title: A549_TMPyP4 Treatment_48hrs_Replicate1

status: Public on Aug 25 2008

city: Delhi

first: Anjali

last: Verma

state: Delhi

address: Mall road

department: Structural Biology and Genome Informatics Division

country: India

institute: Institute of Genomics and Integrative Biology

description: A549 cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. Cells were washed twice with 1X PBS before RNA isolation.

hyb_protocol: Hybridization was done in DigEasy hybridization buffer (Roche). To prevent non-specific hybridizations single stranded DNA from salmon testes and yeast transfer RNA were used. Hybridizations were performed at 37ºC for 16hrs.

scan_protocol: Slides were scanned at 10um resolution with Genepix pro 6.0 scanner using two different lasers, for Cy5 (635nm) and for Cy3 (532 nm).

data_processing: GenePixPro 6.0, Data was normalized so that the mean of the ratio of medians (635/532) of all features is equal to 1 using software Acuity 4.0 (Molecular Devices).The data (normalized values) is expressed as log2 ratio.  Within sample normalization (not across samples) was performed. After normalization, the data was filtered to include only those elements which contained only a small percentage (< 3) of saturated pixels, were not flagged bad or found absent (flags = 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) = 0.6) and were detectable above background (SNR = 3).

source_name: A549 cell culture

label_protocol: Labeling was done with the help of cRNA target synthesis and labeling kit provided by Roche, as per manufacturer protocol.

growth_protocol: Cells were grown in 25cm2 canted flasks in the presence of air, 95%, 5% CO2 at 37ºC. The cells were grown in Dulbecco's modified eagle medium (DMEM), 3.7 g/L sodium bicarbonate, 90%; fetal bovine serum, 10%. After treatments the cells were grown in minimum exposure to light

extract_protocol: Total RNA was isolated with Trizol reagent as per manufacturer protocol(SIGMA).

treatment_protocol: Cells were grown to 50% confluency before TMPyP4 treatments (100 uM final concentration in complete medium), in minimum exposure to light

tag: A549 cells are epithelial cells derived from lung carcinoma.This is a hypotriploid human cell line with the modal chromosome number of 12, occurring in 24% of cells

label: Cy5, treated


title: HFQ_LB_OD=2_BR2

status: Public on Aug 23 2008

type: mixed

city: Norwich

first: Sacha

last: Lucchini

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: Institute of Food Research

description: Intensity ratios of RNA (channel 2) divided by DNA (channel 1) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

hyb_protocol: Slides blocked with DCE according to protocol at PMID 11266573. For hybridisation and washing protocols see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

scan_protocol: Axon GenePix4000A, 10nm resolution scan & see http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

data_processing: Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios.

molecule: genomic DNA

organism: Salmonella enterica

source_name: Reference genomic DNA

label_protocol: Channel Label Protocol: Labelling protocol at http://www.ifr.ac.uk/Safety/Microarrays/default.html#protocols

growth_protocol: S. Typhimurium grown to stationary phase

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)

molecule: total RNA

label_protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

growth_protocol: S. Typhimurium grown to OD600=2 in LB under aeration

extract_protocol: Total RNA isolation protocol at http://www.ifr.ac.uk/safety/Microarrays/protocols.html

tag: Salmonella enterica serovar Typhimurium SL1344 hfq-


title: CTRL_LB_SPI-1_BR2

description: Intensity ratios of RNA (channel 1) divided by DNA (channel 2) signals minus respective background signals. Total array is 16 blocks arranged in 4X4 configuration.

label_protocol: Channel Label Protocol: Labelling protocol at http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols

tag: Salmonella enterica serovar Typhimurium SL1344

growth_protocol: S. Typhimurium grown under SPI-1 inducing conditions: overnight growth in LB-broth containing 0.3M NaCl, under oxygen tension.


title: HFQ_LB_SPI-1_BR1


title: HFQ_LB_OD=2_BR1


title: HFQ_LB_OD=2_BR3


title: CTRL_LB_OD=2_BR1


title: A549_TMPyP4 Treatment_48hrs_Dyeswap2

type: RNA

organism: Homo sapiens

label: Cy5, control


title: A/J mice on control diet at time 0 (TechRep2)

status: Public on Aug 27 2008

city: Cleveleand

first: Joseph

last: Nadeau

state: OH

address: 10900 Euclid Avenue

department: Genetics

country: USA

institute: Case Western Reserve University

description: No additional information

hyb_protocol: THE INSTITUTE FOR GENOMIC RESEARCHStandard Operating Procedure TITLE: MICROARRAY LABELED PROBE HYBRIDIZATION PAGE: 1 of 5 SOP #: M005 REVISION LEVEL: 3 EFFECTIVE DATE: 9/11/02 AUTHOR:Jeremy Hasseman PRIMARY REVIEWERS:Emily Chen, Ivana Yang 1. PURPOSE This protocol describes the hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with PCR amplified cDNA. 2. SCOPE This procedural format is currently utilized by Human Colon Cancer and Mouse microarray projects under the supervision of John Quackenbush within the Mammalian Genomics Dept. 3. MATERIALS 3.1 20X Saline-Sodium Citrate (SSC) (Sigma; Cat # S-6639) 3.2 10% Sodium Dodecyl Sulfate (SDS)(Life Technologies; Cat # 15553-035) 3.3 Bovine Serum Albumin (BSA) (Sigma; Cat # A-9418) 3.4 Formamide, redistilled (Life Technologies; Cat # 15515-081) 3.5 Isopropanol (Fisher Scientific; Cat # A451-1) 3.6 Coplin jar (VWR; Cat # 25457-200) 3.7 Human COT1-DNA (Life Technologies; Cat # 15279-011) 3.8 Mouse COT1-DNA (Life Technologies; Cat # 18440-016) 3.9 Poly(A)-DNA (Pharmacia; Cat # 27-7836-01) 3.10 Microscope Cover Glass (Fisher Scientific; Cat # 12-545J) 3.11 Corning UltraGAPSä Coated Slides (bar-coded) (Corning; Cat # 40015) 3.12 Hybridization chamber (Corning Costar; Cat #2551) 3.13 1 L .22 mm CA (cellulose acetate) Filter System (Corning; Cat #430517) 3.14 Pressurized air duster (Fellowes; Cat # 99790) or clean in-house pressurized air source 4. PROCEDURE 4.1 UV Cross-linking and Prehybridizaton 4.1.1 Aminosilane coated slides (Corning UltraGAPSä Coated Slides) spotted with cDNA in 50% DMSO are UV cross-linked at ~120 mJ. 4.1.2 Prepare prehybridization buffer (5X SSC, 0.1% SDS, 1% BSA) and sterilize by filtration using a CA filter. Preheat at 42oC for ~30 minutes before use. 4.1.3 Place the printed slide(s) to be used for the hybridization in a Coplin jar containing preheated prehybridization buffer and incubate at 42oC for 45 minutes. 4.1.4 Washing Slides - Fill two Coplin jars with MilliQ water and another with isopropanol. - With forceps carefully grasp slide by the labeled end and vertically dip slide into the first Coplin jar (water) so that the slide is completely submerged. Dip slide four or five times. - Dip the slide again in the water five times but only submerging the slide enough to wash the printed array itself. - Using the same technique dip slide into the second Coplin jar (water). - Finally dip slide into the third Coplin jar (isopropanol) submerging the slide completely. Note: Replace each water wash after every five slides. 4.1.5 Drying Slides - Carefully but quickly blow-dry the front of the slide with compressed air. Note: To avoid blowing debris from the forceps onto the array, first blow from where the array ends toward the forceps. Then dry the array itself by blowing down the slide away from the forceps. - Finally dry the back of the slide. - Note the general appearance of the slide. Streaking or mottling on the slide surface indicates further washing is necessary. - Repeat the water/water/isopropanol wash cycle as necessary to clean the slide. Blow-dry between each cycle. 4.1.6 Use slides immediately following prehybridization to ensure optimal hybridization efficiency. 4.2 Hybridization 4.2.1 Prepare 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS). 4.2.2 Prepare Poly(A)-DNA by dissolving stock Poly(A)-DNA in a neutral buffer (i.e. 10 mM Tris, pH 7) to a final concentration of 20 mg/mL. 4.2.3 Prepare COT1-DNA (stock conc.1mg/mL) by ethanol precipitation: - Add 2 to 3 volumes of ethanol and 0.1 volumes of 3 M Sodium Acetate (NaOAc) to the stock tube. - Mix well and place on dry ice for 20-30 minutes or in -20oC freezer overnight. - Centrifuge for 20-30 minutes in a cold room microfuge at maximum angular velocity. - Remove supernatant and allow excess ethanol to dry off. - Dissolve precipitated COT1 in a neutral buffer (i.e. 10 mM Tris, pH 7) to the final concentration of 20mg/mL. 4.2.4 Resuspend labeled probe (Cy3/Cy5 probe mixture: see SOP-M004) in 24 mL of 1X hybridization buffer. Note: Expose Cy labeled probe to light as little as possible during the hybridization process. 4.2.5 To block nonspecific hybridization add: COT1-DNA (20 mg/mL) ... 1mL Poly(A)-DNA (20mg/mL) ... 1mL Note: The COT1-DNA is organism specific: add mouse COT1 to labeled mouse probes and human COT1-DNA to labeled human probes. 4.2.6 To denature, heat the probe mixture at 95oC for 3 minutes and snap cool on ice for 30 sec. 4.2.7 Centrifuge the probe mixture at maximum angular velocity for 1 minute. Keep at room temperature and use immediately. 4.2.8 To Apply Labeled Probe Mixture - Place a prehybridized microarray slide (array side up) between the guide teeth in the bottom half of a hybridization chamber. - Pipette the labeled probe mixture (~26 mL) to the slide surface near one end of the array print area keeping bubbles to a minimum. - Take a 22mm x 60mm microscope glass coverslip, dust it with compressed air, and grasp one end with forceps. - Holding the coverslip over the array print area, lower the end nearest the pool of cDNA probe until solution wicks to the surface of the coverslip. - Gradually lower the opposite end of the coverslip (held by the forceps) onto the slide. The solution may take a minute or two to wick across the entire length of the slide. - After probe has wicked across the slide carefully adjust the coverslips position with the tip of the forceps so that there is an even margin between the edge of the coverslip and the edge of the slide. - Work any large bubbles toward the edge by gently tapping the coverslip surface; small bubbles will absolve themselves during hybridization. 4.2.9 To the small wells at each end of the chamber add 10 mL of water (20mL total), cover, and seal the chamber. 4.2.10 Wrap the chamber in foil (light-tight) and incubate in a 42oC water bath for 16-20 hours. To ensure chamber remains level and does not float to the surface place a small weight upon it. Note: Do not flip the hybridization chamber upside down during hybridization; this may cause the coverslip to shift from the slide and adversely affect the hybridization. 4.2.11 Prepare a low stringency wash buffer (~500mL) containing 1X SSC and 0.2% SDS and a high-stringency wash buffer (~500mL) containing 0.1X SSC and 0.2% SDS. 4.2.12 After the incubation remove foil and unseal hybridization chamber. Remove the slide from the chamber, taking care not to disturb the coverslip. 4.2.13 To remove coverslip submerge slide in a dish containing low stringency wash buffer (preheated to 42oC). With forceps shake the slide gently to loosen the coverslip. With time the coverslip will slide free of the slide surface. Note: Once the slide has been hybridized it should be exposed to light as little as possible. Therefore, all staining dishes should be covered with foil to make them light tight. 4.2.14 After the coverslip is removed place slide in a staining dish containing lower stringency wash buffer (preheated to 42oC) and agitate for 4 minutes. 4.2.15 Wash the slide in a staining dish with high stringency wash buffer by agitating for 4 minutes at room temperature. 4.2.16 Wash the slide in 0.1X SSC agitating for 4 minutes at room temperature. (alternatively one can wash twice in 0.1X SSC agitating for 2.5 minutes to minimize SDS carryover.) 4.2.17 Finally dip the slide in a Coplin jar filled with water several times and blow dry using the same technique as step 4.1.4. 4.2.18 Place slides in a light tight slide box until they can be scanned, preferably as soon as possible.

