title: Pseudomonas + UV+ Aphid+ rep3

status: Public on Nov 25 2008

type: RNA

city: Manchester

first: Daniel

last: Jameson

address: 3.614 Stopford Building

department: Faculty of Life Sciences

country: United Kingdom

institute: University of Manchester

description: Gene expression data from aphid infested, UV-B treated Arabidopsis thaliana

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip system 3000 Hi Res Scanner

data_processing: The data as presented here were normalised with RMA and de-logged (Bioconductor affy library 1.8.1). Subsequent analysis in Genespring 7.1 was undertaken after default per-chip and per-gene normalisation within replicate groups.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana leaf, Pseudomonas, UV-B and aphid treated

label_protocol: Fifteen micrograms of total RNA was converted to first-strand cDNA in the following 20 uL reaction: 4 ul of  5 first strand cDNA buffer(1x), 1 ul T7 (dT)24(100pmol), 2ul  0.1M DTT (10mM DTT) (Invitrogen), 1ul 10mM dNTP mix (500 uM each)  and  2ul  of 400 U Superscript II (Invitrogen). The mixture was incubated at 42  for 1 h  after which the second strand cDNA synthesis was performed in the following 150 ul reaction mixture: 20 ul first strand cDNA, 91ul  of DEPC Water, 30ul of 5x Second strand cDNA buffer(1x), 3ul of 10mM dNTP mix (200uM each) 1ul (10U/ul) E.Coli DNA ligase(10U), 4ul (10U/ul) E.Coli DNA Pol. I (40U) and 1ul (2U/ul ) E. Coli RNase H (2U). The mixture was incubated at 16 for 2 h. The resulted double stranded  cDNA was cleaned up using GeneChip sample clean up module before labelling with biotin.  Labelling was done with Affymetrix labelling kit using the following components in 40 ul reaction mix: 6ul  of  template DNA, 14ul DH2O,  4ul 10X IVT labeling buffer, 12ul IVT labeling NTP mix and 4ul  IVT labelling enzyme mix. The mixture was incubated at 37 for 16 h. Labeled cRNAs were cleaned by using GeneChip sample clean up module. Fragmentation was carried out using 15ug of cRNA (1-21ul) with 6ul.5X fragmentation buffer. The final volume was adjusted using RNase-free water and incubated at 94 for 35 min. Hybridization was performed by following Affymetrix Eukaryotic target hybridization protocol.

growth_protocol: Arabidopsis thaliana seeds were ethanol sterilised (70% EtOH, 5 ddsH2O rinses), vernalised at 4oC for 3 days and then sown on plates containing sterile 1.0% phytagel-MS basal medium (Murashige and Skoog 1962) without sucrose, pH to 5.6-5.8. Plated seeds were vernalised for a further four days before being transferred to the growth chamber (Environmental control chamber  Model no. AR66L, Percieval Scientific Inc. USA). Light regime was 8/16hrs day/night (provided by 32 W Fluorescent bulbs- # F32T8/TL741, Philips giving ~ 256 PAR/uMoles). Temperature was 21oC for day and 18oC at night. The relative humidity was set to 60+10%. On day 15 after transfer to the growth chamber plates were flooded with 1 OD of Pseudomonas aeruginosa strain 7NR cell suspension in 10 mM of Magnesium sulphate and incubated at room temperature for one hour. Fifteen seedlings per tray were transplanted to half size seed trays filled with autoclaved (twice with the gap of 3 days at 120 for 20 minutes) John Innes Compost No: 1. Plants were exposed to the UV-B (9 KJ m-2 day-1) for 7 days at day 21 after transplantation. 28 days after transplantation plants were infested with two caterpillars (Tricoplusia ni) of size 0.5-1cm for 24 hours.

extract_protocol: Total RNA was extracted using RNeasy plant mini kit for plants, following manufacturer's instructions (QIAGEN Ltd., UK). RNA samples were cleaned of contaminating DNA by on-column DNAse treatment using RNase free DNase set (QIAGEN) while using the cleanup column included in the kit.

treatment_protocol: 15 individual plants from same tray snap frozen in NO2(l) and pooled.

tag: Ecotype

value: COL4 (NASC N933)

tag: Age

value: 44 days


title: Pseudomonas + UV- rep3

source_name: Arabidopsis thaliana leaf, Pseudomonas treated


title: Pseudomonas + UV+ rep4

source_name: Arabidopsis thaliana leaf, Pseudomonas and UV-B treated


title: Pseudomonas + UV+ Caterpillar+ rep5

source_name: Arabidopsis thaliana leaf, Pseudomonas, UV-B and caterpillar treated


title: Pseudomonas + UV+ Caterpillar+ rep1


title: Pseudomonas + UV+ Caterpillar+ rep3


title: Pseudomonas + UV+ rep1


title: Pseudomonas + UV+ rep2


title: Pseudomonas + UV- Caterpillar+ rep5

source_name: Arabidopsis thaliana leaf, Pseudomonas and caterpillar treated


title: Pseudomonas + UV+ Aphid+ rep4


title: Pseudomonas + UV- rep5


title: Pseudomonas + UV+ Caterpillar+ rep2


title: Pseudomonas + UV+ Aphid+ rep5


title: Pseudomonas + UV+ Aphid+ rep2


title: Pseudomonas + UV- rep1


title: Pseudomonas + UV- rep2


title: Pseudomonas + UV+ rep5


title: Pseudomonas + UV- Caterpillar+ rep3


title: Pseudomonas + UV+ Caterpillar+ rep4


title: Pseudomonas + UV+ rep3


title: Pseudomonas + UV- Caterpillar+ rep1


title: Pseudomonas + UV- Aphid+ rep2

source_name: Arabidopsis thaliana leaf, Pseudomonas and aphid treated


title: Pseudomonas + UV+ Aphid+ rep1


title: Pseudomonas + UV- Caterpillar+ rep2


title: Pseudomonas + UV- rep4


title: Pseudomonas + UV- Aphid+ rep4


title: Pseudomonas + UV- Caterpillar+ rep4


title: Pseudomonas + UV- Aphid+ rep5


title: Pseudomonas - UV- Caterpillar+ rep5

source_name: Arabidopsis thaliana leaf, caterpillar treated


title: Pseudomonas + UV- Aphid+ rep1


title: Pseudomonas - UV- rep5

source_name: Arabidopsis thaliana leaf


title: Pseudomonas - UV- Caterpillar+ rep1


title: Pseudomonas - UV- rep2


title: Pseudomonas - UV- Caterpillar+ rep4


title: Pseudomonas - UV- rep1


title: Pseudomonas - UV- Aphid+ rep5

source_name: Arabidopsis thaliana leaf, aphid treated


title: Pseudomonas - UV- Caterpillar+ rep3


title: Pseudomonas - UV- Aphid+ rep2


title: Pseudomonas - UV- Caterpillar+ rep2


title: Pseudomonas - UV- rep3


title: Pseudomonas + UV- Aphid+ rep3


title: Pseudomonas - UV+ Caterpillar+ rep1

source_name: Arabidopsis thaliana leaf, UV-B and caterpillar treated


title: Pseudomonas - UV+ Caterpillar+ rep4


title: Pseudomonas - UV+ rep4

source_name: Arabidopsis thaliana leaf, UV-B treated


title: Pseudomonas - UV+ rep3


title: Pseudomonas - UV+ Caterpillar+ rep2


title: Pseudomonas - UV- Aphid+ rep4


title: Pseudomonas - UV- rep4


title: Pseudomonas - UV- Aphid+ rep1


title: Pseudomonas - UV+ rep5


title: Pseudomonas - UV+ Caterpillar+ rep3


title: Pseudomonas - UV+ Aphid+ rep5

source_name: Arabidopsis thaliana leaf, UV-B and aphid treated


title: Pseudomonas - UV+ rep1


title: Pseudomonas - UV+ rep2


title: Pseudomonas - UV+ Aphid+ rep4


title: Pseudomonas - UV+ Caterpillar+ rep5


title: Pseudomonas - UV- Aphid+ rep3


title: Pseudomonas - UV+ Aphid+ rep3


title: Pseudomonas - UV+ Aphid+ rep2


title: Pseudomonas - UV+ Aphid+ rep1


title: HaCaT_4hr vs 8hr_low dose UVB (Y25_L4L5)

status: Public on Nov 18 2008

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

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

hyb_protocol: 3 DNA array 50 kit protocol (Genisphere)

scan_protocol: Barcode=12494746  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=2.94 3.52  Temperature=27.67  ScanPower=33 33

data_processing: Data processing will detailed description in http://140.114.106.30/publication/cho/

organism: Homo sapiens

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

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

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 8 hr

tag: HaCaT Cell line, Gender

value: male, Tissue:skin keratinocytes

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 4 hr


title: HaCaT_1hr_Ctrl/ low dose UVB (Y4_C2L2)

scan_protocol: Barcode=12499119  PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=3.06 3.45  Temperature=30.42  ScanPower=100 33

label_protocol: 3 DNA array 50 kit protocol (Genisphere)

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 1 hr

treatment_protocol: No treatment (control sample), and then incubate for 1 hr


title: HaCaT_2hr_high dose UVB/ Ctrl (Y9_H3C3)

scan_protocol: Barcode=12494691  PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=2.99 3.53  Temperature=28.65  ScanPower=100 33

treatment_protocol: No treatment (control sample), and then incubate for 2 hr

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 2 hr


title: HaCaT_0.5hr_low dose/ high dose UVB (Y2_L1H1)

scan_protocol: Barcode=12499117  PMTVolts=800 600  Scanner=GenePix 4000B [84942]  LaserPower=3.03 3.55  Temperature=30.36  ScanPower=33 33

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 0.5 hr

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 0.5 hr


title: HaCaT_2hr_ Ctrl/ low dose UVB (Y7_C3L3)

scan_protocol: Barcode=12494693  PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=3.17 3.48  Temperature=29.41  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 2 hr


title: HaCaT_1hr_ low dose/ high dose UVB (Y5_L2H2)

scan_protocol: Barcode=12494695  PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=2.94 3.59  Temperature=27.64  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 1 hr


title: HaCaT_0.5hr vs 1hr_low dose UVB (Y22_L1L2)

scan_protocol: Barcode=12518861  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=2.94 3.64  Temperature=30.87  ScanPower=33 33


title: HaCaT_1hr_ high dose UVB/ Ctrl (Y6_H2C2)

scan_protocol: Barcode=12494694 PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=3.03 3.47  Temperature=30.23  ScanPower=100 33


title: HaCaT_0.5hr_high dose UVB/ Ctrl ( Y3_H1C1)

scan_protocol: Barcode=12499118  PMTVolts=600 600  Scanner=GenePix 4000B [84942]  LaserPower=3.11 3.43  Temperature=31.39  ScanPower=33 33

treatment_protocol: No treatment (control sample), and then incubate for 0.5 hr


title: HaCaT_4hr_high dose/ Ctrl (Y12_H4C4)

scan_protocol: Barcode=12494806  PMTVolts=650 600  Scanner=GenePix 4000B [84942]  LaserPower=3.11 3.41  Temperature=30.94  ScanPower=100 33

treatment_protocol: No treatment (control sample), and then incubate for 4 hr

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 4 hr


title: HaCaT_16hr_high dose UVB/ Ctrl (Y18_H6C6)

scan_protocol: Barcode=12497969  PMTVolts=680 630  Scanner=GenePix 4000B [84942]  LaserPower=3.14 3.59  Temperature=32.67  ScanPower=100 33

treatment_protocol: No treatment (control sample), and then incubate for 16 hr

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 16 hr


title: HaCaT_4hr_low dose/ high dose UVB (Y11_L4H4)

scan_protocol: Barcode=12494807  PMTVolts=650 600  Scanner=GenePix 4000B [84942]  LaserPower=3.13 3.5  Temperature=29.44  ScanPower=100 33


title: HaCaT_2hr vs 4hr_low dose UVB (Y24_L3L4)

scan_protocol: Barcode=12494745  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=3.04 3.66  Temperature=30.26  ScanPower=33 33


title: HaCaT_16hr_low dose/ high dose UVB (Y17_L6H6)

scan_protocol: Barcode=12497970  PMTVolts=680 630  Scanner=GenePix 4000B [84942]  LaserPower=3.2 3.65  Temperature=32.55  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 16 hr


title: HaCaT_20hr vs 0.5hr_low dose UVB (Y28_L7L1)

scan_protocol: Barcode=12494749  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=3.01 3.52  Temperature=31.18  ScanPower=33 33

treatment_protocol: Cells exposed to UVB 233 J/m2, and then incubate for 0.5 hr

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 20 hr


title: HaCaT_16hr vs 20hr_low dose UVB (Y27_L6L7)

scan_protocol: Barcode=12494748  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=3.01 3.65  Temperature=28.83  ScanPower=33 33


title: HaCaT_8hr vs 16hr_low dose UVB (Y26_L5L6)

scan_protocol: Barcode=12494747  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=3.05 3.57  Temperature=31.36  ScanPower=33 33

