title: placenta_Erhualian pigs_gestation day 90-2_rep1

status: Public on Jun 20 2009

type: RNA

city: Wuhan

first: Shuhong

last: Zhao

address: Shizishan Road Number 1, Hongshan Area, Wuhan , Hubei Provience, China

department: College of Animal Science and Technology

country: China

institute: Huazhong Agricultural University

description: No

hyb_protocol: 1.Mix the following components together(Hybridization solution).    Fragmented cRNA: 5 μg;    Control Oligonucleotide B2(3nM): 1.7 μL;    20× Eukaryotic Hybridization Controls(bioB, bioC, bioD, cre): 5 μL;   Herring Sperm DNA(10mg/mL): 1 μL;    Acetylated BSA(50mg/mL): 1 μL;    2× Hybridization Buffer: 50 μL;    DMSO: 10μL;    H2O: 31.3μL; 2. Equilibrate probe array to room temperature immediately before use. 3. Heat the hybridization cocktail to 99°C for 5 minutes in a heat block. 4. Meanwhile, wet the array by filling it through one of the septa with appropriate volume of 1X Hybridization Buffer using a micropipettor and appropriate tips. 5. Incubate the probe array filled with 1X Hybridization Buffer at 45°C for 10 minutes with rotation. 6. Transfer the hybridization cocktail that has been heated at 99°C, in step 3, to a 45°C heat block for 5 minutes. 7. Spin hybridization cocktail(s) at maximum speed in a microcentrifuge for 5 minutes to remove any insoluble material from the hybridization mixture. 8. Remove the buffer solution from the probe array cartridge and fill with appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube. 9. Place probe array into the Hybridization Oven, set to 45°C. Avoid stress to the motor; load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm. 10. Hybridize at 45℃ for 16 h with constant rotation at 60rpm. 11. After 16 hours of hybridization, remove the hybridization cocktail from the probe array and fill the probe array completely with the appropriate volume of the following Non-Stringent Wash Buffer(Wash Buffer A:6X SSPE, 0.01% Tween-20). Post Hyb Wash #1: 10 cycles of 2 mixes/cycle with Wash Buffer A at 25°C. 12. Preparing the Staining Reagents. 12.1 SAPE Stain Solution(Mix well and divide into two aliquots of 600 μL each to be used for stains 1 and 3):     2X Stain Buffer  600.0 μL;     50 mg/mL BSA 48.0 μL;      1 mg/mL Streptavidin Phycoerythrin (SAPE) 12.0 μL;      DI H20 540.0 μL; 12.2 Antibody Solution:       2X Stain Buffer 300.0 μL;       50 mg/mL BSA 24.0 μL;       10 mg/mL Goat IgG Stock 6.0 μL;       0.5 mg/mL biotinylated antibody 3.6 μL;       DI H20 266.4 μL; 13. Post Hyb Wash #2: 4 cycles of 15 mixes/cycle with Wash Buffer B(100 mM MES, 0.1M [Na+], 0.01% Tween-20) at 50°C. 14. Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. 15. Post Stain Wash: 10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C. 16. 2nd Stain: Stain the probe array for 10 minutes in antibody solution at 25°C. 17. 3rd Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C. 18. Final Wash: 15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C. Annotation: Chips were washed and stained with a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The probe arrays were scanned using the Affymetrix® GeneChip® Scanner 3000. Apply the spots just before scanning: 1. On the back of the probe array cartridge, clean excess fluid from around septa. 2. Carefully apply one Tough-Spots to each of the two septa. Press to ensure that the spots remain flat. If the Tough-Spots do not apply smoothly, that is, if you observe bumps, bubbles, tears, or curled edges, do not attempt to smooth out the spot. Remove the spot and apply a new spot. 3. Insert the cartridge into the scanner and test the autofocus to ensure that the Tough-Spots do not interfere with the focus. Scanning the Probe Array: 1. Select Run → Scanner from the menu bar. Alternatively, click the Start Scan icon in the tool bar. ⇒ The Scanner dialog box appears with a drop-down list of experiments that have not been run. 2. Select the experiment name that corresponds to the probe array to be scanned. A previously run experiment can also be selected by using the Include Scanned Experiments option box. After selecting this option, previously scanned experiments appear in the drop-down list. 3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required. 4. Once the experiment has been selected, click the Start button. ⇒ A dialog box prompts you to load an array into the scanner. 5. If you are using the GeneArray® Scanner, click the Options button to check for the correct pixel value and wavelength of the laser beam. ■ Pixel value = 3 μm ■ Wavelength = 570 nm If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed. 6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner. 7. Click OK in the Start Scanner dialog box. ⇒ The scanner begins scanning the probe array and acquiring data. When Scan in Progress is selected from the View menu, the probe array image appears on the screen as the scan progresses.

data_processing: There are 11 paired perfect match (PM) and mismatch (MM) 25-mer probes in the Affymetrix GeneChip porcine genome array for each probeset representing a gene. The signals from these probe pairs are used to determine whether a given gene is expressed and to measure the gene expression level. The probe-pair (PM-MM) data were used to detect the expression level of genes on the array (present call, marginal call, and absent call) by MAS 5.0 (Wilcoxon signed rank test). Raw data from .CEL files were converted to gene signal files by MAS 5.0 (Ver.2.3.1). Natural logarithms were then taken on quantile normalization（GeneSpring 7.31. Identification of DE genes was conducted using SAS (Ver.8.1, T-test). The p value cutoff for DE genes was set at 0.05.

label: biotin

molecule: total RNA

organism: Sus scrofa

source_name: porcine placenta_Erhualian pigs_gestation day 90

label_protocol:
GeneChip® IVT Labeling Kit (Affymetrix) protocol:
1.Transfer the needed amount of template cDNA (12 μL) to RNase-free  microfuge tubes and add Rnase-free Water(8 μL), 10× IVT Labeling Buffer (4 μL), IVT Labeling NTP Mix(12 μL), IVT Labeling Enzyme Mix(4 μL) in the order.
2. Carefully mix the reagents and collect the mixture at the bottom of the tube by brief (5 second) microcentrifugation.
3. Incubate at 37°C for 16 hours. To prevent condensation that may result from water bath-style incubators,incubations are best performed in oven incubators for even temperature distribution, or in a thermal cycler.
4.Store labeled cRNA at -20°C, or -70°C if not purifying immediately.

extract_protocol: placentas from Erhualian gestation day75 and 90 or Large White gestation day 75 and 90 all were snap frozen in liquid nitrogen after collection and stored at –80℃ until RNA extraction. TRIzol (Invitrogen) and RNeasy Mini Kit (QIAGEN) were used for RNA extractions and purifications respectively followed by manufacturer’s instructions. RNA quality and concentration were checked by Agilent Bioanalyser 2100.

