title: Asynch-Muscle-Rep1

description:
Sample name: Asynch Muscle IP Replicate 1
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: WAT from Glimepiride-treated Zucker diabetic fatty rat Replicate2

status: Public on Mar 23 2012

type: RNA

city: Seoul

first: Seong

last: Je kyung

country: South Korea

institute: Seoul National University

hyb_protocol: labeled two cDNA probe solutions containing hybridization buffer (Genocheck, Korea) were mixed on equal amount and HybriWell FL Sealing System (Grace bio-labs, U.S.A) were applied to the microarrays and placed in a humidified chamber at 62℃ for 14 h. Then, the microarrays were sequentially washed

scan_protocol: Scanned on an Axon GenePix scanarray 4000(Axon 4000, USA) Software

data_processing: All analysis of microarray data was carried the limma package in R. Log2 ratios were calculated using print-tip loess normalization method and quantile normalization was applied across arrays

molecule: total RNA

organism: Rattus norvegicus

source_name: Epididimal Fat of Glimepiride-treated ZDF rat

label_protocol: we used the Superscript TMⅡ (Invitrogen, U.S.A) RNase H Reverse Transcriptase to synthesize cDNA. The reverse transcription mixture included 400 U Superscript RNase H-reverse transcriptase, 15 mM dATP, dTTP and dGTP, 0.6 mM dCTP and 3 mM Cy3 or Cy5 labeled dCTP (NEN Life Science Product Inc.  MA, USA).

extract_protocol: Total RNA was extracted from the different tissues after drug treatment using Trizol reagent (Invitrogen Co., U.S.A) according to the manufacturer’s instructions.

treatment_protocol: Metformin (Glucophage, 300mg/kg/day) and glimepiride (Amaryl, 200mg/kg/day) were given by oral injection to ZDF rats for 2 weeks in each groups and rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) was given to ZDF rats for 1 week according to the manufacture’s protocols and recommendations

tag: tissue

value: Epididimal Fat

tag: age

value: 12-weeks old

tag: gender

value: Male

tag: strain

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

tag: treatment

value: glimepiride (Amaryl, 200mg/kg/day) daily for 2weeks by oral gavage

source_name: Epididimal Fat of ZDF rat


title: RVSMC treated without Ang II (0h), biological rep2

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

country: USA

institute: City of Hope

description:
Gene expression data from RVSMC without Ang II stimulation
D939_(2_Ctrl.2)_(RaGene-1_0-st-v1).CEL

hyb_protocol: Affymetrix GeneChip Whole Transcript (WT) Gene 1.0 Array hybridization protocol using 5.5 ug fragmented and biotinylated cDNA (sense strand), hybridized at 45 C for ~16 hrs, and the Rat Gene 1.0 Arrays were stained and washed using Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip Rat Gene 1.0 ST Arrays were scanned using the GeneChip Scanner 3000 7G controlled by Affymetrix GeneChip Command Console Software (AGCC).

data_processing: raw CEL files were imported to Partek Genomic Suite and pre-processed using Robust Multichip Average (RMA) method

label: biotin

source_name: vascular smooth muscle cells,  no Ang II stimulation

label_protocol: Affymetrix GeneChip Whole Transcript (WT) Sense Target labeling Protocol V4 using 100 ng total RNA to start the labeling reaction.

growth_protocol: rat vascular smooth muscle cells were cultured in M199 medium supplemented with 10% FBS.

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

treatment_protocol: serum depleted for 48h and treated with or without Ang II (100nM) for 1h, 3h or 24h.

tag: stain

value: Sprague-Dawley

value: aorta

tag: development

value: differentiated

tag: cell type

value: vascular smooth muscle cells

tag: agent

value: untreated

tag: time

value: control


title: WAT from Glimepiride-treated Zucker diabetic fatty rat Replicate3


title: 14227280 - wt_22_2 vs sphk2_22_2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Role of PI4 kinase and Long-chain bases kinases in response to cold stress

hyb_protocol: sphk2_22_2 Cy5 / wt_22_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - media: Murashige and Skoog (MS) medium  hygrometry: 80%  temperature: 22°C  light: 80 micro Enstein

extract_protocol: sphk_22_2:18ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

value: mutant sphk2

extract_protocol: wt_22_2:13ug. (Qiagen_RNeasy.pdf)

value: wild type


title: HS_02

type: genomic

city: Paris

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

description: childhood adrenocortical tumor

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: standard Illumina protocol

extract_protocol: Proteinase K method. The detailed protocol can be found in PMID:18786438.

tag: geographical origin

value: Brazil

tag: genger

tag: histological type

value: Carcinoma

tag: tnm

tag: tp53 mutation

tag: virilization

value: Yes

tag: cushing  syndrome

value: No

value: Surgery

tag: follow-up (months)

value: Alive (90)


title: HS_01

description: childhood adrenocortical tumor

value: Female

value: Adenoma

value: Alive (45)


title: HS_05

description: childhood adrenocortical tumor

value: Surgery+Chemotherapy


title: WAT from Glimepiride-treated Zucker diabetic fatty rat Replicate1

tag: tissue

value: Epididimal Fat

tag: age

value: 12-weeks old

tag: gender

value: Male

tag: strain

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

value: glimepiride (Amaryl, 200mg/kg/day) daily for 2weeks by oral gavage


title: Asynch-Intestine-Rep3

city: Boulder

first: Min

last: Han

state: CO

address: Campus Box 347

department: Molecular Cellular and Developmental Biology

institute: Univeristy of Colardo, Boulder/HHMI

description:
Sample name: Asynch Intestine IP Replicate 3
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.