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 8 hr


title: HaCaT_20hr_Ctrl/ low dose UVB (Y19_C7L7)

scan_protocol: Barcode=12518860  PMTVolts=700 630  Scanner=GenePix 4000B [84942]  LaserPower=3.08 3.64  Temperature=31.58  ScanPower=100 33

treatment_protocol: No treatment (control sample), and then incubate for 20 hr


title: HaCaT_1hr vs 2hr_low dose UVB (Y23_L2L3)

scan_protocol: Barcode=12518862  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=2.92 3.63  Temperature=29.38  ScanPower=33 33

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 1 hr


title: HaCaT_20hr_high dose UVB/ Ctrl (Y21_H7C7)

scan_protocol: Barcode=12497968  PMTVolts=660 630  Scanner=GenePix 4000B [84942]  LaserPower=3.22 3.63  Temperature=32.13  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 20 hr


title: HaCaT_2hr_low dose/ high dose UVB (Y8_L3H3)

scan_protocol: Barcode=12494692  PMTVolts=730 600  Scanner=GenePix 4000B [84942]  LaserPower=3.09 3.47  Temperature=29.78  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 2 hr


title: HaCaT_0.5hr_Ctrl/ low dose UVB (Y1_C1L1)

scan_protocol: Barcode=12499116  PMTVolts=700 600  Scanner=GenePix 4000B [84942]  LaserPower=3.2 3.45  Temperature=32  ScanPower=100 33


title: HaCaT_16hr_Ctrl/ low dose UVB (Y16_C6L6)

scan_protocol: Barcode=12497971  PMTVolts=680 630  Scanner=GenePix 4000B [84942]  LaserPower=3.21 3.64  Temperature=32.4  ScanPower=100 33


title: HaCaT_8hr_Ctrl/ low dose UVB (Y13_C5L5)

scan_protocol: Barcode=12498024  PMTVolts=730 620  Scanner=GenePix 4000B [84942]  LaserPower=3.04 3.63  Temperature=29.93  ScanPower=33 33

treatment_protocol: No treatment (control sample), and then incubate for 8 hr


title: HaCaT_8hr_low dose/ high dose UVB (Y14_L5H5)

scan_protocol: Barcode=12498028  PMTVolts=730 610  Scanner=GenePix 4000B [84942]  LaserPower=2.99 3.64  Temperature=31.3  ScanPower=33 33

treatment_protocol: Cells exposed to UVB 582.5 J/m2 , and then incubate for 8 hr


title: HaCaT_20hr_low dose/ high dose UVB (Y20_L7H7)

scan_protocol: Barcode=12494684  PMTVolts=700 630  Scanner=GenePix 4000B [84942]  LaserPower=3.08 3.63  Temperature=31.79  ScanPower=100 33


title: XIAP knockout MEF unstimulated

status: Public on Nov 12 2008

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

description: Fibroblasts from wild-type and XIAP knockout mice were analyzed with and without TNFa stimulation (4 hours). This sample represents the XIAP knockout cells, unstimulated.

hyb_protocol: Before hybridization, the cocktails were heated to 94°C for 5 minutes, equilibrated at 45°C for 5 minutes, and then clarified by centrifugation (16,000 x g) at room temperature for 5 minutes. Aliquots of this hybridization cocktail containing 15 µg of fragmented cRNA were hybridized at 45°C for 16 hours in a rotisserie oven at 60 rpm. The arrays were washed using non-stringent buffer (6xSSPE: 0.9 M sodium chloride, 0.06 M sodium phosphate, 6 mM EDTA pH 7.4)  at 25°C, followed by stringent buffer (100 mmol/L MES, pH 6.7, 0.1 mol/L NaCl, 0.01% Tween 20) at 50°C. The arrays were stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), washed with 6xSSPE, incubated with biotinylated anti-streptavidin IgG, stained again with streptavidin-phycoerythrin, and washed again with 6xSSPE.

scan_protocol: The arrays were scanned using the GeneArray scanner (Affymetrix).

data_processing: Image analysis was performed with GeneChip software (Affymetrix, MAS 5.0). Normalization was performed by global scaling, with the arrays scaled to an average intensity of 500.

label: biotin-11-CTP, biotin-16-UTP

organism: Mus musculus

source_name: total RNA from unstimulated XIAP knockout MEF

label_protocol: Briefly, 5 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using a cDNA synthesis kit (Superscript Choice System; Life Technologies, Inc., Rockville, MD) that uses an oligo(dT)24 primer containing a T7 RNA polymerase promoter 3' to the polyT (Geneset, La Jolla, CA), followed by second-strand synthesis. Labeled cRNA was prepared from the double-stranded cDNA by in vitro transcription using T7 RNA polymerase in the presence of biotin-11-CTP and biotin-16-UTP (Enzo, Farmington, NY). The labeled cRNA was purified over RNeasy columns (Qiagen, Valencia, CA). Fifteen µg of cRNA was fragmented at 94°C for 35 minutes in 40 mmol/L of Tris-acetate, pH 8.1, 100 mmol/L of potassium acetate, and 30 mmol/L of magnesium acetate. The cRNA was then used to prepare 300 µl of hybridization cocktail (100 mmol/L MES, 1 mol/L NaCl, 20 mmol/L ethylenediaminetetraacetic acid, 0.01% Tween 20) containing 0.1 mg/ml of herring sperm DNA (Promega, Madison, WI) and 500 µg/ml of acetylated bovine serum albumin (Life Technologies, Inc.).

growth_protocol: Cells were cultured in DMEM+10%FCS containing L-glutamine, pen/strep. They were passaged 1:10 every 3 days.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: no treatment

tag: mouse fibroblasts from BL/6 XIAP knockout mice, immortalized


title: wild-type MEF TNFa

description: Fibroblasts from wild-type and XIAP knockout mice were analyzed with and without TNFa stimulation (4 hours). This sample represents the wt cells stimulated with TNFa.

source_name: total RNA from TNFa stimulated MEF

treatment_protocol: Confluent cells were stimulated with 20 ng/ml TNFa (final conc.) for 4 hours.

tag: mouse fibroblasts from BL/6 mice, immortalized


title: HaCaT_8hr_high dose UVB/ Ctrl (Y15_H5C5)

scan_protocol: Barcode=12498025  PMTVolts=650 550  Scanner=GenePix 4000B [84942]  LaserPower=3 3.59  Temperature=30.39  ScanPower=33 33


title: XIAP knockout MEF TNFa

description: Fibroblasts from wild-type and XIAP knockout mice were analyzed with and without TNFa stimulation (4 hours). This sample represents the XIAP knockout cells, stimulated with TNFa.

source_name: total RNA from TNFa stimulated XIAP knockout MEF


title: wild-type MEF unstimulated

description: Fibroblasts from wild-type and XIAP knockout mice were analyzed with and without TNFa stimulation (4 hours). This sample represents the wt cells, unstimulated.

source_name: total RNA from unstimulated MEF


title: HaCaT_4hr_Ctrl/ low dose UVB (Y10_C4L4)

scan_protocol: Barcode=12494808  PMTVolts=650 600  Scanner=GenePix 4000B [84942]  LaserPower=3.03 3.59  Temperature=28.4  ScanPower=100 33

treatment_protocol: Cells exposed to UVB 233 J/m2 , and then incubate for 4 hr


title: L1 vs L2_3H

status: Public on Nov 11 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University

description: RNA was isolated from LCM-collected L1 and L2 cells that were derived from five to ten SAMs to generate one biological replication. PicoPure RNA Isolation Kit (Arcturus/Molecular Devices) was used for RNA isolation as per manufacturer’s instruction. In total, six biological replications were used for each microarray platform (see below). Approximately 1 ng of total RNA from each of the L1 and L2 RNA samples was used as starting material for RNA amplification. RiboAmp HS RNA Amplification Kit (Arcturus/Molecular Devices) was used as per manufacturer’s instruction. Each RNA sample yielded 30 to 90 g of amplified RNA (aRNA). Five to ten micrograms of each aRNA sample (the same amount of aRNA was used within each replication) were indirectly labeled with Cy dye and hybridized to the GPL2557, GPL2572, and GPL3538 sample platforms.

hyb_protocol: Microarray slides were prehybridized in 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% SDS, and 0.1 mg/ml bovine serum albumin at 42oC for 45 min, then rinsed with autoclaved, Millipore water, dipped in isopropanol, and dried by centrifugation. Each target was resuspended in 30 l hybridization solution (5X SSC, 0.1% SDS, 0.2 g/l of yeast tRNA, 0.2 g/l of polyadenylic acid, 25% super-pure (99.5%) formamide (Fisher Scientific). Targets hybridized to the same slide were mixed, heated at 95oC for 3 min, collected by centrifugation, applied to a prehybridized microarray slide and covered with a 24 x 60 mm LiferSlip (Erie Scientific Company). Ten microliters of 3X SSC were added to each of the two slots of the hybridization chamber (TeleChem).  The array was then sealed, submerged in a 42oC water bath and incubated for 12 to 18 h. Subsequently, each array was washed in 1X SSC and 0.2% SDS for two minutes, 0.1X SSC and 0.2% SDS for two minutes, and 0.1X SSC for two minutes, followed by a quick rinse in autoclaved, Millipore water. Arrays were then dried via centrifugation. This protocol is also available at our project web site: http://maize-meristems.plantgenomics.iastate.edu/resources/protocols/

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a ScanArray 5000 (Packard). The following setting was used as initial laser power and PMT gain, respectively: 82 and 63 for Cy3 and 77 and 58 for Cy5. These values were slightly adjusted depending on slides to have enough signals for the lowest scans and to have approximately the same amounts of signals between the two channels for the majority of the spots. For each successive scan, laser power and PMT gain were increased by two to three units and three to four units, respectively. Each slide was scanned seven times. Subsequently, three scans for each slide (“low/L”, “medium/M” and “high/H”) were selected for statistical analyses. In details “L” means Low laser power and PMT, “M” means Medium laser power and PMT and “H” means High laser power and PMT.

data_processing: Spots were removed for bad PCR and empty on the microarrays. All data were background corrected and then an R implementation of the lowess normalization method (Dudoit and Fridlyand, 2002, Genome Biol: 3 RESEARCH0036) was used to normalize the two channels for each combination of slide and scan intensity. The data were centered around 0 for each slide. Subsequently, the data from each scan was used to conduct a mixed linear model analysis separately for each of 44,654 spots using a strategy similar to that of Wolfinger et al. (2001, J Comput Biol 8: 625-637). Following the statistical analysis, an additional 6,608 spots were removed from the data set because of concerns regarding the quality of the associated DNA sequences; 384 control spots that contained exogenous DNA were also removed. As a result, this study reports the gene expression patterns of 37,662 “informative” spots.

organism: Zea mays

source_name: L1 of a shoot apical meristem (SAM). L1 is a single cell layered tunica, which will become epidermal cell layers of the matured plant.

label_protocol: Five to ten micrograms of amplified RNA (within each replication the same amount of amplified RNA was used for both L1 and L2) was labeled with Cy3 or Cy5 according to Nakazono et al. (2003, Plant Cell 15: 583-596) with slight modifications. Details of fluorescent target synthesis are available at our project website (http://maize-meristems.plantgenomics.iastate.edu/resources/protocols/). To remove dye-specific effects in the statistical analyses, Cy dyes were swapped between the RNA samples with odd and even numbers of the replications.

growth_protocol:
Maize (Zea mays inbred line B73) kernels were planted ~2 cm deep in plastic pots (8.5 cm x 8.5 cm wide at the top and 7.5 cm deep) filled with SB 300 Universal (Sun Gro Horticulture). Pots were placed in an environmental control room (PGW-40, Percival Scientific). The light intensity at the growth medium surface was kept between 760 to 810 mol/m2s as measured with a quantum meter (Model QMSW, Apogee Instruments). Temperature and light cycles were set at 25C with 15-hour light conditions and at 20C with 9-hour dark conditions. Pots were watered with a solution containing 0.7 mM calcium nitrate. Tissue blocks including SAMs (3 mm x 2 mm x 1 mm) were harvested from 14-day-old seedlings and processed to prepare paraffin sections. This protocol is also available at our project web site:
http://maize-meristems.plantgenomics.iastate.edu/resources/protocols/

extract_protocol: PicoPure RNA Isolation Kit (Arcturus/Molecular Devices) was used to extract total RNA from LCM-collected L1 and L2 cells of maize SAMs according to the manual. The RNA samples were treated with RNase-free DNase I (Stratagene) on column using the DNase Incubation Buffer provided with PALM RNA ExtractionKit (P.A.L.M. Microlaser Technologies) according to the manual of PicoPure RNA Isolation Kit. Approximately 1 ng of Dnase I-treated total RNA from each sample was then amplified with RiboAmp HS RNA Amplification Kit (Arcturus/Molecular Devices).