scan_protocol: Array images were scanned using the GenePix 4000A scanner (Axon Instruments, Union City, CA). Cy5 PM volt at 750, Cy3 PM volt at 680.

data_processing: Array spot intensities were acquired using TIGR Spotfinder as outlined in (Yang et al. 2002, Genome Biol 3: research0062) and normalized using global Lowess regression using MIDAS (Saeed et al. 2003, Biotechniques 34:374-378) set at a smoothing parameter of 0.3 and filtered for inconsistent flip-dye pairs at two standard deviation cutoff.

organism: Mus musculus

source_name: Stratagene universal mouse reference RNA

label_protocol: THE INSTITUTE FOR GENOMIC RESEARCH Standard Operating Procedure TITLE: AMINOALLYL LABELING OF RNA FOR MICROARRAYS SOP #: M004 REVISION LEVEL: 2 EFFECTIVE DATE: 3/4/02 AUTHOR: Jeremy Hasseman PRIMARY REVIEWERS: Emily Chen, Ivana Yang 1. PURPOSE This protocol describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules. 2. SCOPE This procedural format is utilized by Human Colon Cancer and Mouse microarray projects under the supervision of John Quackenbush within the Eukaryotic Genomics Dept. MATERIALS 3.1 5-(3-aminoallyl)-2^deoxyuridine-5^-triphosphate (AA-dUTP) (Sigma; Cat # A0410) 3.2 100 mM dNTP Set PCR grade (Life Technologies; Cat # 10297-018) 3.3 Random Hexamer primers (3mg/mL) (Life Technologies; Cat # 48190- 011) 3.4 SuperScript II RT (200U/uL) (Life Technologies; Cat # 18064-014) 3.5 Cy-3 ester (AmershamPharmacia; Cat # PA23001) 3.6 Cy-5 ester (AmershamPharmacia; Cat # PA25001) 3.7 QIAquick PCR Purification Kit (Qiagen; Cat # 28106) 3.8 RNeasy® Mini Kit (Qiagen; Cat # 74106) 3.9 Microcon YM-30 Centrifugal Filter Devices (Millipore; Cat # 42410) 4. REAGENT PREPARATION 4.1 Phosphate Buffers 4.1.1 Prepare 2 solutions: 1M K2HPO4 and 1M KH2PO4 4.1.2 To make a 1M Phosphate buffer (KPO4, pH 8.5-8.7) combine: 1M K2HPO4 ..9.5 mL 1M KH2PO4 ..0.5 mL 4.1.3 For 100 mL Phosphate wash buffer (5 mM KPO4, pH 8.0, 80% EtOH) mix: 1 M KPO4 pH 8.5... 0.5 mL MilliQ water ... 15.25 mL 95% ethanol ... 84.25 mL Note: Wash buffer will be slightly cloudy. 4.1.4 Phosphate elution buffer is made by diluting 1 M KPO4, pH 8.5 to 4 mM with MilliQ water. 4.2 Aminoallyl dUTP 4.2.1 For a final concentration of 100mM add 19.1 µL of 0.1 M KPO4 buffer (pH 7.5) to a stock vial containing 1 mg of aa-dUTP. Gently vortex to mix and transfer the aa-dUTP solution into a new microfuge tube. Store at -20oC. 4.2.2 Measure the concentration of the aa-dUTP solution by diluting an aliquot 1:5000 in 0.1 M KPO4 (pH 7.5) and measuring the OD289. (Stock concentration in mM = OD289 x 704) 4.3 Labeling Mix (50X) with 2:3 aa-dUTP: dTTP ratio 4.3.1 Mix the following reagents: Final concentration dATP (100 mM) 5µL... (25 mM) dCTP (100 mM) 5µL... (25 mM) dGTP (100 mM) 5µL... (25 mM) dTTP (100 mM) 3µL... (15 mM) aa-dUTP (100 mM) 2µL... (10 mM) Total: 20µL 4.3.1 Store unused solution at -20oC. 4.4 Sodium Carbonate Buffer (Na2CO3): 1M, pH 9.0 4.4.1 Dissolve 10.8 g Na2CO3 in 80 mL of MilliQ water and adjust pH to 9.0 with 12 N HCl; bring volume up to 100 mL with MilliQ water. 4.4.2 To make a 0.1 M solution for the dye coupling reaction dilute 1:10 with water. Note: Carbonate buffer changes composition over time; make it fresh every couple of weeks to a month. 4.5 Cy-dye esters 4.5.1 Cy3-ester and Cy5-ester are provided as a dried product in 5 tubes. Resuspend a tube of dye ester in 73 uL of DMSO before use. 4.5.2 Wrap all reaction tubes with foil and keep covered as much as possible in order to prevent photobleaching of the dyes. Note: Dye esters must either be used immediately or aliquotted and stored at -80oC. Any introduced water to the dye esters will result in a lower coupling efficiency due to the hydrolysis of the dye esters. Since DMSO is hygroscopic (absorbs water from the atmosphere) store it well sealed in desiccant. 5. PROCEDURE 5.1 Aminoallyl Labeling 5.1.1 To 10 ug of total RNA (or 2 ug poly(A+) RNA) which has been DNase I-treated and Qiagen RNeasy purified, add 2 uL Random Hexamer primers (3mg/mL) and bring the final volume up to 18.5 uL with RNase-free water. 5.1.2 Mix well and incubate at 70oC for 10 minutes. 5.1.3 Snap-freeze in dry ice/ethanol bath for 30 seconds, centrifuge briefly at >10,000 rpm and continue at room temperature. 5.1.4 Add: 5X First Strand buffer .. 6 uL 0.1 M DTT .. 3 uL 50X aminoallyl-dNTP mix .. 0.6 uL SuperScript II RT (200U/uL) .. 2 uL 5.1.5 Mix and incubate at 42oC for 3 hours to overnight. 5.1.6 To hydrolyze RNA, add: 1 M NaOH 10 uL 0.5 M EDTA 10 uL mix and incubate at 65oC for 15 minutes. 5.1.7 Add 10 uL of 1 M HCl to neutralize pH. (Alternatively, one can add 25 uL 1 M HEPES pH 7.0 or 25 uL 1 M Tris pH 7.4) 5.2 Reaction Purification I: Removal of unincorporated aa-dUTP and free amines (use either the Qiagen or the Microcon method) Qiagen Cleanup Method: Note: This purification protocol is modified from the Qiagen QIAquick PCR purification kit protocol. The phosphate wash and elution buffers (prepared in 4.1.3 and 4.1.4) are substituted for the Qiagen supplied buffers because the Qiagen buffers contain free amines which compete with the Cy dye coupling reaction. 5.2.1 Mix cDNA reaction with 300 uL (5X reaction volume) buffer PB (Qiagen supplied) and transfer to QIAquick column. 5.2.2 Place the column in a 2 ml collection tube (Qiagen supplied) and centrifuge at ~13,000 rpm for 1 minute. Empty collection tube. 5.2.3 To wash, add 750 uL phosphate wash buffer to the column and centrifuge at ~13,000 rpm for 1 minute. 5.2.4 Empty the collection tube and repeat the wash and centrifugation step (5.2.3). 5.2.5 Empty the collection tube and centrifuge column an additional 1 minute at maximum speed. 5.2.6 Transfer column to a new 1.5 mL microfuge tube and carefully add 30 uL phosphate elution buffer (see 4.1.4) to the center of the column membrane. 5.2.7 Incubate for 1 minute at room temperature. 5.2.8 Elute by centrifugation at ~13,000 rpm for 1 minute. 5.2.9 Elute a second time into the same tube by repeating steps 5.2.6- 5.2.8. The final elution volume should be ~60 uL. 5.2.10 Dry sample in a speed vac. or~ Microcon YM-30 Cleanup Method: 5.2.1 Place the Microcon sample reservoir into a collection microfuge tube. Add 375 uL of water to the cDNA reaction tube and then pipette the sample into the Microcon sample reservoir/collection microfuge tube without touching the membrane. 5.2.2 Centrifuge at 12,000 rpm for 6-10 min. Note: Never centrifuge column to dryness as this will decrease product recovery. Adjust spin time to allow for optimal filtration while allowing enough solution to remain for sufficient recovery. 5.2.3 Empty collection microfuge tube. 5.2.4 To wash add 450 uL of water to the sample reservoir/collection microfuge tube and centrifuge at 12,000 rpm for 6-10 minutes. 5.2.5 Empty collection microfuge tube and repeat previous wash step. 5.2.6 Invert Microcon sample reservoir into a new collection microfuge tube and centrifuge at 12,000 rpm for 1 minute to collect purified sample. 5.2.7 Dry the sample in a speed vac. 5.3 Coupling aa-cDNA to Cy Dye Ester. 5.3.1 Resuspend aminoallyl-labeled cDNA in 4.5 uL 0.1 M sodium carbonate buffer (Na2CO3), pH 9.0. Note: Carbonate buffer changes composition over time so make sure you make it fresh every couple of weeks to a month. 5.3.2 Add 4.5 uL of the appropriate NHS-ester Cy dye (prepared in DMSO: see 4.5) Note: To prevent photobleaching of the Cy dyes wrap all reaction tubes in foil and keep them sequestered from light as much as possible. 5.3.3 Incubate the reaction for 1 hour in the dark at room temperature. 5.4 Reaction Purification II: Removal of uncoupled dye (Qiagen PCR Purification Kit) 5.4.1 To the reaction add 35 uL 100 mM NaOAc pH 5.2. 5.4.2 Add 250 uL (5X reaction volume) Buffer PB (Qiagen supplied). 5.4.3 Place a QIAquick spin column in a 2 mL collection tube (Qiagen supplied), apply the sample to the column, and centrifuge at ~13,000 for 1 minute. Empty collection tube. 5.4.4 To wash, add 0.75 mL Buffer PE (Qiagen supplied) to the column and centrifuge at ~13,000 for 1 minute. Note: Make sure Buffer PE has added ethanol before using (see label for correct volume). 5.4.5 Empty collection tube and centrifuge column for an additional 1 minute at maximum speed. 5.4.6 Place column in a clean 1.5 mL microfuge tube and carefully add 30 uL Buffer EB (Qiagen supplied) to the center of the column membrane. 5.4.7 Incubate for 1 minute at room temperature. 5.4.8 Elute by centrifugation at ~13,000 rpm for 1 minute. 5.4.9 Elute a second time into the same tube by repeating steps 5.4.6- 5.4.8. The final elution volume should be ~60 uL. Note: This protocol is modified from the Qiagen QIAquick Spin Handbook (04/2000, pg. 18). 5.5 Analysis of Labeling Reaction 5.5.1 Use a 50 uL Beckman quartz MicroCuvette to analyze the entire undiluted sample in a spectrophotometer. 5.5.2 Wash the cuvette with water and blow dry with compressed air duster. 5.5.3 Pipette sample into cuvette and place cuvette in spectrophotometer. 5.5.4 For each sample measure absorbance at 260 nm and either 550 nm for Cy3 or 650 nm for Cy5, as appropriate. 5.5.5 Pipette sample from cuvette back into the original sample tube. 5.5.6 For each sample calculate the total picomoles of cDNA synthesized using: pmol nucleotides = [OD260 * volume (uL) * 37 ng/uL * 1000 pg/ng] 324.5 pg/pmol Note: 1 OD260 = 37 ng/uL for cDNA; 324.5 pg/pmol average molecular weight of a dNTP) 5.5.7 For each sample calculate the total picomoles of dye incorporation (Cy3 or Cy5 accordingly) using: pmol Cy3 = OD550 * volume (uL) 0.15 pmol Cy5 = OD650 * volume (uL) 0.25 nucleotides/dye ratio = pmol cDNA pmol Cy dye Note: >200 pmol of dye incorporation per sample and a ratio of less than 50 nucleotides/dye molecules is optimal for hybridizations (see Microarray Cookbook II) 5.5.8 After analysis mix together the two differentially labeled probes (Cy3 vs. Cy5) which will be hybridized to the same microarray slide. 5.5.9 Dry the Cy3/Cy5 probe mixture to completion in a speed vac and continue with SOP: M005 for the hybridization of the probe to a microarray slide.