tag: Pig age:gestation day 90; Pig tissue

value: fetal placenta; Erhualian pig


title: placenta_Large White pigs_gestation day 90-3_rep1

description: No

source_name: porcine placenta_Large White_pigs_gestation day 90

value: fetal placenta; Large White pig


title: placenta_Large White pigs_gestation day 90-1_rep1

description: No


title: placenta_Large White pigs_gestation day 75-2_rep1

description: No

source_name: porcine placenta_Large White_pigs_gestation day 75

tag: Pig age:gestation day 75; Pig tissue


title: 9S_a

status: Public on Jun 23 2009

city: Little Rock

first: Ying

last: Su

state: AR

address: 1120 Marshall St. South Campus

department: physiology

country: USA

institute: UAMS

description: Bacterial sequence-derived probes on the arrays served as external controls for hybridization, whereas the housekeeping genes β-actin and GAPDH served as endogenous controls and for monitoring the quality of the RNA target.

hyb_protocol: 10 ug of cRNA was hybridized for 16 hours to an Affymetrix (Santa Clara, CA) rat RAE230A GeneChip (3-4 chips used per diet group), followed by incubations with streptavidin-conjugated phycoerythrin, and then with polyclonal anti-streptavidin antibody coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using an Agilent GeneArray laser scanner. Images were analyzed using Affymetrix MAS 5.0 software.

data_processing: Value column are raw signal intensity generated from MAS 5.0.

organism: Homo sapiens

source_name: Hec-1-A cell

label_protocol: 8ug RNA was used for cDNA synthesis using a T7-(deoxythymidine)24 primer and Superscript II (Life Technologies, Inc., Gaithersburg, MD). The resulting cDNA was used with the ENZO BioArray High Yield RNA Transcript labeling kit (ENZO, Farmingdale, NY) to synthesize biotin-labeled cRNA. The cRNA was purified on RNeasy spin columns (QIAGEN) and subjected to chemical fragmentation (size range of 35 to 200 bp). Three replicate cRNA targets were made in parallel starting from each RNA pool.

growth_protocol: the 4S and 2AS sub-lines were propagated to near confluence. The 9S and 3AS sub-lines were propagated on a different occasion than for the 4S and 2AS cell lines.

extract_protocol: TriTRIzol extraction procedure, followed by a cleanup using QIAGEN RNeasy Mini kit.

treatment_protocol: The 4S and 9S sub-lines were derived from the original human HEC-1-A endometrial carcinoma cell line and contain a stably transfected expression plasmid encoding full-length Krüppel-like factor 9 (KLF9), whereas the 2AS and 3AS sub-lines contain a stably transfected plasmid encoding an antisense (AS) RNA to KLF9. All cell lines were derived concurrently (Zhang, 01). The ‘sense’ (S) and ‘antisense’ (AS) cell lines differ in relative levels of KLF9 protein and activity, with sense greater than antisense, respectively.

tag: HEC-1-A human endometrial carcinoma cells


title: placenta_Large White pigs_gestation day 75-1_rep1

description: No


title: placenta_Erhualian pigs_gestation day 90-1_rep1

description: No


title: 2AS_a


title: SLVL09

city: New York

first: Katia

last: Basso

state: NY

address: 1150 St. Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description: CD19-positive cells purified by magnetic cell separation from peripheral blood of splenic lymphoma with villous lymphocytes patients. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GCOS1.2

source_name: Splenic Lymphoma with villous lymphocytes

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

extract_protocol: Total RNA was purified using the TRIzol reagent


title: 4S_b


title: 2AS_b


title: 4S_a


title: placenta_Large White pigs_gestation day 90-2_rep1

description: No


title: 3AS_a


title: SLVL10

tag: Splenic Lymphoma with villous lymphocytes


title: SLVL01


title: SLVL02


title: 3AS_b


title: SLVL07


title: FLB06

description: Follicular lymphoma biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Follicular lymphoma biopsy

tag: Follicular lymphoma


title: FLB07


title: 9S_b

source_name: Hec-1-A cells

treatment_protocol: stable transfect with either sense KLF9 or Anti-sense kLF9 plasmid


title: FLB04


title: FLB05


title: placenta_Erhualian pigs_gestation day 90-3_rep1

description: No


title: SLVL12


title: FLB01


title: FLB03


title: SLVL11


title: placenta_Erhualian pigs_gestation day 75-1_rep1

description: No

tag: Pig age:gestation day 75; Pig tissue:placenta;


title: placenta_Large White pigs_gestation day 75-3_rep1

description: No


title: placenta_Erhualian pigs_gestation day 75-3_rep1

description: No

source_name: porcine placenta_Erhualian pigs_gestation day 75


title: BLPD17

description: Burkitt lymphoma biopsy. The frozen tissue was homogeneized in Trizol reagent and RNA was purified following manufacturer instructions. Targets were produced starting from 5 ug of total RNA following standard Affymetrix protocol.

source_name: Burkitt lymphoma biopsy

tag: Burkitt lymphoma


title: placenta_Erhualian pigs_gestation day 75-2_rep1

description: No


title: SLVL05


title: BLPD12


title: SLVL06


title: SLVL08


title: SLVL03


title: BLPD10


title: BLPD13


title: BLPD14


title: FLB02


title: BLPD04


title: BLPD03


title: BLPD18


title: C_ni_rep1

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Grapevine downy mildew caused by the Oomycete Plasmopara viticola is one of the most important diseases affecting Vitis spp. However, all cultivated European grapevine varieties are susceptible to P. viticola and the resistance needs to be introduced from other Vitaceae. Segregating populations derived from Muscadinia rotundifolia, a species closely related to Vitis, lead to the identification and mapping of two resistance genes, named Rpv1 and Rpv2. The macroscopic phenotypes of the resistance mediated by the two loci are different. Rpv2 plants completely inhibit P. viticola sporulation and produce very small necrotic lesions. In contrast, Rpv1 plants allow a rather limited but visible sporulation of P. viticola. The aim of the study is to understand the gene expression changes associated with downy mildew resistance mediated by these two loci. Gene expression patterns after P. viticola inoculation or mock inoculation are compared in incompatible (resistant plants bearing Rpv1 or Rpv2 locus) and compatible (susceptible plants with no resistance loci) interactions, using the Vitis vinifera GeneChip from Affymetrix.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Vitis rotundifolia

source_name: Rpv1-/Rpv2+, mock-inoculated with water

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: leaf - Plants were grown in the greenhouse in potting soil (compost) during three months (March, April, May)

treatment_protocol: Name:ni - pathogen - control,pathogen infection,mock inoculation:time 6hour . The sixth leaves from the top of plants were used. One leaf disc (14 mm diameter) was punched from each of the 18 plants and mock inoculated with sterile bidistilled water by contact of the abaxial leaf surface in one petri dish. Six hours later, discs were collected and frozen.

tag: Vitis (41528 population) - Age

value: 13 month. Dev.stage (Boyes et al. Plant Cell 2001):green cuttings with 10 developed leaves.