tag: Inbred line

tag: Developmental stage

value: Vegetative SAMs from 14-day old seedlings

tag: Sample name

source_name: L2 of a SAM. L2 is a corpus, which will become internal part the matured plant.

value: 14-day old seedlings


title: L1 vs L2_5H


title: L1 vs L2_1M


title: L1 vs L2_12H

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a Pro Scan Array HT (PerkinElmer). Each slide was scanned nine times with increasing laser power (44 to 100 with seven intervals) and fixed PMT gain (~60 for Cy5 and ~70 for Cy3) settings. PMT gain settings were slightly adjusted depending on slides to have approximately the same amounts of signals between the two channels for the majority of the spots. Subsequently, three scans for each slide (“low/L”, “medium/M” and “high/H”) were selected for statistical analyses. In details “L” means Low laser power and PMT, “M” means Medium laser power and PMT and “H” means High laser power and PMT.


title: L1 vs L2_6H


title: L1 vs L2_4L


title: L1 vs L2_2H


title: L1 vs L2_5L


title: L1 vs L2_1H


title: L1 vs L2_2M


title: L1 vs L2_10H


title: L1 vs L2_1L


title: L1 vs L2_3L


title: L1 vs L2_5M


title: L1 vs L2_8H


title: L1 vs L2_9H


title: L1 vs L2_6M


title: L1 vs L2_3M


title: L1 vs L2_4M


title: L1 vs L2_6L


title: L1 vs L2-2L


title: L1 vs L2_11H


title: L1 vs L2_4H


title: L1 vs L2_10M


title: L1 vs L2_9M


title: L1 vs L2_12M


title: L1 vs L2_11M


title: L1 vs L2_18H


title: L1 vs L2_7M


title: L1 vs L2_7H


title: L1 vs L2_12L


title: L1 vs L2_8M


title: L1 vs L2_11L


title: L1 vs L2_10L


title: L1 vs L2_14H


title: L1 vs L2_18M


title: L1 vs L2_15H


title: L1 vs L2_9L


title: L1 vs L2_16L


title: L1 vs L2_17H


title: L1 vs L2_13H


title: L1 vs L2_15L


title: L1 vs L2_17M


title: L1 vs L2_16H


title: L1 vs L2_18L


title: L1 vs L2_17L


title: BB050802-Th1

status: Public on Nov 07 2008

city: Detroit

first: wenbo

last: xu

state: MI

address: 3127 Scott Hall ,540 East Canfield

institute: wayne state university

description: Treated with cytokines typical of Th1 cells for 6 hours; recombinant rat IL-2, interferon-g, TNF-a, and g-CSF, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Rat RG-U34A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.  Normalization Factor- 1.0, TGT=500 (all probe sets)

data_processing: All cel files were read and normalized by dChip v1.2, normalized data were analysed by GeneSpring software

organism: Rattus norvegicus

source_name: brain; treated with cytokines typical of Th1 cells

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

growth_protocol: Mixed CNS glial cultures were prepared from neonatal rat brain using a modification of the shakeoff technique (McCarthy and deVellis, J. Cell. Biol. 85:890-902, 1980; Dyer and Benjamins, J. Neurosci. 8:4307-4318, 1988)

extract_protocol: Total RNA was isolated from cells 2-3 times for each time point. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were maintained in defined medium with 2% fetal bovine serum for 6-8 days, then treated with cytokine mixtures representative of Th1, Th2 or monocyte/macrophage cytokines for 6 hours (Lisak, et al., Mult. Scler. 12:149-168, 2006)

tag: CNS mixed glial cultures from 2-3 day old Sprague-Dawley rats


title: BB050802-mono macro

description: Treated with cytokines typical of monocyte/macrophages for 6 hours; recombinant rat IL1a, IL1b, IL-12p40, and TNF-a, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

source_name: brain; treated with cytokines typical of monocyte/macrophages


title: BB050802-control

description: Maintained in defined medium with 2% fetal bovine serum

source_name: brain; control


title: L1 vs L2_15M


title: L1 vs L2_13L


title: L1 vs L2_13M


title: L1 vs L2_7L


title: BB050802-Th2

description: Treated with cytokines typical of Th2 cells for 6 hours; recombinant rat IL-5, IL-10,  G-CSF and porcine TGF-b1, all at 10 ng/ml in defined medium with 2% fetal bovine serum.

source_name: brain; treated with cytokines typical of Th2 cells


title: L1 vs L2_14L


title: WT dendritic cell control4

status: Public on Oct 01 2008

city: New York

first: Stefan

last: Worgall

state: NY

address: 515 East 71st Street

department: Genetic Medicine

institute: Weill Cornell Medical College

description: Gene expression data from WT dendritic cell control without Pseudosmonas aeruginosa infection

hyb_protocol: The labeled cRNA was first hybridized to the test chip and then, when satisfactory, to the MG-U74Av2 GeneChip for 16 hr.

scan_protocol: The GeneChips were processed in the fluidics station under the control of the Microarray Suite software (Affymetrix) to receive the appropriate reagents and washed for detection of hybridized biotinylated cRNA and then manually transferred to the scanner for data acquisition.

data_processing: The image data on each individual microarray chip was scaled to arbitrary target intensity, using the Microarray Suite version 5.0. The raw data was normalized using the GeneSpring GX 7.3.1 software (Agilent Technologies, Santa Clara, CA) by setting measurements <0.01 to 0.01, followed by per-chip normalization to the 50th percentile of the measurements for the array, and per-gene by normalizing to the median measurement for the gene across all the arrays in the data set. Data from probe sets representing genes that failed the Affymetrix detection criterion (labeled “Absent ”or  “A”, or   “Marginal”or  “M”) in over 90% of microarrays were eliminated from further assessment. All further analyses were carried out on the remaining 6,474 genes selected using this criterion.

source_name: WT dendritic cell control

label_protocol: Double stranded cDNA was purified by phenol chloroform extraction and precipitation and the size distribution assessed by agarose gel electrophoresis. This material was then used for synthesis of the biotinylated RNA transcript using the BioArray HighYield reagents (Enzo, New York, NY), purified by the RNeasy kit (Qiagen, Valencia, CA) and fragmented immediately before use.

growth_protocol: Bone marrow-derived DC, generated from mouse bone marrow precursors from the CF mice and their WT littermates, were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100ug/ml) (Invitrogen Corporation, CA), recombinant murine granulocyte-macrophage colony-stimulating factor (GM-CSF, 10ng/ml; R&D System, Minneapolis, Minn) and recombinant murine interleukin-4 (IL-4, 2 ng/ml; R&D System, Minneapolis, Minn).

extract_protocol: Total RNA was extracted from the DC using TRIzol followed by RNeasy (Qiagen, Valencia, CA) to remove residual DNA. First strand cDNA was synthesized using the T7-(dT)24 primer (sequence 5'-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT)24-3', HPLC purified from Oligos Etc., Wilsonville, OR) and converted to double stranded cDNA using Superscript Choice system (Life Technologies). Double stranded cDNA was purified by phenol chloroform extraction and precipitation and the size distribution assessed by agarose gel electrophoresis.

treatment_protocol: The P.aeruginosa strain used was the laboratory strain PAK (kindly provided by A. Prince, Columbia University, NY). Bacteria were grown from frozen stocks in tryptic soy broth (Difco, Detroit, MI) at 37  C to mid-log phase, washed three times with phosphate buffered saline (PBS) pH 7.4 (Invitrogen Corporation, CA), and resuspended in the infection media at the desired concentration as determined by spectrophotometry. DC were incubated for 4 h with 10 CFU of PAK per cell in RPMI 1640 supplemented with 25mM Hepes (Biosource International, MD) and then harvested for RNA extraction.

tag: dendritic cell control from WT mice without Pseudosmonas aeruginosa infection


title: CHC600T-Cy3

status: Public on Nov 01 2008

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description:
For more details on microarray procedures, see Graudens et al. Genome Biol (2006) 7:R19.
Quality Controls of RNA samples: Concentration and purity of the RNA preparation was checked first by UV-spectrophotometry using the Ultrospec3100 pro (GE Healthcare, USA) and 5-mm cuvettes. The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Quality of each total RNA was measured by microfuidic/capillary electrophoresis using RNA 6000 Nano LabChip® kits with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and the results assessed by human inspection and with two-user independent classifiers evaluation as described previously [Imbeaud et al., NAR, 2005]. Only samples that reached the anticipated purity and integrity parameters (RIN >= 6; DegFact <= 13) were introduced within the microarray pipeline process. Quality Controls of IVT transcription: Double stranded cDNA (ds-cDNA) and amplified RNA (aRNA) products were analyzed for purity and concentration by UV spectrophotometry, using the Ultrospec3100 pro and 5-mm cuvettes (GE Healthcare, USA). The absorbance (A) was measured from 200 nm to 350 nm. A235, A260, A280 and A320 were determined and A260:A280 ratios were calculated. Three metrics were considered based on the A260 measurement. First, efficiency of the reverse transcription (ds-cDNA quantity/total RNA quantity) and IVT (aRNA quantity/ds-cDNA quantity) reaction efficiencies were computed. The yield of amplification was quantified (aRNA quantity/mRNA quantity), with the assumption that total RNA contains 2% of mRNA. Finally, an aliquot (1 µl) of the IVT reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol. An mRNA nano assay was run on the chip, and the size of the aRNA was compared with the molecular weight markers. On one hand, ds-cDNA product with unsatisfactory reverse transcription reaction efficiency (RT ≤ 0.4) and purity (A260:A280 ratios ≤ 1.6) were removed from the IVT reaction pipeline. On the other hand, aRNA products with unsatisfactory yield of amplification (amplification < 1,000) and integrity (mean size < 1,000 nucleotides) were removed from subsequent analyses. Only samples that reached the expected purity and integrity parameters described above were introduced within the microarray labeling and hybridization pipelines. Quality Controls of Cy-Dye target labeling: Purity and concentration of each target was checked by UV spectrophotometry, using the Ultrospec3100 pro and 70-mm cuvettes (GE Healthcare). Based on the absorbance measured at 256 nm, 550 nm and 650 nm and considering extinction factor for Cy3- and Cy5-dye respectively of 0.15 and 0.25, the yield of cDNA synthesis and dye incorporation rate were computed. An aliquot (1 µl) of the purified labeling reaction was loaded onto RNA 6000 Nano Labchip® using a Agilent 2100 Bioanalyzer (Agilent Technologies, USA). The chip was prepared according to the manufacturer’s protocol and a mRNA nano assay was run on the chip. The shape and sizes of the Cy-dye targets were compared with the molecular weight markers. Targets with unsatisfactory yield of incorporation (dye incorporation rate < 10; A256:A550 or 650 < 2) and integrity (size < 200 nucleotides) were removed from subsequent analyses. The shape of the Cy-dye probes should present a smeared profile with no clearly identified additional peaks.

hyb_protocol: A mixture of equimolar aliquots (20 pmol) of each labeled target (DATA and REF) was incubated at 95°C for 4 min in the presence of 1.5 µg Oligo-A80 (Eurogentec, USA) and 1 µg human Cot-I DNA® (Invitrogen, USA). Fragmented labeled cDNA was then placed onto 11K_VJF-ARRAY slides in a 30 µl hybridization solution (50% formamide, GE Healthcare, USA) and covered by a coverslip. The slides were subsequently hybridized in a humid hybridization cabinet (GE Healthcare, USA) for 16 hr at 42°C. Then the hybridized slides were washed in 1xSSC, 0.2% SDS for 10 min at 55°C, twice in 0.1x SSC, 0.2% SDS for 10 min at 55°C and twice in 0.1x SSC for 1 min at room temperature.

scan_protocol: After washing and drying, the arrays were scanned at 532 nm (PMT 600 V) and 635 nm (PMT 650 V) using a 3rd generation array scanner (GE Healthcare, USA) and independent grayscale images (8 bits, Tiff) were generated for each pair of samples to be compared.

data_processing: Foreground (raw) data - ARMDens - were local background-subtracted (corners between spots - median value) and normalized using a Lowess (locally weighted linear regression) transformation. The following selection criteria were applied: all spots having a mean signal (after background subtraction) less than that of the background and below that of the negative controls in both Cy3 and Cy5 channels were systematically excluded; the data were also filtered to exclude spots flagged as missing or corrupted in one array. We next calculated the expression ratios (DATA/REF) in all analyses; the provided VALUE corresponds to the log, base 2 ratios. Replicate spots on the array (n=2) are considered separately.

