue using Trizol (Invitrogen Co., Carlsbad, CA).  After extraction, RNA was shipped on dry ice to the University of Arizona.  Target labeling via RNA amplification and hybridization were in accordance to standard protocols posted on the Maize Microarray Project website (http://www.maizearray.org/maize_protocols.shtml ).  Briefly, the target labeling protocol utilizes the Ambion Message Amp II kit to produce cRNA which is indirectly labeled using a dye coupling reaction.  All arrays are prehybridized in 1% BSA, 5X SSC, 0.1% SDS.  The resulting labeled cRNA (3 ug/slide) is hybridized to the arrays using a 50% formamide, 5X SSC, 0.1% SDS hybridization buffer at 42 C overnight and the arrays are washed using a series of high stringency washes.    Official IBM ID Stapleton Laboratory ID Mo005 M2 Mo014 M7 Mo016 M9 Mo017 M10 Mo021 M11 Mo033 M22 Mo034 M23 Mo045 M29 Mo057 M36 Mo060 M38 Mo067 M43 Mo077 M47 Mo265 M51 Mo267 M53 Mo317 M69 Mo325 M73 Mo341 M77 Mo344 M78 Mo352 M81 Mo355 M83 Mo364 M86 Mo365 M87 Mo368 M88 Mo369 M89 Mo383 M55(akaM93)

hyb_protocol: Hybridization with indirectly labeled mRNA (SGED_SOP_6.1.1, SGED_SOP_6.2.1-4)

scan_protocol: Axon 4000B scanner. Both the 635nm (red, Cy5) and 532nm (green, Cy3) channels are scanned simultaneously at 100% laser power, the PMT set between 600 and 950. Slides are scanned at a resolution of 10micron

data_processing: The TIFF images were quantified using Genepix 5.0. Local background was subtracted from the signal value and the data was normalized using the quantile method in the limma package of bioconductor.

molecule: polyA RNA

organism: Zea mays

label_protocol: Amino allyl labeling and direct labeling (SGED_SOP_5.1.1 + SGED_SOP_6.1.1)

growth_protocol: See Experimental Description

extract_protocol: Phenol method with carbohydrate-enriched tissue such as tubers and trizol for other tissues such as leaves (SGED_SOP_3.1.1 + SGED_SOP_3.3.1)

treatment_protocol: UV or Control Treatment

tag: Zea mays, Leaf, Abiotic stress control

source_name: SampleM2_UV treated B

tag: Zea mays, Leaf, Abiotic stress


title: MA_0035; location: Charleston Harbor, SC


title: 6GR_B

source_name: SampleM2_UV treated C


title: MA_0047; location: Indian River Lagoon, FL


title: 9GR_B

source_name: SampleM9_UV treated B


title: MA_0023; location: Charleston Harbor, SC


title: MA_0089; location: Sarasota, FL


title: MA_0025; location: Charleston Harbor, SC


title: MA_0029; location: Charleston Harbor, SC


title: MA_0019; location: Charleston Harbor, SC


title: MA_0091; location: Sarasota, FL


title: MA_0017; location: Charleston Harbor, SC


title: MA_0021; location: Charleston Harbor, SC


title: MA_0057; location: Indian River Lagoon, FL


title: MA_0102; location: Sarasota, FL


title: MA_0005; location: Indian River Lagoon, FL


title: MA_0011; location: Charleston Harbor, SC


title: MA_0007; location: Indian River Lagoon, FL


title: 56GR_B

source_name: SampleM88_UV treated C


title: MA_0013; location: Charleston Harbor, SC


title: 51GR_B

source_name: SampleM86_UV treated B


title: 52GR_B

source_name: SampleM86_UV treated C


title: 12GR_B

source_name: SampleM10_UV treated C


title: 46GR_B

source_name: SampleM78_UV treated C


title: 11GR_B

source_name: SampleM10_UV treated B


title: 8GR_B

source_name: SampleM7_UV treated C


title: 10GR_B

source_name: SampleM9_UV treated C


title: 39GR_B

source_name: SampleM69_UV treated B


title: 43GR_B

source_name: SampleM77_UV treated B


title: 41GR_B

source_name: SampleM73_UV treated B


title: 58GR_B

source_name: SampleM89_UV treated C


title: 7GR_B

source_name: SampleM7_UV treated B


title: 38GR_B

source_name: SampleM55_UV treated C


title: 54GR_B

source_name: SampleM87_UV treated C


title: 57GR_B

source_name: SampleM89_UV treated B


title: 55GR_B

source_name: SampleM88_UV treated B


title: 50GR_B

source_name: SampleM83_UV treated C


title: 37GR_B

source_name: SampleM55_UV treated B


title: 40GR_B

source_name: SampleM69_UV treated C


title: 53GR_B

source_name: SampleM87_UV treated B


title: 48GR_B

source_name: SampleM81_UV treated C


title: 42GR_B

source_name: SampleM73_UV treated C


title: 31GR_B

source_name: SampleM51_UV treated B


title: 44GR_B

source_name: SampleM77_UV treated C


title: 35GR_B

source_name: SampleM53_UV treated B


title: 47GR_B

source_name: SampleM81_UV treated B


title: 45GR_B

source_name: SampleM78_UV treated B


title: 34GR_B

source_name: SampleM95_UV treated C


title: 33GR_B

source_name: SampleM95_UV treated B


title: 26GR_B


title: 36GR_B

source_name: SampleM53_UV treated C


title: 52GR_A

source_name: SampleM86_UV treated C


title: 49GR_B

source_name: SampleM83_UV treated B


title: 24GR_B

source_name: SampleM38_UV treated C


title: 27GR_B

source_name: SampleM43_UV treated B


title: 55GR_A

source_name: SampleM88_UV treated B


title: 58GR_A

source_name: SampleM89_UV treated C


title: 23GR_B

source_name: SampleM38_UV treated B


title: 57GR_A

source_name: SampleM89_UV treated B


title: 51GR_A

source_name: SampleM86_UV treated B


title: 29GR_B

source_name: SampleM47_UV treated B


title: 28GR_B

source_name: SampleM43_UV treated C


title: 54GR_A

source_name: SampleM87_UV treated C


title: 22GR_B

source_name: SampleM36_UV treated C


title: 47GR_A

source_name: SampleM81_UV treated B


title: 50GR_A

source_name: SampleM83_UV treated C


title: 30GR_B

source_name: SampleM47_UV treated C


title: 21GR_B

source_name: SampleM36_UV treated B


title: 56GR_A

source_name: SampleM88_UV treated C


title: 53GR_A

source_name: SampleM87_UV treated B


title: 25GR_B

source_name: SampleM95_UV treated B


title: 48GR_A

source_name: SampleM81_UV treated C


title: 45GR_A

source_name: SampleM78_UV treated B


title: 49GR_A

source_name: SampleM83_UV treated B


title: 46GR_A

source_name: SampleM78_UV treated C


title: 39GR_A

source_name: SampleM69_UV treated B


title: 43GR_A

source_name: SampleM77_UV treated B


title: 18GR_B

source_name: SampleM23_UV treated C


title: 20GR_B

source_name: SampleM29_UV treated C


title: 44GR_A

source_name: SampleM77_UV treated C


title: 40GR_A

source_name: SampleM69_UV treated C


title: 42GR_A

source_name: SampleM73_UV treated C


title: 36GR_A

source_name: SampleM53_UV treated C


title: 35GR_A

source_name: SampleM53_UV treated B


title: 34GR_A

source_name: SampleM95_UV treated C


title: 41GR_A

source_name: SampleM73_UV treated B


title: 14GR_B

source_name: SampleM11_UV treated C


title: 38GR_A

source_name: SampleM55_UV treated C


title: 29GR_A

source_name: SampleM47_UV treated B


title: 15GR_B

source_name: SampleM22_UV treated B


title: 13GR_B

source_name: SampleM11_UV treated B


title: 37GR_A

source_name: SampleM55_UV treated B


title: 16GR_B

source_name: SampleM22_UV treated C


title: 32GR_A

source_name: SampleM51_UV treated C


title: 17GR_B

source_name: SampleM23_UV treated B


title: 32GR_B


title: 30GR_A

source_name: SampleM47_UV treated C


title: 33GR_A

source_name: SampleM95_UV treated B


title: 27GR_A

source_name: SampleM43_UV treated B


title: 22GR_A

source_name: SampleM36_UV treated C


title: 24GR_A

source_name: SampleM38_UV treated C


title: 23GR_A

source_name: SampleM38_UV treated B


title: 28GR_A

source_name: SampleM43_UV treated C


title: 31GR_A

source_name: SampleM51_UV treated B


title: 26GR_A

source_name: SampleM95_UV treated C


title: 15GR_A


title: 25GR_A


title: 16GR_A


title: 19GR_A

source_name: SampleM29_UV treated B


title: 11GR_A

source_name: SampleM10_UV treated B


title: 21GR_A

source_name: SampleM36_UV treated B


title: 18GR_A

source_name: SampleM23_UV treated C


title: 14GR_A

source_name: SampleM11_UV treated C


title: 20GR_A

source_name: SampleM29_UV treated C


title: 19GR_B


title: 9GR_A

source_name: SampleM9_UV treated B


title: 17GR_A

source_name: SampleM23_UV treated B


title: 7GR_A

source_name: SampleM7_UV treated B


title: 13GR_A

source_name: SampleM11_UV treated B


title: 10GR_A

source_name: SampleM9_UV treated C


title: Sample_155

status: Public on Feb 12 2009

city: West Point

first: Michael

last: Nebozhyn

state: PA

address: Mail Stop WP53B-120, 770 Sumneytown Pike, Building 53, P.O. Box 4

department: GpGx/Computational System biology

institute: Merck, Inc

description: VALUEs represent averaged data for both channels from a fluor-reverse pair

