title: 12g 2_7_a YLK144 2% glucose

description: 12g 2_7_a YLK144 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:49:00 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 12g 2_7_a YLK144 2% glucose


title: 15E 3_3_d YLK159 1% ethanol

status: Public on Apr 15 2008

type: RNA

city: Princeton

first: Erin

middle: N

last: Smith

state: NJ

address: 110 Carl Icahn Labs

department: Ecology and Evolutionary Biology

country: USA

institute: Princeton University

description: 15E 3_3_d YLK159 1% ethanol

hyb_protocol: Hybridization date : 2005-12-10 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:00:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : Unknown
Datafile type : Agilent result file

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: BYg+RMg+BYE+RME

label_protocol:
Type of label : Cy3
Low RNA Input Fluorescent Linear Amplification Kit Protocol, Version 4, January 2006, Agilent Technologies, Publication 5185-58

growth_protocol: media : common reference: mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions

extract_protocol: Extraction method : "Hot acid/phenol, Qiagen Rneasy Kit"

tag: Strain Name

value: common reference:mixture of BY4716 and RM11-1a RNA from glucose and ethanol conditions

source_name: 15E 3_3_d YLK159 1% ethanol

label_protocol:
Type of label : Cy5
Low RNA Input Fluorescent Linear Amplification Kit Protocol, Version 4, January 2006, Agilent Technologies, Publication 5185-58

growth_protocol: media : "ethanol carbon source: 6.7g/L YNB (Sigma Y0626), 10mL/L ethanol, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"


title: Soybean-Bayfield-2-RMA

city: Ste-Anne-de-Bellevue

first: Martina

last: Stromvik

state: Quebec

address: 21,111 Lakeshore Rd

department: Department of Plant Science

country: Canada

institute: McGill University

description: Sample 2 from the Bayfield soybean strain.  The second of five samples for this strain.

hyb_protocol: Target preparation, hybridization and scanning were carried out at the McGill University and Genome Quebec Innovation Centre Microarray platform using the protocol recommended by Affymetrix ().  Labelled cRNA were cleaned and fragmented using the Sample Cleanup Module reagents (Qiagen).  Spike controls B2, bio-B, bio-C, bio-D, and Cre-x were added to the hybridization cocktail before overnight hybridization at 45°C for 16 h.

scan_protocol: Arrays were washed and stained in an Affymetrix fluidics Station prior to scanning on the GeneChip Scanner 3000 (Affymetrix).  Image acquisition and processing was done with the Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: R and the BioConductor packages (Gentleman et al., 2004) such as affy, limma, cluster, and made4 were used for data analysis.  This sample was pre-processed using the RMA method.

label: biotin

organism: Glycine max

source_name: Soybean strain Bayfield

label_protocol: 5µg of total RNA was used to generate double-stranded cDNA using a T7-linked oligo(dT) primer and SuperScript II reverse transcriptase (Invitrogen) following the instructions for the One cycle-cDNA synthesis kit (from Affymetrix).  cRNA were synthesized using the IVT labelling kit from Affymetrix, resulting in biotinylated cRNA.

growth_protocol: Grown in growth changers in ambient humidity, 16h photoperiod, and 25/19°C day/night temperatures.  10 seeds sown into two 20 cm pots.

extract_protocol: At the V2 growth stage (Fehr et al. 1971), completely unrolled first trifoliate leaves were harvested by cutting  the petiole a few millimeters below the leaflets, immediately frozen in liquid nitrogen and stored at -80°C.  RNA was extracted using the RNeasy Plant Mini Kit (Quiagen, Valencia, CA).

tag: Strain

value: Bayfield

tag: Growth stage


title: BY9g BY4716 0 2% glu

description: BY9g BY4716 0 2% glu

hyb_protocol: Hybridization date : 2005-12-13 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:05:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY9g BY4716 0 2% glu

growth_protocol: media : "glucose carbon source: 6.7g/L YNB (Sigma Y0626), 20g/L glucose, 100 mg/L leucine, 100mg/L lysine, 20mg/L uracil"


title: Soybean-2601R-3-RMA

description: Sample 3 from the 2601R soybean strain.  The second of five samples for this strain.

source_name: Soybean strain 2601R


title: Soybean-Bayfield-1-RMA

description: Sample 1 from the Bayfield soybean strain.  The first of five samples for this strain.


title: BY9E BY4716 0 1% ethanol

description: BY9E BY4716 0 1% ethanol

hyb_protocol: Hybridization date : 2005-12-09 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:10:57 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY9E BY4716 0 1% ethanol


title: 117E 26_2_d YLK587 1% eth

description: 117E 26_2_d YLK587 1% eth

hyb_protocol: Hybridization date : 2005-12-11 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:11:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 117g 26_2_d YLK587 2% glucose

description: 117g 26_2_d YLK587 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:43:54 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: Soybean-2601R-6-RMA

description: Sample 6 from the 2601R soybean strain.  The fifth of five samples for this strain.