label_protocol: Linear Amplification: One-round of RNA amplification was performed on total RNA as described in [Van Gelder et al., 1990; Eberwine et al., 1992] with some modifications. Amplified RNA products were air dried, resuspended in 10µl RNase-free water and then stored at -80°C; 1 µl of the reaction (1/10) was stored to perform quality assessment (Purity, size, yield). Labeling protocol: Targets were synthesized using 1.0 µg amplified RNA, 1 µl anchored oligo-(dT) and 2 µl random nonamers (GE Healthcare, USA) for priming (total volume 11 µl, 10 min, 70°C) in presence of 1 µl spike RNA from Lucidea™ Microarray Human Scorecard v1.1 (GE Healthcare, USA). cDNA products were generated using 1 mM of either Cy3- or Cy5-dCTP (GE Healthcare, USA) and 200 units MMLV RNase H- reverse transcriptase (Promega, USA) at 42°C for 2 to 3 hr. After reverse transcription, the RNA was degraded by adding 2 µl of 2.5 N NaOH and incubating at 37°C for 10 min. The reaction was then neutralized by adding 10 µl of 2 M MOPS (free acid) and Cy3- and Cy5-containing targets were purified twice onto QIAquick PCR columns (Qiagen, Germany) according the manufacturer’s instructions with minor modifications. The Cy-dye targets were controlled during quality assessment (purity, size, yield). Adjusted Cy-dye target yield was calculated to reflect carryover of unlabeled aRNA. Thus, certified targets were air-dried in a vacuum centrifuge for 1.5 hr and resuspended in RNase-free water to reach a 10 pmol/µl concentration.

extract_protocol: Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.

tag: Sample

tag: Gender

value: female

tag: Age at onset

value: 46 years

tag: Disease

value: focal nodular hyperplasia

tag: Tissue

value: tumor liver

extract_protocol: see Provider description

tag: Universal Reference RNA


title: L1 vs L2_16M


title: CHC595T-Cy3

value: 47 years


title: L1 vs L2_14M


title: CHC566T-Cy3

value: 53 years


title: CHC565T-Cy3

value: 44 years


title: CHC600T-Cy5


title: CHC597T-Cy5


title: CHC607T-Cy5

value: 49 years


title: CHC607T-Cy3


title: CHC597T-Cy3


title: WT dendritic cell control3


title: CHC566T-Cy5


title: CHC595T-Cy5


title: CHC561T-Cy5

value: 34 years


title: CHC561T-Cy3


title: CHC565T-Cy5


title: CF dendritic cell control3

description: Gene expression data from CF dendritic cell control without Pseudosmonas aeruginosa infection

source_name: CF dendritic cell control

tag: dendritic cell control from CF mice without Pseudosmonas aeruginosa infection


title: Kidney 1397_2

status: Public on Jun 01 2008

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from five control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: Strain

value: Male

value: 15 weeks

tag: Mouse ID

source_name: Kdn wt pool

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (singel individual mutant mice) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

value: wt (Swiss strain SWR/Ola Hsd)


title: Kidney 1414_1

tag: Age


title: Kidney 1414_1_cf


title: Kidney 1414_2


title: CF dendritic cell control4


title: Kidney 1414_2_cf


title: Kidney 1397_2_cf


title: Kidney 1380_2


title: Kidney 1421_2


title: Kidney 1397_1_cf


title: Kidney 1421_1_cf


title: Kidney 1380_1_cf


title: Kidney 1421_2_cf


title: Kidney 1380_2_cf


title: Kidney 1380_1


title: Kidney 1421_1


title: TM_TA_1mg/ml_rep2

status: Public on May 01 2008

city: Boston

first: Bao Jian

last: Fan

state: MA

address: MEEI, 243 Charles Street

department: Ophthalmology

institute: Harvard Medical School

description: The second slide for TA-1 experiments.

hyb_protocol: 1. For dual color hybridization, combine Cy3- and Cy5-labelled cDNAs into one tube. Dry down the cDNA solution using MicroconYM-30. 1) Insert Microcon sample reservoir into vial. 2) Spin-rinse devices with 25 ul deionized water at 3000 rpm for 2 min. 3) Pipeette 120 ul combined labeled cDNA into sample reservoir, without touching the membrane with the pipette tip. Seal with attached cap. 4) Place assembled device into the centrifuge rotor, align the cap strap toward the center of the rotor. Spin at 8,000 rpm for 8 min. 5) Remove assembly from centrifuge. Separate vial from sample reservoir. 6) Place sample reservoir upside down in a new vial, spin at 3,300 rpm for 3 min. 2. Measure the obtained cDNA volume ( ~ 15 ul). 3. Denature the cDNA by heating at 95 C for 2 min. Leave the tube cap open to further dry the solution to 10.5 ul. 4. Cool the cDNA solution on ice for 30 sec. 5. Add 1.75 ul dA80 (1 mg/ml) and mix well. 6. Incubate the mixure at 75 C for 45 min. 7. Add 8.75 ul microarray hybridization buffer and 14 ul 100% Formamide. Mix well and spin for 15 sec in a microcentrifuge to collect all reaction components at the bottom of the tube. cDNA solution	10.5 ul (30%) dA80 (1 mg/ml)	1.75 ul (5%) 4x Hybridization buffer	8.75 ul (25%) 100% Formamide	14 ul	(40%) Total volume	35 ul	(100%) 8. Pipette the hybridization mixture onto a microarray slide. Carefully place the coverslip on the array. Avoid the formation of air bubbles under the coverslip. 9. Hybridize at 42 C for 16 hours in a humid hybridization chamber. Protect the slides form light during this and subsequent steps.

scan_protocol: Scan the slides with a microarray scanner suitable for detecting Cy3 and Cy5 fluorescence. 1. Lunch ScanArray software, open Lamp1 and Lamp 3, allow warming for 15 min. 2. Quick scan to find out suitable settings for laser power and gain (usually both 80%). 3. Scan with the highest resolution at 5 um. 4. Save both Cy3 and Cy5 images in a TIFF format. 5. Lunch QuantArray software, open Cy3 and Cy5 images to check the quality and process images.

data_processing: Print-tip-loess normalization method and quantile normalization method

label_protocol:
1. Labelling first-strand cDNA with amino allyl-dUTP (in 200 ul tube):
1) Set a thermocycler at 70 C and another at 42 C.
2) Add the following components on ice (Primer annealing):
RNA (25 ug)
Anchored oligo (dT) (3 ul)
Total volume (11 ul)
3) Mix gently by pipetting up and down.
4) Incubate reactions at 70 C for 5 min.
5) Cool reactions at room temperature for 10 min to allow the primers and the mRNA template to anneal.
6) Spin down reactions for 15 sec in a microcentrifuge.
7) Place reactions on ice and add the following components to each, adding the enzyme last. (Extension reaction)
5x CyScript buffer	(4 ul)
0.1 M DTT (2 ul)
Nucleotide mix (1 ul)
AA-dUTP	(1 ul)
Cyscript reverse transcriptase (1 ul)
Total volume (20 ul)
8) Mix by very gently pipetting and spin for 15 sec (Vigorous pipetting will denature the enzyme).
9) Incubate the reactions at 42 C for 90 min.
10) Store the aminoallyl modified cDNA on ice for immediate purification or place at -20 C frost freezer for storage. (Can stop)
2. Purification of cDNA with Cyscribe GFX Purification Kit:
1) Adjust a waterbath to 37 C.
2) Add 2 ul 2.5 M NaOH to each cDNA reaction. (Degradation of mRNA)
3) Mix and spin for 15 sec.
4) Incubate reactions at 37 C for 15 min.
5) Add 10 ul 2 M HEPES free acid to each reaction (Neutralize the reaction).
6) Mix by vortexing and spin for 15 sec.
7) The cDNA reactions are now ready for purification or can be stored at -20 C. (can stop)
8) Add 500 ul capture buffer to each GFX column. (Purification of amilnoallyl-labelled cDNA with CyScribe GFX Purification Kit)
9) Transfer the unpurified aminoallyl-labelled cDNA products (32 ul) into each GFX column, mix the cDNA by gently pipetting up and down 5 times.
10) Centrifuge each column immediately at 13000 rpm for 30 sec.
11) Remove the GFX column and discard the liquid at the bottom of each collection tube. Return each GFX column into the used collection tube.
12) Add 600 ul of 80% ethanol to each column and centrifuge at 13,000 rpm for 30 sec.
13) Remove the GFX column and discard the collected liquid. Repeat the 80% ethanol wash for a total of 3 washes. Discard the liquid and place each column back in the used collection tube.
14) Centrifuge at 13,000 rpm for an additional 10 sec to remove all traces of 80% ethanol in the tip of the column. Discard the collection tube.
15) Transfer each GFX column to a fresh 1.5 ml microcentrifuge tube and add 60 ul of 0.1 M NaHCO3 directly to the top of the glass fiber matrix in each GFX column (Make sure completely covering the membrane).
16) Incubate the GFX column at room temperature for 1-5 min. Centrifuge at 13,000 rpm for 1 min to collect the purified aminoallyl-labelled cDNA.
17) Repeat steps 15 and 16 may increase the yield by 10%.
18) Proceed immediately to the coupling reaction procedure.
3. Post-labelling of amino allyl-modified cDNA with CyDye:
1) Add the purified aminoallyl cDNA directly into one aliquot of CyDye NHS ester in a 1.5 ml tube. Resuspend the NHS ester completely by pipetting several times. Centrifuge at 13,000 rpm for 1 min to collect the liquid at the bottom of the tube.
2) Incubate at room temperature in the dark for 60-90 min.
3) Add 15 ul of 4 M hydroxylamine to each coupling reaction to stop the reaction.
4) Pipette up and down several times to mix the components, and then incubate at room temperature in the dark for 15 min.
5) Purify the CyDye-labelled cDNA immediately according to the following protocol.
4. Purification of CyDye-labelled cDNA:
1) Add 40 ml of absolute ethanol to the wash buffer bottle prior to starting the protocol. Mix well.
2) Add 500 ul of capture buffer to each GFX column.
3) Transfer the unpurified labeled cDNA products into each GFX column, mix the cDNA by gently pipetting up and down 5 times.
4) Centrifue each column immediately at 13,000 rpm for 30 sec.
5) Remove the GFX column and discard the liquid. Return each GFX column to the used collection tube.
6) Add 600 ul of wash buffer to each column and centrifuge at 13,000 rpm for 30 sec.
7) Remove the GFX column and discard the collected liquid. Repeat the wash buffer wash for a total of 3 washes. After the final wash, discard the liquid and place each column back in the used collection tube.
8) Centrifuge each column at 13,000 rpm for an additional 10 sec to remove all wash buffer in the tip of the column. Discard the collection tube.
9) Transfer each GFX column to a fresh 1.5ml microcentrifuge tube , add 60 ul of prewarmed (65 C) elution buffer directly to the top of the glass fiber matrix in each GFX column (Make sure completely covering the membrane).
10) Incubate the GFX column at room temperature for 1-5 min. Centrifuge at 13,000 rpm for 1 min to collect the purified labeled cDNA.
11) Repeat steps 9 and 10 may increase the yield by 10%.
12) Measure the purified cDNA in a spectrophotometer at 260nm (Cy5 at 649nm and  Cy3 dye at 550nm) to calculate the yield of purified cDNA.
Incorporation of CyDye
                = pmol of CyDye in sample/ ug of nucleic acid in sample
Typical yield of labeled cDNA with the recommended purification systems varies from 40 – 100 pmol of Cy3 or Cy5 incorporated into probe using 0.5 ug control mRNA as template.
Frequency of Incorporation (FOI)
= pmol of Dye incorporated x (324.5/ng of cDNA probe).
Probes with FOI values in the range of 20-50 generate strong signals upon hybridization. FOI value <10 will generate weak signals from poor incorporation, whereas, at FOI >70, probes may also produce reduced hybridization signals from possible quenching between CyDyes fluors.