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

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

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

organism: Homo sapiens

source_name: Adipose

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

extract_protocol: Total RNA was isolated from the adipose samples  by Qiagen RNeasy spin columns with DNAse treatment. 2 µg of each sample was precipitated in ethanol and re-suspended in 14 µl of water. Globin mitigation performed using Ambion's GLOBINclear kit (cat# AM1980; Austin, TX) according to manufacturer’s protocol. Briefly, biotinylated globin-specific oligonucleotides are mixed with total RNA and annealed to α and β globin transcripts; streptavidin-coated paramagnetic beads are then added to bind and capture the bound globin mRNAs; the beads are removed using a magnet. GLOBINclear-treated total RNA samples were adjusted to 150 µl, aliquots of which were used for qRT-PCR and microarray experiments.

tag: common reference


title: Sample_157

tag: Sibutramine


title: 8GR_A

source_name: SampleM7_UV treated C


title: Sample_148


title: 6GR_A

source_name: SampleM2_UV treated C


title: Sample_151


title: Sample_153


title: Sample_152


title: Sample_154


title: Sample_150


title: Sample_156


title: Sample_147


title: Sample_146


title: 5GR_A

source_name: SampleM2_UV treated B


title: Sample_145


title: Sample_143


title: Sample_138


title: Sample_140


title: Sample_137


title: Sample_135


title: Sample_141


title: Sample_144


title: Sample_136


title: Sample_142


title: Sample_139


title: Sample_134


title: Sample_130


title: Sample_133


title: Sample_131


title: Sample_125


title: Sample_123


title: Sample_127


title: Sample_129


title: Sample_118


title: Sample_128


title: Sample_126


title: Sample_124


title: Sample_132


title: Sample_122


title: Sample_121


title: Sample_120


title: Sample_113


title: Sample_115


title: Sample_119


title: Sample_105


title: Sample_111


title: Sample_112


title: Sample_102


title: Sample_108


title: Sample_116


title: Sample_114


title: Sample_100


title: Sample_117


title: Sample_110


title: Sample_107


title: Sample_109


title: Sample_98


title: Sample_103


title: Sample_104


title: Sample_106


title: Sample_93


title: Sample_101


title: Sample_95


title: Sample_92


title: Sample_96


title: Sample_94


title: Sample_99


title: Sample_97


title: 12GR_A

source_name: SampleM10_UV treated C


title: Sample_88


title: Sample_90


title: Sample_85


title: Sample_86


title: Sample_79


title: Sample_82


title: Sample_80


title: Sample_72


title: Sample_81


title: Sample_149


title: Sample_77


title: Sample_74


title: Sample_71


title: Sample_87


title: Sample_91


title: Sample_83


title: Sample_84


title: Sample_67


title: Sample_89


title: Sample_68


title: Sample_75


title: Sample_76


title: Sample_69


title: Sample_78


title: Sample_70


title: Sample_59


title: Sample_58


title: Sample_62


title: Sample_64


title: Sample_63


title: Sample_66


title: Sample_65


title: Sample_61


title: Sample_73


title: Sample_60


title: Sample_51


title: Sample_53


title: Sample_55


title: Sample_57


title: Sample_54


title: Sample_46


title: Sample_50


title: Sample_48


title: Sample_49


title: Sample_52


title: Sample_43


title: Sample_56


title: Sample_41


title: Sample_45


title: Sample_44


title: Sample_37


title: Sample_40


title: Sample_31


title: Sample_33


title: Sample_42


title: Sample_35


title: Sample_30


title: Sample_29


title: Sample_25


title: Sample_34


title: Sample_32


title: Sample_28


title: Sample_27


title: Sample_24


title: Sample_26


title: Sample_21


title: Sample_22


title: Sample_20


title: Sample_23


title: Sample_18


title: Sample_15


title: Sample_14


title: Sample_19


title: Sample_17


title: Sample_12


title: Sample_13


title: Sample_9


title: Sample_6


title: Sample_16


title: Sample_11


title: Sample_8


title: Sample_4


title: Sample_10


title: Sample_36


title: PWD_CingulateCortex 251197835427

status: Public on Feb 05 2009

city: Chapel Hill

first: Hanwen

last: Huang

state: NC

address: University of North Carolina

institute: UNC

hyb_protocol: Agilent Hyb. Protocol

scan_protocol: Agilent Scanner

data_processing: The original arrays consist of a total of 22393 transcripts. Data were normalized by the lowess function using the Statistical microarray analysis (SMA) package in R   (http://stat-www.berkeley.edu/users/terry/zarray/Software/smacode.html), and further scale normalized.  Raw data from Nadler et al. (2006) with the addition of another ten strains were normalized as a single dataset. The log-ratio of background-subtracted Cy3 signal to background-subtracted Cy5 signal was calculated for each spot, and used for subsequent analyses. 20868 transcripts remained after the control genes were removed and the 50 probesets spotted 10 times on the array were averaged.  Since the array data was collected over period of two years, we investigated the possibility of a calendar time effect.  We performed principal component analysis (PCA) on all arrays and the first two PCs were plotted against time. A significant time effect was noted in the data. To correct for this effect, arrays were divided into 5 equally sized groups (shown in color), and an ANOVA model applied to each gene with the “defined” time group as a covariate. The residuals from the ANOVA model were treated as the final expression values and used in all the subsequent analyses. PCA analysis on the new adjusted expression indicated this procedure removed the time effect efficiently.

organism: Mus musculus

label_protocol: Agilent Direct Label kit (15ug total RNA input)