title: BLPD15


title: GC020300

description: CD77-positive B-cells purified by magnetic cell separation. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Germinal center centroblasts from tonsil


title: BLPD07


title: FLB08


title: C_i_rep2

source_name: Rpv1-/Rpv2+, inoculated with P. viticola

treatment_protocol: Name:i - pathogen - pathogen infection,p. viticola inoculation:time 6hour . The sixth leaves from the top of plants were used. One leaf disc (14 mm diameter) was punched from each of the 18 plants and inoculated with a suspension of P. viticola sporangia (10000 sporangia per ml) by contact of the abaxial leaf surface in one petri dish. Six hours later, discs were collected and frozen. 10 000 sporangia per ml


title: BLPD08


title: BLPD11


title: BLPD09


title: BLPD16


title: BLPD02


title: B_ni_rep2

source_name: Rpv1+/Rpv2-, mock-inoculated with water


title: CB022500

tag: Germinal center centroblasts from tonsil


title: D_i_rep1

source_name: Rpv1-/Rpv2-, inoculated with P. viticola


title: D_ni_rep2

source_name: Rpv1-/Rpv2-, mock-inoculated with water


title: D_i_rep2


title: D_ni_rep1


title: CC031400

description: CD10-positive CD77-positive B-cells purified by magnetic cell separation. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

source_name: Germinal center centrocytes from tonsil

tag: Germinal center centrocytes from tonsil


title: CB021700


title: BLPD01


title: Cc030800-r


title: Aluminum-4_vs_Ctr-4

status: Public on Jun 16 2009

city: Nashville

first: Suping

last: Zhou

state: TN

address: 3500 John A Merritt Blvd

department: IAGER

institute: Tennessee State University

hyb_protocol: 1.5 ug (~ 100 pmol) of Cy3 labeled  aRNA for Al treated samples, and 1.5 ug Cy5 (~ 100 pmol) labeled aRNA for control samples  were mixed and loaded onto each slides.

scan_protocol: Images were captured with a GenePix 4000B slide scanner and data obtained with the Genepix 6.0 software (Molecular Devices).

data_processing: Raw data were loaded into GeneSpring (v.7) (Agilent Technologies, Inc., USA) using the GenePix-format defaults and normalized with the Lowess curve.

organism: Solanum lycopersicum

source_name: : Root tips of tomato treated with Al

label_protocol: aRNAs were obtained using the Amino Allyl MessageAmp II aRNA Amplification Kit and labeled with cyanine-dye (Cy5/Cy3) (Ambion, USA).

extract_protocol: Total RNA was extracted using Genehunter’s RNA pure kit (Genhunter, USA). Genomic DNA was removed by incubation with DNase I at 37°C for 30 min. The RNA samples were purified by extraction in phenol: chloroform (1:1), precipitated with ethanol, and resuspended in diethyl pyrocarbonate- treated water. The quality and quantity of the RNA was monitored in 2.0% denatured agarose gels and a ND-1000 nanodrop spectrometer (Nanodrop Technologies, USA). DNA-free RNA extracts were used for further analysis.

treatment_protocol: Tomato (Solanum esculentum Mill cv. ‘Money Maker’) seeds (Seedman, USA) were surface sterilized by submerging in 50% bleach (sodium hypochloride) for 10 min followed by three washes with sterile distilled water. For seed germination, six clean seeds were placed in a 500 ml flask containing 300 ml Modified Magnavaca’s solution (Magnavaca, 1982) adjusted to pH 4.5 and incubated on a shaker (150 rpm) at 25°C for four days. Germinating seeds were then transferred to fresh Modified Magnavaca’s solution supplemented with 20 μM AlK(SO4)2 (Fisher Scientific, USA). Seedlings serving as controls were placed in Magnavaca’s solution without the Al. Cultures were maintained for 12 additional days, and the solution was replaced every four days. At the termination of the experiment, root tips of ~2 cm in length were dissected and soaked in a pre-chilled RNA extraction buffer (Genehunter, USA). Each replicate of treatment/ control has 20 flasks, and root tips from the 20 flasks were pooled to make one RNA extraction. Six RNA extraction replicates were preformed for Al treated and control tissues.

tag: Root tips in Modified Magnavaca’s solution supplemented with 20 μM AlK(SO4)2

source_name: Root tips of tomato without Al treatment

tag: Root tips in Modified Magnavaca’s solution grown without supplementation with Al


title: C_i_rep1


title: C_ni_rep2


title: CB071102


title: Aluminum-5_vs_Ctr-5

source_name: Root tips of tomato treated with Al


title: B_i_rep2

source_name: Rpv1+/Rpv2-, inoculated with P. viticola


title: Aluminum-2_vs_Ctr-2

value: Root tips in Modified Magnavaca’s solution grown without supplementation with Al


title: CB100103


title: Aluminum-6_vs_Ctr-6


title: B_i_rep1


title: heifers with PI fetuses (BVDV), day 160 of pregnancy, 5th replicate

status: Public on Jun 15 2009

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description: Gene expression after ncpBVDV infection

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse GeneChip 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed with DChip 2006, build 12.21.06, using default settings for model-based summation of expression values, and following normalization to invariant set of probes.

organism: Bos taurus

source_name: Total white blood cells from ncpBVDV-infected heifers with PI, TI or control fetuses

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle Affymetrix protocol from 3.5 micrograms total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Extraction of total RNA was performed from Trireagent BD for blood derivatives according to the manufacturer's instructions.

treatment_protocol: Blood sample collected at day160 of gestation

tag: Total white blood cells


title: Aluminum-3_vs_Ctr-3


title: heifers with TI fetuses (BVDV), day 190 of pregnancy, 1st replicate

description: Gene expression after ncpBVDV infection

treatment_protocol: Blood sample collected at day 190 of gestation


title: heifers with TI fetuses (BVDV), day 190 of pregnancy, 2nd replicate

description: Gene expression after ncpBVDV infection


title: B_ni_rep1


title: heifers with TI fetuses (BVDV), day 190 of pregnancy, 3rd replicate

description: Gene expression after ncpBVDV infection


title: heifers with PI fetuses (BVDV), day 160 of pregnancy, 4th replicate

description: Gene expression after ncpBVDV infection


title: heifers with PI fetuses (BVDV), day 160 of pregnancy, 3rd replicate

description: Gene expression after ncpBVDV infection


title: heifers with PI fetuses (BVDV), day 190 of pregnancy, 3rd replicate

description: Gene expression after ncpBVDV infection


title: heifers with PI fetuses (BVDV), day 160 of pregnancy, 1st replicate

description: Gene expression after ncpBVDV infection


title: control, day 160 of pregnancy, 3rd replicate

description: Gene expression after ncpBVDV infection

treatment_protocol: Blood sample collected at day 160 of gestation


title: heifers with PI fetuses (BVDV), day 190 of pregnancy, 2nd replicate

description: Gene expression after ncpBVDV infection


title: Wide-type + FOXM1B

status: Public on Jun 13 2009

type: genomic

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

description: Apart from control wild-type non-transformed SVpgC2a cells, all SVFN cells exhibit anchorage-independent growth properties.