extract_protocol:
1. Disrupt cells by Buffer RLT:
Add the appropriate volume of Buffer RLT. Vortex or pipet to mix.
2. Homogenize the sample:
Pipet the lysate directly on to a QIAshredder spin column, centrifuge for 2 min at maximum speed (13,200 rpm).
3. Add 1 volume (350 ul or 600 ul) of 70% ethanol to the homogenized lysate, and mix well by pipetting. Do not centrifuge.
4. Apply up to 700 ul of the sample, including any precipitate that may have formed, to an RNeasy mini column placed in a 2-ml collection tube. Close the tube gently, and centrifuge for 15 sec at 10,000 rpm. Discard the flow-through (not compatible with bleach). If any, add remaining sample, repeat this step.
5. Add 700 ul Buffer RW1 to the RNeasy column. Close the tube gently, and centrifuge for 15s at 10,000 rpm. Discard the flow-through and collection tube.
6. Transfer the RNeasy column into a new 2-ml collection tube (supplied). Pipet 500 ul Buffer RPE onto the RNeasy column. Close the tube gently, and centrifuge for 15 sec at 10,000 rpm. Discard the flow-through.
7. Add another 500 ul Buffer RPE to the RNeasy column. Close the tube gently, and centrifuge for 2 min at 10,000 rpm to dry the RNeasy silica-gel membrane.
8. To elute, transfer the RNeasy column to a new 1.5-ml collection tube (supplied). Pipet 30 - 50 ul RNase-free water directly onto the RNeasy silica-gel membrane. Close the tube gently, centrifuge for 1 min at 10,000 rpm to elute.
9. If the expected RNA yield is > 30 ug, repeat the step 9 with a second volume of RNase-free water. Elute into the same collection tube.

tag: Human trabecular meshwork (TM) cells treated with 0.025% benzyl alcohol (BA) for 12 hours.

tag: Human trabecular meshwork (TM) cells treated with 1 mg/ml triamcinolone acetonide (TA) for 12 hours.


title: TM_TA_0.1mg/ml_rep2

description: The second slide for TA-0.1 experiments.

tag: Human trabecular meshwork (TM) cells treated with 0.0025% benzyl alcohol (BA) for 12 hours.

tag: Human trabecular meshwork (TM) cells treated with 0.1 mg/ml triamcinolone acetonide (TA) for 12 hours.


title: TM_DEX_rep2

description: The second slide for DEX experiments.

tag: Human trabecular meshwork (TM) cells treated with 1.1 uM benzyl alcohol (BA) for 7 days.

tag: Human trabecular meshwork (TM) cells treated with 100 nM dexamethasone (DEX) for 7 days.


title: TM_TA_0.1mg/ml_rep1

description: The first slide for TA-0.1 experiments.

tag: Human trabecular meshwork (TM) cell lines treated with 0.0025% benzyl alcohol (BA) for 12 hours.

tag: Human trabecular meshwork (TM) cell lines treated with 0.1 mg/ml triamcinolone acetonide (TA) for 12 hours.


title: TM_TA_1mg/ml_rep3

description: The thrid slide for TA-1 experiments.


title: TM_TA_1mg/ml_rep1

description: The first slide for TA-1 experiments.


title: TM_DEX_rep3

description: The third slide for DEX experiments.


title: TM_TA_0.1mg/ml_rep3

description: The third slide for TA-0.1 experiments.

tag: Human trabecular meshwork (TM) cells treated with 0.0025%benzyl alcohol (BA) for 12 hours.


title: L1 vs L2_8L

tag: Inbred line

tag: Developmental stage

tag: Sample name


title: TM_DEX_rep1

description: The first slide for DEX experiments.


title: bh20061215m430v2_U_26_PKBa_-_-_R_MEF_24h_1

status: Public on Apr 04 2008

city: Basel

first: Lana

last: Bozulic

address: Maulbeerstr 66

country: Switzerland

institute: FMI

description: this sample is a knockout/reconstituted PKB alpha, treated, 24hrs

hyb_protocol: 10ug of fragmented cRNA was hybridised to Affymetrix MOE430v2 GeneChips as per manufacturer's instructions.

scan_protocol: The chips were scanned in Affymetrix 7G scanner using an automated slide carosel.

data_processing: Transcript expression values were estimated using the GC_RMA function provided by Refiner 3.1 (Genedata, Basel) and statistical analysis was performed using Analyst 3.1 (Genedata, Basel). Genedata's implementation of GC-RMA includes the generation of an Affymetrix detection p-value. A gene was considered to be reliably detected if it had a detection p-value ≤ 0.04 (Affymetrix default, marginal calls ignored) in at least 2/3 of the biological replicates of a condition. A power analysis of our experimental design showed we could expect to have a power of 0.8 to distinguish samples differing by 1.5-fold with a normal standard deviation less than 0.461 and it could resolve differences of 2-fold (power of 0.8) when the normalized standard deviation was less than 0.613.

label: Biotin

source_name: MEF

label_protocol: The Affymetrix labelling protocol was used to label the material as per manufacturer's instructions.

growth_protocol: MEF are grown in DMEM supplemented with 10%FCS, NEAA and L-glutamine. Cells are passaged every 3-4 days by splitting 1:5-1:10.

extract_protocol: TRIZOL RNA extraction protocol, following the manufacturer's instructions.

treatment_protocol: MEF were cultured for 24 hrs in standard conditions, before being gamma-irradiated with 10Gy. 4hrs or 24hrs after irradiation RNA was isolated using TRIZOL following manufacturer's instructions.

tag: genotypes

value: wt PKBalpha, ko PKBalpha, ko/rescued PKBalpha

tag: gender

tag: passage

tag: gamma-IR

tag: recovery after IR

value: 4hrs, 24hrs


title: bh20061215m430v2_U_18_PKBa_-_-_MEF_24h_2

description: this sample is a knockout, treated, 24hrs


title: bh20061215m430v2_U_23_PKBa_-_-_R_MEF_4h_1

description: this sample is a knockout/reconstituted PKB alpha, treated, 4hrs


title: bh20061215m430v2_U_21_PKBa_-_-_R_MEF_-_2

description: this sample is a knockout/reconstituted PKB alpha, untreated


title: bh20061215m430v2_U_22_PKBa_-_-_R_MEF_4h_0


title: bh20061215m430v2_U_13_PKBa_-_-_MEF_4h_0

description: this sample is a knockout, treated, 4hrs


title: bh20061215m430v2_U_15_PKBa_-_-_MEF_4h_2


title: bh20061215m430v2_U_14_PKBa_-_-_MEF_4h_1


title: bh20061215m430v2_U_27_PKBa_-_-_R_MEF_24h_2


title: bh20061215m430v2_U_19_PKBa_-_-_R_MEF_-_0


title: bh20061215m430v2_U_11_PKBa_-_-_MEF_-_1

description: this sample is a knockout, untreated control

source_name: mouse embryonic fibroblasts


title: bh20061215m430v2_U_24_PKBa_-_-_R_MEF_4h_2


title: bh20061215m430v2_U_17_PKBa_-_-_MEF_24h_1


title: bh20061215m430v2_U_12_PKBa_-_-_MEF_-_2


title: bh20061215m430v2_U_20_PKBa_-_-_R_MEF_-_1


title: Kidney 1397_1

tag: Strain

tag: Gender

tag: Age

tag: Mouse ID


title: bh20061215m430v2_U_07_PKBa-MEF-WT_24h_0

description: this sample is a wild-type, untreated control.


title: bh20061215m430v2_U_05_PKBa-MEF-WT_4h_1


title: bh20061215m430v2_U_25_PKBa_-_-_R_MEF_24h_0


title: bh20061215m430v2_U_08_PKBa-MEF-WT_24h_1


title: bh20061215m430v2_U_10_PKBa_-_-_MEF_-_0


title: bh20061215m430v2_U_06_PKBa-MEF-WT_4h_2


title: bh20061215m430v2_U_03_PKBa-MEF-WT_-_2


title: bh20061215m430v2_U_16_PKBa_-_-_MEF_24h_0


title: bh20061215m430v2_U_09_PKBa-MEF-WT_24h_2


title: 48h - replicate 2

status: Public on Mar 30 2008

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Biological replicate 2 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 48h.

hyb_protocol: Labeled RNA from infected and uninfected cells was hybridized using the Agilent Technologies (Santa Clara, CA   95051, United States) human 1A oligo microarrays (V2), containing over 22000 60-mer probes, according to the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: The microarrays were scanned with a GenePix 4200 autoloader (Axon instruments) scanner. Segmentation, computation of the absolute foreground intensities, and estimation of local background from the scanned images was performed with the Axon GenePix Pro v. 6.0 software

data_processing: The data were then imported into the R package BioConductor. Background correction and quality assessment of the dataset were carried out using the BioConductor package limma. The background-corrected log ratios were then normalized using the VSN method implemented in the BioConductor package vsn.

source_name: Total RNA from human epithelial cell line after 48h infection with Chlamydia penumodiae labeled with Cyanine-3 (green).

label_protocol: Precipitated RNA was dissolved in 25 microl 1 x TE buffer and labeled with Agilent Fluorescent Direct Labeling Kit according to the manufacturer’s instructions.

growth_protocol: Human epithelial cells (HL) were cultured in RPMI 1640 medium supplemented with 7.5% fetal Bovine serum (FBS), (BioWhittaker Europe, Verviers, Belgium), 2 mM glutamine, and 20  µg/ml streptomycin (HL medium) in a 5% CO2 atmosphere at 37°C.

extract_protocol: Total RNA was extracted with RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: HL cells were grown in 6-well plates (Cellstar® TC-Plate 6 Well, (# 657 160) Greiner, Frickenhausen, Germany). The HL cells in confluent wells (average 3.5 x 106 cells) were infected with 7,0 x 106 purified C. pneumoniae EBs using centrifugation at 550 x g, 60 min RT. After infection, the cells were washed once with phosphate-buffered saline (PBS), fresh culture medium was added to the wells, and the plates were placed into a 5% CO2 atmosphere at 37°C for different periods.

tag: Human epithelial cell line (HL)

source_name: Total RNA from human epithelial cell line grown for 48h from the beginning of the experiment labeled with Cyanine-5 (red).

treatment_protocol: Uninfected control cells


title: 72h - replicate 2

description: Biological replicate 2 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 72h.

source_name: Total RNA from human epithelial cell line after 72h infection with Chlamydia penumodiae labeled with Cyanine-3 (green).

source_name: Total RNA from human epithelial cell line grown for 72h from the beginning of the experiment labeled with Cyanine-5 (red).


title: 24h - replicate 2

description: Biological replicate 2 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 24h.

source_name: Total RNA from human epithelial cell line after 24h infection with Chlamydia penumodiae labeled with Cyanine-3 (green).

source_name: Total RNA from human epithelial cell line grown for 24h from the beginning of the experiment labeled with Cyanine-5 (red).


title: 72h - replicate 1

description: Biological replicate 1 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 72h.


title: bh20061215m430v2_U_02_PKBa-MEF-WT_-_1

source_name: Mouse embryonic fibroblasts


title: bh20061215m430v2_U_04_PKBa-MEF-WT_4h_0


title: bh20061215m430v2_U_01_PKBa-MEF-WT_-_0


title: 12h - replicate 2

description: Biological replicate 2 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 12h.

source_name: Total RNA from human epithelial cell line after 12h infection with Chlamydia penumodiae labeled with Cyanine-3 (green).

source_name: Total RNA from human epithelial cell line grown for 12h from the beginning of the experiment labeled with Cyanine-5 (red).


title: p53_01 JOS 181.1.36 ds

status: Public on Feb 01 2008

type: genomic

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

country: Netherlands

institute: Genentech

description: Primary mouse mammary tumor aCGH analysis. Platform is the NKI 6k BAC array. Goal is to discover recurrent genomic aberrations in several similar mammary tumors. This is the dye-swap experiment.

hyb_protocol: The DNA pellet was redissolved with 60 µL of hybridization buffer (50% formamide, 10% dextran  sulfate, 0.1% Tween20, 2xSSC, and 10mM Tris-HCl, pH7.4) and 600µg yeast t-RNA (Invitrogen). Probe DNA was denatured for 10 Min at 70°C and incubated for 1h at 37°C prior to applicationon the prehybridized BAC microarray slides. Array slides were prehybridized for 1 h at 37°C with 90 µL of denatured hybridization buffer containing 540µg herring sperm DNA and 90µg of mouse C0t-1 DNA. Hybridization was performed without cover slips, in a humid chamber. In brief, a rubber cement ringwas applied around the microarray. After application of the hybridization solution on the array, slides were incubated in a light tight humid chamber on an orbital shaker (400 rpm) for 48 h at 37°C. Slides were washed serially in solution 1 (PBS containing 0.05% Tween 20) for 10 min at room temperature, in solution 2 (50% formamide, 2X SSC) at 42°C for 30 min, and in solution 1 at room temperature for 10 min. Finally, slides were spin-dried for 3 min at 1000 rpm.