extract_protocol: TRIzol followed by Qiagen Rneasy Cleanup

tag: Age 6-8 weeks

source_name: Stratagene Mouse Universal Reference RNA


title: Sample_7


title: DBA/2J_Hippocampus 16011978014881

tag: Stratagene Mouse Universal Reference RNA


title: SPRET/Ei_OlfactoryBulb 251197835431


title: SPRET/Ei_CingulateCortex 251197834903


title: Sample_2


title: SPRET/Ei_OlfactoryBulb 251197835430


title: Sample_3


title: PWD_OlfactoryBulb 251197835428


title: SPRET/Ei_Hippocampus 251197834881


title: SPRET/Ei_BasalGanglia 251197834878


title: SPRET/Ei_OlfactoryBulb 251197834904


title: Sample_1


title: SPRET/Ei_CingulateCortex 251197834902


title: SPRET/Ei_FrontalCortex 251197834880


title: SPRET/Ei_CingulateCortex 251197835429


title: SPRET/Ei_Hippocampus 251197834876


title: SPRET/Ei_FrontalCortex 251197834875


title: SPRET/Ei_Cerebellum 251197834874


title: SPRET/Ei_BasalGanglia 251197834873


title: SPRET/Ei_Amygdala 251197834872


title: CAST/Ei_Hippocampus 251197833796


title: CAST/Ei_FrontalCortex 251197833795


title: Sample_38


title: PWD_Amygdala 251197834817


title: CAST/Ei_OlfactoryBulb 251197833770


title: PWD_Hippocampus 251197834821


title: CAST/Ei_Cerebellum 251197833794


title: PWD_FrontalCortex 251197834820


title: CAST/Ei_BasalGanglia 251197833793


title: CAST/Ei_CingulateCortex 251197833769


title: Sample_39


title: CAST/Ei_BasalGanglia 251197833758


title: CAST/Ei_CingulateCortex 251197833767


title: CAST/Ei_Amygdala 251197833792


title: MOLF/Ei_Hippocampus 251197833745


title: CAST/Ei_FrontalCortex 251197833760


title: SPRET/Ei_Cerebellum 251197834879


title: Sample_5


title: PWD_BasalGanglia 251197834818


title: CAST/Ei_OlfactoryBulb 251197833768


title: MOLF/Ei_CingulateCortex 251197833746


title: CAST/Ei_CingulateCortex 251197833771


title: SPRET/Ei_Amygdala 251197834877


title: Sample_47


title: CAST/Ei_Hippocampus 251197833761


title: CAST/Ei_Amygdala 251197833757


title: MOLF/Ei_FrontalCortex 251197833744


title: CAST/Ei_Cerebellum 251197833759


title: PWD_Cerebellum 251197834819


title: MOLF/Ei_BasalGanglia 251197833742


title: SPRET/Ei_FrontalCortex 251197832750


title: MOLF/Ei_OlfactoryBulb 251197833711


title: PL/J_CingulateCortex 251197833709


title: SPRET/Ei_Hippocampus 251197832751


title: PWD_FrontalCortex 251197832715


title: NOD/LtJ_Hippocampus 251197832741


title: NOD/LtJ_Amygdala 251197832737


title: SPRET/Ei_BasalGanglia 251197832748


title: PL/J_CingulateCortex 251197833707


title: PWD_Hippocampus 251197832716


title: PWD_Amygdala 251197832712


title: SPRET/Ei_Cerebellum 251197832749


title: PWD_CingulateCortex 251197832711


title: PWD_CingulateCortex 251197832708


title: PWD_OlfactoryBulb 251197832710


title: PWD_Cerebellum 251197832714


title: SPRET/Ei_Amygdala 251197832747


title: PWD_Hippocampus 251197832706


title: NOD/LtJ_BasalGanglia 251197832738


title: PWD_BasalGanglia 251197832713


title: NOD/LtJ_FrontalCortex 251197832740


title: CAST/Ei_OlfactoryBulb 251197832707


title: PWD_FrontalCortex 251197832705


title: PL/J_OlfactoryBulb 251197833710


title: MOLF/Ei_Cerebellum 251197833743


title: PWD_Cerebellum 251197832704


title: PL/J_OlfactoryBulb 251197833708


title: SWR/J_OlfactoryBulb 251197832698


title: PWD_BasalGanglia 251197832703


title: NZB/B1NJ_CingulateCortex 251197832696


title: SWR/J_CingulateCortex 251197832689


title: NOD/LtJ_CingulateCortex 251197832694


title: NZB/B1NJ_BasalGanglia 251197832683


title: PWD_Amygdala 251197832702


title: NZB/B1NJ_OlfactoryBulb 251197832688


title: NZB/B1NJ_Hippocampus 251197832686


title: NZB/B1NJ_FrontalCortex 251197832685


title: PWD_OlfactoryBulb 251197832692


title: NZB/B1NJ_OlfactoryBulb 251197832697


title: NZB/B1NJ_CingulateCortex 251197832690


title: CAST/Ei_Hippocampus 251197832661


title: CAST/Ei_FrontalCortex 251197832660


title: CAST/Ei_BasalGanglia 251197832658


title: NZB/B1NJ_Hippocampus 251197832656


title: NZB/B1NJ_Cerebellum 251197832684


title: CAST/Ei_Amygdala 251197832657


title: NZB/B1NJ_FrontalCortex 251197832655


title: NOD/LtJ_OlfactoryBulb 251197832695


title: SWR/J_FrontalCortex 251197832650


title: NZB/B1NJ_OlfactoryBulb 251197832691


title: NZB/B1NJ_Cerebellum 251197832654


title: NOD/LtJ_Cerebellum 251197832739


title: CAST/Ei_Cerebellum 251197832659


title: SWR/J_BasalGanglia 251197832648


title: NZB/B1NJ_BasalGanglia 251197832653


title: SWR/J_Amygdala 251197832647


title: NZB/B1NJ_BasalGanglia 251197832643


title: NZB/B1NJ_Cerebellum 251197832644


title: PERA/EiJ_CingulateCortex 251197832637


title: PERA/EiJ_OlfactoryBulb 251197832636


title: NZB/B1NJ_FrontalCortex 251197832645


title: PERA/EiJ_FrontalCortex 251197832633


title: NZB/B1NJ_Amygdala 251197832642


title: SWR/J_Cerebellum 251197832649


title: PERA/EiJ_OlfactoryBulb 251197832640


title: PERA/EiJ_CingulateCortex 251197832639


title: SWR/J_Hippocampus 251197832651


title: NZB/B1NJ_Hippocampus 251197832646


title: NZB/B1NJ_Amygdala 251197832652


title: PERA/EiJ_Hippocampus 251197832624


title: PERA/EiJ_OlfactoryBulb 251197832638


title: PERA/EiJ_Hippocampus 251197832634


title: PERA/EiJ_Cerebellum 251197832632


title: PERA/EiJ_Amygdala 251197832630


title: NZB/B1NJ_CingulateCortex 251197832687


title: PERA/EiJ_FrontalCortex 251197832608


title: PL/J_Amygdala 251197832615


title: PERA/EiJ_Cerebellum 251197832622


title: PL/J_Cerebellum 251197832617


title: PL/J_BasalGanglia 251197832616


title: PL/J_FrontalCortex 251197832618


title: PERA/EiJ_FrontalCortex 251197832623


title: PL/J_Hippocampus 251197832619


title: PERA/EiJ_BasalGanglia 251197832606


title: PERA/EiJ_Amygdala 251197832620


title: PERA/EiJ_BasalGanglia 251197832621


title: SWR/J_Hippocampus 251197832604


title: PERA/EiJ_Cerebellum 251197832607


title: PERA/EiJ_Hippocampus 251197832609


title: SWR/J_FrontalCortex 251197832603


title: SWR/J_Cerebellum 251197832602


title: PERA/EiJ_BasalGanglia 251197832631


title: PERA/EiJ_Amygdala 251197832605


title: SWR/J_OlfactoryBulb 251197832594


title: SWR/J_Amygdala 251197832600


title: SWR/J_BasalGanglia 251197832601


title: SWR/J_CingulateCortex 251197832591


title: SWR/J_CingulateCortex 251197832593


title: SWR/J_OlfactoryBulb 251197832592


title: PL/J_FrontalCortex 251197832578


title: SWR/J_BasalGanglia 251197832586


title: SWR/J_Cerebellum 251197832587


title: MOLF/Ei_OlfactoryBulb 251197832521


title: SWR/J_Hippocampus 251197832590


title: MOLF/Ei_Cerebellum 251197832510


title: MOLF/Ei_CingulateCortex 251197832516


title: PL/J_CingulateCortex 251197832518


title: NZB/B1NJ_Amygdala 251197832682


title: SWR/J_FrontalCortex 251197832588


title: PL/J_Hippocampus 251197832579


title: PL/J_Hippocampus 251197832499


title: MOLF/Ei_FrontalCortex 251197832511


title: MOLF/Ei_Hippocampus 251197832512


title: PL/J_BasalGanglia 251197832576


title: PL/J_Amygdala 251197832575


title: SWR/J_Amygdala 251197832585


title: MOLF/Ei_BasalGanglia 251197832509


title: PL/J_FrontalCortex 251197832498


title: MOLF/Ei_Amygdala 251197832508


title: PL/J_BasalGanglia 251197832496


title: PL/J_Amygdala 251197832495


title: PL/J_Cerebellum 251197832497


title: C58/J_FrontalCortex 251197831576


title: PL/J_Cerebellum 251197832577


title: PL/J_OlfactoryBulb 251197832520


title: PERA/EiJ_CingulateCortex 251197832635


title: C58/J_BasalGanglia 251197831574


title: C58/J_Hippocampus 251197831561


title: NOD/LtJ_Amygdala 251197831555


title: C58/J_Cerebellum 251197831559


title: C58/J_FrontalCortex 251197831560


title: C58/J_Amygdala 251197831557


title: C58/J_Cerebellum 251197831575


title: BTBR_OlfactoryBulb 251197827596


title: NOD/LtJ_CingulateCortex 251197831058


title: NOD/LtJ_Cerebellum 251197831540


title: NOD/LtJ_OlfactoryBulb 251197831061


title: C58/J_BasalGanglia 251197831558


title: NOD/LtJ_BasalGanglia 251197831556


title: NOD/LtJ_Cerebellum 251197831052


title: NOD/LtJ_Amygdala 251197831050


title: C58/J_Hippocampus 251197831577


title: NOD/LtJ_BasalGanglia 251197831051


title: NOD/LtJ_CingulateCortex 251197831060


title: NOD/LtJ_OlfactoryBulb 251197831059


title: C58/J_OlfactoryBulb 251197831057


title: BTBR_CingulateCortex 251197827593


title: NOD/LtJ_FrontalCortex 251197831541


title: NOD/LtJ_FrontalCortex 251197831053


title: NOD/LtJ_Hippocampus 251197831054


title: SJL/J_CingulateCortex 251197827591


title: C58/J_Hippocampus 251197827540


title: SJL/J_OlfactoryBulb 251197827594


title: NOD/LtJ_Hippocampus 251197831542


title: C58/J_Cerebellum 251197827538


title: SJL/J_Cerebellum 251197827533


title: FVB/NJ_Amygdala 251197827519


title: SJL/J_Hippocampus 251197827535


title: BTBR_FrontalCortex 251197827513


title: C57L/J_Amygdala 251197827518


title: SJL/J_FrontalCortex 251197827534