hyb_protocol: Hybridization Application 1.0 PURPOSE: To provide a standard operating procedure for hybridization of fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass slides. 2.0 SPECIAL NOTES: 3.0 AUTHORS: Mike Heinz 4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0 5.0 REQUIRED MATERIALS AND EQUIPMENT: Labeled probe Hybridization chamber apparatus Hybridization oven Heat block 4xSSC Air gun/ canister Timers Microcentrifuge Hybridization buffer (check vendor) Forceps Microarray(s) Pipettes Coverslips (Erie Scientific) 6.0 DEFINITIONS: 7.0 PROCEDURE: 7.1 Set up 7.1.1 Using an air gun canister, blow off all hybridization chamber parts to ensure they are clean, especially the microarray and the coverslip. 7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip apparatus. Make sure that the coverslip is appropriately placed over the entire arrayed area. 7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization chamber. 7.1.4 If frozen, remove probes from the -20C freezer and thaw at room temperature in the dark if frozen. Ensure that each probe has enough volume for the hybridization (ie. For a 25x25mm coverslip, 20ul is needed to cover the array surface). Each probe should have at least +2ul of probe in the tube compared to that of the volume to be applied to the array. If a probe does not contain the appropriate volume, add hybridization buffer (use appropriate vendor) to reach desired volume. Make sure to mix the solution if adding hyb buffer. 7.1.5 By checking the paperwork/ jobticket, make sure that the appropriate probes have been thawed and that the appropriate arrays have been placed in the chambers. 7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for appropriate denaturing temperatures and times). 7.1.7 Centrifuge the probes for 1 min. at max speed. 7.2 Application 7.2.1 Carefully pipette 20ul (or other amount) under the coverslip covering the arrayed surface. Ensure that the array is completely covered. If not completely covered, pipette additional probe under the coverslip in increments of 2ul. Note any bubbles or abnormalities. 7.2.2 Apply the coverglass and clamps. Using the torque wrench, tighten the clamps. Make sure that the metal arms of the clamps are not resting on the edge of the coverglass. Also, make certain that the wrench is set at 46 lb/in. 7.2.3 Place the hybridization chambers in the hybrization box, then place the hyb. box in the oven at 42C and hybridize overnight (minimum of 12 hours). Make certain to place the chambers in the hyb. box so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0.

data_processing: Microarray data (median spot value – median local background) was first filtered to remove low-signal spots (spots with values < 25 in either the channel representing the Total RNA or the channel representing IP RNA).   For each remaining probe, the enrichment value was defined as IP/Total.  We next calculated the percent rank of the enrichment value for all spots within a given biological replicate.  Finally, for any given probe (representing a specific mRNA) the mean value of all non-missing percent ranks was calculated.  A given probe was defined as “testable” if at least two biological replicates yielded non-missing values (i.e. at least two replicates yielded sufficiently robust signal in both the IP and Total RNA channels).  For all testable mRNAs, a p-value for enrichment was calculated by using a one-tailed t-test for each percent rank value compared to all percent rank values within the dataset.  Therefore, for a given mRNA, the enrichment value is represented as the mean percent rank over all biological replicates as well as a p-value indicating statistical significance of the percent ranks compared to the whole data set.  This methodology was based on previous work (Roy et al., 2002).  p value cut-offs for enrichment were p < 0.01 for all tissue-specific IPs, with the exception of the L4-syncrhonized worms in which we chose a cut-off of p < 0.001.  An mRNA was considered to be IP-enriched if it showed above average enrichment (i.e. mean percent rank was greater than 0.500) and the p-value for its enrichment was below the indicated cut-off.

organism: Caenorhabditis elegans

source_name: Total RNA from Pges-1::ain-2::gfp

label_protocol: The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

growth_protocol: For experiments on asynchronous worms, worms were grown to high density on HB101 and harvested when well-fed.  For synchroinization at L4, worms were grown to gravid adults on 20x10cm NGM plates with a thick lawn of HB101 E. coli.  Just prior to starvation, worms were washed from the plates, and embryos were isolated by the hypochlorite method followed by sucrose floatation to remove carcasses.  The purified embryos were rinsed several times with M9, and allowed to hatch for 20 h at 20oC in M9.  The synchronized L1s were then mixed with HB101 and allowed to grow for 48 h at 20oC before they were harvested, sucrose floated to remove remaining HB101, split in two, and distributed between 30x10cm peptone-enhanced (0.35% final) plates seeded with OP50 or PA14.  The worms were exposed to each bacterium at 25oC for 8 h before harvesting, cross-linking and subsequent IP.

extract_protocol: This was performed essentially as previously described (Zhang et al., 2007; Zhang et al., 2009). Worm cultures were expanded on 10 cm nematode growth medium (NGM) plates seeded with thick lawns of HB101 (KanR) E. coli.  For each experiment, approximately 20 plates of worms were grown to high density, without allowing starvation.  Worms were harvested and immediately cross-linked with 0.5% formaldehyde in M9 at 4oC for 1 h as performed by Roy et al. (Roy et al., 2002).  Cross-linked samples were washed twice with M9, snap-frozen in liquid nitrogen and stored at -80oC for subsequent lysis and IP.  Frozen samples were then homogenized with a mortar and pestle under liquid nitrogen.  The homogenate was extracted with three volumes lysis buffer [25 mM HEPES-NaOH (pH 7.4), 150 mM NaCl, 1 mM DTT, 10% glycerol, 1% Triton X-100, Complete Protease Inhibitors (Roche), 100 U/ml recombinant ribonuclease inhibitor (RNaseOUT by Invitrogen)].  The lysate was then clarified by centrifugation at 20,000xg for 20 min at 4oC.  The supernatant was then pre-cleared by incubation with 25 μl/ml protein A sepharose (Sigma) for 1 h at 4oC.  The cleared supernatant was then subjected to immunoprecipation with the 10 μg/ml 3E6 anti-GFP monoclonal antibody for 2 h, as previously described (Zhang et al., 2007; Zhang et al., 2009).  Immediately before addition of protein A sepharose beads, several 50 μl aliquots of lysate were removed and de-crosslinked as previously described (Roy et al., 2002).  The de-crosslinked aliquots were mixed with 1 ml of Trizol (Invitrogen) and used as Total RNA for subsequent microarray analysis.  After incubation with protein A sepharose and washing, as previously described, complexes precipitating with the protein A sepharose beads were decrosslinked twice, according to the method of Roy et al.  The de-crosslinked RNA was then mixed with Trizol, and split into two aliquots – one for microarray analysis and one for miRNA cloning.

treatment_protocol: In all instances, worms harvested, well-fed, from 10cm NGM plates.