hyb_protocol: Standard Affymetrix 10K XbaI protocol was used

scan_protocol: Affymetrix fluidics Station 400

data_processing: Affymetrix GCOS 1.4 and GTYPE 4.0

molecule: genomic DNA

source_name: Wild-type SVpgC2a transduced with FOXM1B

growth_protocol: Cells were grown in DMEM with 10% FCS in a humidified 5%CO2/95% air tissue culture incubator

extract_protocol: Standard genomic DNA salt precipitation method was used to extract gDNA from cells

tag: Non-transformed cells


title: Transformed clone 7 (SVFN7)

source_name: Transformed FOXM1B-induced clone 7

label_protocol: Standard Affymetrix 10K XbaI protocol was used

tag: Transformed cells


title: Aluminum-1_vs_Ctr-1


title: heifers with PI fetuses (BVDV), day 190 of pregnancy, 1st replicate

description: Gene expression after ncpBVDV infection


title: control, day 190 of pregnancy, 2nd replicate

description: Gene expression after ncpBVDV infection


title: control, day 190 of pregnancy, 3rd replicate

description: Gene expression after ncpBVDV infection


title: Transformed clone 4 (SVFN4)

source_name: Transformed FOXM1B-induced clone 4


title: Transformed clone 5 (SVFN5)

source_name: Transformed FOXM1B-induced clone 5


title: Transformed clone 3 (SVFN3)

source_name: Transformed FOXM1B-induced clone 3


title: Transformed clone 8 (SVFN8)

source_name: Transformed FOXM1B-induced clone 8


title: Wild-type control

source_name: Wild-type SVpgC2a with no treatment


title: heifers with PI fetuses (BVDV), day 160 of pregnancy, 2nd replicate

description: Gene expression after ncpBVDV infection


title: control, day 160 of pregnancy, 4th replicate

description: Gene expression after ncpBVDV infection


title: control, day 160 of pregnancy, 1st replicate

description: Gene expression after ncpBVDV infection


title: control, day 190 of pregnancy, 1st replicate

description: Gene expression after ncpBVDV infection


title: control, day 160 of pregnancy, 2nd replicate

description: Gene expression after ncpBVDV infection


title: Transformed clone 2 (SVFN2)

source_name: Transformed FOXM1B-induced clone 2


title: Transformed clone 6 (SVFN6)

source_name: Transformed FOXM1B-induced clone 6


title: 13749434 - Col0-3937-3 vs Col0-buffer-3

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

description: BOS1 signaling pathway in Arabidopsis thaliana / Erwinia chrysanthemi interaction

hyb_protocol: Col0-buffer-3 Cy5 / Col0-3937-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,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 indirect, amplification=yes, DNA 5 ug. 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: aerial - Media 		soil hygrometry 		70% Temperature 		19°C / 24°C Light 		8 hours

extract_protocol: Col0-buffer-3:4ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:Buffer - control buffer - control buffer,buffer:time 24hour . Rapid dipping aerial parts of six weeks old Arabidopsis plants in 50 mM KPO4 pH 7 buffer containing 0.01% (vol/vol) of the Silwet L-77 surfactant (van Meeuwen Chemicals BV, Weesp, The Netherlands). Infected plant were immediately incubated under following conditions : 100% hygrometry, 19°C / 24°C, day:night 8:16 hours. After incubation (24 hours)

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

extract_protocol: Col0-3937-3:10ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:3937 - biotic stress - pathogen infection,erwinia chrysanthemi-3937:quantity 1e+07cfu/ml time 24hour . Wild type and mutant Arabidopsis lines infection by wild type Erwinia chrysanthemi strains. Infections were performed by rapid dipping aerial parts of six weeks old Arabidopsis plants in 10^8 cfu / ml bacterial suspension in 50 mM KPO4 pH 7 buffer containing 0.01% (vol/vol) of the Silwet L-77 surfactant (van Meeuwen Chemicals BV, Weesp, The Netherlands). Infected plant were immediately incubated under following conditions : 100% hygrometry, 19°C / 24°C, day:night 8:16 hours. After incubation (24 hours), aerial parts were harvested.


title: Transformed clone 1 (SVFN1)

source_name: Transformed FOXM1B-induced clone 1


title: 13749433 - Col0-pelbc-2 vs Col0-3937-2

hyb_protocol: Col0-3937-2 Cy5 / Col0-pelbc-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-3937-2:15ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

extract_protocol: Col0-pelbc-2:7ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

treatment_protocol: Name:pelbc - biotic stress - pathogen infection,erwinia chrysanthemi-pelbc mutant:quantity 1e+07cfu/ml time 24hour . Wild type and mutant Arabidopsis lines infection by pelbc mutant Erwinia chrysanthemi strain. Infections were performed by rapid dipping aerial parts of six weeks old Arabidopsis plants in 10^8 cfu / ml bacterial suspension in 50 mM KPO4 pH 7 buffer containing 0.01% (vol/vol) of the Silwet L-77 surfactant (van Meeuwen Chemicals BV, Weesp, The Netherlands). Infected plant were immediately incubated under following conditions : 100% hygrometry, 19°C / 24°C, day:night 8:16 hours. After incubation (24 hours)


title: 13749439 - bos1-3937-3 vs Col0-3937-3

hyb_protocol: Col0-3937-3 Cy5 / bos1-3937-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: bos1-3937-3:7ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

tag: Arabidopsis thaliana (col-0)  mutant (bos1) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13749437 - Col0-pelbc-3 vs Col0-3937-3

hyb_protocol: Col0-3937-3 Cy5 / Col0-pelbc-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-pelbc-3:6ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13705694 - bos1-3937-1 vs Col0-3937-1

hyb_protocol: Col0-3937-1 Cy5 / bos1-3937-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-3937-1:16ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.

extract_protocol: bos1-3937-1:7ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13749431 - Col0-buffer-2 vs Col0-3937-2

hyb_protocol: Col0-3937-2 Cy5 / Col0-buffer-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-buffer-2:7ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13705696 - bos1-3937-2 vs Col0-3937-2

hyb_protocol: Col0-3937-2 Cy5 / bos1-3937-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: bos1-3937-2:8ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13749438 - Col0-3937-3 vs bos1-3937-3

hyb_protocol: bos1-3937-3 Cy5 / Col0-3937-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749435 - Col0-buffer-3 vs Col0-3937-3

hyb_protocol: Col0-3937-3 Cy5 / Col0-buffer-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749436 - Col0-3937-3 vs Col0-pelbc-3

hyb_protocol: Col0-pelbc-3 Cy5 / Col0-3937-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749432 - Col0-3937-2 vs Col0-pelbc-2

hyb_protocol: Col0-pelbc-2 Cy5 / Col0-3937-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13749430 - Col0-3937-2 vs Col0-buffer-2

hyb_protocol: Col0-buffer-2 Cy5 / Col0-3937-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: SLVL04

description: CD3-negative cells purified by magnetic cell separation from peripheral blood of splenic lymphoma with villous lymphocytes patients. Targets were produced starting from 6 ug of total RNA following standard Affymetrix protocol.