title: C58/J_Amygdala 251197827536


title: BTBR_Hippocampus 251197827514


title: SJL/J_OlfactoryBulb 251197827592


title: BTBR_Cerebellum 251197827512


title: BTBR_BasalGanglia 251197827511


title: C3H/HeJ_Amygdala 251197827522


title: C58/J_FrontalCortex 251197827539


title: SJL/J_Amygdala 251197827531


title: C57BL/6J_BasalGanglia 251197827517


title: DBA/2J_Amygdala 251197827515


title: C58/J_CingulateCortex 251197827523


title: C57BL/6J_Amygdala 251197827516


title: SJL/J_Cerebellum 251197827434


title: SJL/J_Hippocampus 251197827436


title: SJL/J_FrontalCortex 251197827435


title: SJL/J_CingulateCortex 251197827437


title: BTBR_Amygdala 251197827510


title: SJL/J_BasalGanglia 251197827433


title: BTBR_BasalGanglia 251197827414


title: BTBR_Cerebellum 251197827415


title: BTBR_Amygdala 251197827413


title: C58/J_OlfactoryBulb 251197827401


title: SJL/J_FrontalCortex 251197827280


title: C58/J_OlfactoryBulb 251197827521


title: SJL/J_CingulateCortex 251197827397


title: BTBR_FrontalCortex 251197827416


title: SJL/J_BasalGanglia 251197827532


title: SJL/J_Hippocampus 251197827281


title: SJL/J_Cerebellum 251197827279


title: BALB/cByJ_OlfactoryBulb 251197826383


title: FVB/NJ_CingulateCortex 251197826381


title: BALB/cByJ_OlfactoryBulb 251197826384


title: BALB/cByJ_CingulateCortex 251197826382


title: SJL/J_BasalGanglia 251197827278


title: BTBR_Hippocampus 251197827417


title: BALB/cByJ_OlfactoryBulb 251197826380


title: BALB/cByJ_Hippocampus 251197826379


title: SJL/J_Amygdala 251197827399


title: C58/J_CingulateCortex 251197827400


title: SJL/J_Amygdala 251197827277


title: BALB/cByJ_FrontalCortex 251197826378


title: BALB/cByJ_Cerebellum 251197826377


title: SJL/J_OlfactoryBulb 251197827398


title: C58/J_Amygdala 251197831573


title: BTBR_OlfactoryBulb 251197826358


title: BTBR_CingulateCortex 251197826359


title: C58/J_BasalGanglia 251197827537


title: BTBR_Hippocampus 251197826191


title: BTBR_FrontalCortex 251197826190


title: BTBR_OlfactoryBulb 251197826360


title: BALB/cByJ_Amygdala 251197826375


title: BTBR_Amygdala 251197826187


title: BTBR_BasalGanglia 251197826188


title: BTBR_Cerebellum 251197826189


title: BALB/cByJ_BasalGanglia 251197826376


title: BALB/cByJ_Cerebellum 251197825554


title: C57L/J_FrontalCortex 251197825539


title: BALB/cByJ_Amygdala 251197825552


title: BTBR_CingulateCortex 251197826338


title: C57L/J_Hippocampus 251197825540


title: C57BL/6J_FrontalCortex 251197825549


title: C57L/J_Cerebellum 251197825502


title: BALB/cByJ_BasalGanglia 251197825553


title: C57L/J_Amygdala 251197825499


title: BALB/cByJ_FrontalCortex 251197825445


title: BALB/cByJ_Cerebellum 251197825444


title: BALB/cByJ_Hippocampus 251197825446


title: FVB/NJ_CingulateCortex 251197825432


title: BALB/cByJ_BasalGanglia 251197825443


title: BALB/cByJ_Amygdala 251197825440


title: C57L/J_BasalGanglia 251197825500


title: BALB/cByJ_CingulateCortex 251197825429


title: BALB/cByJ_FrontalCortex 251197825376


title: AKR/J_Amygdala 251197822068


title: C57L/J_FrontalCortex 251197822055


title: C57L/J_CingulateCortex 251197822057


title: C3H/HeJ_Amygdala 251197822069


title: 129/SvlmJ_Amygdala 251197822065


title: A/J_Amygdala 251197822066


title: BALB/cByJ_Hippocampus 251197825428


title: C57BL/6J_Hippocampus 251197822005


title: C57BL/6J_BasalGanglia 251197822002


title: C57L/J_Hippocampus 251197822056


title: C58/J_CingulateCortex 251197827520


title: DBA/2J_Amygdala 251197822067


title: C57BL/6J_Amygdala 251197822001


title: C57L/J_BasalGanglia 251197822052


title: C57BL/6J_Cerebellum 251197822003


title: C57L/J_Cerebellum 251197822054


title: DBA/2J_CingulateCortex 251197821996


title: C57L/J_OlfactoryBulb 251197821998


title: C3H/HeJ_BasalGanglia 251197821999


title: C57L/J_OlfactoryBulb 251197821995


title: C3H/HeJ_BasalGanglia 251197821997


title: C57L/J_CingulateCortex 251197821994


title: C57BL/6J_CingulateCortex 251197821991


title: 129/SvlmJ_OlfactoryBulb 251197821993


title: AKR/J_CingulateCortex 251197821992


title: C57BL/6J_Amygdala 251197821700


title: AKR/J_BasalGanglia 251197822000


title: FVB/NJ_OlfactoryBulb 251197821699


title: FVB/NJ_OlfactoryBulb 251197820701


title: C57BL/6J_FrontalCortex 251197821644


title: FVB/NJ_Amygdala 251197821697


title: FVB/NJ_FrontalCortex 251197820763


title: FVB/NJ_Hippocampus 251197820764


title: C57L/J_Hippocampus 251197820548


title: C3H/HeJ_Hippocampus 251197820484


title: FVB/NJ_FrontalCortex 251197820513


title: DBA/2J_Amygdala 251197820480


title: C57L/J_BasalGanglia 251197820512


title: FVB/NJ_Cerebellum 251197820765


title: C57BL/6J_Cerebellum 251197820655


title: FVB/NJ_Hippocampus 251197821698


title: A/J_Amygdala 251197820481


title: C57BL/6J_OlfactoryBulb 251197820656


title: FVB/NJ_BasalGanglia 251197820756


title: C57L/J_CingulateCortex 251197820549


title: C57L/J_Amygdala 251197820657


title: C57L/J_OlfactoryBulb 251197820654


title: C57L/J_FrontalCortex 251197820547


title: C3H/HeJ_FrontalCortex 251197820483


title: C57L/J_Cerebellum 251197820546


title: AKR/J_Amygdala 251197820482


title: C3H/HeJ_OlfactoryBulb 251197820485


title: C3H/HeJ_CingulateCortex 251197820486


title: FVB/NJ_Amygdala 251197820479


title: C3H/HeJ_Amygdala 251197820478


title: 129/SvlmJ_Hippocampus 251197818153


title: 129/SvlmJ_Amygdala 251197818149


title: 129/SvlmJ_FrontalCortex 251197818152


title: 129/SvlmJ_Cerebellum 251197818151


title: 129/SvlmJ_BasalGanglia 251197818150


title: AKR/J_OlfactoryBulb 251197818013


title: 129/SvlmJ_Hippocampus 251197818138


title: 129/SvlmJ_Amygdala 251197818134


title: AKR/J_OlfactoryBulb 251197818041


title: AKR/J_FrontalCortex 251197818011


title: AKR/J_CingulateCortex 251197818012


title: 129/SvlmJ_FrontalCortex 251197818137


title: AKR/J_BasalGanglia 251197818010


title: 129/SvlmJ_CingulateCortex 251197818042


title: 129/SvlmJ_Cerebellum 251197818136


title: 129/SvlmJ_Cerebellum 251197818000


title: 129/SvlmJ_OlfactoryBulb 251197818039


title: 129/SvlmJ_CingulateCortex 251197818003


title: 129/SvlmJ_BasalGanglia 251197817999


title: 129/SvlmJ_Hippocampus 251197818002


title: 129/SvlmJ_BasalGanglia 251197818135


title: 129/SvlmJ_CingulateCortex 251197817993


title: 129/SvlmJ_FrontalCortex 251197818001


title: FVB/NJ_BasalGanglia 251197817990


title: BALB/cByJ_CingulateCortex 251197825434


title: C57BL/6J_CingulateCortex 16011978017650


title: C57BL/6J_OlfactoryBulb 16011978017651


title: A/J_FrontalCortex 251197817989


title: AKR/J_CingulateCortex 251197818040


title: FVB/NJ_Cerebellum 251197817991


title: A/J_Hippocampus 16011978017140


title: C57BL/6J_FrontalCortex 16011978017649


title: A/J_BasalGanglia 16011978017137


title: C3H/HeJ_OlfactoryBulb 16011978017111


title: A/J_CingulateCortex 16011978017647


title: A/J_FrontalCortex 16011978017139


title: A/J_Cerebellum 16011978017138


title: AKR/J_OlfactoryBulb 16011978017110


title: AKR/J_FrontalCortex 16011978017108


title: A/J_CingulateCortex 16011978017141


title: A/J_OlfactoryBulb 16011978016813


title: C57BL/6J_Hippocampus 16011978016810


title: C3H/HeJ_FrontalCortex 16011978017094


title: C3H/HeJ_BasalGanglia 16011978017092


title: C3H/HeJ_Cerebellum 16011978017093


title: C3H/HeJ_CingulateCortex 16011978017095


title: AKR/J_BasalGanglia 16011978017107


title: A/J_OlfactoryBulb 16011978017648


title: C3H/HeJ_Cerebellum 16011978016760


title: AKR/J_Amygdala 251197818009


title: 129/SvlmJ_OlfactoryBulb 16011978016463


title: A/J_FrontalCortex 16011978016443


title: A/J_OlfactoryBulb 16011978016759


title: A/J_CingulateCortex 16011978016445


title: FVB/NJ_BasalGanglia 16011978016431


title: FVB/NJ_Hippocampus 16011978016434


title: FVB/NJ_OlfactoryBulb 16011978016435


title: A/J_Cerebellum 16011978016442


title: C57BL/6J_Hippocampus 16011978014895


title: A/J_Cerebellum 16011978016323


title: C57BL/6J_Cerebellum 16011978014893


title: A/J_Amygdala 16011978016321


title: C57BL/6J_BasalGanglia 16011978014892


title: C57BL/6J_FrontalCortex 16011978014894


title: A/J_BasalGanglia 16011978016441


title: A/J_Hippocampus 16011978016325


title: A/J_BasalGanglia 16011978016322


title: C57BL/6J_CingulateCortex 16011978014896


title: AKR/J_Cerebellum 16011978014889


title: C3H/HeJ_OlfactoryBulb 16011978014898


title: FVB/NJ_FrontalCortex 16011978016433


title: C57BL/6J_Cerebellum 16011978014890


title: DBA/2J_Hippocampus 16011978014887


title: FVB/NJ_Cerebellum 16011978016432


title: AKR/J_Cerebellum 16011978014891


title: DBA/2J_FrontalCortex 16011978014886


title: DBA/2J_BasalGanglia 16011978014884


title: DBA/2J_Cerebellum 16011978014885


title: DBA/2J_CingulateCortex 16011978014882


title: DBA/2J_OlfactoryBulb 16011978014746