extract_protocol: Total RNA from each cell line were extracted, treated with DNase, and pooled into a single RNA pool. Further details can be obtained from Stratagene.

tag: Stratagene's universal mouse reference RNA (Catalog #740100). Total RNA from 11 mouse cell lines embryo, embryo (fibroblast), kidney, liver (hepatocyte), lung (alveolar macrophasge), B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, testis.

source_name: A/J mice on control diet at time 0

extract_protocol:
Mice were sacrificed with CO2. Tissues were frozen immediately on dry ice, and stored at –80 ºC until use. Tissues were cut on dry ice and weighed immediately to prevent thawing of tissue.
Trizol Protocol (GibcoBRL): Pooled liver tissues from 8 replicate animals (240mg total) were placed in 6mL Trizol (GibcoBRL), homogenized with polytron homogenizer. Sample was incubated for 5 minutes at room temperature, spun for 10 minutes to remove cellular debris. Chloroform was added to supernatant, shaken by hand for 15 seconds, incubated for 10 minutes at room temperature, and spun for 15 minutes at 12000g at 4ºC. Aqueous phase was transferred to a new tube and 3mL of isopropanol was added, mixed, incubated for 10 minutes at room temperature, and spun for 15 minutes at 12000g at 4ºC. The pellet was washed with 75% ethanol, air dried for 5 minutes, and dissolved in DEPC treated water with heating at 60ºC for 10 minutes. 100ug of RNA were treated with 10 units of DNase (Ambion) in 1mL reaction for 1 hour at 37ºC. RNA were precipitated with 1/10th volume of 3M sodium acetate (pH 5.2) and 2 volumes of absolute ethanol at –80ºC for 30 minutes and spun at 4ºC for 20 minutes. Pellet was dissolved in 100uL of DEPC treated water.
RNeasy Protocol (Qiagen): 350uL of RLT buffer was added to the 100uL of RNA, mixed, then 250uL of absolute ethanol was added. Mixture was placed in RNeasy mini spin-column and centrifuged for 15 seconds at 8000g. The column was washed twice with 500uL of RPE buffer. The column was centrifuged for 15 seconds at 8000g for the first wash and maximum speed for 2 minutes for the second wash. The column was spun one more time at 8000g for 1 minute to remove any remaining buffer. To elute RNA, 30uL of DEPC treated water was added to the column, incubated for 5 minutes, and spun for 1 minute at 8000g. Quality of RNA samples was examined on clean agarose gel and the quantity of RNA was measured with spectrophotometer.

tag: Eight 6-weeks old female A/J mice were purchased from the Jackson laboratory. Mice were placed on a control diet (Basal Diet #7024 from TestDiet) for one week to become adjusted to this diet. Mice were sacrificed on day 0 of experiment (7-weeks old) with CO2 and liver tissue was immediately isolated, frozen on dry ice, and stored in -80C until use. All mice shared the same animal room with controlled temperature (21ºC), humidity, and 12 h light-dark cycle. Mice were housed in micro-ventilated cages with corn cob bedding. Mice were provided with food and water ad libitum.


title: A549_TMPyP4 Treatment_48hrs_Replicate2


title: HFQ_LB_SPI-1_BR3


title: CTRL_LB_SPI-1_BR3


title: Sample 5 swapped

status: Public on Aug 22 2008

city: Wako

first: Charles

last: Plessy

state: Saitama

address: 2-1 Hirosawa

department: DRI

country: Japan

institute: RIKEN

description: Sample 5 swapped

hyb_protocol: The mixture of Cy3- and Cy5-labeled probes was applied at 75 °C onto arrays, and hybridized for 3 h at 65 °C, 3 h at 55 °C and 12 h at 50 °C in the dark, using GeneMachines HybStation (Genomic Solutions), an automatic hybridizer. After hybridization, the slides were washed once in 2 × saline-sodium citrate (SSC) and 0.2 % SDS at 53 °C, in 1 × SSC and 0.2% SDS at 53 °C, in 2 × SSC at 24 °C, and in 0.2 × SSC for 5 min at 24 °C using one cycle of 10 s flow and 1 s hold, and 15 (first wash) or 13 (other washes) cycles of 1 s flow and 10 s hold, and then dried by spinning for 1 min.

scan_protocol: The scanning was done using an Axon GenPix 4000B scanner (Axon Instruments, Union City, CA) at 10 µm resolution. PMT voltage settings were varied to obtain maximum signal intensities with < 5 % probe saturation. TIFF images were captured and analyzed with GenePix 6.0 (Axon Ins.) software and Acuity 4.0 (Axon Ins.).

data_processing: Lowess (locally weighted scatter plot for smoother) analysis was used for normalizing microarray data. Within-print-tip-group normalization was conducted by using loess.smooth function in the statistical software package R (R development core team, 2004). In short, this lowess normalization approach is to use the dependence of M = log₂ ( Cy5 / Cy3 ) on A = log₂ (Cy5 × Cy3 ) for estimating its normalizing curve, which is a function of A (Cleverland et al, 1988). Due to its estimation procedure, its normalization curve is considered as estimated mostly based on unexpressed clones (which should be a majority) in each small segment of A {Yang, 2002 #29} (we used 50 segments). We tried to further ensure this point in our lowess normalization; For each segment of A, the standard deviation of M values was calculated and lowess normalization curve was estimated by using only data points whose M values fell into a range within three times the standard deviation in each A segment. Once the normalization curve was estimated, data points out of the range were also normalized.

source_name: FACS-sorted visual cortex cells, GFP positive

label_protocol: Probes were prepared following the method of Xiang et al (2002, PubMed ID 12089562), except that [QUANTITY] ng of RNA were used per slide, and that the probes were dried and resuspended in 6 µl of water.

growth_protocol: 12 light/dark cycle with access to food ad libitum.

extract_protocol: Total RNA was extracted from FACS-sorted cells (Wagatsuma et al, in prep.) using the RNEasy Lipid Tissue Mini kit from Qiagen according to the manufacturer's instructions.

tag: Strain

tag: Age

value: 28 or 29 days

tag: Transgene

value: parvalbuming-egfp BAC (Meyer et al, 2002)

source_name: FACS-sorted visual cortex cells, GFP negative


title: CTRL_LB_OD=2_BR3


title: CTRL_LB_OD=2_BR2


title: A549_TMPyP4 Treatment_48hrs_Dyeswap1


title: Sample 4 standard

description: Sample 4 standard


title: Sample 4 swapped

description: Sample 4 swapped


title: Sample 2 swapped

description: Sample 2 swapped


title: Sample 3 swapped

description: Sample 3 swapped


title: Sample 3 standard

description: Sample 3 standard


title: Sample 5 standard

description: Sample 5 standard


title: Sample 2 standard

description: Sample 2 standard; this sample discarded after failing quality criteria.


title: Sample 1 swapped

description: Sample 1 swapped


title: Sample 1 standard

description: Sample 1 standard


title: WT colon repl1

status: Public on Aug 15 2008

city: Cincinnati

first: Xiaonan

last: Han

address: 3333 Burnet Ave.

department: Gastroenterology

institute: Cincinnati Children's Hospital Medical Center

description: gene expression data from adult mouse colon

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the mouse MOE-430 GeneChip array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: The data was analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Mm430_Mm_REFSEQ_8), then normalized to the REF colon repl1 and the mean of the 3 WT colon samples

label: biotin

source_name: wild type mouse colon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA  amplified with TargetAmp 1-round Aminoallyl-aRNA Amplication Kit 101 (Epicentre, WI) (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Mini kit (QIAGEN, Hilden, Germany)

tag: genotype

value: wild type

tag: gender

value: female


title: WT colon repl3


title: WT colon repl2


title: STAT5b-/- colon repl2

source_name: STAT5b deficient mouse colon


title: REF colon repl1


title: STAT5b-/- colon repl1

data_processing: The data was analyzed with GeneSpring version 7.3 using RMA normalization with a custom CDF file(Mm430_Mm_REFSEQ_8), then normalized to the REF colon repl2 and the mean of the 3 WT colon samples

value: male


title: Cy3-tachykinins-16h & Cy5-Control-16h

status: Public on Aug 19 2008

city: Osaka

first: Honoo

last: Satake

address: 1-1-1 Wakayamadai, Shimamoto, Mishima

institute: Suntory Inst. for Bioorg. Res.

description: - RNA quality control with Agilent Bioanalyzer 2100

hyb_protocol: Hybridization and washing protocols were according to the manufacturer's instructions (Agilent Technologies).

scan_protocol: The microarrays were scanned with a GenePix4000B DNA Microarray Scanner (Axon Instruments, Foster City, CA). The resulting fluorescence intensity for each spot was quantified using GENEPIX PRO 4.0 microarray analysis software (Axon Instruments).

data_processing: Quantified images were exported into text files for statistical analysis. After removing the flagged features and subtracting the background value we took the logarithm (base 2) of the intensity signals.

organism: Ciona intestinalis

label_protocol: Total RNA was labeled with Cy3 using an Agilent Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol:
RNA from the ovary was isolated with TRIzol Reagent according to the manufactures standard protocol method
Subsequent sample "clean-up" using QIAGEN's RNeasy Total RNA Isolation kit

treatment_protocol: Incubation of the Ciona ovary in seawater in the presence of 100 nM Ci-TK at 18 C for 15 hrs.

tag: Ci-TK-stimulated ovary

treatment_protocol: Incubation of the Ciona ovary in seawater in the absence of 100 nM Ci-TK at 18 C for 15 hrs

tag: Negative control


title: STAT5b-/- colon repl3


title: REF colon repl2


title: Cy3-Control-16h & Cy5-tachykinins-16h


title: CHR_KIDNEY_4

status: Public on Aug 13 2008

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression ratios were obtained from human Chromophobe kidney tumor tissues. Normal reference and Papillary subtype raw files can be obtained from GSE7023.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 6 entrez gene ID CDF was used.

label: R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml  ( we use 6 ul per reaction )

source_name: chromophobe renal tumor tissue

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: chromophobe renal tumor


title: CHR_KIDNEY_5


title: CHR_KIDNEY_2


title: CHR_KIDNEY_3


title: CHR_KIDNEY_1


title: ON_KIDNEY_7

description: Gene expression ratios were obtained by comparing normal human kidney tissue to human kidney tumor tissues. Tumor subtypes include Papillary type 1, and Oncocytoma. Normal and Papillary tissue raw files can be obtained from GSE7023.

source_name: oncocytoma renal tumor tissue

tag: oncocytoma renal tumor tissue


title: ON_KIDNEY_6


title: CHR_KIDNEY_6


title: CHR_KIDNEY_9


title: ON_KIDNEY_8


title: CHR_KIDNEY_10


title: CHR_KIDNEY_8


title: ON_KIDNEY_10


title: CHR_KIDNEY_7


title: ON_KIDNEY_5


title: ON_KIDNEY_9


title: ON_KIDNEY_3


title: ON_KIDNEY_4


title: CHR_KIDNEY_9_SNP_Hind

type: genomic

description: Human kidney tumor tissues. Tumor subtypes is Chromophobe.