scan_protocol: Agilent Scanner G2505B, Agilent Technologies

data_processing: Fluorescent intensities were normalized per block to the median raw Cy5:Cy3 ratio. All experiments were performed in fluor-reversed pairs of two-color hybridizations. All values were converted to log2 values to weight gains and losses equally. Weighted averages, errors, and confidence levels were computed from quadruple measurements obtained from duplicate spots on arrays from both hybridizations, accordingto the Rosetta Error Model (Hughes et al. 2000, http://download.cell.com/supplementarydata/cell/102/1/109/DC1/ErModlv2.htm). In this model, errors in the measurements of Cy5:Cy3 ratio are estimated usingcontrol experiments where two identical DNA samples are independently labeled with Cy3 and Cy5, respectively. The resulting distribution of the log2-transformed ratios provides a model for the error distribution. This distribution widens with decreasingintensity, and the error model is designed to fit this intensity dependence closely.

molecule: genomic DNA

source_name: mouse 01JOS181

label_protocol: Digested genomic DNA was labeled with Cy3- or Cy5-dCTP by random priming(Bioprime Labeling Kit, Invitrogen). Briefly, 1 µg of DNA was denatured in random primer solution. To this mixture was added 15 µL 10X dNTP mix (0.5 mM dCTP, 2 mM dATP, 2 mM dTTP, and 2 mM dGTP), 6 µL Cy3- or Cy5-dCTP (1 mM, NEN), 3 µL Klenow enzyme and distilled water to a final volume of 150 µL. After 37°C overnight incubation, labeled genomic DNA was purified through Sephadex G-50 columns and precipitated together with 135 µg of mouse C0t-1 DNA (Invitrogen).

growth_protocol: described in Jonkers et al, Nature Genetics, 2001, vol. 29, 418-425, PMID: 11694875, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=11694875

extract_protocol: Genomic DNA was extracted and purified by standard methods (Sambrook and Russel 2001; Molecular Cloning, a laboratory handbook). Test DNA and control DNA were digested with HaeIII for 2 h.

value: K14cre; p53F/F

tag: Tissue

value: Spleen

label_protocol: described in Chung et al., Genome Research, 2004, vol.14, 188-196, PMID: 14707179, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=14707179

value: p53 deficient mammary epithelial tumor


title: p53_01 JOS 80.2.36 ds

source_name: mouse 01JOS80

treatment_protocol: described in Jonkers et al, Nature Genetics, 2001, vol. 29, 418-425, PMID: 11694875, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=11694875

value: female

extract_protocol: described in Chung et al., Genome Research, 2004, vol.14, 188-196, PMID: 14707179, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=14707179


title: 24h - replicate 1

description: Biological replicate 1 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 24h.


title: p53_03 JOS 155.2.36 ds

source_name: mouse 03JOS155


title: p53_01 JOS 169.36 ds

source_name: mouse 01JOS169


title: 48h - replicate 1

description: Biological replicate 1 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 48h.


title: p53_01 JOS 66.36 ds

source_name: mouse 01JOS66


title: p53_03 JOS 154.1.36 ds

source_name: mouse 03JOS154


title: p53_03 JOS 29.36 ds

source_name: mouse 03JOS29


title: p53_01 JOS 181.2.36 ds


title: P53_01 JOS 80.1.36 ds


title: 12h - replicate 1

description: Biological replicate 1 of 2. Human epithelial cell lines infected with Chlamydia pneumoniae and control grown for 12h.


title: p53_03 JOS 154.2.36 ds


title: p53_01 JOS 65.36 ds

source_name: mouse 01JOS65


title: p53_01 JOS 127.1.36 ds

source_name: mouse 01JOS127


title: p53_03 JOS 154.3.36 ds


title: p53_03 JOS 105.36 ds

source_name: mouse 03JOS105


title: p53_03 JOS 155.1.36 ds


title: p53_03 JOS 03.36 ds

source_name: mouse 03JOS03


title: p53_01 JOS 165.36 ds

source_name: mouse 01JOS165


title: p53_03 JOS 154.1.36

description: Primary mouse mammary tumor aCGH analysis. Platform is the NKI 6k BAC array. Goal is to discover recurrent genomic aberrations in several similar mammary tumors.


title: p53_01 JOS 181.1.36


title: p53_03 JOS 155.2.36


title: p53_01 JOS 80.2.36


title: p53_01 JOS 181.2.36


title: p53_01 JOS 169.36


title: P53_01 JOS 80.1.36


title: p53_03 JOS 154.2.36


title: p53_03 JOS 29.36


title: p53_01 JOS 66.36


title: p53_03 JOS 105.36


title: p53_03 JOS 03.36


title: p53_01 JOS 165.36


title: p53_02 JOS 92.36 ds

source_name: mouse 02JOS92


title: p53_03 JOS 14.36

source_name: mouse 03JOS14


title: p53_01 JOS 127.1.36


title: p53_03 JOS 155.1.36


title: p53_01 JOS 65.36


title: p53_03 JOS 154.3.36


title: Control sample, Sample_ID = 125b, DNA

status: Public on Jan 05 2008

city: Baltimore

first: Aik Choon

last: Tan

state: MD

address: 1650 Orleans Street, RM 1M86

department: The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

institute: Johns Hopkins University

hyb_protocol: Array image processing and signal extraction were done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)

scan_protocol: Arrays were imaged using Illumina BeadArray Reader scanner (Illumina).

data_processing: Image analysis and data extraction software were as described previously (Oliphant, A., Barker, D.L., Stuelpnagel, J.R., and Chee, M.S. 2002. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 32: S56-S61.; Galinsky, V.L. 2003. Automatic registration of microarray images II: Hexagonal grid. Bioinformatics 19: 1832-1836.). Each sequence type is represented by an average of thirty beads on the array. Bead signals are computed with weighted averages of pixel intensities, and local background is subtracted. Sequence-type signal is calculated by averaging corresponding bead signals with outliers removed (using median absolute deviation).

source_name: genomic DNA from ASO1

label_protocol: GoldenGate® assay was done as described previously (Fan JB et al, Illumina Universal bead arrays, 2006)

extract_protocol: RNA was extracted from four to five 5-um sections using an RNA extraction kit (Roche High Pure RNA Paraffin kit), yielding 0.5 - 3 ug of total RNA.