title: DBA/2J_OlfactoryBulb 16011978014883


title: DBA/2J_Hippocampus 16011978014744


title: C57BL/6J_OlfactoryBulb 16011978013169


title: AKR/J_Hippocampus 16011978013183


title: DBA/2J_OlfactoryBulb 16011978014745


title: DBA/2J_BasalGanglia 16011978014737


title: DBA/2J_CingulateCortex 16011978014747


title: DBA/2J_FrontalCortex 16011978014742


title: C3H/HeJ_Hippocampus 16011978013164


title: AKR/J_Hippocampus 16011978012362


title: C3H/HeJ_FrontalCortex 16011978014748


title: C3H/HeJ_Hippocampus 16011978013182


title: DBA/2J_FrontalCortex 16011978014739


title: DBA/2J_Cerebellum 16011978014738


title: AKR/J_Cerebellum 16011978013167


title: DBA/2J_Cerebellum 16011978014741


title: Mouse 21 Steady state d4pi post-PBS injection

status: Public on Feb 04 2009

city: Oklahoma City

first: Douglas

last: Drevets

state: OK

address: 921 NE 13th St

department: Medicine-Infectious Diseases

institute: University of Oklahoma Health Sciences Center

description: The expression levels of the individual genes were analyzed using Array Vision Software (Imaging Research Inc., Ontario, Canada).  This software is designed to determine density of each array element (discrete hybridization site) on the membrane which reflects the total amount of hybridization signal emitted from each site.  In our system, this signal is expressed as Molecular Dynamic Counts.  The background or nonspecific hybridization signal was measured and subtracted from the signal of each individual element and the output was the raw data, shown as the arithmetic means of the signals for the genes which were spotted in duplicate

hyb_protocol: We chose to use the Atlas 5K plastic mouse array (Clontech) cDNA array that provides reliable evaluation of 5,030 genes.  Each Atlas Array was placed in a hybridization bottle containing deionized H2O.  The water was poured off allowing the membrane to adhere to the inside walls of the bottle and to prevent the membrane from drying the prepared ExpressHyb (Clontech).  Then sheared salmon testes solutions were added.  The membranes were prehybridized for 30 min with continuous rotation at 68°C.  The probes were prepared for hybridization by adding 5 ml of Cot-1 DNA to the labeled probe and incubating in a boiling water bath for 2 min and then cooled on ice for 2 min.  Without pouring the concentrated probe directly on the surface of the membrane, the mixture was added to the array and the prehybridization solution.  The samples were hybridized overnight with continuous rotation at 68°C.  The next day, the hybridization solution was discarded in the appropriate container for radioactive waste and replaced with 200 microL of pre-warmed Wash Solution 1.  This 30 min wash step at 68°C was repeated three more times.  One 30 min wash in 200 microL pre-warmed Wash Solution 2 at 68°C was followed by a 5-min wash in 200 microL of 2X SSC with agitation at room temperature.  Using forceps, the array was carefully removed from the container and the excess wash solution will be shaken off.  The damp membranes were immediately wrapped in plastic wrap and placed on the phosphorimaging screens (Molecular Dynamics, Piscataway, NJ) for an overnight exposure.

scan_protocol: The damp membranes were immediately wrapped in plastic wrap and placed on the phosphorimaging screens (Molecular Dynamics, Piscataway, NJ) for an overnight exposure.  The exposed phosphorimaging screens were aligned on the glass plate of the Storm Phosphorimaging System (Molecular Dynamics).  The appropriate scan area will be selected, and data was acquired for analysis.

data_processing: Data were processed further when loaded onto GeneSpring GX v. 7.3.1.  Data were normalized per chip to the median of the chip then further normalized per gene to the median of the PBS-injected (steady state) control samples.

source_name: Half perfused brain divided along sagittal sulcus from PBS-injected mouse 4 days post-infection

label_protocol:
Total RNA from mouse brain was labeled using the Atlas Pure Total RNA Labeling System (catalog #7906-1, BD Clontech, Palo Alto, CA).  A master mix was prepared for all labeling reactions and reagents combined at room temperature.  Total RNA was combined with 1 microL of CDS primer mix in a 0.5-ml PCR tube and placed in a preheated PCR thermal cycler at 70°C for 2 min.  The temperature of the thermal cycler was reduced to 50°C and incubated for 2 min.  During this incubation, 1 microL per reaction of MMLV Reverse Transcriptase was added to the Master Mix.  After completion of the 2-min incubation at 50°C, 8 ml of the Master Mix was added to each reaction tube, and the tubes were incubated in the thermal cycler for another 25 min at 50°C.  The reaction was stopped by the addition of 1 microL of 10X termination mix.
A NucleoSpin Extraction Spin column was placed into a 2-ml collection tube and the sample was pipetted onto the column.  The samples were centrifuged at 14,000 rpm for 2 min, and the collection tube containing the flow-through was discarded into the appropriate container for radioactive waste.  The NucleoSpin column was inserted into a fresh 2-ml collection tube and 400 microL of buffer NT3 was added to the column.  Samples were centrifuged at 14,000 rpm for 2 min and the collection tubes and flow-through discarded.  This step was repeated two more times.  The NucleoSpin column was transferred to a clean 1.5-ml microcentrifuge tube.  Then 100 microLof Buffer NE was added and the column allowed to soak for 2 min.  The samples were centrifuged at 14,000 rpm for 2 min to elute the purified probe.  Scintillation counting checked the radioactivity of the probe.

growth_protocol: Listeria monocytogenes strain EGD was grown for 4.5 hrs from stock aliquots in brain heart infusion at 37 degrees C.  Grown culture was diluted in sterile PBS prior to injection.  Uninfected controls received sterile PBS only.

extract_protocol:
Total RNA from mouse brain was isolated using the Atlas Pure Total RNA Labeling System (catalog #7906-1, BD Clontech, Palo Alto, CA). Tissue was homogenized with 3 ml of denaturing solution and incubated on ice for 10 min.  The homogenate was poured into a 15 ml centrifuge tube and centrifuged at 12,000 rpm (15,000 X G) for 5 min at 4°C to remove cellular debris.  The entire supernatant was transferred to a new centrifuge tube and 6 ml of saturated phenol was added.  The tubes was capped, vortexed for 1 min and incubated on ice for 5 min.  1.8 ml of chloroform was added to each tube, vortexed for 1 min and incubated on ice for 5 min.  Samples were centrifuged at 12,000 rpm for 10 min at 4°C.  The upper phase containing the RNA was transferred to a new tube.  To each tube, 4.8 ml of saturated phenol was added, vortexed, and incubated on ice for 5 min. An additional phenol:chloroform extraction using the above volumes was performed.  The upper  phase was transferred to a new centrifuge tube and 6 ml of isopropanol was added to each tube.  The solution was gently mixed and incubated on ice for 10 min.  The samples were centrifuged at 12,000 rpm for 15 min at 4°C.  After removal of the supernatant, 3 ml of 80% ethanol was added to the RNA pellet.  The samples were centrifuged at 12,000 rpm for 5 min at 4°C.  The pellet was air dried for approximately 10 min and resuspended in enough RNase-free water to yield an RNA concentration of 2 mg/ml.
Samples of total RNA were prepared in 1.5 ml microcentrifuge tubes containing 10X DNase buffer, DNase (1 unit/ml), ANTI-RNase (Ambion) and brought to a final volume of 1 ml with deionized water.  The reactions were incubated at 37°C for 30 min in an air incubator.  At the end of the incubation period, 100 microL of 10X termination mix was added and mixed well by pipetting.  Each sample was split into two 1.5 microcentrifuge tubes containing 550 microL each.  To these tubes, 500 microL of saturated phenol and 300 microL of chloroform were added.  Samples were vortexed thoroughly and centrifuged at 14,000 rpm for 10 min at 4°C.   The upper aqueous layer was transferred to a fresh 1.5 microcentrifuge tube and 550 microL of chloroform was added to each tube.  Samples were centrifuged at 14, 000 rpm for 10 min at 4°C to separate the phases.  The aqueous top layer was placed in a 1.5 ml centrifuge tube and to each tube was added 1/10 volume of 2 M NaOAc and 2.5 volumes of 95% ethanol.  The mixture was vortexed and incubated on ice for 10 min.  Tubes were centrifuged at 14,000 rpm for 15 min at 4°C.  The supernatant and all traces of ethanol were removed and 500 microL of 80% ethanol was gently layered over the pellet.  Following a final spin at 14,000 rpm for 5 min at 4°C, the supernatant was carefully removed and the pellet was air dried for approximately 10 min.  The precipitate was dissolved in the appropriate volume of RNase-free H2O.