hyb_protocol: Following fragmentation, 40 ug of genomic DNA was hybridized for 16 hr at 48C on Affymetrix GeneChip Human Mapping 50K chip, either Xba Array or Hind array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Files were processed by Affymetrix GCOS 1.4 with default analysis settings.

source_name: Chromophobe renal tumor tissue

label_protocol: 40 ug per Xba1 chip and 40 ug per HindIII chip.  Purified pooled 3 Xba1 PCRs with 3 pooled HindIII PCRs.

extract_protocol: extraction of total Genomic DNA was performed using Genomed JETquick tissue DNA Maxi Kit ( part # 452050), according to manufacturers instructions.

tag: Chromophobe Renal Tumor


title: CHR_KIDNEY_1_SNP_Hind


title: ON_KIDNEY_10_SNP_Hind

description: Human kidney tumor tissues. Tumor subtypes is Oncocytoma.

tag: Oncocytoma Renal Tumor


title: CHR_KIDNEY_11_SNP_Hind


title: ON_KIDNEY_2


title: ON_KIDNEY_9_SNP_Xba


title: ON_KIDNEY_2_SNP_Hind


title: ON_KIDNEY_9_SNP_Hind


title: ON_KIDNEY_2_SNP_Xba


title: CHR_KIDNEY_11_SNP_Xba


title: ON_KIDNEY_1


title: Cerebellum GABAergic cells replicate 3

status: Public on Aug 12 2008

city: Cologne

first: Olaf

last: Hardt

state: NRW

address: Stöckheimer Weg 1

department: MACSmolecular Business Unit, Research and Development

country: Germany

institute: Miltenyi Biotec GmbH

description: Biological replicate 3 of 3. P1 GABAergic neurons from cerebellum vs. total brain reference.

hyb_protocol: Agilent whole mouse genome 44k microarrays were hybridized according to the manufactures instructions (http://www.chem.agilent.com/scripts). Briefly, 2.5 µg of combined Cy3- and Cy5-labeled and purified cDNAs were adjusted to a volume of 200 µl and denatured 5 min at 95°C. After adding of 50 µl control targets (Agilent) and 250 µl 2x Hybridization Buffer (Agilent), samples were incubated on the microarrays at 65°C for >16 h. Afterwards microarrays were washed with Wash Buffer I (Agilent) for 1 min at 37°C, with Wasch Buffer II (Agilent) for 1 min at 25°C, and dried after 30 s incubation in Acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies, Palo Alto, USA).

data_processing: Scanned images were analyzed using the Agilent Feature Extraction software (Version 8.1.1.1) by which the local background was subtracted and a rank consistency based probe selection for Lowess normalization was done. After filtering the data with respect to signal significance a two-tailed t test was used to determine the signal versus background significance.

molecule: polyA RNA

source_name: amplified cDNA  from murine P1 cerebellar GABAergic neurons labeled with Cyanine-5 (red).

label_protocol: 250 ng of each of the cDNAs was labeled with Cy5- (sample) or Cy3-dCTP (common reference) in a Klenow Fragment (10 units per sample) reaction for 2 h at 37°C before heat inactivating at 70°C for 5 min. Labeled cDNA was purified using the CyScribe GFX Purification Kit (GE Healthcare) and quantified by OD measurement.

growth_protocol: Animals were kept under standard conditions on a C57Bl/6 background.

extract_protocol: Flow-sorted cells were immediately subjected to SuperAmpTM lysis buffer. mRNA was isolated via magnetic bead technology, reversely transcribed to cDNA, and amplified in a global PCR using the SuperAmpTM Technology (Miltenyi Biotec). For the common reference, RNA was extracted from whole brain of four age-matched mice using the NucleoSpin® RNA Clean-up Kit (Macherey Nagel) and amplified equally to the flow-sorted cells.

treatment_protocol: GABAergic eGFP+ cells from whole brains were isolated from four GAD67-eGFP mice at P1. For the isolation of cells from different areas, brains of six P1 old mice were dissected into olfactory bulb, cortex, striatum, and cerebellum. Brain tissue was dissociated to single cell suspensions using the Neuronal Tissue Dissociation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Cells were resuspended in PBS (Gibco) and sorted on a FACS Vantage SE cell sorter (Becton Dickinson).

tag: postnatal day 1 old (C57Bl6, GAD67-eGFP) mice, GABAergic cells from cerebellar tissue

source_name: amplified cDNA  from murine P1 whole brain RNA labeled with Cyanine-3 (red).

tag: postnatal day 1 old (C57Bl6) mice


title: ON_KIDNEY_1_SNP_Hind


title: ON_KIDNEY_1_SNP_Xba


title: Striatum GABAergic cells replicate 2

description: Biological replicate 2 of 3. P1 GABAergic neurons from striatum vs. total brain reference.

source_name: amplified cDNA  from murine P1 striatal GABAergic neurons labeled with Cyanine-5 (red).

tag: postnatal day 1 old (C57Bl6, GAD67-eGFP) mice, GABAergic cells from striatal tissue


title: CHR_KIDNEY_9_SNP_Xba


title: Cerebellum GABAergic cells replicate 1

description: Biological replicate 1 of 3. P1 GABAergic neurons from cerebellum vs. total brain reference.


title: Cerebellum GABAergic cells replicate 2

description: Biological replicate 2 of 3. P1 GABAergic neurons from cerebellum vs. total brain reference.


title: ON_KIDNEY_10_SNP_Xba


title: CHR_KIDNEY_1_SNP_Xba


title: Striatum GABAergic cells replicate 3

description: Biological replicate 3 of 3. P1 GABAergic neurons from striatum vs. total brain reference.


title: Olfactory bulb GABAergic cells replicate 3

description: Biological replicate 3 of 3. P1 GABAergic neurons from olfactory bulb vs. total brain reference.

source_name: amplified cDNA  from murine P1 olfactory bulb GABAergic neurons labeled with Cyanine-5 (red).

tag: postnatal day 1 old (C57Bl6, GAD67-eGFP) mice, GABAergic cells from olfactory bulb tissue


title: Olfactory bulb GABAergic cells replicate 1

description: Biological replicate 1 of 3. P1 GABAergic neurons from olfactory bulb vs. total brain reference.


title: Cortex GABAergic cells replicate 3

description: Biological replicate 3 of 3. P1 GABAergic neurons from cortex vs. total brain reference.

source_name: amplified cDNA  from murine P1 cortical GABAergic neurons labeled with Cyanine-5 (red).

tag: postnatal day 1 old (C57Bl6, GAD67-eGFP) mice, GABAergic cells from cortical tissue


title: Olfactory bulb GABAergic cells replicate 2

description: Biological replicate 2 of 3. P1 GABAergic neurons from olfactory bulb vs. total brain reference.


title: Cortex GABAergic cells replicate 1

description: Biological replicate 1 of 3. P1 GABAergic neurons from cortex vs. total brain reference.


title: Cortex GABAergic cells replicate 2

description: Biological replicate 2 of 3. P1 GABAergic neurons from cortex vs. total brain reference.


title: Whole brain GABAergic cells replicate 4

description: Biological replicate 4 of 4. P1 GABAergic neurons from whole brain vs. total brain reference.

source_name: amplified cDNA  from murine P1 whole brain GABAergic neurons labeled with Cyanine-5 (red).

tag: postnatal day 1 old (C57Bl6, GAD67-eGFP) mice, GABAergic cells from whole brain tissue


title: Whole brain GABAergic cells replicate 3

description: Biological replicate 3 of 4. P1 GABAergic neurons from whole brain vs. total brain reference.


title: Whole brain GABAergic cells replicate 2

description: Biological replicate 2 of 4. P1 GABAergic neurons from whole brain vs. total brain reference.


title: Whole brain GABAergic cells replicate 1

description: Biological replicate 1 of 4. P1 GABAergic neurons from whole brain vs. total brain reference.


title: KO - 3 mo - repeat 4 - Cy5 - mAdbID:74670

status: Public on Aug 09 2008

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Cellular and Molecular Biology Section

institute: National Cancer institute/NIH

description: mAdb experiment ID: 74670

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.42 Temperature: 36.13

data_processing:
mAdb Data Processing Protocol (v. 2)
Calculation Method: After background correction, ratios were median centered based on signals greater than 100 in both channels and linear transformed to obtain the log and linear values given in the data table.

source_name: WT Liver - Pooled -Cy3

label_protocol:
Cy3 Labeling Protocol
Other: The Cy3 and Cy5 dyes (Amersham Biosciences) were also dissolved in 20 ìl of water. For the coupling reaction, 2 ìl of dye was added to each sample, and the mix was left in a dark box for an hour. Labeled cDNA was purified again with a MinElute kit (Qiagen ), and Cy3- and Cy5-labeled target and reference samples were combined.

extract_protocol:
CsCl Gradient Extraction Protocol
Extraction method: CsCl gradient centrifugation
Other: Total RNA was isolated from snap-frozen liver tissue using the CsCl gradient centrifugation method.

tag: Strain

tag: Gender

value: 12 weeks

tag: Tissue

value: liver

tag: Developmental stage

value: adult

source_name: KO4 - Met Knock-out - 3 months - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: The Cy3 and Cy5 dyes (Amersham Biosciences) were also dissolved in 20 ìl of water. For the coupling reaction, 2 ìl of dye was added to each sample, and the mix was left in a dark box for an hour. Labeled cDNA was purified again with a MinElute kit (Qiagen ), and Cy3- and Cy5-labeled target and reference samples were combined.

treatment_protocol:
Treatment type: compound
Agent: N-nitrosodiethylamine
Treatment dose: 10 ug/g of body weight
Treatment time: 3 months

tag: genotype/variation gene knock out

tag: genotype/variation

value: Alb-Cre +/-; Met Fl/Fl


title: KO - 3 mo - repeat 4 - Cy3 - mAdbID:74675

description: mAdb experiment ID: 74675

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.58 Temperature: 39.19

source_name: WT Liver - Pooled -Cy5

tag: Age

source_name: KO4 - Met Knock-out - 3 months - Cy3


title: WT - Cre Control - 3 mo - repeat 5 - Cy3 - mAdbID:74673

description: mAdb experiment ID: 74673

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.26 Temperature: 38.23

source_name: WT5 - Cre Control - 3 months - Cy3

value: Alb-Cre +/-


title: KO - 3 mo - repeat 5 - Cy3 - mAdbID:74676

description: mAdb experiment ID: 74676

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.58 Temperature: 39.73

source_name: KO5 - Met Knock-out - 3 months - Cy3


title: KO - 3 mo - repeat 3 - Cy3 - mAdbID:74674

description: mAdb experiment ID: 74674

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.61 Temperature: 38.73

source_name: KO3 - Met Knock-out - 3 months - Cy3


title: WT - Cre Control - 3 mo - repeat 5 - Cy5 - mAdbID:74668

description: mAdb experiment ID: 74668

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.51;; 1.34 Temperature: 34.68

source_name: WT5 - Cre Control - 3 months - Cy5


title: Striatum GABAergic cells replicate 1

description: Biological replicate 1 of 3. P1 GABAergic neurons from striatum vs. total brain reference.