tag: Stage

value: asynchronous

value: Intestine

tag: rip antibody

source_name: IP RNA from Pges-1::ain-2::gfp

value: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120; various  lots)


title: HS_08

description: childhood adrenocortical tumor

value: Brazil

value: Carcinoma

tag: treatment


title: HS_04

description: childhood adrenocortical tumor

value: Yes

value: No


title: HS_07

description: childhood adrenocortical tumor

value: Surgery

value: Alive (92)


title: Asynch-Intestine-Rep2

description:
Sample name: Asynch Intestine IP Replicate 2
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: 14227291 - wt_4_1 vs wt_12_1

hyb_protocol: wt_12_1 Cy5 / wt_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: wt_12_1:16ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:cold stress 12 degrees - abiotic stress - temperature,temperature:quantity 12 time 4hour . Plantlets of wild type and mutant were grown vitro for 14 days in a growth chamber (80% humidity, 80 micro Enstein without photoperiod). The 15th day, a part of wild type plantlets, pi4kinaseb1b2 and sphingosine kinase2 mutants were transferred at 4°C during 4 hours (80 micro Enstein) for a cold stress. Another part of wild type and sphk2 mutant were transferred at 12°C during 4 hours (80 micro Enstein) for a cold stress.

tag: ecotype

value: columbia

value: wild type

value: cold stress 12 degrees - abiotic stress - quantity 12 time 4hour

extract_protocol: wt_4_1:15ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:cold stress 4 degrees - abiotic stress - temperature,temperature:quantity 4 time 4hour . Plantlets of wild type and mutant were grown vitro for 14 days in a growth chamber (80% humidity, 80 micro Enstein without photoperiod). The 15th day, a part of wild type plantlets, pi4kinaseb1b2 and sphingosine kinase2 mutants were transferred at 4°C during 4 hours (80 micro Enstein) for a cold stress. Another part of wild type and sphk2 mutant were transferred at 12°C during 4 hours (80 micro Enstein) for a cold stress.

value: cold stress 4 degrees - abiotic stress -  quantity 4 time 4hour


title: Pancreas from Glimepiride-treated Zucker diabetic fatty rat Replicate2

source_name: Pancreas of Glimepiride-treated ZDF rat

value: Pancreas

value: 12-weeks old

source_name: Pancreas of of ZDF rat


title: Asynch-Intestine-Rep1

description:
Sample name: Asynch Intestine IP Replicate 1
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: 14227277 - wt_4_2 vs b1/b2_4_2

hyb_protocol: b1/b2_4_2 Cy5 / wt_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: b1/b2_4_2:19ug. (Qiagen_RNeasy.pdf)

tag: genotype/variation

value: mutant b1/b2

extract_protocol: wt_4_2:15ug. (Qiagen_RNeasy.pdf)


title: Asynch-Intestine-Rep4

description:
Sample name: Asynch Intestine IP Replicate 4
Total and IP RNA from a given biological replicate was Trizol-extracted according to the manufacturer’s protocol and shipped to the Microarray Core Laboratory at Washington University in St. Louis.  RNA was amplified once with the MessageAmp aRNA kit (Ambion), labeled with cy3 or cy5 with the MicroMax ASAP kit (Perkin Elmer), and hybrized to a single two color long oligomer-spotted microarray for C. elegans made by the Genome Sequencing Center at Washington University (http://genome.wustl.edu/services/microarray/caenorhabditis_elegans).  Four biological replicates, cultured, harvested, and IP-ed on different days, were prepared from each of the Pges-1::ain-2::gfp and Pmyo-3::ain-2::gfp strains, as well as five biological replicates of L4-synchronized Pges-1::ain-2::gfp, and five biological replicates were prepared for the Pain-2::gfp negative control strain.  Dye swapping occurred for each biological replicate to eliminate biases introduced during the labeling process.


title: 14227278 - b1/b2_4_2 vs wt_4_2

hyb_protocol: wt_4_2 Cy5 / b1/b2_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: EoE patient #6_after treatment

city: Providence

first: Shaolei

last: Lu

state: Rhode Island

address: 593 Eddy Steet

department: Pathology

institute: Rhode Island Hospital

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-6A

hyb_protocol: Hybridized for 17 hr at 45C and 60 rpm in an Affymetrix Hybridization Oven to Affymetrix Gene ST 1.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450 and fluidics protocol FS450_0007.

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

data_processing: The data were analyzed with Affymetrix Command Console and Expression Console using Affymetrix default analysis settings and global scaling as normalization method. Differential gene expression was analysed using Partek Genomics Suite software version 6.6 beta using RMA analysis mode and default settings.

source_name: EoE patient_after treatment

label_protocol: Fifty nanograms of total RNA was amplified and transcribed into cDNA using the Ovation FFPE WTA system (Nugen Technologies, San Carlos, CA).  Five to ten micrograms of amplified cDNA from the amplification above was fragmented and labeled for Affymetrix array analysis using the Encore Biotin Module (Nugen Technologies).

extract_protocol: Tissue sections (10mm) were cut and mounted onto plain glass slides.  If the biopsy section contained only epithelium, the sections were scraped from the slides and RNA was extracted using the RecoverAll Total Nucleic Acid Extraction kit for FFPE tissues (Ambion).  If biopsy sections contained sub-epithelium, the sections were deparaffinized, stained, dehydrated through graded alcohols using the Paradise FFPE reagent System (Applied Biosystems, Foster City, CA) and subjected to LCM within 2 hr of deparaffinization.  About 20000 epithelial cells were captured on LCM Macro CapSure caps (Applied Biosystems) using the Arcturus XT LCM instrument (Applied Biosystems).  Total RNA was extracted from the caps also using the RecoverAll kit as above, and subjected to analysis by the Agilent Bioanalyzer using an RNA 6000 Nano or Pico LabChip (Agilent Technologies)

tag: age range

value: Pediatric patient

tag: clinical procedure

value: Biopsy

tag: disease status

value: After glucocorticoid steroid treatment

value: epithelium

tag: histology procedure

value: Formalin-fixed paraffin-embedded


title: Pancreas from Glimepiride-treated Zucker diabetic fatty rat Replicate1

value: Male

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

value: glimepiride (Amaryl, 200mg/kg/day) daily for 2weeks by oral gavage


title: 14227273 - wt_4_2 vs wt_12_2

hyb_protocol: wt_12_2 Cy5 / wt_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: wt_12_2:16ug. (Qiagen_RNeasy.pdf)


title: EoE patient #6_before treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-6B