hyb_protocol: Standard Affymetrix procedures

source_name: Splenic Lymphoma with villous lymphocytes


title: 13705695 - Col0-3937-2 vs bos1-3937-2

hyb_protocol: bos1-3937-2 Cy5 / Col0-3937-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13705691 - Col0-3937-1 vs Col0-pelbc-1

hyb_protocol: Col0-pelbc-1 Cy5 / Col0-3937-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-pelbc-1:6ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13705690 - Col0-buffer-1 vs Col0-3937-1

hyb_protocol: Col0-3937-1 Cy5 / Col0-buffer-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Col0-buffer-1:6ug. Total RNA Isolation - Guanidinium thiocyanate method Reagents All the solutions should be treated with DEPc 2 ml/L Guanidinium solution 4M stock (3 months on bench) 250.0 g Guanidinium (Fluka) 293.0 ml H2O 17.6 ml 0.75 M sodium citrate pH7 26.4 ml 10% sarcosyl 200 ml total Denaturing Guanidinium solution 0.36 ml 2-mercaptoethanol for 50 ml of the stock solution CsCl buffer For 100 ml Weigh 95.97 g CsCl, dissolved it in 0.1 M EDTA to 100 ml, add 200 µl DEPc Weigh the bottle and autoclave 20', check the weigh Protocol Grind 1g of frozen tissue in a mortar under liquid nitrogen to a fine powder. Transfer the powder with a cold spatula in a homogenizer containing 7 ml of the denaturing solution. Mix well by vortexing. Put the mixture to a centrifuge tube to spin down the membranes and debris 10 000 rpm for 10' Load the supernatant onto a 5.7M CsCl cushion (3ml) equilibrated with EDTA. Centrifuge for at least 15 h at 35 000 rpm at 19°C. Remove most of the solution, invert quickly the tube and let it dry for 10'. Cut off the bottom of the tube and dissolve the RNA pellet with100 µl H2O. Add the same volume of phenol-chloroforme, mix well and centrifuge for 3'. Collect the aqueous phase and re-extract the organic phase with 100 µl H2O. Collect the two fractions and re-extract twice with chloroform. Precipitate the RNA with 0.3 M NaAcetate final concentration and 2.5 volume of ethanol for at least 1 h. Spin down the precipitate at 13 000 rpm, 4 °C, 20' and wash the pellet twice with 70% ethanol. Dry the pellet and dissolve it in 100 µl H2O in order to measure the concentration. Keep the RNA at -70°C.


title: 13705689 - Col0-3937-1 vs Col0-buffer-1

hyb_protocol: Col0-buffer-1 Cy5 / Col0-3937-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 30d SM muscle of Cmat/+, biological rep 3 [RMA]

status: Public on Jun 10 2009

city: West Lafayette

first: Christopher

middle: A

last: Bidwell

state: IN

address: 125 South Russell Street

department: Animal Sciences

institute: Purdue University

description: gene expression data using bovine platform

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were hybridized for 16hr at 45C on GeneChip Bovine Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Images were interpreted with Microarray Suite version 5.0 (MAS5.0) in GCOS with no scaling or normalization. Images were also interpreted by RMA using Bioconductor package of R.
The VALUEs below represent RMA signals.

organism: Ovis aries

source_name: 30 day old lamb semimembranosus muscle

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Lambs were housed indoors and allowed to nurse ewes fed grain based diet until collection.

extract_protocol: Tissue homogenized in 4M guanidinium thiocyanate, 25mM EDTA, 1% sodium-N-lauroyl-sarcosine. Homogenates ultracentrifuged on 5.7M CsCl cusion. RNA purified and DNase treated with Nucleospin RNA II columns (Machery-Nagel Inc.).

treatment_protocol: Lambs were euthanized, semimembranosus muscle excised and fixed in RNAlater (Ambion).

tag: genotype Cmat/+, age 30 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 80d SM muscle of +/+, biological rep 1 [RMA]

source_name: 80 day old lamb semimembranosus muscle

tag: genotype +/+, age 80 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 13705692 - Col0-pelbc-1 vs Col0-3937-1

hyb_protocol: Col0-3937-1 Cy5 / Col0-pelbc-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 30d SM muscle of C/C, biological rep 2 [RMA]

tag: genotype C/C, age 30 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 13705693 - Col0-3937-1 vs bos1-3937-1

hyb_protocol: bos1-3937-1 Cy5 / Col0-3937-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 30d SM muscle of C/C, biological rep 3 [RMA]


title: 80d SM muscle of +/+, biological rep 2 [RMA]


title: 30d SM muscle of Cmat/+, biological rep 2 [RMA]


title: 30d SM muscle of Cmat/+, biological rep 1 [RMA]


title: 30d SM muscle of +/+, biological rep 1 [RMA]

tag: genotype +/+, age 30 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 80d SM muscle of +/Cpat, biological rep 1 [RMA]

tag: genotype +/Cpat, age 80 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 30d SM muscle of C/C, biological rep 1 [RMA]


title: 20d SM muscle of +/+, biological rep 2 [RMA]

source_name: 20 day old lamb semimembranosus muscle

tag: genotype +/+, age 20 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 30d SM muscle of +/Cpat, biological rep 1 [RMA]

tag: genotype +/Cpat, age 30 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 10d SM muscle of +/+, biological rep 1 [RMA]

source_name: 10 day old lamb semimembranosus muscle

tag: genotype +/+, age 10 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 10d SM muscle of +/Cpat, biological rep 2 [RMA]

tag: genotype +/Cpat, age 10 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 80d SM muscle of +/Cpat, biological rep 2 [RMA]


title: 20d SM muscle of +/Cpat, biological rep 2 [RMA]

tag: genotype +/Cpat, age 20 days, breed 1/2 suffolk 1/2 dorset, muscle semimembranosus


title: 30d SM muscle of +/+, biological rep 2 [RMA]


title: 20d SM muscle of +/+, biological rep 1 [RMA]


title: 30d SM muscle of +/Cpat, biological rep 2 [RMA]


title: 10d SM muscle of +/+, biological rep 2 [RMA]


title: 20d SM muscle of +/Cpat, biological rep 1 [RMA]


title: 10d SM muscle of +/Cpat, biological rep 1 [RMA]


title: 80d SM muscle of +/+, biological rep 2

data_processing:
Images were interpreted with Microarray Suite version 5.0 (MAS5.0) in GCOS with no scaling or normalization. Images were also interpreted by RMA using Bioconductor package of R.
The VALUEs below represent MAS5.0 signals.


title: 80d SM muscle of +/+, biological rep 1


title: 80d SM muscle of +/Cpat, biological rep 2


title: 30d SM muscle of Cmat/+, biological rep 1


title: 30d SM muscle of Cmat/+, biological rep 3


title: 20d SM muscle of +/+, biological rep 1


title: 30d SM muscle of +/Cpat, biological rep 2


title: 20d SM muscle of +/+, biological rep 2


title: 30d SM muscle of +/+, biological rep 1


title: 20d SM muscle of +/Cpat, biological rep 1


title: 20d SM muscle of +/Cpat, biological rep 2


title: 30d SM muscle of +/+, biological rep 2


title: 10d SM muscle of +/+, biological rep 2


title: 10d SM muscle of +/+, biological rep 1


title: 30d SM muscle of C/C, biological rep 3


title: 30d SM muscle of +/Cpat, biological rep 1


title: 30d SM muscle of C/C, biological rep 2


title: 30d SM muscle of Cmat/+, biological rep 2


title: 80d SM muscle of +/Cpat, biological rep 1


title: 30d SM muscle of C/C, biological rep 1


title: DU145_preNeg_rep2

status: Public on Jun 05 2009

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale Tumori

description: DU145 cells transfected with Pre-miR™ miRNA Precursor Molecule negative control #1(Ambion)