title: KO - 3 mo - repeat 1 - Cy5 - mAdbID:74593

description: mAdb experiment ID: 74593

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.32 Temperature: 42.18

source_name: KO1 - Met Knock-out - 3 months - Cy5


title: KO - 3 mo - repeat 1 - Cy3 - mAdbID:74592

description: mAdb experiment ID: 74592

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.62;; 1.33 Temperature: 43.39

source_name: KO1 - Met Knock-out - 3 months - Cy3


title: KO - 3 mo - repeat 3 - Cy5 - mAdbID:74669

description: mAdb experiment ID: 74669

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.45 Temperature: 35.32

source_name: KO3 - Met Knock-out - 3 months - Cy5


title: WT - Cre Control - 3 mo - repeat 4 - Cy5 - mAdbID:74667

description: mAdb experiment ID: 74667

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.6 Temperature: 32.98

source_name: WT4 - Cre Control - 3 months - Cy5


title: KO - 3 mo - repeat 2 - Cy3 - mAdbID:74594

description: mAdb experiment ID: 74594

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.65;; 1.3 Temperature: 43.59

source_name: KO2 - Met Knock-out - 3 months - Cy3


title: WT - Cre Control - 3 mo - repeat 3 - Cy3 - mAdbID:74591

description: mAdb experiment ID: 74591

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.64;; 1.31 Temperature: 43.14

source_name: WT3 - Cre Control - 3 months - Cy3


title: WT - Cre Control - 3 mo - repeat 2 - Cy3 - mAdbID:74589

description: mAdb experiment ID: 74589

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.62;; 1.35 Temperature: 42.99

source_name: WT2 - Cre Control - 3 months - Cy3


title: KO - 5 mo - repeat 5 - Cy3 - mAdbID:74141

description: mAdb experiment ID: 74141

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.3 Temperature: 36.78

source_name: KO5 - Met Knock-out - 5 months - Cy3

treatment_protocol:
Treatment type: compound
Agent: N-nitrosodiethylamine
Treatment dose: 10 ug/g of body weight
Treatment time: 5 months

value: 20 weeks


title: KO - 5 mo - repeat 4 - Cy3 - mAdbID:74139

description: mAdb experiment ID: 74139

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.31 Temperature: 36.03

source_name: KO4 - Met Knock-out - 5 months - Cy3


title: KO - 3 mo - repeat 2 - Cy5 - mAdbID:74595

description: mAdb experiment ID: 74595

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.59;; 1.3 Temperature: 42.53

source_name: WT Liver - Pooled -Cy3

source_name: KO2 - Met Knock-out - 3 months - Cy5


title: KO - 5 mo - repeat 4 - Cy5 - mAdbID:74138

description: mAdb experiment ID: 74138

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.58 Temperature: 32.62

source_name: KO4 - Met Knock-out - 5 months - Cy5


title: WT - Cre Control - 3 mo - repeat 3 - Cy5 - mAdbID:74590

description: mAdb experiment ID: 74590

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.34 Temperature: 41.85

source_name: WT3 - Cre Control - 3 months - Cy5


title: WT - Cre Control - 3 mo - repeat 1 - Cy5 - mAdbID:74586

description: mAdb experiment ID: 74586

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.42 Temperature: 41.24

source_name: WT1 - Cre Control - 3 months - Cy5


title: KO - 5 mo - repeat 3 - Cy5 - mAdbID:74137

description: mAdb experiment ID: 74137

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.3 Temperature: 31.37

source_name: KO3 - Met Knock-out - 5 months - Cy5


title: KO - 3 mo - repeat 5 - Cy5 - mAdbID:74671

description: mAdb experiment ID: 74671

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.37 Temperature: 36.93

source_name: KO5 - Met Knock-out - 3 months - Cy5


title: WT - Cre Control - 3 mo - repeat 2 - Cy5 - mAdbID:74588

description: mAdb experiment ID: 74588

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.55;; 1.34 Temperature: 41.58

source_name: WT2 - Cre Control - 3 months - Cy5


title: KO - 5 mo - repeat 1 - Cy3 - mAdbID:74108

description: mAdb experiment ID: 74108

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.54;; 1.34 Temperature: 34.13

source_name: WT Liver - Pooled -Cy5

source_name: KO1 - Met Knock-out - 5 months - Cy3


title: KO - 5 mo - repeat 5 - Cy5 - mAdbID:74140

description: mAdb experiment ID: 74140

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.47;; 1.28 Temperature: 33.32

source_name: KO5 - Met Knock-out - 5 months - Cy5


title: KO - 5 mo - repeat 2 - Cy3 - mAdbID:74110

description: mAdb experiment ID: 74110

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.5;; 1.33 Temperature: 34.93

source_name: KO2 - Met Knock-out - 5 months - Cy3


title: KO - 5 mo - repeat 1 - Cy5 - mAdbID:74107

description: mAdb experiment ID: 74107

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.49;; 1.34 Temperature: 33.84

source_name: KO1 - Met Knock-out - 5 months - Cy5


title: WT - Cre Control - 5 mo - repeat 5 - Cy3 - mAdbID:74106

description: mAdb experiment ID: 74106

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.61;; 1.33 Temperature: 42.1

source_name: WT5 - Cre Control - 5 months - Cy3


title: WT - Cre Control - 3 mo - repeat 1 - Cy3 - mAdbID:74587

description: mAdb experiment ID: 74587

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.61;; 1.35 Temperature: 42.78

source_name: WT1 - Cre Control - 3 months - Cy3


title: WT - Cre Control - 3 mo - repeat 4 - Cy3 - mAdbID:74672

description: mAdb experiment ID: 74672

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.29 Temperature: 37.67

source_name: WT4 - Cre Control - 3 months - Cy3


title: WT - Cre Control - 5 mo - repeat 4 - Cy3 - mAdbID:74104

description: mAdb experiment ID: 74104

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.6;; 1.34 Temperature: 41.77

source_name: WT4 - Cre Control - 5 months - Cy3


title: WT - Cre Control - 5 mo - repeat 5 - Cy5 - mAdbID:74105

description: mAdb experiment ID: 74105

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.56 Temperature: 40.72

source_name: WT Liver - Pooled -Cy3

source_name: WT5 - Cre Control - 5 months - Cy5


title: WT - Cre Control - 5 mo - repeat 2 - Cy5 - mAdbID:74099

description: mAdb experiment ID: 74099

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.29 Temperature: 38.93

source_name: WT2 - Cre Control - 5 months - Cy5


title: WT - Cre Control - 5 mo - repeat 3 - Cy3 - mAdbID:74102

description: mAdb experiment ID: 74102

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.55 Temperature: 41.5

source_name: WT3 - Cre Control - 5 months - Cy3


title: WT - Cre Control - 5 mo - repeat 2 - Cy3 - mAdbID:74100

description: mAdb experiment ID: 74100

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.57;; 1.35 Temperature: 41.32

source_name: WT2 - Cre Control - 5 months - Cy3


title: WT - Cre Control - 5 mo - repeat 1 - Cy3 - mAdbID:74098

description: mAdb experiment ID: 74098

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.58;; 1.35 Temperature: 41.05

source_name: WT1 - Cre Control - 5 months - Cy3


title: WT - Cre Control - 5 mo - repeat 1 - Cy5 - mAdbID:74097

description: mAdb experiment ID: 74097

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.52;; 1.29 Temperature: 38.4

source_name: WT1 - Cre Control - 5 months - Cy5


title: WT - Cre Control - 5 mo - repeat 3 - Cy5 - mAdbID:74101

description: mAdb experiment ID: 74101

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.53;; 1.58 Temperature: 39.54

source_name: WT3 - Cre Control - 5 months - Cy5


title: MCL MD307

status: Public on Aug 08 2008

city: Vancouver

first: Ronald

middle: J

last: deLeeuw

state: British Columbia

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Centre

description: MCL MD307

hyb_protocol: DIG easy, 45ºC, 40hr

scan_protocol: Applied Precision AutoE CCD scanner, 9.675um

data_processing: Applied Precision SoftWoRx analysis software, Scale factor=1, median background normalization.  Stepwise normalization procedure (Khojasteh M., et al BMC Bioinformatics 6, 274)

source_name: Leukemic MCL

label_protocol: random priming

extract_protocol: Proteinase K digestion, phenol extraction, ethanol precipitation

tag: leukemic MCL, 65yo male

source_name: pooled normal male genomic DNA

extract_protocol: unknown, purchased from Novagen, San Diego, CA

tag: pool of at least 8 individuals purchased from Novagen


title: MCL 99-26032

description: MCL 99-26032

source_name: Classic MCL

tag: lymph node tissue, 63yo male, classic MCL


title: MCL MD346

description: MCL MD346

tag: leukemic MCL, 82yo male


title: MCL 98-22730

description: MCL 98-22730

tag: lymph node tissue, 73yo male, classic MCL


title: MCL 99-27781

description: MCL 99-27781

tag: lymph node tissue, 80yo male, classic MCL


title: MCL 99-19395

description: MCL 99-19395

tag: lymph node tissue, 37yo female, classic MCL


title: MCL 98-18113

description: MCL 98-18113

source_name: Blastoid MCL

tag: lymph node tissue, 66yo male, blastoid MCL


title: MCL 97-28480

description: MCL 97-28480

tag: lymph node tissue, 71yo male, classic MCL


title: MCL 98-27836

description: MCL 98-27836

tag: lymph node tissue, 48yo male, classic MCL


title: MCL MD146

description: MCL MD146


title: MCL 97-18950

description: MCL 97-18950

tag: lymph node tissue, 84yo female, classic MCL

source_name: pooled normal female genomic DNA


title: MCL 99-10429

description: MCL 99-10429

tag: lymph node tissue, 42yo female, classic MCL


title: MCL 98-13331

description: MCL 98-13331

tag: lymph node tissue, 42yo male, classic MCL


title: MCL 98-19743

description: MCL 98-19743

tag: lymph node tissue, 54yo male, blastoid MCL


title: MCL 99-14390

description: MCL 99-14390

tag: lymph node tissue, 56yo male, classic MCL


title: MCL 95-23866

description: MCL 95-23866

tag: lymph node tissue, 65yo male, blastoid MCL


title: MCL 96-13855

description: MCL 96-13855

tag: lymph node tissue, 86yo female, classic MCL


title: MCL 97-24857

description: MCL 97-24857

tag: lymph node tissue, 59yo male, classic MCL


title: MCL 92-56466

description: MCL 92-56466

tag: lymph node tissue, 76yo male, blastoid MCL

tag: pool of at least 8 individuals purchased from Novagen


title: MCL MD629

description: MCL MD629

tag: leukemic MCL, 69yo male


title: MCL 86-67262

description: MCL 86-67262

tag: lymph node tissue, 83yo male, blastoid MCL


title: MCL 94-13463

description: MCL 94-13463


title: MCL 85-64225

description: MCL 85-64225

tag: lymph node tissue, 44yo female, classic MCL


title: MCL 85-62401

description: MCL 85-62401

tag: lymph node tissue, 73yo male, classic MCL


title: MCL 93-10926

description: MCL 93-10926

tag: lymph node tissue, 85yo female, blastoid MCL


title: MCL 94-26991

description: MCL 94-26991

tag: lymph node tissue, 72yo male, classic MCL


title: MCL 05-14395

description: MCL 05-14395

tag: Lymph node tissue, 75yo male, blastoid MCL


title: MCL 93-31511

description: MCL 93-31511

tag: lymph node tissue, 78yo female, blastoid MCL


title: MCL 05-13982

description: MCL 05-13982

tag: Lymph node tissue, 73yo female, classic MCL


title: MCL 04-10848

description: MCL 04-10848

tag: Lymph node tissue, 77yo female, blastoid MCL


title: MCL 0424272

description: MCL 0424272

tag: Lymph node tissue, 70yo male, histology MCL


title: MCL 05-18379

description: MCL 05-18379

tag: Lymph node tissue, 89yo male, blastoid MCL


title: MCL 0426157

description: MCL 0426157

tag: Lymph node tissue, 80yo male, classic MCL


title: WT - Cre Control - 5 mo - repeat 4 - Cy5 - mAdbID:74103

description: mAdb experiment ID: 74103

scan_protocol: Creator: GenePix Pro 5.1.0.11 Scanner: GenePix 4000A [54243] ScanPower: 100;; 100 LaserPower: 2.56;; 1.41 Temperature: 39.94