source_name: EoE patient_before treatment

value: Before glucocorticoid steroid treatment


title: Muscle from Glimepiride-treated Zucker diabetic fatty rat Replicate2

source_name: Gastronemious of Glimepiride-treated ZDF rat

value: Gastronemious

source_name: Gastronemious of ZDF rat


title: Muscle from Glimepiride-treated Zucker diabetic fatty rat Replicate3


title: 14227272 - wt_22_2 vs wt_4_2

hyb_protocol: wt_4_2 Cy5 / wt_22_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia


title: EoE patient #5_after treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-5A


title: EoE patient #4_after treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-4A


title: EoE patient #5_before treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-5B


title: Liver from Glimepiride-treated Zucker diabetic fatty rat Replicate2

source_name: Liver of Glimepiride-treated ZDF rat

value: liver

source_name: Liver of ZDF rat


title: EoE patient #4_before treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-4B


title: HS_045

description: blood sample

tag: geographical origin

value: Brazil

tag: genger

value: Female

tag: histological type

value: Paired blood sample corresponding to tumor HS_11

tag: tnm

tag: tp53 mutation


title: 14227271 - wt_4_2 vs wt_22_2

hyb_protocol: wt_22_2 Cy5 / wt_4_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wild type

tag: age

value: cold stress 4 degrees - abiotic stress -  quantity 4 time 4hour


title: Liver from Glimepiride-treated Zucker diabetic fatty rat Replicate3

tag: tissue

value: 12-weeks old

tag: gender


title: Liver from Glimepiride-treated Zucker diabetic fatty rat Replicate1

tag: strain


title: HS_03

description: childhood adrenocortical tumor

value: Carcinoma

tag: virilization

value: Yes

tag: cushing  syndrome

value: No

value: Surgery+Chemotherapy

tag: follow-up (months)


title: 14227274 - wt_12_2 vs wt_4_2

hyb_protocol: wt_4_2 Cy5 / wt_12_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: genotype/variation

tag: treatment

value: cold stress 12 degrees - abiotic stress - quantity 12 time 4hour


title: 14227269 - b1/b2_22_2 vs wt_22_2

hyb_protocol: wt_22_2 Cy5 / b1/b2_22_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: b1/b2_22_2:19ug. (Qiagen_RNeasy.pdf)

value: mutant b1/b2


title: Muscle from Glimepiride-treated Zucker diabetic fatty rat Replicate1

value: Male

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

value: glimepiride (Amaryl, 200mg/kg/day) daily for 2weeks by oral gavage


title: 14227265 - b1/b2_4_1 vs wt_4_1

hyb_protocol: wt_4_1 Cy5 / b1/b2_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia

extract_protocol: b1/b2_4_1:15ug. (Qiagen_RNeasy.pdf)


title: 14227264 - wt_4_1 vs b1/b2_4_1

hyb_protocol: b1/b2_4_1 Cy5 / wt_4_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: WAT from Metformin-treated Zucker diabetic fatty rat Replicate3

source_name: Epididimal Fat of Metformin-treated ZDF rat

value: Epididimal Fat

value: Metformin(300mg/kg/day) daily for 2weeks by oral gavage


title: EoE patient #2_before treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-2B

tag: age range

value: Pediatric patient

tag: clinical procedure

value: Biopsy

tag: disease status

value: Before glucocorticoid steroid treatment

value: epithelium

value: Formalin-fixed paraffin-embedded


title: HS_043

description: blood sample

tag: geographical origin

value: Brazil

tag: genger

value: Female

value: Paired blood sample corresponding to tumor HS_09


title: EoE patient #2_after treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-2A

value: After glucocorticoid steroid treatment

tag: histology procedure


title: exp-3_pH-6_vs_pH-4_color-swap

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description: Sample 10

hyb_protocol: Preparation of the slides was performed in 50 ml Falcon tubes. All reagents were from the OpArray system from Eurofins MWG Operon. Slides were incubated at 42°C in Pre-Hyb solution for 1 h, then the slides were transferred to Wash 1 solution (1.25 ml Wash B and 48.75 ml H2O) and incubated for 5 min at 37°C. Slides were washed with H2O and dried in a centrifuge (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Hybridization was carried out for 16–18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: For post-hybridization, slides were washed at 37°C in Wash 2 solution (5 ml Wash A, 2.5 ml Wash B and 42.5 ml H2O) and Wash 3 solution (5 ml Wash A and 45 ml H2O) for 10 minutes each. Slides were rotated in Wash 4 solution (1 ml Wash A and 49 ml H2O) for 5 min at room temperature. Finally, the slides were dried by centrifugation (Sigma Laboratory Centrifuge 4K15C, 5 min, 521 x g). Fluorescence of the hybridized DNA microarrays was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) at 10 µm resolution with a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (http://www.bioconductor.org). For further analysis, the processed and loess-normalized data as well as detailed experimental information according to MIAME (Brazma et al., 2001) were stored in the in-house microarray database (Polen and Wendisch, 2004). DNA microarray experiments were repeated independently three times for G. oxydans ΔqrcABC versus wild type and G. oxydans grown at pH 4 versus pH 6 and four times for G. oxydans grown at oxygen limitation versus oxygen saturation in biological replicates. To filter for differentially expressed genes, the following criteria had to be fulfilled: (i) flags ≥0 (GenePix Pro 6.0), (ii) signal/noise ≥5 for Cy5 (F635Median/B635Median, GenePix Pro 6.0) or Cy3 (F532Median/B532Median, GenePix Pro 6.0), (iii) mRNA ratio ≥2.0 (lower ones allowed in the case of operons) or ≤0.5 (higher ones allowed in the case of operons), (iv) in a paired Student’s t test, relative RNA levels had to be significantly different from all spots (p < 0.05).  The (test/reference) is the same as (O2 limitation/excess), (mutant/WT), and (pH4/pH6).