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: BeadStudio Gene Expression Module v_3; cubic spline normalization; filtering: detection p-value<0.05

source_name: negative control

label_protocol: standard Illumina protocol (Cy3)

extract_protocol: Three days after transfection, cells were harvested and total RNA extracted using Trizol Reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Transfection with 20nM Pre-miR™ miRNA Precursor Molecules (Ambion), using Lipofectamine2000 (Invitrogen).

tag: DU145 cells


title: DU145_preNeg_rep1

tag: transfected with Pre-miR™ miRNA Precursor Molecule negative control #1(Ambion)


title: DU145_preNeg_rep3


title: DU145_preNeg_rep4


title: DU145_pre205_rep3

description: DU145 cells transfected with Pre-miR™ miRNA Precursor Molecule miR-205 (Ambion)


title: DU145_pre205_rep2

tag: transfected with Pre-miR™ miRNA Precursor Molecule miR-205 (Ambion)


title: DU145_pre205_rep1


title: WT Mouse heart 4Wk TAC Replicate 1

status: Public on Jun 03 2009

city: Chapel Hill

first: Monte

middle: S

last: Willis

state: NC

address: 103 Mason Farm Road

department: Pathology & Laboratory Medicine

institute: UNC

description: Biological replicate 1 of 3. Wt 4 week post band heart.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner. Images were quantified using Genepix Pro (version 6.0).

data_processing: LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal by Genepix Pro V 6.0, and uploaded to UNC microarray database (http:\\genome.unc.edu). Data was subsequently downloaded and filtered for features present in less than 70% of arrays.

organism: Mus musculus

source_name: WT Mouse heart, 4week post TAC replicate 1

label_protocol: 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

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

treatment_protocol: Trans-aortic constriction placed

tag: Cardiac tissue

tag: 4 Weeks post TAC

source_name: whole mouse neonates (day 1)

tag: Strain

tag: Age

value: postnatal Day 1

tag: Tissue

value: whole pup


title: 10d SM muscle of +/Cpat, biological rep 2


title: MURF1 Tg Mouse Heart 4Wk TAC Replicate 1

description: Biological replicate 1 of 3. MURF1 Tg 4 week post band heart.

source_name: MURF1 Tg mouse heart, 4week post TAC replicate 1


title: MURF1 Tg Mouse Heart 1Wk TAC Replicate 3

description: Biological replicate 3 of 3. MURF1 Tg 1 week post band heart.

source_name: MURF1 Tg mouse heart, 1week post TAC replicate 3

tag: 1 Week post TAC


title: MURF1 Tg Mouse Heart 1Wk TAC Replicate 1

description: Biological replicate 1 of 3. MURF1 Tg 1 week post band heart.

source_name: MURF1 Tg mouse heart, 1week post TAC replicate 1


title: MURF1 Tg Mouse Heart 1Wk TAC Replicate 2

description: Biological replicate 2 of 3. MURF1 Tg 1 week post band heart.

source_name: MURF1 Tg mouse heart, 1week post TAC replicate 2


title: WT Mouse heart 4Wk TAC Replicate 2

description: Biological replicate 2 of 3. Wt 4 week post band heart.

source_name: WT Mouse heart, 4week post TAC replicate 2


title: 10d SM muscle of +/Cpat, biological rep 1


title: WT Mouse heart 1Wk TAC Replicate 1

description: Biological replicate 1 of 3. Wt 1 week post band heart.

source_name: WT Mouse heart, 1week post TAC replicate 1


title: WT Mouse heart baseline Replicate 2

description: Biological replicate 2 of 4. Wt Baseline heart.

source_name: WT Mouse heart, untreated replicate 2

tag: untreated


title: WT Mouse heart baseline Replicate 3

description: Biological replicate 3 of 4. Wt Baseline heart.

source_name: WT Mouse heart, untreated replicate 3


title: rad4delta rad23delta strain R3

status: Public on Jun 01 2009

city: Cardiff

first: Julia

last: Smirnova

address: Tenovus building Ground Floor

department: Cardiff School of Medicine

institute: University of Cardiff

description: roarray experiments were performed using a yeast S98 chip oligonucleotide array (Affymetrix, Inc.) according to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manuals.affx). Approximately 1 µg of total RNA was processed into biotinylated cRNA according to Affymetrix protocols; 15-µg biotinylated cRNA targets were fragmented and hybridized to the arrays at 45°C for 16 h. The arrays were then processed using Affymetrix fluidics protocol EukGE-WS2 (V4 450) and stained with R-phycoerythrin conjugated to streptavidin (Molecular Probes, Inc). Microarray images were acquired using the 2500 GeneChip scanner (Affymetrix) and Microarray Suite version 5.0 software. Robust multichip average normalization and further analysis were carried out using the Affymetrix library of procedures (Affy version 1.5.8) in Bioconductor (version 1.5) (http://www.bioconductor.org) within R (version 2.0.1) (http://www.r-project.com; 16).

hyb_protocol: Eukaryotic Target preparation Manual

scan_protocol: Eukaryotic Target preparation Manual

data_processing: RMA

organism: Saccharomyces cerevisiae

source_name: University Of Cardiff, Simon Reed lab

label_protocol: Affymetrix Genechip Expression Amplification one-cycle target labeling reagents

growth_protocol: Grow cells in YPD till they reach OD 0.5-0.6

extract_protocol: Trizol Total RNA purification protocol can be found http://www.cogeme.man.ac.uk/services/transcriptoneservicefacility/index.asp

treatment_protocol: untreated

tag: BY4742 MAT alpha hisdelta1leu2delta0 lys2delta0 ura3delta0 YER162c::his3 YEL037c::kanMX4


title: WT Mouse heart 1Wk TAC Replicate 2

description: Biological replicate 2 of 3. Wt 1 week post band heart.

source_name: WT Mouse heart, 1week post TAC replicate 2


title: MURF1 Tg Mouse Heart 4Wk TAC Replicate 2

description: Biological replicate 2 of 3. MURF1 Tg 4 week post band heart.

source_name: MURF1 Tg mouse heart, 4week post TAC replicate 2


title: WT Mouse heart 4Wk TAC Replicate 3

description: Biological replicate 3 of 3. Wt 4 week post band heart.

source_name: WT Mouse heart, 4week post TAC replicate 3


title: MURF1 Tg Mouse Heart baseline Replicate 2

description: Biological replicate 2 of 3. MURF1 Tg Baseline heart.

source_name: MURF1 Tg mouse heart, untreated replicate 2


title: WT Mouse heart 1Wk TAC Replicate 3

description: Biological replicate 3 of 3. Wt 1 week post band heart.