tag: CEPH family

value: CEPH 1423

tag: CEPH pedigree

value: MOTHER

source_name: genomic DNA from ASO2


title: Control sample, Sample_ID = 126a, DNA

value: CEPH 1349

value: SON


title: Control sample, Sample_ID = 123b, DNA

value: CEPH 1421


title: Control sample, Sample_ID = 125a, DNA


title: Control sample, Sample_ID = 124a, DNA

value: CEPH 1418

value: DAUGHTER


title: Control sample, Sample_ID = 124b, DNA


title: Control sample, Sample_ID = 123a, DNA


title: p53_02 JOS 92.36


title: Control sample, Sample_ID = 122b, DNA

value: CEPH 1424


title: Control sample, Sample_ID = 121b, DNA

value: FATHER


title: Control sample, Sample_ID = 120b, DNA


title: Control sample, Sample_ID = 120a, DNA


title: Control sample, Sample_ID = 119a, DNA

value: CEPH 1413


title: Control sample, Sample_ID = 117a, DNA


title: Control sample, Sample_ID = 118a, DNA

value: CEPH 1420


title: Control sample, Sample_ID = 117b, DNA


title: Control sample, Sample_ID = 116b, DNA


title: Control sample, Sample_ID = 118b, DNA


title: Control sample, Sample_ID = 119b, DNA


title: Control sample, Sample_ID = 116a, DNA


title: Control sample, Sample_ID = 113b, DNA


title: Control sample, Sample_ID = 122a, DNA


title: Control sample, Sample_ID = 114a, DNA

value: CEPH 1375


title: Pancreatic cancer sample, Sample_ID = 11b, DNA


title: Pancreatic cancer sample, Sample_ID = 11a, DNA


title: Control sample, Sample_ID = 113a, DNA


title: Control sample, Sample_ID = 112b, DNA

value: CEPH 1416


title: Control sample, Sample_ID = 110b, DNA


title: Control sample, Sample_ID = 112a, DNA


title: Control sample, Sample_ID = 121a, DNA


title: Control sample, Sample_ID = 111b, DNA


title: Control sample, Sample_ID = 110a, DNA


title: Control sample, Sample_ID = 111a, DNA


title: Control sample, Sample_ID = 114b, DNA


title: Pancreatic cancer sample, Sample_ID = 10b, DNA


title: Pancreatic cancer sample, Sample_ID = 10a, DNA


title: Control sample, Sample_ID = 154b, DNA

value: CEPH 1346


title: Control sample, Sample_ID = 155a, DNA

value: CEPH 1345


title: Control sample, Sample_ID = 153b, DNA

value: CEPH 1340


title: Control sample, Sample_ID = 154a, DNA


title: Pancreatic cancer sample, Sample_ID = 109, DNA


title: Pancreatic cancer sample, Sample_ID = 108, DNA


title: Pancreatic cancer sample, Sample_ID = 106, DNA


title: Control sample, Sample_ID = 153a, DNA


title: Pancreatic cancer sample, Sample_ID = 107, DNA


title: Control sample, Sample_ID = 151a, DNA


title: Control sample, Sample_ID = 151b, DNA


title: Control sample, Sample_ID = 152a, DNA


title: Control sample, Sample_ID = 152b, DNA


title: Control sample, Sample_ID = 150b, DNA

value: CEPH 1344


title: Control sample, Sample_ID = 150a, DNA


title: p53_03 JOS 14.36 ds

value: K14cre; p53F/F

value: female

value: Spleen

value: p53 deficient mammary epithelial tumor


title: Pancreatic cancer sample, Sample_ID = 104, DNA


title: Pancreatic cancer sample, Sample_ID = 15, DNA


title: Pancreatic cancer sample, Sample_ID = 14b, DNA


title: Pancreatic cancer sample, Sample_ID = 14a, DNA


title: Pancreatic cancer sample, Sample_ID = 105, DNA


title: Pancreatic cancer sample, Sample_ID = 103, DNA


title: Pancreatic cancer sample, Sample_ID = 102, DNA


title: Control sample, Sample_ID = 149b, DNA


title: Pancreatic cancer sample, Sample_ID = 101, DNA


title: Control sample, Sample_ID = 149a, DNA


title: Pancreatic cancer sample, Sample_ID = 100, DNA


title: Control sample, Sample_ID = 148a, DNA


title: Control sample, Sample_ID = 148b, DNA


title: Pancreatic cancer sample, Sample_ID = 99a, RNA

source_name: RNA from ASO1

source_name: RNA from ASO2


title: Pancreatic cancer sample, Sample_ID = 9b, RNA


title: Control sample, Sample_ID = 147b, DNA

value: CEPH 1350


title: Pancreatic cancer sample, Sample_ID = 98b, RNA


title: Control sample, Sample_ID = 146b, DNA

value: MOTHER


title: Pancreatic cancer sample, Sample_ID = 9a, RNA


title: Pancreatic cancer sample, Sample_ID = 98a, RNA


title: Pancreatic cancer sample, Sample_ID = 99b, RNA


title: Pancreatic cancer sample, Sample_ID = 97b, RNA


title: Control sample, Sample_ID = 146a, DNA


title: Control sample, Sample_ID = 145b, DNA

value: CEPH 1362


title: Control sample, Sample_ID = 145a, DNA


title: Pancreatic cancer sample, Sample_ID = 96b, RNA


title: Pancreatic cancer sample, Sample_ID = 96a, RNA


title: Pancreatic cancer sample, Sample_ID = 95b, RNA


title: Pancreatic cancer sample, Sample_ID = 97a, RNA


title: Control sample, Sample_ID = 144a, DNA

value: SON


title: Pancreatic cancer sample, Sample_ID = 94b, RNA


title: Control sample, Sample_ID = 143a, DNA

value: FATHER


title: Pancreatic cancer sample, Sample_ID = 95a, RNA


title: Control sample, Sample_ID = 142a, DNA

value: CEPH 1341


title: Control sample, Sample_ID = 143b, DNA


title: Pancreatic cancer sample, Sample_ID = 94a, RNA


title: Control sample, Sample_ID = 142b, DNA


title: Pancreatic cancer sample, Sample_ID = 13a, DNA


title: Control sample, Sample_ID = 141b, DNA


title: Pancreatic cancer sample, Sample_ID = 93a, RNA


title: Pancreatic cancer sample, Sample_ID = 92b, RNA


title: Pancreatic cancer sample, Sample_ID = 13b, DNA


title: Pancreatic cancer sample, Sample_ID = 92a, RNA


title: Pancreatic cancer sample, Sample_ID = 91b, RNA


title: Control sample, Sample_ID = 139b, DNA


title: Control sample, Sample_ID = 141a, DNA


title: Control sample, Sample_ID = 139a, DNA


title: Pancreatic cancer sample, Sample_ID = 90a, RNA


title: Pancreatic cancer sample, Sample_ID = 91a, RNA


title: Pancreatic cancer sample, Sample_ID = 90b, RNA


title: Pancreatic cancer sample, Sample_ID = 93b, RNA


title: Pancreatic cancer sample, Sample_ID = 8b, RNA


title: Control sample, Sample_ID = 136b, DNA


title: Pancreatic cancer sample, Sample_ID = 8a, RNA


title: Control sample, Sample_ID = 138b, DNA

value: CEPH 1421


title: Control sample, Sample_ID = 138a, DNA


title: Control sample, Sample_ID = 137b, DNA

value: CEPH 1420

value: DAUGHTER


title: Control sample, Sample_ID = 137a, DNA


title: Control sample, Sample_ID = 136a, DNA


title: Pancreatic cancer sample, Sample_ID = 89b, RNA


title: Pancreatic cancer sample, Sample_ID = 88a, RNA


title: Pancreatic cancer sample, Sample_ID = 89a, RNA


title: Pancreatic cancer sample, Sample_ID = 88b, RNA


title: Control sample, Sample_ID = 144b, DNA

value: CEPH 1346


title: Control sample, Sample_ID = 135b, DNA

value: CEPH 1416


title: Control sample, Sample_ID = 134b, DNA

value: CEPH 1424


title: Pancreatic cancer sample, Sample_ID = 87a, RNA


title: Pancreatic cancer sample, Sample_ID = 87b, RNA


title: Control sample, Sample_ID = 135a, DNA


title: Control sample, Sample_ID = 134a, DNA


title: Pancreatic cancer sample, Sample_ID = 86b, RNA


title: Control sample, Sample_ID = 133a, DNA


title: Control sample, Sample_ID = 133b, DNA


title: Control sample, Sample_ID = 132b, DNA

value: CEPH 1413


title: Control sample, Sample_ID = 132a, DNA


title: Pancreatic cancer sample, Sample_ID = 85b, RNA


title: Pancreatic cancer sample, Sample_ID = 86a, RNA


title: Pancreatic cancer sample, Sample_ID = 84a, RNA


title: Pancreatic cancer sample, Sample_ID = 83b, RNA


title: Pancreatic cancer sample, Sample_ID = 85a, RNA


title: Pancreatic cancer sample, Sample_ID = 83a, RNA


title: Control sample, Sample_ID = 131a, DNA

value: CEPH 1349


title: Control sample, Sample_ID = 130a, DNA


title: Control sample, Sample_ID = 128b, DNA


title: Control sample, Sample_ID = 129b, DNA


title: Control sample, Sample_ID = 129a, DNA


title: Control sample, Sample_ID = 128a, DNA


title: Pancreatic cancer sample, Sample_ID = 81b, RNA


title: Pancreatic cancer sample, Sample_ID = 82a, RNA


title: Pancreatic cancer sample, Sample_ID = 82b, RNA


title: Control sample, Sample_ID = 130b, DNA


title: Pancreatic cancer sample, Sample_ID = 80b, RNA


title: Pancreatic cancer sample, Sample_ID = 81a, RNA


title: Control sample, Sample_ID = 126b, DNA


title: Control sample, Sample_ID = 126a, DNA


title: Pancreatic cancer sample, Sample_ID = 79b, RNA


title: Pancreatic cancer sample, Sample_ID = 80a, RNA


title: Control sample, Sample_ID = 125b, DNA

value: CEPH 1423


title: Control sample, Sample_ID = 124b, DNA

value: CEPH 1418


title: Control sample, Sample_ID = 125a, DNA


title: Pancreatic cancer sample, Sample_ID = 78b, RNA


title: Pancreatic cancer sample, Sample_ID = 79a, RNA


title: Pancreatic cancer sample, Sample_ID = 78a, RNA


title: Pancreatic cancer sample, Sample_ID = 77b, RNA


title: Control sample, Sample_ID = 124a, DNA


title: Control sample, Sample_ID = 123b, DNA


title: Pancreatic cancer sample, Sample_ID = 76b, RNA


title: Pancreatic cancer sample, Sample_ID = 76a, RNA


title: Control sample, Sample_ID = 123a, DNA


title: Control sample, Sample_ID = 122b, DNA


title: Pancreatic cancer sample, Sample_ID = 77a, RNA


title: Pancreatic cancer sample, Sample_ID = 75b, RNA


title: Control sample, Sample_ID = 122a, DNA


title: Pancreatic cancer sample, Sample_ID = 74b, RNA


title: Pancreatic cancer sample, Sample_ID = 75a, RNA


title: Pancreatic cancer sample, Sample_ID = 84b, RNA


title: Pancreatic cancer sample, Sample_ID = 74a, RNA


title: Control sample, Sample_ID = 121a, DNA


title: Pancreatic cancer sample, Sample_ID = 71b, RNA


title: Control sample, Sample_ID = 120b, DNA


title: Control sample, Sample_ID = 131b, DNA


title: Control sample, Sample_ID = 121b, DNA


title: Control sample, Sample_ID = 120a, DNA


title: Pancreatic cancer sample, Sample_ID = 12, DNA


title: Pancreatic cancer sample, Sample_ID = 11b, DNA


title: Pancreatic cancer sample, Sample_ID = 6b, RNA


title: Pancreatic cancer sample, Sample_ID = 71a, RNA


title: Pancreatic cancer sample, Sample_ID = 70b, RNA


title: Pancreatic cancer sample, Sample_ID = 6a, RNA


title: Pancreatic cancer sample, Sample_ID = 70a, RNA


title: Pancreatic cancer sample, Sample_ID = 11a, DNA


title: Control sample, Sample_ID = 119b, DNA


title: Control sample, Sample_ID = 119a, DNA


title: Pancreatic cancer sample, Sample_ID = 69b, RNA


title: Control sample, Sample_ID = 118b, DNA


title: Pancreatic cancer sample, Sample_ID = 69a, RNA


title: Control sample, Sample_ID = 118a, DNA


title: Control sample, Sample_ID = 117a, DNA


title: Control sample, Sample_ID = 116b, DNA


title: Pancreatic cancer sample, Sample_ID = 68b, RNA


title: Pancreatic cancer sample, Sample_ID = 67b, RNA


title: Pancreatic cancer sample, Sample_ID = 68a, RNA


title: Control sample, Sample_ID = 113a, DNA


title: Control sample, Sample_ID = 114a, DNA

value: CEPH 1375


title: Control sample, Sample_ID = 113b, DNA


title: Pancreatic cancer sample, Sample_ID = 66b, RNA


title: Pancreatic cancer sample, Sample_ID = 67a, RNA


title: Control sample, Sample_ID = 117b, DNA


title: Control sample, Sample_ID = 112b, DNA


title: Control sample, Sample_ID = 116a, DNA


title: Pancreatic cancer sample, Sample_ID = 66a, RNA


title: Pancreatic cancer sample, Sample_ID = 65b, RNA


title: Pancreatic cancer sample, Sample_ID = 63b, RNA


title: Pancreatic cancer sample, Sample_ID = 65a, RNA


title: Pancreatic cancer sample, Sample_ID = 64a, RNA


title: Pancreatic cancer sample, Sample_ID = 62b, RNA


title: Control sample, Sample_ID = 112a, DNA


title: Control sample, Sample_ID = 111b, DNA


title: Control sample, Sample_ID = 111a, DNA


title: Pancreatic cancer sample, Sample_ID = 63a, RNA


title: Pancreatic cancer sample, Sample_ID = 62a, RNA


title: Control sample, Sample_ID = 114b, DNA


title: Control sample, Sample_ID = 110a, DNA


title: Pancreatic cancer sample, Sample_ID = 64b, RNA


title: Pancreatic cancer sample, Sample_ID = 61b, RNA


title: Pancreatic cancer sample, Sample_ID = 61a, RNA


title: Control sample, Sample_ID = 110b, DNA


title: Pancreatic cancer sample, Sample_ID = 60a, RNA


title: Pancreatic cancer sample, Sample_ID = 60b, RNA


title: Pancreatic cancer sample, Sample_ID = 5b, RNA


title: Pancreatic cancer sample, Sample_ID = 10a, DNA


title: Pancreatic cancer sample, Sample_ID = 10b, DNA


title: Pancreatic cancer sample, Sample_ID = 109, DNA


title: Pancreatic cancer sample, Sample_ID = 108, DNA


title: Pancreatic cancer sample, Sample_ID = 107, DNA


title: Pancreatic cancer sample, Sample_ID = 105, DNA


title: Pancreatic cancer sample, Sample_ID = 55a, RNA


title: Pancreatic cancer sample, Sample_ID = 54b, RNA


title: Pancreatic cancer sample, Sample_ID = 106, DNA


title: Pancreatic cancer sample, Sample_ID = 5a, RNA


title: Pancreatic cancer sample, Sample_ID = 104, DNA


title: Pancreatic cancer sample, Sample_ID = 101, DNA


title: Pancreatic cancer sample, Sample_ID = 100, DNA


title: Pancreatic cancer sample, Sample_ID = 55b, RNA