treatment_protocol:
Adult female C57BL/6 mice, 8-10 weeks old were utilized for this experiment.  The experimental group consisted of 25 animals that were infected at by intravenous injection of 0.1 ml endotoxin-free phosphate-buffered saline (PBS) containing 1-2 LD50 L. monocytogenes strain EGD (approximately 4.0 log10 CFU bacteria).  The control group of 25 littermates and were injected with PBS only.  Groups of 5 mice were harvested at 24 hour intervals for 4 days.
During tissue harvest, mice were anesthetized by injection of ketamine/xylazine and exsanguinated by cardiac puncture.  The animals were then perfused via the left ventricle with 30 ml of sterile, endotoxin-free PBS, and the brain was removed aseptically.  The brain was divided along the sagittal fissure into 2 approximately equal parts.  One portion of each organ was frozen in liquid nitrogen, the other portion was weighed and used for culture.  Brain halves frozen in liquid nitrogen were stored at -80 degrees C until further utilized

tag: Sex

value: Female

tag: Strain

tag: Age

value: 8-10 weeks

tag: Injected with sterile PBS

tag: Hours post infection or injection

value: half transcardially perfused brain cut along sagittal sulcus


title: Mouse 21 Infected d4pi with Listeria monocytogenes

source_name: Half perfused brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 4 days post-infection

tag: Infected Lethal dose Listeria monocytogenes EGD

tag: Tissue


title: DBA/2J_BasalGanglia 16011978014740


title: C3H/HeJ_Cerebellum 16011978013166


title: Mouse 22 Infected d4pi with Listeria monocytogenes


title: Mouse 22 Steady state d4pi post-PBS injection


title: AKR/J_Hippocampus 16011978013165


title: C3H/HeJ_Hippocampus 16011978012361


title: Mouse 23 Infected d4pi with Listeria monocytogenes


title: FVB/NJ_CingulateCortex 251197820762


title: Mouse 20 Steady state d4pi post-PBS injection


title: Mouse 20 Infected d4pi with Listeria monocytogenes


title: Mouse 17 Steady state d3pi post-PBS injection

source_name: Half perfused brain divided along sagittal sulcus from PBS-injected mouse 3 days post-infection


title: Mouse 19 Infected d4pi with Listeria monocytogenes


title: Mouse 18 Infected d3pi with Listeria monocytogenes

source_name: Half perfused brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 3 days post-infection


title: A/J_Hippocampus 16011978016444


title: AKR/J_OlfactoryBulb 251197817992


title: Mouse 18 Steady state d4pi post-PBS injection

source_name: Half perfused brain divided along sagittal sulcus from PBS-injected) mouse 4 days post-infection


title: Mouse 15 Steady state d3pi post-PBS injection

source_name: Half perfused brain divided along sagittal sulcus from PBS-injected mouse 2 days post-infection


title: Mouse 19 Steady state d4pi post-PBS injection


title: Mouse 13 Infected d3pi with Listeria monocytogenes


title: Mouse 16 Infected d3pi with Listeria monocytogenes


title: Mouse 16 Steady state d3pi post-PBS injection


title: Mouse 11 Steady state d2pi post-PBS injection


title: Mouse 11 Infected d2pi with Listeria monocytogenes

source_name: Half perfused brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 2 days post-infection


title: Mouse 15 Infected d3pi with Listeria monocytogenes


title: Mouse 12 Steady state d3pi post-PBS injection


title: Mouse 13 Steady state d3pi post-PBS injection


title: C3H/HeJ_CingulateCortex 16011978014749


title: Mouse 12 Infected d2pi with Listeria monocytogenes


title: Mouse 14 Infected d3pi with Listeria monocytogenes


title: Mouse 8 Infected d2pi with Listeria monocytogenes


title: C3H/HeJ_Cerebellum 16011978014888


title: Mouse 9 Steady state d2pi post-PBS injection


title: Mouse 10 Steady state d2pi post-PBS injection


title: Mouse 8 Steady state d1pi post-PBS injection

source_name: Half perfused brain divided along sagittal sulcus from  PBS-injected mouse 2 days post-infection


title: Mouse 9 Infected d2pi with Listeria monocytogenes


title: Mouse 7 Steady state d2pi post-PBS injection


title: Mouse 5 Infected d1pi with Listeria monocytogenes

source_name: Half perfused brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 1 day post-infection

tag: Infected Lethal dose Listeria monocytogenes EGD or Injected sterile PBS


title: Mouse 3 Infected d1pi with Listeria monocytogenes


title: Mouse 5 Steady state d1pi post-PBS injection

source_name: Half perfused brain divided along sagittal sulcus from PBS-injected mouse 1 day post-infection


title: Mouse 1 Steady state d1pi post-PBS injection


title: Mouse 3 steady state 1 day Post-PBS injection


title: Mouse 4 Infected d1pi with Listeria monocytogenes


title: Mouse 4 Steady state d1pi post-PBS injection

tag: Injected sterile PBS


title: Mouse 7 Infected d2pi with Listeria monocytogenes


title: Mouse 2 Infected d1pi with Listeria monocytogenes

source_name: Half of perfused brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 1 day post-infection


title: Mouse 1 steady state 1 day Post-PBS injection

source_name: Half of a perfused brain divided along sagittal sulcus from PBS-injected mouse 1 day post-infection


title: Mouse 1 Infected d1pi with Listeria monocytogenes

hyb_protocol: We chose to use the Atlas 5K plastic mouse array (Clontech) cDNA array that provides reliable evaluation of 5,030 genes.  Each Atlas Array was placed in a hybridization bottle containing deionized H2O.  The water was poured off allowing the membrane to adhere to the inside walls of the bottle and to prevent the membrane from drying the prepared ExpressHyb (Clontech).  Then sheared salmon testes solutions were added.  The membranes were prehybridized for 30 min with continuous rotation at 68 °C.  The probes were prepared for hybridization by adding 5 ml of Cot-1 DNA to the labeled probe and incubating in a boiling water bath for 2 min and then cooled on ice for 2 min.  Without pouring the concentrated probe directly on the surface of the membrane, the mixture was added to the array and the prehybridization solution.  The samples were hybridized overnight with continuous rotation at 68 °C.  The next day, the hybridization solution was discarded in the appropriate container for radioactive waste and replaced with 200 microL of pre-warmed Wash Solution 1.  This 30 min wash step at 68 °C was repeated three more times.  One 30 min wash in 200 microL pre-warmed Wash Solution 2 at 68 °C was followed by a 5-min wash in 200 microL of 2X SSC with agitation at room temperature.  Using forceps, the array was carefully removed from the container and the excess wash solution will be shaken off.  The damp membranes were immediately wrapped in plastic wrap and placed on the phosphorimaging screens (Molecular Dynamics, Piscataway, NJ) for an overnight exposure.

source_name: Half brain divided along sagittal sulcus from Listeria monocytogenes infected mouse 1 day post-infection

label_protocol:
Total RNA from mouse brain was labeled using the Atlas Pure Total RNA Labeling System (catalog #7906-1, BD Clontech, Palo Alto, CA).A master mix was prepared for all labeling reactions and reagents combined at room temperature.  Total RNA was combined with 1 microLof CDS primer mix in a 0.5-ml PCR tube and placed in a preheated PCR thermal cycler at 70 °C for 2 min.  The temperature of the thermal cycler was reduced to 50 °C and incubated for 2 min.  During this incubation, 1 microL per reaction of MMLV Reverse Transcriptase was added to the Master Mix.  After completion of the 2-min incubation at 50 °C, 8 ml of the Master Mix was added to each reaction tube, and the tubes were incubated in the thermal cycler for another 25 min at 50 °C.  The reaction was stopped by the addition of 1 microL of 10X  termination mix.
A NucleoSpin Extraction Spin column was placed into a 2-ml collection tube and the sample was pipetted onto the column.  The samples were centrifuged at 14,000 rpm for 2 min, and the collection tube containing the flow-through was discarded into the appropriate container for radioactive waste.  The NucleoSpin column was inserted into a fresh 2-ml collection tube and 400 microL of buffer NT3 was added to the column.  Samples were centrifuged at 14,000 rpm for 2 min and the collection tubes and flow-through discarded.  This step was repeated two more times.  The NucleoSpin column was transferred to a clean 1.5-ml microcentrifuge tube.  Then 100 microLof Buffer NE was added and the column allowed to soak for 2 min.  The samples were centrifuged at 14,000 rpm for 2 min to elute the purified probe.  Scintillation counting checked the radioactivity of the probe.