source_name: WT Mouse heart, 1week post TAC replicate 3


title: DU145_pre205_rep4


title: OCI-Ly3 Dox 3 days + Ikk Inhibitor 24 hours - mAdbID:81135

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 81135

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

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 850;; 750 ScanPower: 100;; 100 LaserPower: 1.7655;; 2.24464 Temperature: 37.3582

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: OCI-Ly3 - Ikk Inhibitor (24 hours)

label_protocol:
Cy3 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy3-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

extract_protocol:
Trizol Reagent Extraction Protocol
Extraction method: Trizol Reagent
Other: Total RNA was prepared using the Trizol reagent (Gibco BRL) according to manufacturer's instructions.

treatment_protocol:
Treatment type: compound
Agent: Ikk Inhibitor (MLN120b)
Treatment dose: 12.5 uM (Ikk Inhibitor)
Treatment time: 24 hr (Ikk Inhibitor)
In-vivo treatment: Treated 24 hours of Ikk inhibitor (MLN120b).

tag: Cell line

value: OCI-Ly3 Cell Line

source_name: OCI-Ly3 - Dox 3 days + Ikk Inhib 24 hrs

label_protocol:
Cy5 Labeling Protocol
Other: Isolated RNA (50 ug) was reverse transcribed by oligo dT-primed polymerization using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA). The targets were coupled to Cy5-conjugated deoxynucleotides (Amersham Biosciences, Piscataway, NJ) for 1 hour at room temperature. Probes were combined and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA).

treatment_protocol:
Treatment type: compound
Agent: Doxycycline; Ikk Inhibitor (MLN120b)
Treatment dose: 20 ng/ml (Dox); 12.5 uM (Ikk Inhibitor)
Treatment time: 3 days (Dox); 24 hr (Ikk Inhibitor)
In-vivo treatment: Treated 2 days with Doxycycline followed by 24 hours of Ikk inhibitor (MLN120b).


title: MURF1 Tg Mouse Heart baseline Replicate 3

description: Biological replicate 3 of 3. MURF1 Tg Baseline heart.

source_name: MURF1 Tg mouse heart, untreated replicate 3

source_name: whole mouse neonates (day 1)


title: OCI-Ly3 Dox 3 days - mAdbID:81679

description: mAdb experiment ID: 81679

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 800;; 750 ScanPower: 100;; 100 LaserPower: 1.65;; 2.3 Temperature: 35.48

source_name: Untreated OCI-Ly3

source_name: OCI-Ly3 - Dox 3 days

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 3 days


title: WT Mouse heart baseline Replicate 1

description: Biological replicate 1 of 4. Wt Baseline heart.

source_name: WT Mouse heart, untreated replicate 1


title: rad4delta rad23delta strain R1


title: MURF1 Tg Mouse Heart 4Wk TAC Replicate 3

description: Biological replicate 3 of 3. MURF1 Tg 4 week post band heart.

source_name: MURF1 Tg mouse heart, 4week post TAC replicate 3


title: rad4delta rad23delta strain R2


title: OCI-Ly3 Dox 2 days - mAdbID:81678

description: mAdb experiment ID: 81678

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000A [55478] PMTVolts: 760;; 710 ScanPower: 100;; 100 LaserPower: 1.61;; 2.28 Temperature: 34.64

source_name: OCI-Ly3 - Dox 2 days

treatment_protocol:
Treatment type: compound
Agent: Doxycycline
Treatment dose: 20 ng/ml
Treatment time: 2 days


title: rad23delta strain Euroscarf Y10278 R1

source_name: Euroscarf

tag: BY4742 MAT alpha hisdelta1leu2delta0 lys2delta0 ura3delta0 YEL037c::kanMX4


title: WT Mouse heart baseline Replicate 4

description: Biological replicate 4 of 4. Wt Baseline heart.

source_name: WT Mouse heart, untreated replicate 4


title: Male NOD Lacrimal Placebo, biological rep 3 b

status: Public on Feb 01 2009

city: Boston

first: David

last: Sullivan

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

description: Lacrimal gland gene expression in male NOD mice.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on GE Healthcare/Amersham Biosciences CodeLink UniSet Mouse I Bioarray. Bioarrays were washed and stained with streptavidin-Alexa 647 and washed again.

scan_protocol: Bioarrays were scanned with a ScanArray Express HT scanner using ScanArray Express software.

data_processing: Data were analyzed with the CodeLink Image Analysis software using the default settings and normalized using global scaling to a median target intensity  on each array of 1.0.

source_name: Lacrimal glands from male NOD mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

extract_protocol: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.


title: OCI-Ly3 Dox 2 days + Ikk Inhibitor 3 hours - mAdbID:81325

description: mAdb experiment ID: 81325

scan_protocol: Creator: GenePix Pro 3.0.6.89 Scanner: GenePix 4000B [82703] PMTVolts: 790;; 690 ScanPower: 100;; 100 LaserPower: 2.91;; 3.02 Temperature: 30.05

source_name: OCI-Ly3 - Ikk Inhibitor (3 hours)

treatment_protocol:
Treatment type: compound
Agent: Ikk Inhibitor (MLN120b)
Treatment dose: 12.5 uM (Ikk Inhibitor)
Treatment time: 3 hr (Ikk Inhibitor)
In-vivo treatment: Treated 3 hours of Ikk inhibitor (MLN120b).

source_name: OCI-Ly3 - Dox 2 days + Ikk Inhib 3 hrs

treatment_protocol:
Treatment type: compound
Agent: Doxycycline; Ikk Inhibitor (MLN120b)
Treatment dose: 20 ng/ml (Dox); 12.5 uM (Ikk Inhibitor)
Treatment time: 2 days+3 hr (Dox); 3 hr (Ikk Inhibitor)
In-vivo treatment: Treated 2 days with Doxycycline followed by 3 hours of Ikk inhibitor (MLN120b).


title: Male NOD Lacrimal Placebo, biological rep 2 b


title: rad23delta strain Euroscarf Y10278 R3

source_name: e


title: rad4delta strain Euroscarf Y16158 R3

tag: BY4742 MAT alpha hisdelta1leu2delta0 lys2delta0 ura3delta0 YER162c::kanMX4


title: MURF1 Tg Mouse Heart baseline Replicate 1

description: Biological replicate 1 of 3. MURF1 Tg Baseline heart.

source_name: MURF1 Tg mouse heart, untreated replicate 1


title: WT strain Euroscarf Y10000 R1

description: Microarray experiments were performed using a yeast S98 chip oligonucleotide array (Affymetrix, Inc.) according to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manuals.affx). Approximately 1 µg of  total RNA was processed into biotinylated cRNA according to Affymetrix protocols; 15-µg biotinylated cRNA targets were fragmented and hybridized to the arrays at 45°C for 16 h. The arrays were then processed using Affymetrix fluidics protocol EukGE-WS2 (V4 450) and stained with R-phycoerythrin conjugated to streptavidin (Molecular Probes, Inc). Microarray images were acquired using the 2500 GeneChip scanner (Affymetrix) and Microarray Suite version 5.0 software. Robust multichip average normalization and further analysis were carried out using the Affymetrix library of procedures (Affy version 1.5.8) in Bioconductor (version 1.5) (http://www.bioconductor.org) within R (version 2.0.1) (http://www.r-project.com; 16).