title: Pancreatic cancer sample, Sample_ID = 54a, RNA


title: Pancreatic cancer sample, Sample_ID = 53a, RNA


title: Pancreatic cancer sample, Sample_ID = 103, DNA


title: Pancreatic cancer sample, Sample_ID = 52a, RNA


title: Pancreatic cancer sample, Sample_ID = 52b, RNA


title: Pancreatic cancer sample, Sample_ID = 53b, RNA


title: Pancreatic cancer sample, Sample_ID = 1, DNA


title: Pancreatic cancer sample, Sample_ID = 50b, RNA


title: Pancreatic cancer sample, Sample_ID = 102, DNA


title: Pancreatic cancer sample, Sample_ID = 9a, RNA


title: Pancreatic cancer sample, Sample_ID = 9b, RNA


title: Pancreatic cancer sample, Sample_ID = 99b, RNA


title: Pancreatic cancer sample, Sample_ID = 4b, RNA


title: Pancreatic cancer sample, Sample_ID = 99a, RNA


title: Pancreatic cancer sample, Sample_ID = 98b, RNA


title: Pancreatic cancer sample, Sample_ID = 48a, RNA


title: Pancreatic cancer sample, Sample_ID = 48b, RNA


title: Pancreatic cancer sample, Sample_ID = 97b, RNA


title: Pancreatic cancer sample, Sample_ID = 96b, RNA


title: Pancreatic cancer sample, Sample_ID = 95b, RNA


title: Pancreatic cancer sample, Sample_ID = 49b, RNA


title: Pancreatic cancer sample, Sample_ID = 49a, RNA


title: Pancreatic cancer sample, Sample_ID = 47a, RNA


title: Pancreatic cancer sample, Sample_ID = 50a, RNA


title: Pancreatic cancer sample, Sample_ID = 98a, RNA


title: Pancreatic cancer sample, Sample_ID = 46a, RNA


title: Pancreatic cancer sample, Sample_ID = 47b, RNA


title: Pancreatic cancer sample, Sample_ID = 94a, RNA


title: Pancreatic cancer sample, Sample_ID = 4a, RNA


title: Pancreatic cancer sample, Sample_ID = 97a, RNA


title: Pancreatic cancer sample, Sample_ID = 45a, RNA


title: Pancreatic cancer sample, Sample_ID = 45b, RNA


title: Pancreatic cancer sample, Sample_ID = 44b, RNA


title: Pancreatic cancer sample, Sample_ID = 94b, RNA


title: Pancreatic cancer sample, Sample_ID = 96a, RNA


title: Pancreatic cancer sample, Sample_ID = 46b, RNA


title: Pancreatic cancer sample, Sample_ID = 43b, RNA


title: Pancreatic cancer sample, Sample_ID = 95a, RNA


title: Pancreatic cancer sample, Sample_ID = 41b, RNA


title: Pancreatic cancer sample, Sample_ID = 90b, RNA


title: Pancreatic cancer sample, Sample_ID = 93a, RNA


title: Pancreatic cancer sample, Sample_ID = 91a, RNA


title: Pancreatic cancer sample, Sample_ID = 91b, RNA


title: Pancreatic cancer sample, Sample_ID = 92b, RNA


title: Pancreatic cancer sample, Sample_ID = 92a, RNA


title: Pancreatic cancer sample, Sample_ID = 93b, RNA


title: Pancreatic cancer sample, Sample_ID = 42a, RNA


title: Pancreatic cancer sample, Sample_ID = 89b, RNA


title: Pancreatic cancer sample, Sample_ID = 8b, RNA


title: Pancreatic cancer sample, Sample_ID = 40b, RNA


title: Pancreatic cancer sample, Sample_ID = 41a, RNA


title: Pancreatic cancer sample, Sample_ID = 43a, RNA


title: Pancreatic cancer sample, Sample_ID = 44a, RNA


title: Pancreatic cancer sample, Sample_ID = 42b, RNA


title: Pancreatic cancer sample, Sample_ID = 87a, RNA


title: Pancreatic cancer sample, Sample_ID = 8a, RNA


title: Pancreatic cancer sample, Sample_ID = 87b, RNA


title: Pancreatic cancer sample, Sample_ID = 88a, RNA


title: Pancreatic cancer sample, Sample_ID = 40a, RNA


title: Pancreatic cancer sample, Sample_ID = 89a, RNA


title: Pancreatic cancer sample, Sample_ID = 3a, RNA


title: Pancreatic cancer sample, Sample_ID = 39b, RNA


title: Pancreatic cancer sample, Sample_ID = 90a, RNA


title: Pancreatic cancer sample, Sample_ID = 86b, RNA


title: Pancreatic cancer sample, Sample_ID = 88b, RNA


title: Pancreatic cancer sample, Sample_ID = 84a, RNA


title: Pancreatic cancer sample, Sample_ID = 84b, RNA


title: Pancreatic cancer sample, Sample_ID = 85b, RNA


title: Pancreatic cancer sample, Sample_ID = 85a, RNA


title: Pancreatic cancer sample, Sample_ID = 86a, RNA


title: Pancreatic cancer sample, Sample_ID = 3b, RNA


title: Pancreatic cancer sample, Sample_ID = 36b, RNA


title: Pancreatic cancer sample, Sample_ID = 37a, RNA


title: Pancreatic cancer sample, Sample_ID = 38a, RNA


title: Pancreatic cancer sample, Sample_ID = 38b, RNA


title: Pancreatic cancer sample, Sample_ID = 37b, RNA


title: Pancreatic cancer sample, Sample_ID = 83a, RNA


title: Pancreatic cancer sample, Sample_ID = 39a, RNA


title: Pancreatic cancer sample, Sample_ID = 82a, RNA


title: Pancreatic cancer sample, Sample_ID = 82b, RNA


title: Pancreatic cancer sample, Sample_ID = 36a, RNA


title: Pancreatic cancer sample, Sample_ID = 81b, RNA


title: Pancreatic cancer sample, Sample_ID = 33a, RNA


title: Pancreatic cancer sample, Sample_ID = 35b, RNA


title: Pancreatic cancer sample, Sample_ID = 33b, RNA


title: Pancreatic cancer sample, Sample_ID = 35a, RNA


title: Pancreatic cancer sample, Sample_ID = 34b, RNA


title: Pancreatic cancer sample, Sample_ID = 34a, RNA


title: Pancreatic cancer sample, Sample_ID = 83b, RNA


title: Pancreatic cancer sample, Sample_ID = 32b, RNA


title: Pancreatic cancer sample, Sample_ID = 81a, RNA


title: Pancreatic cancer sample, Sample_ID = 80a, RNA


title: Pancreatic cancer sample, Sample_ID = 31b, RNA


title: Pancreatic cancer sample, Sample_ID = 7b, RNA


title: Pancreatic cancer sample, Sample_ID = 31a, RNA


title: Pancreatic cancer sample, Sample_ID = 2b, RNA


title: Pancreatic cancer sample, Sample_ID = 80b, RNA


title: Pancreatic cancer sample, Sample_ID = 78b, RNA


title: Pancreatic cancer sample, Sample_ID = 7a, RNA


title: Pancreatic cancer sample, Sample_ID = 2a, RNA


title: Pancreatic cancer sample, Sample_ID = 32a, RNA


title: Pancreatic cancer sample, Sample_ID = 79b, RNA


title: Pancreatic cancer sample, Sample_ID = 26b, RNA


title: Pancreatic cancer sample, Sample_ID = 28a, RNA


title: Pancreatic cancer sample, Sample_ID = 78a, RNA


title: Pancreatic cancer sample, Sample_ID = 27a, RNA


title: Pancreatic cancer sample, Sample_ID = 76b, RNA


title: Pancreatic cancer sample, Sample_ID = 77a, RNA


title: Pancreatic cancer sample, Sample_ID = 76a, RNA


title: Pancreatic cancer sample, Sample_ID = 74b, RNA


title: Pancreatic cancer sample, Sample_ID = 26a, RNA


title: Pancreatic cancer sample, Sample_ID = 28b, RNA


title: Pancreatic cancer sample, Sample_ID = 79a, RNA


title: Pancreatic cancer sample, Sample_ID = 25b, RNA


title: Pancreatic cancer sample, Sample_ID = 75b, RNA


title: Pancreatic cancer sample, Sample_ID = 25a, RNA


title: Pancreatic cancer sample, Sample_ID = 24b, RNA


title: Pancreatic cancer sample, Sample_ID = 77b, RNA


title: Pancreatic cancer sample, Sample_ID = 24a, RNA


title: Pancreatic cancer sample, Sample_ID = 27b, RNA


title: Pancreatic cancer sample, Sample_ID = 75a, RNA


title: Pancreatic cancer sample, Sample_ID = 74a, RNA


title: Pancreatic cancer sample, Sample_ID = 71b, RNA


title: Pancreatic cancer sample, Sample_ID = 23b, RNA


title: Pancreatic cancer sample, Sample_ID = 23a, RNA


title: Pancreatic cancer sample, Sample_ID = 71a, RNA


title: Pancreatic cancer sample, Sample_ID = 22b, RNA


title: Pancreatic cancer sample, Sample_ID = 22a, RNA


title: Pancreatic cancer sample, Sample_ID = 70a, RNA


title: Pancreatic cancer sample, Sample_ID = 70b, RNA


title: Pancreatic cancer sample, Sample_ID = 1b, RNA


title: Pancreatic cancer sample, Sample_ID = 20a, RNA


title: Pancreatic cancer sample, Sample_ID = 20b, RNA


title: Pancreatic cancer sample, Sample_ID = 69a, RNA


title: Pancreatic cancer sample, Sample_ID = 6a, RNA


title: Pancreatic cancer sample, Sample_ID = 19b, RNA


title: Pancreatic cancer sample, Sample_ID = 69b, RNA


title: Pancreatic cancer sample, Sample_ID = 18b, RNA


title: Pancreatic cancer sample, Sample_ID = 68a, RNA


title: Pancreatic cancer sample, Sample_ID = 6b, RNA


title: Pancreatic cancer sample, Sample_ID = 68b, RNA


title: Pancreatic cancer sample, Sample_ID = 1a, RNA


title: Pancreatic cancer sample, Sample_ID = 18a, RNA


title: Pancreatic cancer sample, Sample_ID = 67a, RNA


title: Pancreatic cancer sample, Sample_ID = 67b, RNA


title: Pancreatic cancer sample, Sample_ID = 17a, RNA


title: Pancreatic cancer sample, Sample_ID = 66b, RNA


title: Pancreatic cancer sample, Sample_ID = 16b, RNA


title: Pancreatic cancer sample, Sample_ID = 16a, RNA


title: Pancreatic cancer sample, Sample_ID = 15b, RNA


title: Pancreatic cancer sample, Sample_ID = 66a, RNA


title: Pancreatic cancer sample, Sample_ID = 17b, RNA


title: Pancreatic cancer sample, Sample_ID = 65b, RNA


title: Pancreatic cancer sample, Sample_ID = 65a, RNA


title: Pancreatic cancer sample, Sample_ID = 64b, RNA


title: Pancreatic cancer sample, Sample_ID = 19a, RNA


title: Pancreatic cancer sample, Sample_ID = 63b, RNA


title: Pancreatic cancer sample, Sample_ID = 64a, RNA


title: Pancreatic cancer sample, Sample_ID = 15a, RNA


title: Control sample, Sample_ID = 157a, RNA

value: CEPH 1350


title: Control sample, Sample_ID = 157b, RNA

value: MOTHER


title: Control sample, Sample_ID = 156b, RNA


title: Pancreatic cancer sample, Sample_ID = 63a, RNA


title: Pancreatic cancer sample, Sample_ID = 62b, RNA


title: Control sample, Sample_ID = 154b, RNA


title: Pancreatic cancer sample, Sample_ID = 61a, RNA


title: Control sample, Sample_ID = 156a, RNA


title: Control sample, Sample_ID = 155b, RNA

value: CEPH 1345


title: Pancreatic cancer sample, Sample_ID = 61b, RNA


title: Pancreatic cancer sample, Sample_ID = 62a, RNA


title: Control sample, Sample_ID = 155a, RNA


title: Pancreatic cancer sample, Sample_ID = 60a, RNA


title: Control sample, Sample_ID = 152b, RNA


title: Control sample, Sample_ID = 154a, RNA


title: Pancreatic cancer sample, Sample_ID = 5b, RNA


title: Pancreatic cancer sample, Sample_ID = 5a, RNA


title: Pancreatic cancer sample, Sample_ID = 55b, RNA


title: Control sample, Sample_ID = 153b, RNA

value: CEPH 1340

value: SON


title: Pancreatic cancer sample, Sample_ID = 60b, RNA


title: Control sample, Sample_ID = 153a, RNA


title: Control sample, Sample_ID = 150b, RNA

value: CEPH 1344


title: Control sample, Sample_ID = 151a, RNA

value: FATHER


title: Control sample, Sample_ID = 151b, RNA


title: Pancreatic cancer sample, Sample_ID = 54b, RNA


title: Control sample, Sample_ID = 152a, RNA


title: Pancreatic cancer sample, Sample_ID = 55a, RNA


title: Control sample, Sample_ID = 150a, RNA


title: Pancreatic cancer sample, Sample_ID = 54a, RNA


title: Pancreatic cancer sample, Sample_ID = 53a, RNA


title: Pancreatic cancer sample, Sample_ID = 14b, RNA


title: Pancreatic cancer sample, Sample_ID = 14a, RNA


title: Control sample, Sample_ID = 149b, RNA


title: Pancreatic cancer sample, Sample_ID = 52a, RNA


title: Control sample, Sample_ID = 149a, RNA


title: Pancreatic cancer sample, Sample_ID = 50b, RNA


title: Pancreatic cancer sample, Sample_ID = 53b, RNA


title: Pancreatic cancer sample, Sample_ID = 52b, RNA


title: Control sample, Sample_ID = 148a, RNA


title: Control sample, Sample_ID = 147a, RNA


title: Control sample, Sample_ID = 147b, RNA


title: Pancreatic cancer sample, Sample_ID = 48b, RNA


title: Pancreatic cancer sample, Sample_ID = 4a, RNA


title: Pancreatic cancer sample, Sample_ID = 4b, RNA


title: Pancreatic cancer sample, Sample_ID = 48a, RNA


title: Control sample, Sample_ID = 148b, RNA


title: Pancreatic cancer sample, Sample_ID = 46b, RNA


title: Pancreatic cancer sample, Sample_ID = 47b, RNA


title: Pancreatic cancer sample, Sample_ID = 50a, RNA


title: Pancreatic cancer sample, Sample_ID = 47a, RNA


title: Control sample, Sample_ID = 145b, RNA

value: CEPH 1362


title: Control sample, Sample_ID = 146a, RNA


title: Control sample, Sample_ID = 146b, RNA


title: Pancreatic cancer sample, Sample_ID = 45b, RNA


title: Pancreatic cancer sample, Sample_ID = 45a, RNA


title: Pancreatic cancer sample, Sample_ID = 46a, RNA


title: Control sample, Sample_ID = 143b, RNA


title: Control sample, Sample_ID = 144b, RNA


title: Control sample, Sample_ID = 144a, RNA


title: Control sample, Sample_ID = 143a, RNA


title: Control sample, Sample_ID = 142b, RNA

value: CEPH 1341


title: Pancreatic cancer sample, Sample_ID = 44b, RNA


title: Pancreatic cancer sample, Sample_ID = 44a, RNA


title: Control sample, Sample_ID = 145a, RNA


title: Control sample, Sample_ID = 142a, RNA


title: Control sample, Sample_ID = 141b, RNA


title: Pancreatic cancer sample, Sample_ID = 43b, RNA


title: Pancreatic cancer sample, Sample_ID = 13b, RNA


title: Pancreatic cancer sample, Sample_ID = 42b, RNA


title: Control sample, Sample_ID = 138a, RNA

value: CEPH 1421


title: Pancreatic cancer sample, Sample_ID = 42a, RNA


title: Control sample, Sample_ID = 139a, RNA


title: Pancreatic cancer sample, Sample_ID = 41b, RNA


title: Control sample, Sample_ID = 139b, RNA


title: Control sample, Sample_ID = 141a, RNA