organism: Gluconobacter oxydans 621H

label_protocol: cDNA synthesis for DNA microarray analysis was performed as described (Polen et al., 2007). 25 µg RNA was used for random hexamer-primed synthesis of fluorescently-labeled cDNA with the fluorescent nucleotide analogues Cy3-dUTP and Cy5-dUTP (GE Healthcare, Freiburg, Germany). The mixture contained 3 µl 1 mM Cy3-dUTP or Cy5-dUTP, 3 µl 0.1 M DTT, 6 µl 5x first strand buffer (Invitrogen, Karlsruhe, Germany), 0.6 µl dNTP-mix (25 mM each of dATP, dCTP, and dGTP and 10 mM dTTP) and 2 µl Superscript II reverse transcriptase (Invitrogen, Darmstadt, Germany). The mixture was incubated for 10 min at room temperature and 110 min at 42 °C, stopped by addition of 10 μl 0.1 N NaOH, incubated for 10 min at 70 °C, and then neutralized by addition of 10 μl 0.1 N HCl. The sensors were purified by washing three times with water on a Microcon column (Millipore, YM-30).

growth_protocol: Precultures of G. oxydans were grown in shaking flasks at 30°C and 220 rpm in complex medium (mannitol medium) containing 80 g l-1 mannitol, 5 g l-1 yeast extract, 2.5 g l-1 MgSO4 x 7H2O, and 0.5 g l-1 glycerol. The initial pH of the medium was 6.0. For DNA microarray analysis, cells were grown in 200 ml of the same medium in a parallel bioreactor system (Dasgip, Jülich, Germany) for controlled growth conditions (control of pH and oxygen availability) in four 250 ml bioreactors. Each reactor was equipped with electrodes for measuring the pH value and the concentration of dissolved oxygen (DO) in the medium. The carbon dioxide concentration in the exhaust air was measured continuously by an infrared spectrometer. The pH values and oxygen levels used are given in the respective results sections. The pH was kept at pH 6.0 or pH 4.0 by automatic titration of 2 M NaOH and 2 M HCL. The oxygen availability was kept constant at 15% dissolved oxygen (DO) by mixing air, O2 and N2. Oxygen-limited conditions were brought about by gassing the culture with 2% O2/98% N2, resulting in a dissolved oxygen concentration of 0%. Calibration was performed by gassing with air (100% DO) and N2 (0% DO). ). Control and recording of all data was carried out by the software “Fedbatch Pro” (Dasgip, Jülich, Germany.”

extract_protocol: 25 ml of a G. oxydans culture was added to 25 g of crushed ice in a Falcon tube which had been pre-cooled in liquid nitrogen. The cells were sedimented by centrifugation for 3 min at 4 °C and 10,397 x g and after removal of the supernatant the tube with the cell pellet was immersed in liquid nitrogen and then stored at -70°C. For total RNA preparation, the RNeasy system (Qiagen, Hilden, Germany) was used. The cell pellet was resuspended in 700 µl of RLT buffer containing 7 µl ß-mercaptoethanol and transferred to two vials each containing 0.5 g of 0.1-mm diameter zirconium silica beads (Roth, Karlsruhe, Germany). Cells were disrupted by 4 x 30 s bead beating using a Silamat S5 (Ivoclar Vivadent, Ellwangen, Germany). The lysate was centrifuged at 8,000 x g for 2 min and the supernatant was mixed with 250 µl ethanol (-20 °C). RNA was extracted with two RNeasy mini-columns following the manufacturer’s instructions. DNA digestion was performed for 20 min on column by adding 30 Kuniz U RNase-free DNase. RNA concentration and quality were checked photometrically and on formaldehyde gels according to standard procedures (Sambrook and Russell, 2001).

value: wild type

tag: growth condition


title: exp-2_pH-4_vs_pH-6

description: Sample 9


title: HS_041

description: blood sample

tag: histological type

value: Paired blood sample corresponding to tumor HS_04

tag: tnm

tag: tp53 mutation


title: 14227267 - wt_22_2 vs b1/b2_22_2

hyb_protocol: b1/b2_22_2 Cy5 / wt_22_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mutant b1/b2

tag: age


title: HS_040

description: blood sample

value: Paired blood sample corresponding to tumor HS_03

tag: virilization


title: exp-1_pH-4_vs_pH-6

description: Sample 8


title: WAT from Metformin-treated Zucker diabetic fatty rat Replicate2

hyb_protocol: labeled two cDNA probe solutions containing hybridization buffer (Genocheck, Korea) were mixed on equal amount and HybriWell FL Sealing System (Grace bio-labs, U.S.A) were applied to the microarrays and placed in a humidified chamber at 62℃ for 14 h. Then, the microarrays were sequentially washed

tag: tissue

value: 12-weeks old

tag: gender

value: Male

tag: strain

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: exp-1_Delta-qcrABC_vs_WT

description: Sample 5

source_name: ΔqrcABC_pH4_15% DO

tag: genotype/variation

value: ΔqrcABC mutant

value: pH-4, 15% dissolve oxygen

source_name: WT_pH4_15% DO


title: EoE patient #1_after treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-1A

value: Pediatric patient

value: Biopsy


title: WAT from Metformin-treated Zucker diabetic fatty rat Replicate1

value: Epididimal Fat

tag: treatment

value: Metformin(300mg/kg/day) daily for 2weeks by oral gavage


title: exp-3_Delta-qcrABC_vs_WT

description: Sample 7


title: exp-2_WT_vs_Delta-qcrABC_color-swap

description: Sample 6


title: Pancreas from Metformin-treated Zucker diabetic fatty rat Replicate1

source_name: Pancreas of Metformin-treated ZDF rat

value: Pancreas


title: exp-4_O2-limitation_vs_O2-excess

description: Sample 4


title: Pancreas from Glimepiride-treated Zucker diabetic fatty rat Replicate3

value: glimepiride (Amaryl, 200mg/kg/day) daily for 2weeks by oral gavage


title: EoE patient #1_before treatment

description:
Fresh bipspies were fixed right away and porcessed within the same day.
EE-1B

tag: age range

value: Before glucocorticoid steroid treatment

value: epithelium

value: Formalin-fixed paraffin-embedded


title: 13561265 - N0.25C7.5-2 vs N0.25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-2 Cy5 / N0.25C7.5-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

growth_protocol: cell culture/primary cell - Cells are grown in 50ml of Gamborg medium + 0.1mg/l 2,4-D in sterile 250 ml erlenmeyers.

extract_protocol: N0.25C15-2:6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N.25C15 - growth conditions - nitrogen concentration,nitrate:quantity 0.25mM time 1week . Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

value: cell culture

extract_protocol: N0.25C7.5-2:4ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N.25C7.5 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 0.25 mM Sucrose : 7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:0.25 mM Sucrose:7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: Pancreas from Metformin-treated Zucker diabetic fatty rat Replicate2

extract_protocol: Total RNA was extracted from the different tissues after drug treatment using Trizol reagent (Invitrogen Co., U.S.A) according to the manufacturer’s instructions.