tag: Strain

tag: Gender

tag: Age

tag: Tissue

tag: Developmental stage

source_name: WT4 - Cre Control - 5 months - Cy5

tag: genotype/variation


title: MCL 0126790

description: MCL 0126790

tag: Lymph node tissue, 69yo male, classic MCL

tag: pool of at least 8 individuals purchased from Novagen


title: MCL 03-10497

description: MCL 03-10497

tag: Lymph node tissue, 74yo female, classic MCL


title: MCL 02-25451

description: MCL 02-25451

tag: Lymph node tissue, 55yo male, classic MCL


title: MCL 03-11565

description: MCL 03-11565

tag: Lymph node tissue, 52yo female, classic MCL


title: MCL 03-14255

description: MCL 03-14255

tag: Lymph node tissue, 57yo male, classic MCL


title: MCL 03-22255

description: MCL 03-22255

tag: Lymph node tissue, 67yo male, classic MCL


title: MCL 02-28146

description: MCL 02-28146

tag: Lymph node tissue, 49yo male, blastoid MCL


title: MCL 01-26449

description: MCL 01-26449

tag: Lymph node tissue, 69yo male, blastoid MCL


title: Surrounding normal prostate tissue patient 21

status: Public on Aug 06 2008

first: Robert

middle: Scott

last: Hudson

address: National Cancer Institute Room Blgd.37/3044

department: NCI

institute: NIH

hyb_protocol: The chips were hybridized on Tecan HS 4800 hybridization station. Chips were pre-hybridized at 25C for 30 min in the buffer of 6x SSPE/ 30% formamide/ 1x Denhardt's solution. The chips were further hybridized with labeled target in 6x SSPE/ 30% formamide at 25C for 18 hr. Hybridization, post-hybridization washing in 0.75x TNT (Tris, sodium, Tween 20) (see PNAS) at 37C for 40 mins. The chips were stained by streptavidin-alexa647 (1:500) dilution in TNT for 30 mins. Post-staining washing in 1x TNT FOR 40 min. Rinse with water and spin dry.

scan_protocol: Arrays were scanned on the GenePix scanner and analyzed using the GenePix Pro software package.

data_processing: median-centralized normalized data (in log scale)

source_name: Normal prostate

label_protocol: Refer to Liu et al (PNAS 101: 9740-9744 (2004)). 5 ug of total RNA was labeled in reverse transcription at 37C for 90 mins by using biotin-labeled rand-octomer oligo primer. The RT reaction mix was further denatured by using 0.5 N NaOH / 1 mM EDTA at 65C for 15 mins and neutralized by 1 M Tris HCl pH 7.6. Biotin signal was detected with an Alexa 647-Streptavidin conjugate.

growth_protocol: not applicable

extract_protocol: TRIzol

treatment_protocol: not applicable

tag: race

value: African American

tag: smoking status

value: Unknown

tag: gleason sum

tag: pt stage

tag: extraprostatic extension

value: Multifocal

tag: perineural invasion

value: Yes

tag: seminal vesicle invasion

tag: are surgical margins involved

value: Tumor focal at margin

tag: angio lymphatic invasion

value: No


title: Surrounding normal prostate tissue protate cancer patient C

value: Caucasian

value: Never

value: All surgical margins are free of tumor


title: MCL MD533

description: MCL MD533

tag: leukemic MCL, 75yo male

tag: pool of at least 8 individuals purchased from Novagen


title: Surrounding normal prostate tissue patient 4

value: Past


title: Prostate tumor patient 76

source_name: Adenocarcinoma (NOS) of the prostate


title: Surrounding normal prostate tissue patient 45

value: Current


title: Surrounding normal prostate tissue patient 31

value: Focal


title: Prostate tumor patient 77


title: Surrounding normal prostate tissue patient D

value: Caucasian, Smoking Status:Current


title: Surrounding normal prostate tissue patient 16


title: Surrounding normal prostate tissue patient 76


title: intestine_cysticfibrosis_1

first: Gary

last: Shull

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min.  For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.  The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.  To test for differentially expressed genes, a hierarchical Bayes procedure, IBMT (Sartor et al., BMC Bioinf, 2006) was used.

label: Cy5, Cy3

source_name: total RNA from whole small intestine; Wild Type

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

growth_protocol: Adult mice.  CFTR KO mice were maintained on an oral, osmotic laxative (Colyte) to prevent early mortality.

extract_protocol: Total RNA was extracted from whole small intestine using Tri-Reagent according to the manufacturer's instructions.

tag: strain

value: C57BL/6J mice

source_name: total RNA from whole small intestine; CFTR KO


title: Surrounding normal prostate tissue protate cancer patient A


title: Surrounding normal prostate tissue protate cancer patient B


title: MCL 01-23645

description: MCL 01-23645

tag: Lymph node tissue, 88yo female, classic MCL


title: MCL 05-23234

description: MCL 05-23234

tag: lymph node tissue, 64yo female, classic MCL


title: MCL 01-15563

description: MCL 01-15563

tag: lymph node tissue, 53yo male, classic MCL


title: Prostate tumor patient 74


title: Surrounding normal prostate tissue patient 57


title: Prostate tumor patient 73


title: Prostate tumor patient 72


title: Prostate tumor patient 70


title: Prostate tumor patient 65


title: Surrounding normal prostate tissue patient 72


title: MCL 01-28037

description: MCL 01-28037

tag: Lymph node tissue, 32yo male, classic MCL


title: Prostate tumor patient 68


title: Surrounding normal prostate tissue patient 65


title: MCL 04-40616

description: MCL 04-40616

tag: Lymph node tissue, 75yo male, blastoid MCL


title: Prostate tumor patient 61

tag: race


title: Surrounding normal prostate tissue patient 63

source_name: normal prostate

tag: smoking status


title: Prostate tumor patient 59

tag: gleason sum


title: MCL 00-14259

description: MCL 00-14259

tag: Lymph node tissue, 57yo male, classic MCL


title: Prostate tumor patient 58

tag: pt stage

tag: extraprostatic extension


title: MCL 01-14081

description: MCL 01-14081

tag: Lymph node tissue, 77yo male, classic MCL


title: Prostate tumor patient 56

tag: perineural invasion

tag: seminal vesicle invasion

value: Yes Are Surgical margins involved:All surgical margins are free of tumor


title: Prostate tumor patient 57

tag: are surgical margins involved

tag: angio lymphatic invasion


title: Prostate tumor patient 49


title: Prostate tumor patient 54


title: Prostate tumor patient 60


title: Surrounding normal prostate tissue patient 70


title: Prostate tumor patient 51


title: Prostate tumor patient 48


title: Prostate tumor patient 44


title: Prostate tumor patient 47


title: MCL 01-10814

description: MCL 01-10814

tag: Lymph node tissue, 56yo male, classic MCL

tag: pool of at least 8 individuals purchased from Novagen


title: Prostate tumor patient 45


title: Prostate tumor patient 52


title: Prostate tumor patient 43

value: Established


title: Prostate tumor patient 53


title: Surrounding normal prostate tissue patient 68


title: MCL 01-11260

description: MCL 01-11260


title: Prostate tumor patient 42


title: MCL 00-13921

description: MCL 00-13921

tag: lymph node tissue, 59yo male, classic MCL


title: Prostate tumor patient 37


title: Prostate tumor patient 36


title: Prostate tumor patient 38


title: Prostate tumor patient 40


title: Prostate tumor patient 39


title: Prostate tumor patient 33


title: Prostate tumor patient 30


title: Prostate tumor patient 55


title: Prostate tumor patient 41


title: Prostate tumor patient 34


title: Prostate tumor patient 27


title: Prostate tumor patient 35


title: Prostate tumor patient 29


title: Prostate tumor patient 23


title: Prostate tumor patient 20


title: Prostate tumor patient 15


title: Prostate tumor patient 16


title: Prostate tumor patient 17


title: Prostate tumor patient 28


title: Prostate tumor patient 14


title: Prostate tumor patient 26


title: control chip10

city: Mannheim

first: Xiaolei

last: Yu

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Total RNA was isolated.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: SAS Microarray Solution 1.0

source_name: Total RNA of HuH-7 cells, control

label_protocol: Total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA isolation of HuH-7 cells was performed.

tag: HuH-7 cells, control


title: Prostate tumor patient 18

source_name: hr


title: Prostate tumor patient 22


title: control chip9

description: Total RNA was isolated.

tag: Total RNA of HuH-7 cells, control


title: Prostate tumor patient 7

value: Tumor widespread at margin


title: Prostate tumor patient 8


title: ds1 A chip5

description: Total RNA isolation was performed 3 days after transfection of IGF-II-specific siRNAs.

source_name: Total RNA of HuH-7 cells, 3 days after transfection of ds1

label_protocol: total RNA was processed to produce biotinylated cRNA targets.

tag: HuH-7 cells, transfection of ds1


title: Prostate tumor patient 13

tag: race

value: African American


title: Prostate tumor patient 5

tag: smoking status


title: Prostate tumor patient 9

tag: gleason sum


title: Prostate tumor patient 6


title: Prostate tumor patient 21

value: Unknown


title: Prostate tumor patient 12

value: African American, Smoking Status:Unknown


title: Prostate tumor patient 10

value: Yes


title: Prostate tumor patient 2


title: Prostate tumor patient 1


title: Prostate tumor patient 4

value: Tumor focal at margin


title: SOM-rep3

city: Turku

first: Lea

last: Sistonen

address: Tykistokatu 6 B

department: Biology

country: Finland

institute: Åbo Akademi University

description: Biological replicate 3

hyb_protocol: The labeled ChIP DNA was precipitated and hybridized in buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C and then washed. Hybridizations were performed per manufacturer's protocols http://www.nimblegen.com/products/lit/lit.html

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturers's protocol: http://www.nimblegen.com/products/lit/lit.html

data_processing: The ChIP-chip data was normalized with Lowess normalization method and normalized log2 ratio (HSF2 ChIP/Input DNA) was produced for each biological replicate. The promoter values were calculated as average log2 ratios over all probes for each promoter. To identify the HSF2 target population, we used a non-arbitrary analysis method called RankProd described in Breitling et al. 2004. RankProd has been published as an R/Bioconductor package.

source_name: Amplified HSF2 ChIP DNA from mouse wild-type testis labeled with Cy5.

label_protocol: For NimbleGen arrays, ChIP DNA prepared from testes was directly labeled by klenow random priming with Cy5 or Cy3 nonamers per manufacturer's protocol: http://www.nimblegen.com/products/lit/lit.html

growth_protocol: Pathogen-free mice were housed under controlled environmental conditions and fed with complete pelleted chow and allowed tap water. The mice were killed by CO2 asphyxiation. All mice were handled in accordance with the institutional animal care policies of the Åbo Akademi University (Turku, Finland).

extract_protocol:
Isolated testes were cross-linked with a final concentration of 1% formaldehyde. Quenching was performed with 125 mM glycine. Testes were lysed in 4 ml lysis buffer. Chromatin samples were sonicated with Bioruptor (Diagenode) to an approximate size of 100-500 bp. Immunoprecipitation was performed after preclearing with 50% slurry of
protein G-coated Sepharose beads (Amersham Biosciences), at 4C over night. HSF2 antibody was used for immunoprecipitation and an input sample was obtained after the immunoprecipitation. Immunocomplexes were washed eight times. Cross-links were reversed by incubation of samples over night at 65C and DNA was purified and resuspended in water.
DNA amplification of material obtained from three biological replicates, needed for microarray hybridizations. Whole ChIP samples and 20 ng of the input samples were used for the ligation-mediated PCR (LM-PCR). The DNA was blunted using dNTP mix (Promega) and T4 DNA polymerase (New England Biolabs), purified and dissolved in water.
Purified DNA was ligated using T4 DNA ligase (New England Biolabs) and annealed with linkers made from HPLC-purified oligos; oligo 1: 5’-gcg gtg acc ggg aga tct gaa ttc-3’ and oligo 2: 5’-gaa ttc aga tc-3’. DNA was purified again and dissolved in water. LM-PCR was performed using Taq Polymerase (New England Biolabs) and Pfu Polymerase (Stratagen).