extract_protocol:
Total RNA from mouse brain was isolated using the Atlas Pure Total RNA Labeling System (catalog #7906-1, BD Clontech, Palo Alto, CA). Tissue was homogenized with 3 ml of denaturing solution and incubated on ice for 10 min.  The homogenate was poured into a 15 ml centrifuge tube and centrifuged at 12,000 rpm (15,000 X G) for 5 min at 4 °C to remove cellular debris.  The entire supernatant was transferred to a new centrifuge tube and 6 ml of saturated phenol was added.  The tubes was capped, vortexed for 1 min and incubated on ice for 5 min.  1.8 ml of chloroform was added to each tube, vortexed for 1 min and incubated on ice for 5 min.  Samples were centrifuged at 12,000 rpm for 10 min at 4 °C.  The upper phase containing the RNA was transferred to a new tube.  To each tube, 4.8 ml of saturated phenol was added, vortexed, and incubated on ice for 5 min. An additional phenol:chloroform extraction using the above volumes was performed.  The upper phase was transferred to a new centrifuge tube and 6 ml of isopropanol was added to each tube.  The solution was gently mixed and incubated on ice for 10 min.  The samples were centrifuged at 12,000 rpm for 15 min at 4 °C.  After removal of the supernatant, 3 ml of 80% ethanol was added to the RNA pellet.  The samples were centrifuged at 12,000 rpm for 5 min at 4 °C.  The pellet was air dried for approximately 10 min and resuspended in enough RNase-free water to yield an RNA concentration of 2 mg/ml.
Samples of total RNA were prepared in 1.5 ml microcentrifuge tubes containing 10X DNase buffer, DNase (1 unit/ml), ANTI-RNase (Ambion) and brought to a final volume of 1 ml with deionized water.  The reactions were incubated at 37 °C for 30 min in an air incubator.  At the end of the incubation period, 100 microL of 10X termination mix was added and mixed well by pipetting.  Each sample was split into two 1.5 microcentrifuge tubes containing 550 microL each.  To these tubes, 500 microL of saturated phenol and 300 microL of chloroform were added.  Samples were vortexed thoroughly and centrifuged at 14,000 rpm for 10 min at 4 °C.   The upper aqueous layer was transferred to a fresh 1.5 microcentrifuge tube and 550 microL of chloroform was added to each tube.  Samples were centrifuged at 14, 000 rpm for 10 min at 4 °C to separate the phases.  The aqueous top layer was placed in a 1.5 ml centrifuge tube and to each tube was added 1/10 volume of 2 M NaOAc and 2.5 volumes of 95% ethanol.  The mixture was vortexed and incubated on ice for 10 min.  Tubes were centrifuged at 14,000 rpm for 15 min at 4 °C.  The supernatant and all traces of ethanol were removed and 500 microL of 80% ethanol was gently layered over the pellet.  Following a final spin at 14,000 rpm for 5 min at 4 °C, the supernatant was carefully removed and the pellet was air dried for approximately 10 min.  The precipitate was dissolved in the appropriate volume of RNase-free H2O.

tag: hours post infection or injection


title: M9

status: Public on Feb 01 2009

type: genomic

city: Toronto

first: Susan

last: Done

address: 610 University Ave

country: Canada

institute: Ontario Cancer Institute

description: run in duplicate

hyb_protocol: Labeled products were combined, 80μg of Human Cot-1 DNA and 200mg of yeast tRNA (Invitrogen) were added.  The mixture was concentrated in a speed-vac at 37°C down to 10μl and resuspended in 80μl of DIG Easy Hybe buffer (Roche, Switzerland), denatured at 100°C for 1.5 min., cooled on ice and incubated for 30 min at 37°C, then hybridized to 19K human cDNA arrays (University Health Network Microarray Centre, Toronto, Canada, www.microarrays.ca) for 16 hours at 42°C.

scan_protocol: GenePix 4000B slide scanner and GenePix Pro 6.0 software package (Molecular Devices, California, USA)

data_processing: Samples run in duplicate, Log2 ratios of duplicates averaged, filtered to exclude cDNA clones without mapping info and those spots flagged as anomalous, cenetered by the median and scale normalized.

molecule: genomic DNA

source_name: Metastasis into more distal LN

label_protocol: 1.0μg of amplified test and reference DNA was mixed with 21.5μl ddH2O and 20μl of 2.5X Random Primer/Reaction Mix Buffer (Invitrogen, www.invitrogen.com), boiled for 5 min. and 5μl of ‘low C’ dNTP mix with either 2.5μl Cy5-dCTP (Amersham Biosciences, USA) for test or Cy3 for the reference DNA with 1μl of Klenow solution, then incubated at 37°C for 2 hrs.  The reaction was stopped by adding EDTA, then 450μl of TE pH 7.4 added and the mix loaded onto a micron-30 filter (Fisher/Millipore), spun for 8-10 min. at 10,000 rpm, inverted and spun for 1 min to recover the purified probe.

extract_protocol: DNA extracted  using a QIAGEN DNA Mini Kit (QUIAGEN Inc., Canada) after a 72 hr period in lysis buffer at 56°C.  DNA from 12 normal lymph nodes was prepared similarly and pooled for the reference sample.  The single cell comparative genomic hybridization protocol (SCOMP) was used for genome amplification

tag: Microdissected sections of fresh fixed paraffin embedded tissue

source_name: Pooled normal lymph nodes


title: M20

description: run in duplicate

source_name: Metastasis into sentinel LN


title: M21

description: run in duplicate


title: M18

description: run in duplicate


title: IDC17

description: run in duplicate

source_name: IDC with detected metastasis into sentinel lymph node


title: IDC18

description: run in duplicate


title: Egr1 Chip-on-Chip, M12 untreated vs. UV treated, duplicate 2, SetB Array

status: Public on Feb 02 2009

city: San Diego

first: Yipeng

last: Wang

state: CA

institute: Vaccine Research Institute of San Diego

hyb_protocol: Following Corning Pre-Hyb, Hybridization and Washing Protocol.

scan_protocol: Array was scanned using Perkin-Elmer Scanner.

data_processing: Intensity data was extracted using Quantarray. Ratio was calculated using limma package (www.bioconductor.org) with background subtraction, print-tip loess within array normalization and scale between array normalization.

source_name: untreated M12 cell line, duplicate 2

label_protocol: Ready-To-Go DNA -dCTP labeling beads (Amersham Pharmacia Biotech)

extract_protocol: Chromatin Immunoprecipitation

tag: Egr1 Chip sample from untreated M12 cell line

source_name: UV treated M12 cell line, duplicate 2

tag: Egr1 Chip sample from UV treated M12 cell line


title: M22

description: run in duplicate


title: M19

description: run in duplicate


title: M17

description: run in duplicate


title: Egr1 Chip-on-Chip, M12 untreated vs. UV treated, duplicate 2, SetA Array


title: IDC19

description: run in duplicate


title: Egr1 Chip-on-Chip, M12 untreated va. UV treated, duplicate 1, SetB Array

source_name: untreated M12 cell line, duplicate 1

source_name: UV treated M12 cell line, duplicate 1


title: M13

description: run in duplicate


title: M14

description: run in duplicate


title: Egr1 Chip-on-Chip, M12 untreated va. UV treated, duplicate 1, SetA Array


title: IDC16

description: run in duplicate


title: IDC6

description: run in duplicate

source_name: IDC without known metastases into axillary lymph nodes


title: M15

description: run in duplicate


title: IDC7

description: run in duplicate


title: IDC8

description: run in duplicate


title: IDC12

description: run in duplicate


title: IDC15

description: run in duplicate


title: IDC10

description: run in duplicate


title: IDC9

description: run in duplicate


title: IDC11

description: run in duplicate


title: IDC14

description: run in duplicate


title: IDC13

description: run in duplicate


title: IDC2

description: run in duplicate


title: IDC5

description: run in duplicate


title: IDC4

description: run in duplicate


title: IDC3

description: run in duplicate


title: IDC1

description: run in duplicate


title: Breast invasive duct carcinoma IDC22

description: run in duplicate

source_name: Breast invasive duct carcinoma

tag: DNA


title: Breast invasive duct carcinoma IDC23

description: run in duplicate


title: card9 control

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technical University Munich

description: macrophages from wt mice, not stimulated

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure; Affymetrix Scanner 3000 7G

data_processing: rma background correction and normalization. Linear values

label: biotin, PE

source_name: Macrophages

label_protocol: samples were processed with the Whole Transcript Assay Kit as recommended by the manufacterer (Affymetrix)

growth_protocol: Macrophages were differentiated from bone marrow cells in cDMEM containing 10 % L-cell conditioned medium for 6 days and prestimulated with 10 ng/ml interferon gamma for 3h