title: 13561268 - N0.25C15-2 vs N0.25C30-2

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C30-2 Cy5 / N0.25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N0.25C30-2:6ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N.25C30 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 0.25 mM Sucrose : 30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:0.25 mM Sucrose:30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13690371 - N0.25C15-2 vs N2.5C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-2 Cy5 / N0.25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N2.5C15-2:39ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C15 - growth conditions - nitrogen concentration,nitrate:quantity 2.5mM time 1week . Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13561267 - N0.25C30-2 vs N0.25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-2 Cy5 / N0.25C30-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Muscle from Metformin-treated Zucker diabetic fatty rat Replicate2

source_name: Gastronemious of Metformin-treated ZDF rat

value: Gastronemious

value: 12-weeks old

value: Male


title: HS_039

description: blood sample

hyb_protocol: standard Illumina protocol

tag: geographical origin

value: Brazil

value: Female

value: Paired blood sample corresponding to tumor HS_01

tag: cushing  syndrome

tag: follow-up (months)


title: Pancreas from Metformin-treated Zucker diabetic fatty rat Replicate3

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: exp-3_O2-limitation_vs_O2-excess

description: Sample 3

value: wild type

tag: growth condition


title: 13561253 - N0.25C15-2 vs N0.25C7.5-2

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C7.5-2 Cy5 / N0.25C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Muscle from Metformin-treated Zucker diabetic fatty rat Replicate3

value: Metformin(300mg/kg/day) daily for 2weeks by oral gavage


title: 13561507 - N0.25C15-1 vs N0.25C30-1

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C30-1 Cy5 / N0.25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N0.25C30-1:27ug. (Qiagen_RNeasy.pdf)

extract_protocol: N0.25C15-1:4ug. (Qiagen_RNeasy.pdf)


title: exp-2_O2-limitation_vs_O2-excess

description: Sample 2


title: LPS.3

city: Corvallis

first: Stephen

last: Ramsey

state: OR

address: Dryden Hall 208A

department: Biomedical Sciences

institute: Oregon State University

hyb_protocol: Biotinylated cRNA was hybridized to an Affymetrix Mouse Exon 1.0 ST GeneChip using standard protocols and reagents from Affymetrix.

scan_protocol: Imaging was performed with the Affymetrix GeneChip Scanner 3000.

data_processing:
Scanned GeneChip images were processed into probe-level intensities (CEL files) using the Affymetrix GeneChip Operating Software.
MoEx10stv1_Mm_ENST.pgf
Probe intensities were quantile normalized and probeset-summarized (at both exon and transcript levels) using the Affymetrix PLIER algorithm, with no background adjustment, as implemented in the Affymetrix Power Tools software suite. The probeset summarization was carried out using probe-to-probeset mappings from the CustomCDF Project based on the Ensembl Transcript databases (CustomCDF Version 13). Values are in log2 scale.

organism: Mus musculus

source_name: Bone marrow-derived macrophages_LPS

label_protocol: Sample mRNA was amplified and labeled with the Affymetrix One-Cycle Eukaryotic Target Labeling Assay protocol and reagents.

growth_protocol: Bone marrow cells collected from femurs were plated on non-tissue culture-treated plastic in complete RPMI medium [RPMI 1640 (Invitrogen) containing L-glutamine, supplemented with 10% (v/v) FBS (Invitrogen, cat #10437), 100 IU/mL penicillin and 100 μg/mL streptomycin (all from Cellgro)] plus 50 ng/mL recombinant human macrophage colony-stimulating factor (rhM-CSF, Chiron) (hereafter, BMDM medium). On day four, the medium was replaced, and on day six, adherent cells were lifted in PBS + 1 mM EDTA, counted, pelleted, resuspended in BMDM medium, and plated into six-well tissue culture plates.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen). RNA quality was analyzed with an Agilent 2100 Bioanalyzer.

treatment_protocol: On day seven, for samples intended for LPS stimulation, LPS (List Biological Labs) was introduced into the culture medium, at 10 ng/mL. Cells were then incubated for 4 hours.

value: female

value: 8-12 weeks

tag: diet

value: normal chow

tag: cell type

value: Bone marrow-derived macrophages

tag: stimulus

value: LPS

tag: stimulus concentration

value: 10 ng/mL

tag: stimulus duration

value: 4 h


title: Muscle from Metformin-treated Zucker diabetic fatty rat Replicate1

tag: tissue

tag: age


title: 13561245 - N0.25C30-1 vs N0.25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-1 Cy5 / N0.25C30-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cell culture

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:0.25 mM Sucrose:30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13690370 - N2.5C15-2 vs N0.25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-2 Cy5 / N2.5C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Liver from Metformin-treated Zucker diabetic fatty rat Replicate3

source_name: Liver of Metformin-treated ZDF rat

value: liver

value: 12-weeks old

tag: gender

value: Male

tag: strain


title: HS_023

description: blood sample

extract_protocol: Proteinase K method. The detailed protocol can be found in PMID:18786438.

value: Brazil

tag: genger

value: Female

tag: age  (months)

tag: histological type

value: Paired blood sample corresponding to tumor HS_14

tag: tnm

tag: tp53 mutation

tag: virilization

tag: treatment


title: exp-1_O2-excess_vs_O2-limitation

description: Sample 1

tag: genotype/variation

value: wild type

tag: growth condition


title: 13561246 - N25C15-1 vs N25C30-1

description: How does the C/N balance act in cells ?

hyb_protocol: N25C30-1 Cy5 / N25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N25C30-1:32ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N25C30 - growth conditions - carbon concentration,sucrose:quantity 30g/l time 1week . Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: N25C15-1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N25C15 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.


title: LPS.1

value: female

tag: diet

tag: cell type

tag: stimulus

tag: stimulus concentration


title: 13561243 - N25C30-1 vs N25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-1 Cy5 / N25C30-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.