treatment_protocol: Adult (60 days old) wild-type mice were used for isolation of testes

tag: Strain

value: B6129SF2/J, Age:60 days, Gender:Male, Tissue:Wild-type testis

source_name: Amplified Input DNA from mouse wild-type testis labeled with Cy3.


title: SOM-rep1

description: Biological replicate 1


title: SOM-rep2

description: Biological replicate 2

source_name: Amplified HSF2 ChIP DNA from mouse wild-type testis labeled with Cy3.

source_name: Amplified Input DNA from mouse wild-type testis labeled with Cy5.


title: P0716 lenalidomide post-treatment

status: Public on Aug 04 2008

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: human myeloma cell  P0716 lenalidomide post-treatment

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

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

label: Biotin

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol

extract_protocol: RNeasy Mini Kit(50)


title: P0677 lenalidomide pre-treatment

description: human myeloma cell  P0677 lenalidomide pre-treatment


title: P0662 lenalidomide pre-treatment

description: human myeloma cell  P0662 lenalidomide pre-treatment


title: P220 lenalidomide pre-treatment

description: human myeloma cell  P220 lenalidomide pre-treatment


title: P616 lenalidomide post-treatment

description: human myeloma cell  P616 lenalidomide post-treatment


title: P548 lenalidomide post-treatment

description: human myeloma cell  P548 lenalidomide post-treatment


title: P616 lenalidomide pre-treatment

description: human myeloma cell  P616 lenalidomide pre-treatment


title: P581 lenalidomide pre-treatment

description: human myeloma cell  P581 lenalidomide pre-treatment


title: P198 lenalidomide pre-treatment

description: human myeloma cell  P198 lenalidomide pre-treatment


title: P548 lenalidomide pre-treatment

description: human myeloma cell  P548 lenalidomide pre-treatment


title: P621 lenalidomide post-treatment

description: human myeloma cell  P621 lenalidomide post-treatment


title: P318 lenalidomide pre-treatment

description: human myeloma cell  P318 lenalidomide pre-treatment


title: P555 lenalidomide post-treatment

description: human myeloma cell  P555 lenalidomide post-treatment


title: P244 lenalidomide post-treatment

description: human myeloma cell  P244 lenalidomide post-treatment


title: P533 lenalidomide pre-treatment

description: human myeloma cell  P533 lenalidomide pre-treatment


title: P72 lenalidomide pre-treatment

description: human myeloma cell  P72 lenalidomide pre-treatment


title: P238 lenalidomide pre-treatment

description: human myeloma cell  P238 lenalidomide pre-treatment


title: P244 lenalidomide pre-treatment

description: human myeloma cell  P244 lenalidomide pre-treatment


title: P617 lenalidomide pre-treatment

description: human myeloma cell  P617 lenalidomide pre-treatment


title: P486 lenalidomide pre-treatment

description: human myeloma cell  P486 lenalidomide pre-treatment


title: P533 lenalidomide post-treatment

description: human myeloma cell  P533 lenalidomide post-treatment


title: P336 lenalidomide post-treatment

description: human myeloma cell  P336 lenalidomide post-treatment


title: P509 lenalidomide pre-treatment

description: human myeloma cell  P509 lenalidomide pre-treatment


title: P557 lenalidomide post-treatment

description: human myeloma cell  P557 lenalidomide post-treatment


title: P555 lenalidomide pre-treatment

description: human myeloma cell  P555 lenalidomide pre-treatment


title: P072 lenalidomide pre-treatment

description: human myeloma cell  P072 lenalidomide pre-treatment


title: P590 lenalidomide pre-treatment

description: human myeloma cell  P590 lenalidomide pre-treatment


title: P619 lenalidomide pre-treatment

description: human myeloma cell  P619 lenalidomide pre-treatment


title: P499 lenalidomide pre-treatment

description: human myeloma cell  P499 lenalidomide pre-treatment


title: P72 lenalidomide post-treatment

description: human myeloma cell  P72 lenalidomide post-treatment


title: P580 lenalidomide post-treatment

description: human myeloma cell  P580 lenalidomide post-treatment


title: P0716 lenalidomide pre-treatment

description: human myeloma cell  P0716 lenalidomide pre-treatment


title: P516 lenalidomide pre-treatment

description: human myeloma cell  P516 lenalidomide pre-treatment


description: human myeloma cell  P244 lenalidomide pre_Cycle_3_Dex-treatment


title: P0619 lenalidomide pre-treatment

description: human myeloma cell  P0619 lenalidomide pre-treatment


title: P543 lenalidomide pre-treatment

description: human myeloma cell  P543 lenalidomide pre-treatment


title: P0677 lenalidomide post-treatment

description: human myeloma cell  P0677 lenalidomide post-treatment


title: P336 lenalidomide pre-treatment

description: human myeloma cell  P336 lenalidomide pre-treatment


title: P621 lenalidomide pre-treatment

description: human myeloma cell  P621 lenalidomide pre-treatment


title: P558 lenalidomide pre-treatment

description: human myeloma cell  P558 lenalidomide pre-treatment


title: P554 lenalidomide pre-treatment

description: human myeloma cell  P554 lenalidomide pre-treatment


title: P0764 lenalidomide pre-treatment

description: human myeloma cell  P0764 lenalidomide pre-treatment


title: P617 lenalidomide post-treatment

description: human myeloma cell  P617 lenalidomide post-treatment


title: P557 lenalidomide pre-treatment

description: human myeloma cell  P557 lenalidomide pre-treatment


title: P547 lenalidomide pre-treatment

description: human myeloma cell  P547 lenalidomide pre-treatment


title: P519 lenalidomide post-treatment

description: human myeloma cell  P519 lenalidomide post-treatment


title: P642 dexamethasone post-treatment

description: human myeloma cell  P642 dexamethasone post-treatment


title: P630 dexamethasone post-treatment

description: human myeloma cell  P630 dexamethasone post-treatment


title: P636 thalidomide pre-treatment

description: human myeloma cell  P636 thalidomide pre-treatment


title: P625 dexamethasone post-treatment

description: human myeloma cell  P625 dexamethasone post-treatment


title: P543 lenalidomide post-treatment

description: human myeloma cell  P543 lenalidomide post-treatment


title: P580 lenalidomide pre-treatment

description: human myeloma cell  P580 lenalidomide pre-treatment


title: P600 thalidomide post-treatment

description: human myeloma cell  P600 thalidomide post-treatment


title: P640 dexamethasone post-treatment

description: human myeloma cell  P640 dexamethasone post-treatment


title: P610 thalidomide pre-treatment

description: human myeloma cell  P610 thalidomide pre-treatment


title: P600 thalidomide pre-treatment

description: human myeloma cell  P600 thalidomide pre-treatment


title: P614 thalidomide post-treatment

description: human myeloma cell  P614 thalidomide post-treatment


title: P594 thalidomide post-treatment

description: human myeloma cell  P594 thalidomide post-treatment


title: P566 dexamethasone post-treatment

description: human myeloma cell  P566 dexamethasone post-treatment


title: P597 thalidomide pre-treatment

description: human myeloma cell  P597 thalidomide pre-treatment


title: P625 dexamethasone pre-treatment

description: human myeloma cell  P625 dexamethasone pre-treatment


title: P610 thalidomide post-treatment

description: human myeloma cell  P610 thalidomide post-treatment


title: P614 thalidomide pre-treatment

description: human myeloma cell  P614 thalidomide pre-treatment


title: P575 dexamethasone post-treatment

description: human myeloma cell  P575 dexamethasone post-treatment


title: P561 thalidomide post-treatment

description: human myeloma cell  P561 thalidomide post-treatment


title: P566 dexamethasone pre-treatment

description: human myeloma cell  P566 dexamethasone pre-treatment


title: P594 thalidomide pre-treatment

description: human myeloma cell  P594 thalidomide pre-treatment


title: P561 thalidomide pre-treatment

description: human myeloma cell  P561 thalidomide pre-treatment


title: P597 thalidomide post-treatment

description: human myeloma cell  P597 thalidomide post-treatment


title: P559 thalidomide post-treatment

description: human myeloma cell  P559 thalidomide post-treatment


title: P559 thalidomide pre-treatment

description: human myeloma cell  P559 thalidomide pre-treatment


title: ds3 A chip7

description: Total RNA isolation was performed 3 days after transfection of IGF-II-specific siRNAs.