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: not stimulated

tag: card9 KO, untreated


title: card9 curdlan

treatment_protocol: cells were stimulated with 100 µg/ml  curdlan for 48h

tag: card9 KO, curdlan


title: Breast invasive duct carcinoma IDC21

description: run in duplicate


title: card9 CpG

treatment_protocol: cells were stimulated with 1 µM CpG for 48h

tag: card9 KO, CpG


title: Breast invasive duct carcinoma IDC20

description: run in duplicate


title: bl6 TDB

treatment_protocol: cells were stimulated with 40 µg/ml TDB for 48h

tag: wt, TDB


title: card9 TDB

tag: card 9 KO, TDB


title: Breast invasive duct carcinoma IDC12

description: run in duplicate


title: bl6 control

tag: wt, untreated


title: Breast invasive duct carcinoma IDC19

description: run in duplicate


title: Breast invasive duct carcinoma IDC15

description: run in duplicate


title: Breast invasive duct carcinoma IDC18

description: run in duplicate


title: Breast invasive duct carcinoma IDC11

description: run in duplicate


title: Breast invasive duct carcinoma IDC08

description: run in duplicate


title: bl6 CpG

tag: wt, CpG treated


title: Breast invasive duct carcinoma IDC13

description: run in duplicate


title: Breast invasive duct carcinoma IDC14

description: run in duplicate


title: Breast invasive duct carcinoma IDC10

description: run in duplicate


title: bl6 curdlan

tag: wt, curdlan


title: Breast invasive duct carcinoma IDC07

description: run in duplicate


title: Breast invasive duct carcinoma IDC17

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS21

description: run in duplicate


title: Breast invasive duct carcinoma IDC09

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS15

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS20

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS19

description: The replicate raw data file GSM257548 _2.gpr (dcis19_2.gpr) for GSM257548 is not available.


title: Breast duct carcinoma in situ associated with invasive cancer DCIS16

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS22

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS18

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS17

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS09

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS10

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS11

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS12

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS08

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS01

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS04

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS13

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS06

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS05

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS07

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS02

description: run in duplicate


title: Breast duct carcinoma in situ associated with invasive cancer DCIS14

description: run in duplicate


title: Breast duct carcinoma in situ, no invasive cancer identified PureDCIS03

description: run in duplicate


title: Y15_UV6C6

status: Public on Jan 30 2009

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: We applied loop design for our microarray experiments in order to reduce the systemic error.

hyb_protocol: 3 DNA array 50 kit protocol (Genisphere)

scan_protocol: "PMTVolts=600	600"	"ScanPower=33	33"	PixelSize=5

data_processing:
Data filtering method:

The following three criteria were used to validate spots: 1) SNR ((signal-background)/ S.D. of background) of Cy3 and Cy5 both greater than 5. 2) Diameter of spot greater than 75 ìm. 3) C.V. (coefficient of variation) of pixels within a spot in the Cy3 and Cy5 channels both less than 100%. After this filtering process, on average about 45% of the spots were identified as valid.

We used MAANOVA, provided by Churchill's group (http://www.jax.org/staff/churchill/labsite/software/anova/readme.html), to perform Lowess fit normalization, and least square estimation for gene expression profiles for our microarray loop design

Details can be found in GSE7060 supplementary file "suppII.pdf".

growth_protocol: Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100μg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone).

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 2 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at time points 0h, 8h and 16hr ,and then harvested at time point 24h

tag: HaCaT Cell line, Gender

value: male, Tissue:skin keratinocytes

treatment_protocol: Cells were harvested at time point 24h without any UVB irradiation


title: Y16_C3UV3

scan_protocol: "PMTVolts=720	550"	"ScanPower=100	100"	PixelSize=5

label_protocol: 3 DNA array 50 kit protocol (Genisphere)

treatment_protocol: Cells were harvested at time point 8.5h without any UVB irradiation

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at time points 0h and 8hr ,and then harvested at time point 8.5h


title: Y9_C1UV1

scan_protocol: "PMTVolts=650	550"	"ScanPower=33	33"	PixelSize=5

treatment_protocol: Cells were harvested at time point 0.5h without any UVB irradiation

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at beginning and harvested at time point 0.5h


title: Y8_UV3UV6

scan_protocol: "PMTVolts=700	600"	"ScanPower=33	33"	PixelSize=5


title: Y7_UV5UV2

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at time points 0h, 8h and 16hr ,and then harvested at time point 16.5h

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at beginning and harvested at time point 8h


title: Y6_UV6UV1

scan_protocol: "PMTVolts=690	600"	"ScanPower=33	33"	PixelSize=5


title: Y5_UV5UV6


title: Y13_C5UV5

scan_protocol: "PMTVolts=730	600"	"ScanPower=33	33"	PixelSize=5

treatment_protocol: Cells were harvested at time point 16.5h without any UVB irradiation


title: Y14_C6UV6


title: Y12_C4UV4

treatment_protocol: Cells were harvested at time point 16h without any UVB irradiation

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at time points 0h and 8h ,and then harvested at time point 16h


title: Y4_UV4UV5


title: Y3_UV3UV4

treatment_protocol: Cells were irradiated by 10 J/m2 UVB at time points 0h and 8hr ,and then harvested at time point 16h


title: Y11_C3UV3


title: Y10_C2UV2

treatment_protocol: Cells were harvested at time point 8h without any UVB irradiation


title: Y1_UV1UV2

scan_protocol: "PMTVolts=720	630"	"ScanPower=33	33"	PixelSize=5

value: male, Tissue:skin keratinocyte


title: 13697373 - ler 3 vs sqe1 3

status: Public on Jan 24 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Arabidopsis transcriptome microarray from wild type and mutant plants.

hyb_protocol: sqe1 3 Cy5 / ler 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: sqe1 3

label_protocol: labeling

growth_protocol: leaf - Media=Pots	 hygrometry=60% RH	 Temperature=23ºC	 Light=130 uM/m2seg Long Day

treatment_protocol: no treatment

tag: Arabidopsis thaliana (landsberg erecta) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: ler 3

tag: Arabidopsis thaliana (landsberg erecta)  - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13697374 - sqe1 3 vs ler 3

hyb_protocol: ler 3 Cy5 / sqe1 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: chc101 control vs B73 control

status: Public on Dec 31 2008

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Hybridization was highly correlated as assessed from correlations between median signal intensities (r2 = 0.97 for both dyes; data not shown) and between log2 ratios of the signals (r2 = 0.94; data not shown).

hyb_protocol: Array hybridizations were carried out according to the manufacturer's instructions. For the experiments, Agilent Technologies microarrays were used, they contained 43,451 maize 60-mer probes and each slide had the same pattern of probes in quadruplicate (4x44 version), that were used to hybridize independent biological samples. Specifically, each array was hybridized with two samples, each of 0.825 μg labeled target cRNA, for 17 hours at 60°C. The samples were hybridized in a double loop design arrangement, as described by Kerr and Churchill et (2001).

scan_protocol: Data were acquired with an Agilent G2565BA scanner.

data_processing:
The slide images were processed with Feature Extraction (Agilent), including normalization of the data. After filtering out saturated spots flagged by Feature Extraction, and for each slide, we first calculated thresholds for background hybridizations with the internal negative controls.
All statistical analyses were performed using either the R package (http://www.r-project.org/) or Microsoft EXCEL (http://www.microsoft.com)

source_name: chc101 control plants

label_protocol: Target cRNA was prepared and labeled with either Cy-3 or Cy-5 dye (PerkinElmer, Boston, MA, USA) from 3 μg of total RNA using an Agilent Low RNA Input Fluorescent Linear Amplification Kit. Array hybridizations were carried out according to the manufacturer's instructions.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen, Carlsbad CA) and purified by ethanol precipitation.  The yield and RNA purity were determined spectrophotometrically with a SpectraMax 250 plate spectrophotometer (Molecular Devices, Sunnyvale, CA, USA) and verified by agarose gel analysis.

tag: chc101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with PE filters to exclude wavelengths lower than 320 nm.

source_name: B73 control plants

tag: B73 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with PE filters to exclude wavelengths lower than 320 nm.


title: Y2_UV2UV3


title: 13697367 - ler 2 vs sqe1 2

hyb_protocol: sqe1 2 Cy5 / ler 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: sqe1 2

source_name: ler 2


title: 13697370 - sqe1 2 vs ler 2

hyb_protocol: ler 2 Cy5 / sqe1 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: mbd101 control vs B73 control

source_name: mbd101 control plants

tag: mbd101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with PE filters to exclude wavelengths lower than 320 nm.


title: UV-B irradiated B73 vs chc101 control

source_name: UV-B irradiated B73 plants

tag: B73 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm.


title: UV-B irradiated  B73 vs  B73 control

source_name: UV-B irradited B73 plants


title: 13697320 - ler 1 vs sqe1 1

hyb_protocol: sqe1 1 Cy5 / ler 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: sqe1 1

source_name: ler 1


title: UV-B irradiated chc101 vs chc101 control

source_name: UV-B irradiated chc101 plants

tag: chc101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm.


title: mbd101 control vs chc101 control