value: Normal nitrogen concentration. 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: WAT from Rosiglitazone-treated Zucker diabetic fatty rat Replicate3

source_name: Epididimal Fat of Rosiglitazone-treated ZDF rat

tag: tissue

value: Epididimal Fat

tag: age

tag: gender

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

value: rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) daily for 2weeks by oral gavage

source_name: Epididimal Fat of ZDF rat


title: Liver from Metformin-treated Zucker diabetic fatty rat Replicate1

tag: strain

value: Metformin(300mg/kg/day) daily for 2weeks by oral gavage


title: 13552332 - N0.25C7.5-1 vs N0.25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-1 Cy5 / N0.25C7.5-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cell culture

extract_protocol: N0.25C7.5-1:4ug. (Qiagen_RNeasy.pdf)

value: Nitrate:0.25 mM Sucrose:7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: LPS.2

value: 8-12 weeks

value: normal chow

value: Bone marrow-derived macrophages

value: LPS

value: 10 ng/mL

tag: stimulus duration

value: 4 h


title: Unstim.2


title: Liver from Metformin-treated Zucker diabetic fatty rat Replicate2

value: liver

value: 12-weeks old

value: Male


title: WAT from Rosiglitazone-treated Zucker diabetic fatty rat Replicate2


title: Unstim.3

value: female


title: 13552329 - N0.25C15-1 vs N0.25C7.5-1

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C7.5-1 Cy5 / N0.25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 12h_Combination_R3

city: Mumbai

first: Muralidhara

last: Padigaru

state: Maharashtra

address: 1, Nirlon Compex, Off Western Express Highway

department: Translational Research

country: India

institute: Piramal Lifesciences India Limited

hyb_protocol: The microarray slides were processed for pre-hybridization using the Pronto hybridization kit as described by the manufacturer. The slides were loaded onto the GeneTac automated hybridization station and primed with the labeled cDNA as per the manufacturer's instructions. A step down hybridization was performed for 18 hours with the following protocol – 6 hrs at 42 degree centigrade, 6 hours at 35 degree centigrade and 6 hours at 30 degree centigrade. At the end of the hybridization cycle, the slides were removed from the hybridization station, washed and processed for scanning as described by the manufacturer (Corning Pronto, USA). The slides were spun dry by centrifugation at 1600 rpm for 10 minutes and loaded onto a laser scanner for scanning the Cy3 and Cy5 intensities.

scan_protocol: The microarray slides were scanned with the “autogain” function of the scanner (GeneTAC UC4) so as to optimize the laser power for amplifying the low intensity spots versus avoiding the over-saturation of the high intensity spots on the slide. The resultant scanned tiff image files were gridded using the GAL file generated from the spotting run with use of the GeneTac Integrator software.

data_processing: Foreground and background intensity values were recorded for every gene in the array using a fixed threshold boundary by GeneTAC Integrator software. Background intensity values were subtracted from the foreground and normalized using global normalization algorithm used by GeneTAC Integrator software. The resultant comma separated file with the background subtracted, globally normalized intensity ratio between the treated versus control (Cy5/Cy3) values were used for statistical analysis.

source_name: pancreatic cancer cell line PANC-1

label_protocol: The total RNA from control PANC-1 cells were labeled with fluorescent dyes Cy3, whereas total RNA from treated cells were labelled with Cy5 using the indirect labeling method. Briefly, twenty micrograms of total RNA from PANC-1 cells were converted to cDNA using modified amino-allyl dUTP. The resultant cDNA was purified using the silica columns provided by the kit and subsequently used for dye conjugation. The purified cDNA was eluted in binding buffer and incubated with the DMSO dissolved Cy3 dye suspension for 3 hours in a thermo mixer at room temperature. Excess dye was quenched using 20mM hydroxylamine and the resultant labeled cDNA was again purified using the silica columns as provided by the kit. The purified and labeled cDNA was eluted using 65μL elution buffer. The exultant was dried under vacuum and resuspended in 65μl of hybridization buffer. The resuspended cDNA was heated at 95 degree centigrade for 5 minutes, flash chilled on ice and microfuged on ice before use in hybridization.

growth_protocol: The pancreatic cancer cell line PANC-1 (ATCC, Manassas, VA) was maintained in RPMI 1640 containing 10% heat inactivated fetal bovine serum (Sigma-Aldrich) and 1% antibiotic and antimycotic solution (Mediatech Inc) at 370C in a humidified atmosphere of 5% CO2.

extract_protocol: On assay completion, PANC-1 cells (treated & control) were harvested with chilled Trizol reagent (Invitrogen Corp, Carlsbad, USA). The volume of Trizol was maintained at 1 ml for every 1 x 106 cells. The cells with Trizol were stored at -80 degree centigrade until used for RNA extraction. The lysates were thawed at room temperature and passed through a 21-gauge needle for 10 times. This ensured that the lysates was uniformly homogenized. Post homogenization, the lysates were allowed to settle for 5 minutes at room temperature. The lysates were then spun at 12000 rpm for 15 minutes in a fixed angle rotor centrifuge at 4 degree centigrade. The upper aqueous phase was then transferred to a new microfuge tube and equal volumes of chilled 70% ethanol were added to the tubes. The ethanol-aqueous phase was mixed gently with a pipette and total RNA was purified using the RNeasy Mini kit (Qiagen, Valencia, USA). The lysates were then transferred to a purification column and spun at 10,000 rpm for 10 seconds. The flow-through is discarded and the column is filled with 500μl of RW1 buffer provided by the kit. The columns are spun at 10,000 rpm for 10 seconds and the flow-through is discarded. The columns are then filled with 500μl of RPE buffer and spun at 10,000 rpm for 10 seconds. The RPE buffer spin is repeated once more and a dry spin is performed by centrifugation of the empty column at 13,000 rpm for 2 minutes. The final elution step was performed by adding 32μl of nuclease free water and spinning the column for 5 minutes at 13,000 rpm. The concentration of the RNA is determined using 1μl of RNA with a Nanodrop spectro-photometer (ND-1000,).

treatment_protocol: PANC-1 cells were treated with single treatment of gemcitabine or P276-00 for 12 hours according to respective dosage (IC10, IC50). For combination treatment, the cells were pre-treated with Gemcitabine [(IC10 (100 nM)] followed by P276-00 [IC50 (1000 nM)] for 12 hours. The control cells were treated with vehicle control for 12 hours.