source_name: Total RNA of HuH-7 cells, 3 days after transfection of ds3

tag: HuH-7 cells, transfection of ds3


title: ds3 B chip8


title: P549 dexamethasone post-treatment

description: human myeloma cell  P549 dexamethasone post-treatment


title: P549 dexamethasone pre-treatment

description: human myeloma cell  P549 dexamethasone pre-treatment


title: ds1 B chip6


title: P541 thalidomide post-treatment

description: human myeloma cell  P541 thalidomide post-treatment


title: P541 thalidomide pre-treatment

description: human myeloma cell  P541 thalidomide pre-treatment


title: P532 dexamethasone pre-treatment

description: human myeloma cell  P532 dexamethasone pre-treatment


title: P532 dexamethasone post-treatment

description: human myeloma cell  P532 dexamethasone post-treatment


title: P511 dexamethasone post-treatment

description: human myeloma cell  P511 dexamethasone post-treatment


title: P474 thalidomide post-treatment

description: human myeloma cell  P474 thalidomide post-treatment


title: P511 dexamethasone pre-treatment

description: human myeloma cell  P511 dexamethasone pre-treatment


title: P510 dexamethasone post-treatment

description: human myeloma cell  P510 dexamethasone post-treatment


title: P522 dexamethasone post-treatment

description: human myeloma cell  P522 dexamethasone post-treatment


title: P510 dexamethasone pre-treatment

description: human myeloma cell  P510 dexamethasone pre-treatment


title: P526 thalidomide pre-treatment

description: human myeloma cell  P526 thalidomide pre-treatment


title: P508 thalidomide post-treatment

description: human myeloma cell  P508 thalidomide post-treatment


title: P522 dexamethasone pre-treatment

description: human myeloma cell  P522 dexamethasone pre-treatment


title: P480 dexamethasone pre-treatment

description: human myeloma cell  P480 dexamethasone pre-treatment


title: P501 dexamethasone pre-treatment

description: human myeloma cell  P501 dexamethasone pre-treatment


title: P517 dexamethasone pre-treatment

description: human myeloma cell  P517 dexamethasone pre-treatment


title: P482 dexamethasone pre-treatment

description: human myeloma cell  P482 dexamethasone pre-treatment


title: P517 dexamethasone post-treatment

description: human myeloma cell  P517 dexamethasone post-treatment


title: P465 dexamethasone post-treatment

description: human myeloma cell  P465 dexamethasone post-treatment


title: P503 dexamethasone post-treatment

description: human myeloma cell  P503 dexamethasone post-treatment


title: P480 dexamethasone post-treatment

description: human myeloma cell  P480 dexamethasone post-treatment


title: P508 thalidomide pre-treatment

description: human myeloma cell  P508 thalidomide pre-treatment


title: P474 thalidomide pre-treatment

description: human myeloma cell  P474 thalidomide pre-treatment


title: P451 thalidomide post-treatment

description: human myeloma cell  P451 thalidomide post-treatment


title: P501 dexamethasone post-treatment

description: human myeloma cell  P501 dexamethasone post-treatment


title: P447 dexamethasone pre-treatment

description: human myeloma cell  P447 dexamethasone pre-treatment


title: P503 dexamethasone pre-treatment

description: human myeloma cell  P503 dexamethasone pre-treatment


title: P451 thalidomide pre-treatment

description: human myeloma cell  P451 thalidomide pre-treatment


title: P447 dexamethasone post-treatment

description: human myeloma cell  P447 dexamethasone post-treatment


title: P434 dexamethasone post-treatment

description: human myeloma cell  P434 dexamethasone post-treatment


title: P421 thalidomide pre-treatment

description: human myeloma cell  P421 thalidomide pre-treatment


title: P405 dexamethasone post-treatment

description: human myeloma cell  P405 dexamethasone post-treatment


title: P492 thalidomide post-treatment

description: human myeloma cell  P492 thalidomide post-treatment


title: P492 thalidomide pre-treatment

description: human myeloma cell  P492 thalidomide pre-treatment


title: P405 dexamethasone pre-treatment

description: human myeloma cell  P405 dexamethasone pre-treatment


title: P421 thalidomide post-treatment

description: human myeloma cell  P421 thalidomide post-treatment


title: P399 thalidomide post-treatment

description: human myeloma cell  P399 thalidomide post-treatment


title: P399 thalidomide pre-treatment

description: human myeloma cell  P399 thalidomide pre-treatment


title: P433 dexamethasone post-treatment

description: human myeloma cell  P433 dexamethasone post-treatment


title: P433 dexamethasone pre-treatment

description: human myeloma cell  P433 dexamethasone pre-treatment


title: P365 thalidomide post-treatment

description: human myeloma cell  P365 thalidomide post-treatment


title: P391 thalidomide post-treatment

description: human myeloma cell  P391 thalidomide post-treatment


title: P391 thalidomide pre-treatment

description: human myeloma cell  P391 thalidomide pre-treatment


title: P365 thalidomide pre-treatment

description: human myeloma cell  P365 thalidomide pre-treatment


title: P357 thalidomide post-treatment

description: human myeloma cell  P357 thalidomide post-treatment


title: P357 thalidomide pre-treatment

description: human myeloma cell  P357 thalidomide pre-treatment


title: P434 dexamethasone pre-treatment

description: human myeloma cell  P434 dexamethasone pre-treatment


title: P387 dexamethasone post-treatment

description: human myeloma cell  P387 dexamethasone post-treatment


title: P371 dexamethasone post-treatment

description: human myeloma cell  P371 dexamethasone post-treatment


title: P354 dexamethasone post-treatment

description: human myeloma cell  P354 dexamethasone post-treatment


title: P354 dexamethasone pre-treatment

description: human myeloma cell  P354 dexamethasone pre-treatment


title: P330 thalidomide post-treatment

description: human myeloma cell  P330 thalidomide post-treatment


title: P281 thalidomide pre-treatment

description: human myeloma cell  P281 thalidomide pre-treatment


title: P324 thalidomide pre-treatment

description: human myeloma cell  P324 thalidomide pre-treatment


title: P281 thalidomide post-treatment

description: human myeloma cell  P281 thalidomide post-treatment


title: P308 dexamethasone pre-treatment

description: human myeloma cell  P308 dexamethasone pre-treatment


title: P301 thalidomide post-treatment

description: human myeloma cell  P301 thalidomide post-treatment


title: P330 thalidomide pre-treatment

description: human myeloma cell  P330 thalidomide pre-treatment


title: P313 dexamethasone post-treatment

description: human myeloma cell  P313 dexamethasone post-treatment


title: P313 dexamethasone pre-treatment

description: human myeloma cell  P313 dexamethasone pre-treatment


title: P255 thalidomide post-treatment

description: human myeloma cell  P255 thalidomide post-treatment


title: P271 thalidomide post-treatment

description: human myeloma cell  P271 thalidomide post-treatment


title: P324 thalidomide post-treatment

description: human myeloma cell  P324 thalidomide post-treatment


title: P270 dexamethasone post-treatment

description: human myeloma cell  P270 dexamethasone post-treatment


title: P251 dexamethasone post-treatment

description: human myeloma cell  P251 dexamethasone post-treatment


title: P343 dexamethasone pre-treatment

description: human myeloma cell  P343 dexamethasone pre-treatment


title: P239 dexamethasone post-treatment

description: human myeloma cell  P239 dexamethasone post-treatment


title: P280 dexamethasone post-treatment

description: human myeloma cell  P280 dexamethasone post-treatment


title: P343 dexamethasone post-treatment

description: human myeloma cell  P343 dexamethasone post-treatment


title: P099 dexamethasone post-treatment

description: human myeloma cell  P099 dexamethasone post-treatment


title: P278 thalidomide post-treatment

description: human myeloma cell  P278 thalidomide post-treatment


title: P154 thalidomide post-treatment

description: human myeloma cell  P154 thalidomide post-treatment


title: P232 thalidomide pre-treatment

description: human myeloma cell  P232 thalidomide pre-treatment


title: P095 dexamethasone pre-treatment

description: human myeloma cell  P095 dexamethasone pre-treatment


title: P095 dexamethasone post-treatment

description: human myeloma cell  P095 dexamethasone post-treatment


title: P154 thalidomide pre-treatment

description: human myeloma cell  P154 thalidomide pre-treatment


title: P175 dexamethasone post-treatment

description: human myeloma cell  P175 dexamethasone post-treatment


title: P237 thalidomide post-treatment

description: human myeloma cell  P237 thalidomide post-treatment


title: P084 thalidomide post-treatment

description: human myeloma cell  P084 thalidomide post-treatment


title: P075 dexamethasone post-treatment

description: human myeloma cell  P075 dexamethasone post-treatment


title: P0740 dexamethasone post-treatment

description: human myeloma cell  P0740 dexamethasone post-treatment


title: P0740 dexamethasone pre-treatment

description: human myeloma cell  P0740 dexamethasone pre-treatment


title: P0741 dexamethasone pre-treatment

description: human myeloma cell  P0741 dexamethasone pre-treatment


title: P308 dexamethasone post-treatment

description: human myeloma cell  P308 dexamethasone post-treatment


title: P0724 dexamethasone pre-treatment

description: human myeloma cell  P0724 dexamethasone pre-treatment


title: P0724 dexamethasone post-treatment

description: human myeloma cell  P0724 dexamethasone post-treatment


title: P0718 thalidomide pre-treatment

description: human myeloma cell  P0718 thalidomide pre-treatment


title: P0705 thalidomide pre-treatment

description: human myeloma cell  P0705 thalidomide pre-treatment


title: P202 thalidomide post-treatment

description: human myeloma cell  P202 thalidomide post-treatment


title: P301 thalidomide pre-treatment

description: human myeloma cell  P301 thalidomide pre-treatment


title: P0725 dexamethasone post-treatment

description: human myeloma cell  P0725 dexamethasone post-treatment


title: P0718 thalidomide post-treatment

description: human myeloma cell  P0718 thalidomide post-treatment


title: P0725 dexamethasone pre-treatment

description: human myeloma cell  P0725 dexamethasone pre-treatment


title: P232 thalidomide post-treatment

description: human myeloma cell  P232 thalidomide post-treatment


title: P0733 dexamethasone post-treatment

description: human myeloma cell  P0733 dexamethasone post-treatment


title: P0733 dexamethasone pre-treatment

description: human myeloma cell  P0733 dexamethasone pre-treatment


title: P0698 thalidomide pre-treatment

description: human myeloma cell  P0698 thalidomide pre-treatment


title: P0705 thalidomide post-treatment

description: human myeloma cell  P0705 thalidomide post-treatment


title: P0702 thalidomide pre-treatment

description: human myeloma cell  P0702 thalidomide pre-treatment


title: P0741 dexamethasone post-treatment

description: human myeloma cell  P0741 dexamethasone post-treatment


title: P0695 thalidomide pre-treatment

description: human myeloma cell  P0695 thalidomide pre-treatment


title: P0702 thalidomide post-treatment

description: human myeloma cell  P0702 thalidomide post-treatment


title: P0698 thalidomide post-treatment

description: human myeloma cell  P0698 thalidomide post-treatment


title: P0695 thalidomide post-treatment

description: human myeloma cell  P0695 thalidomide post-treatment


title: P0692 thalidomide pre-treatment

description: human myeloma cell  P0692 thalidomide pre-treatment


title: P0689 dexamethasone pre-treatment

description: human myeloma cell  P0689 dexamethasone pre-treatment


title: P0692 thalidomide post-treatment

description: human myeloma cell  P0692 thalidomide post-treatment


title: P0689 dexamethasone post-treatment

description: human myeloma cell  P0689 dexamethasone post-treatment


title: P0678 dexamethasone post-treatment

description: human myeloma cell  P0678 dexamethasone post-treatment


title: P0686 dexamethasone post-treatment

description: human myeloma cell  P0686 dexamethasone post-treatment


title: P0678 dexamethasone pre-treatment

description: human myeloma cell  P0678 dexamethasone pre-treatment


title: P0672 dexamethasone pre-treatment

description: human myeloma cell  P0672 dexamethasone pre-treatment


title: P0672 dexamethasone post-treatment

description: human myeloma cell  P0672 dexamethasone post-treatment


title: P0670 thalidomide post-treatment

description: human myeloma cell  P0670 thalidomide post-treatment


title: P0667 dexamethasone pre-treatment

description: human myeloma cell  P0667 dexamethasone pre-treatment


title: P0670 thalidomide pre-treatment

description: human myeloma cell  P0670 thalidomide pre-treatment


title: P0667 dexamethasone post-treatment

description: human myeloma cell  P0667 dexamethasone post-treatment


title: P0666 thalidomide pre-treatment

description: human myeloma cell  P0666 thalidomide pre-treatment


title: P0647 thalidomide pre-treatment

description: human myeloma cell  P0647 thalidomide pre-treatment


title: P0673 thalidomide post-treatment

description: human myeloma cell  P0673 thalidomide post-treatment


title: P0686 dexamethasone pre-treatment

description: human myeloma cell  P0686 dexamethasone pre-treatment


title: P0666 thalidomide post-treatment

description: human myeloma cell  P0666 thalidomide post-treatment


title: P0647 thalidomide post-treatment

description: human myeloma cell  P0647 thalidomide post-treatment


title: P0642 dexamethasone pre-treatment

description: human myeloma cell  P0642 dexamethasone pre-treatment


title: P0673 thalidomide pre-treatment

description: human myeloma cell  P0673 thalidomide pre-treatment


title: P0640 dexamethasone pre-treatment

description: human myeloma cell  P0640 dexamethasone pre-treatment


title: P0575 dexamethasone pre-treatment

description: human myeloma cell  P0575 dexamethasone pre-treatment


title: P0636 thalidomide post-treatment

description: human myeloma cell  P0636 thalidomide post-treatment


title: P0526 thalidomide post-treatment

description: human myeloma cell  P0526 thalidomide post-treatment


title: P0630 dexamethasone pre-treatment

description: human myeloma cell  P0630 dexamethasone pre-treatment


title: P029 thalidomide pre-treatment

description: human myeloma cell  P029 thalidomide pre-treatment


title: P0278 thalidomide pre-treatment

description: human myeloma cell  P0278 thalidomide pre-treatment


title: P0280 dexamethasone pre-treatment

description: human myeloma cell  P0280 dexamethasone pre-treatment


title: P0465 dexamethasone pre-treatment

description: human myeloma cell  P0465 dexamethasone pre-treatment


title: P029 thalidomide post-treatment

description: human myeloma cell  P029 thalidomide post-treatment


title: P0271 thalidomide pre-treatment

description: human myeloma cell  P0271 thalidomide pre-treatment