tag: Mat alpha his3delta1 leu2delta0 ura3delta0


title: Female NOD Lacrimal Placebo, biological rep 1 b

description: Lacrimal gland gene expression in female NOD mice.

source_name: Lacrimal glands from female NOD mice ( glands pooled from 5-8 mice)


title: Female NOD Lacrimal Placebo, biological rep 2 b


title: WT strain  Euroscarf Y10000 R3

tag: Mat alpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: rad4delta strain Euroscarf Y16158 R2

description: Microarray experiments were performed using a yeast S98 chip oligonucleotide array (Affymetrix, Inc.) according to the manufacturer's instructions (http://www.affymetrix.com/support/technical/manuals.affx). Approximately 1 µg of total RNA was processed into biotinylated cRNA according to Affymetrix protocols; 15-µg biotinylated cRNA targets were fragmented and hybridized to the arrays at 45°C for 16 h. The arrays were then processed using Affymetrix fluidics protocol EukGE-WS2 (V4 450) and stained with R-phycoerythrin conjugated to streptavidin (Molecular Probes, Inc). Microarray images were acquired using the 2500 GeneChip scanner (Affymetrix) and Microarray Suite version 5.0 software. Robust multichip average normalization and further analysis were carried out using the Affymetrix library of procedures (Affy version 1.5.8) in Bioconductor (version 1.5) (http://www.bioconductor.org) within R (version 2.0.1) (http://www.r-project.com; 16).


title: Male MRL/lpr Lacrimal Placebo, biological rep 2 b

description: Lacrimal gland gene expression in male MRL/lpr mice.

source_name: Lacrimal glands from male MRL/lpr mice ( glands pooled from 5-8 mice)


title: rad4delta strain Euroscarf Y16158 R1s

tag: BY4742 MAT alpha  hisdelta1leu2delta0 lys2delta0 ura3delta0 YER162c::kanMX4


title: rad23delta strain Euroscarf Y10278 R2


title: WT strain Euroscarf Y10000 R2


title: Female NOD Lacrimal Placebo, biological rep 3 b


title: Male MRL/lpr Lacrimal Placebo, biological rep 3 b


title: Male NOD Lacrimal Placebo, biological rep 1 b


title: Female NOD Lacrimal Testosterone, biological rep 2

description: Lacrimal gland gene expression from female NOD mice treated with testosterone for 21 days.

source_name: Lacrimal glands from testosterone treated female NOD mice ( glands pooled from 2-4 mice).

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.

tag: Female NOD Lacrimal Testosterone


title: Female MRL/lpr Lacrimal Placebo, biological rep 3	b

description: Lacrimal gland gene expression in female MRL/lpr mice.

source_name: Lacrimal glands from female MRL/lpr mice ( glands pooled from 5-8 mice)


title: Male MRL/lpr Lacrimal Placebo, biological rep 1 b


title: Wild Type (Aromatase KO) Meibomian Male , biological rep 2

description: Meibomian gland gene expression from male wild type (aromatase knockout) mice.

source_name: Meibomian glands from male wild type mice ( glands pooled from 5-8 mice)

extract_protocol: Lacrimal glands: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.  Meibomian glands: RNA was purified with two Trizol extractions.

tag: Wild Type (Aromatase KO) Meibomian Male


title: Female MRL/lpr Lacrimal Placebo, biological rep 3

description: Lacrimal gland gene expression from female MRL/lpr mice treated with placebo for 18 days.

source_name: Lacrimal glands from placebo treated female MRL/lpr mice ( glands pooled from 6 mice).

tag: Female MRL/lpr Lacrimal Placebo


title: Female NOD Lacrimal Placebo, biological rep 3

description: Lacrimal gland gene expression from female NOD mice treated with placebo for 21 days.

source_name: Lacrimal glands from placebo treated female NOD ( glands pooled from 2-4 mice).

tag: Female NOD Lacrimal Placebo


title: Female NOD Lacrimal Placebo, biological rep 2


title: Female MRL/lpr Lacrimal Placebo, biological rep 2


title: Female NOD Lacrimal Testosterone, biological rep 3


title: Female NOD Lacrimal Placebo, biological rep 1


title: Female MRL/lpr Lacrimal Placebo, biological rep 1	b


title: Female NOD Lacrimal Testosterone, biological rep 1


title: Wild Type (Aromatase KO) Meibomian Male , biological rep 1


title: Aromatase KO Meibomian Female , biological rep 3

description: Meibomian gland gene expression from female aromatase knockout mice

source_name: Meibomian glands from female aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Aromatase KO Meibomian Female


title: Female MRL/lpr Lacrimal Testosterone, biological rep 3

description: Lacrimal gland gene expression from female MRL/lpr mice treated with testosterone for 18 days.

source_name: Lacrimal glands from testosterone treated female MRL/lpr mice ( glands pooled from 6 mice).

tag: Female MRL/lpr Lacrimal Testosterone


title: Aromatase KO Meibomian Male , biological rep 2

description: Meibomian gland gene expression from male aromatase knockout mice

source_name: Meibomian glands from male aromatase knockout mice ( glands pooled from 5-8 mice)

tag: Aromatase KO Meibomian Male


title: Wild Type (Aromatase KO) Meibomian Male , biological rep 3

data_processing: Data were analyzed with the CodeLink Image Analysis software using the default settings and normalized using global scaling to a median target intensity on each array of 1.0.


title: Female MRL/lpr Lacrimal Testosterone, biological rep 1


title: Aromatase KO Meibomian Male , biological rep 3


title: Aromatase KO Meibomian Female , biological rep 2


title: Aromatase KO Meibomian Male , biological rep 1


title: Female MRL/lpr Lacrimal Placebo, biological rep 1


title: Wild Type (Aromatase KO) Lacrimal Male , biological rep 3

description: Lacrimal gland gene expression from male wild type (aromatase knockout) mice.

source_name: Lacrimal glands from male wild type mice ( glands pooled from 5-8 mice)

tag: Wild Type (Aromatase KO) Lacrimal Male


title: Wild Type (Aromatase KO) Meibomian Female , biological rep 1

description: Meibomian gland gene expression from female wild type (aromatase knockout) mice.

source_name: Meibomian glands from female wild type mice ( glands pooled from 5-8 mice)


title: Wild Type (Aromatase KO) Meibomian Female , biological rep 2


title: Wild Type (Aromatase KO) Lacrimal Male , biological rep 1


title: Female MRL/lpr Lacrimal Testosterone, biological rep 2


title: Aromatase KO Meibomian Female , biological rep 1

description: Meibomian gland gene expression from female aromatase knockout mice.


title: Wild Type (Aromatase KO) Lacrimal Male , biological rep 2


title: Female MRL/lpr Lacrimal Placebo, biological rep 2	b