value: Control (Untreated)

tag: dose

value: Gemcitabine and P276-00


title: 12h_Combination_R2


title: WAT from Rosiglitazone-treated Zucker diabetic fatty rat Replicate1

value: Epididimal Fat

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)

value: rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) daily for 2weeks by oral gavage


title: Atf3KO.oxLDL.2

data_processing:
Scanned GeneChip images were processed into probe-level intensities (CEL files) using the Affymetrix GeneChip Operating Software.
Probe intensities were quantile normalized and probeset-summarized (at both exon and transcript levels) using the Affymetrix PLIER algorithm, with no background adjustment, as implemented in the Affymetrix Power Tools software suite. The probeset summarization was carried out using probe-to-probeset mappings from the CustomCDF Project based on the Ensembl Transcript databases (CustomCDF Version 13). Values are in log2 scale.
MoEx10stv1_Mm_ENST.pgf

treatment_protocol: On day seven, for samples intended for oxLDL stimulation, oxidized LDL (CuSO4-oxidized human low density lipoprotein, from Intracel) was introduced into the culture medium, at 25 ug/mL (protein concentration). Cells were then incubated for 24 hours.

tag: strain background

value: Atf3-/- (Aft3 KO)

value: oxidized low-density lipoprotein (oxLDL)

value: 25 ug/mL


title: Unstim.1

value: 8-12 weeks

value: normal chow

value: Bone marrow-derived macrophages


title: Pancreas from Rosiglitazone-treated Zucker diabetic fatty rat Replicate3

source_name: Pancreas of Rosiglitazone-treated ZDF rat

value: Pancreas

source_name: Pancreas of of ZDF rat


title: 13552320 - N2.5C30-2 vs N2.5C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-2 Cy5 / N2.5C30-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cell culture

extract_protocol: N2.5C30-2:9ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C30 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 2.5 mM Sucrose : 30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:2.5 mM Sucrose:30g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: Atf3KO.oxLDL.3


title: 12h_P276-00_IC50_R3


title: 13552318 - N2.5C7.5-2 vs N2.5C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-2 Cy5 / N2.5C7.5-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:N2.5C15 - growth conditions - nitrogen concentration,nitrate:quantity 2.5mM time 1week.

tag: treatment:

extract_protocol: N2.5C7.5-2:27ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:N2.5C7.5 - growth conditions - carbon and nitrogen concentrations,nitrate and sucrose:time 1week . Nitrate : 2.5 mM Sucrose : 7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.

value: Nitrate:2.5 mM Sucrose:7.5g/l 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: Pancreas from Rosiglitazone-treated Zucker diabetic fatty rat Replicate2

hyb_protocol: labeled two cDNA probe solutions containing hybridization buffer (Genocheck, Korea) were mixed on equal amount and HybriWell FL Sealing System (Grace bio-labs, U.S.A) were applied to the microarrays and placed in a humidified chamber at 62℃ for 14 h. Then, the microarrays were sequentially washed

treatment_protocol: Metformin (Glucophage, 300mg/kg/day) and glimepiride (Amaryl, 200mg/kg/day) were given by oral injection to ZDF rats for 2 weeks in each groups and rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) was given to ZDF rats for 1 week according to the manufacture’s protocols and recommendations

value: 12-weeks old

value: Male

tag: treatment


title: 13552319 - N2.5C15-2 vs N2.5C30-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C30-2 Cy5 / N2.5C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 13552317 - N2.5C15-2 vs N2.5C7.5-2

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C7.5-2 Cy5 / N2.5C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Pancreas from Rosiglitazone-treated Zucker diabetic fatty rat Replicate1


title: 12h_P276-00_IC50_R2

value: Control (Untreated)


title: Atf3KO.unstim.3

tag: genotype/variation

value: female


title: Muscle from Rosiglitazone-treated Zucker diabetic fatty rat Replicate3

source_name: Gastronemious of Rosiglitazone-treated ZDF rat

value: Gastronemious

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)


title: 12h_P276-00_IC50_R1


title: 12h_Combination_R1

value: Gemcitabine and P276-00


title: Muscle from Rosiglitazone-treated Zucker diabetic fatty rat Replicate2

value: rosiglitazone (Avandia, BRL 49653, 15mg/kg/day) daily for 2weeks by oral gavage


title: WT.oxLDL.3

value: wild type

value: oxidized low-density lipoprotein (oxLDL)

value: 25 ug/mL


title: Muscle from Rosiglitazone-treated Zucker diabetic fatty rat Replicate1


title: 13552315 - N2.5C15-1 vs N0.25C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N0.25C15-1 Cy5 / N2.5C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N2.5C15-1:8ug. (Qiagen_RNeasy.pdf)


title: Liver from Rosiglitazone-treated Zucker diabetic fatty rat Replicate3

source_name: Liver of Rosiglitazone-treated ZDF rat

value: liver


title: Atf3KO.unstim.2

value: Atf3-/- (Aft3 KO)

value: 8-12 weeks

value: normal chow

value: Bone marrow-derived macrophages


title: 13561244 - N2.5C15-2 vs N25C15-2

description: How does the C/N balance act in cells ?

hyb_protocol: N25C15-2 Cy5 / N2.5C15-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: N25C15-2:17ug. (Qiagen_RNeasy.pdf)

value: cell culture

value: Normal Nitrogen and sucrose concentrations (control treatment) 5 ml of cells are added to 45 ml of control medium and grown with agitation and light.


title: 12h_Gem_IC50_R2

value: Gemcitabine


title: Atf3KO.unstim.1


title: WT.oxLDL.2


title: 12h_P276-00_IC10_R3

value: Control (Untreated)


title: 12h_Gem_IC50_R3


title: 12h_P276-00_IC10_R2


title: 12h_P276-00_IC10_R1


title: WT.oxLDL.1

value: female


title: 13552316 - N0.25C15-1 vs N2.5C15-1

description: How does the C/N balance act in cells ?

hyb_protocol: N2.5C15-1 Cy5 / N0.25C15-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Normal sucrose concentration 5 ml of cells are added to 45 ml of treatment medium and grown with agitation and light.


title: 12h_Gem_IC50_R1


title: Liver from Rosiglitazone-treated Zucker diabetic fatty rat Replicate2

value: 12-weeks old

value: Male

value: Zucker diabetic fatty rat(ZDF/Crl-Leprfa)