title: BY7g BY4716 0 2% glu

description: BY7g BY4716 0 2% glu

hyb_protocol: Hybridization date : 2005-12-12 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:19:37 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BY7g BY4716 0 2% glu


title: 90E 18_4_c YLK458 1% ethanol

description: 90E 18_4_c YLK458 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:31:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 90E 18_4_c YLK458 1% ethanol


title: BY11g BY4716 0 2% glu

description: BY11g BY4716 0 2% glu


title: 115E 25_4_d YLK575 1% ethanol

description: 115E 25_4_d YLK575 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:06:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 115g 25_4_d YLK575 2% glu

description: 115g 25_4_d YLK575 2% glu

hyb_protocol: Hybridization date : 2005-12-14 Two-Color Microarray-Based Gene Expression Analysis v.5.5, Agilent Technologies, Publication G4140-90050 V.5.5

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:29:25 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 114E 25_3_d YLK571 1% ethanol

description: 114E 25_3_d YLK571 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:48:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 89E 18_3_d YLK455 1% ethanol

description: 89E 18_3_d YLK455 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:15:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 89E 18_3_d YLK455 1% ethanol


title: 89g 18_3_d YLK455 2% glucose

description: 89g 18_3_d YLK455 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:07:48 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 89g 18_3_d YLK455 2% glucose


title: 114g 25_3_d YLK571 2% glucose

description: 114g 25_3_d YLK571 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:36:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 116E 26_1_d YLK583 1% eth

description: 116E 26_1_d YLK583 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 13:48:44 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 113g 25_1_d YLK567 2% glu

description: 113g 25_1_d YLK567 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:40:04 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 73E 14_4_a YLK388 1% ethanol

description: 73E 14_4_a YLK388 1% ethanol

source_name: 73E 14_4_a YLK388 1% ethanol


title: 78g 15_3_b YLK409 2% glucose

description: 78g 15_3_b YLK409 2% glucose

source_name: 78g 15_3_b YLK409 2% glucose


title: 113E 25_1_d YLK567 1% ethanol

description: 113E 25_1_d YLK567 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 13:08:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 111E 23_5_d YLK559 1% ethanol

description: 111E 23_5_d YLK559 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:50:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 110E 23_3_d YLK551 1% ethanol

description: 110E 23_3_d YLK551 1% ethanol


title: 110g 23_3_d YLK551 2% glu

description: 110g 23_3_d YLK551 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:20:52 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 111g 23_5_d YLK559 2% glucose

description: 111g 23_5_d YLK559 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:39:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 10g 2_5_d YLK139 2% glucose

description: 10g 2_5_d YLK139 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:34:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 10g 2_5_d YLK139 2% glucose


title: Soybean-2601R-2-RMA

description: Sample 2 from the 2601R soybean strain.  The first of five samples for this strain.

scan_protocol: Arrays were washed and stained in an Affymetrix fluidics Station prior to scanning on the GeneChip Scanner 3000 (Affymetrix).  Image acquisition and processing was done with the Microarray Analysis Suite 5.0 (Affymetrix).


title: 112E 24_1_d YLK563 1% ethanol

description: 112E 24_1_d YLK563 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 13:28:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 70E 14_1_b YLK377 1% ethanol

description: 70E 14_1_b YLK377 1% ethanol

source_name: 70E 14_1_b YLK377 1% ethanol


title: 10E 2_5_d YLK139 1% eth

description: 10E 2_5_d YLK139 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-14 Scan Time : 12:45:12 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 57E 10_2_d YLK327 1% ethanol

description: 57E 10_2_d YLK327 1% ethanol

source_name: 57E 10_2_d YLK327 1% ethanol


title: 109g 22_5_d YLK543 2% glucose

description: 109g 22_5_d YLK543 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:52:49 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 106E 22_2_d YLK531 1% eth

description: 106E 22_2_d YLK531 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:27:32 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 107E 22_3_b YLK533 1% eth

description: 107E 22_3_b YLK533 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:00:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 107g 22_3_b YLK533 2% glu

description: 107g 22_3_b YLK533 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 15:03:26 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 106g 22_2_d YLK531 2% glu

description: 106g 22_2_d YLK531 2% glu

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:44:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 52g 9_4_d YLK307 2% glucose

description: 52g 9_4_d YLK307 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:39:22 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 52g 9_4_d YLK307 2% glucose


title: 43E 8_2_d YLK271 1% ethanol

description: 43E 8_2_d YLK271 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:03:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 43E 8_2_d YLK271 1% ethanol


title: 105E 21_5_c YLK522 1% ethanol

description: 105E 21_5_c YLK522 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:00:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: BYg+RMg+BYE+RME


title: 104E 21_4_d YLK519 1% eth

description: 104E 21_4_d YLK519 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-12 Scan Time : 12:35:27 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 23E 5_2_d YLK191 1% ethanol

description: 23E 5_2_d YLK191 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:23:35 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 23E 5_2_d YLK191 1% ethanol


title: 24E 5_3_d YLK195 1% ethanol

description: 24E 5_3_d YLK195 1% ethanol

source_name: 24E 5_3_d YLK195 1% ethanol


title: 31g 6_5_d YLK223 2% glucose

description: 31g 6_5_d YLK223 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:55:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 31g 6_5_d YLK223 2% glucose


title: 42E 8_1_a YLK264 1% ethanol

description: 42E 8_1_a YLK264 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 12:47:16 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 42E 8_1_a YLK264 1% ethanol


title: 105g 21_5_c YLK522 2% glucose

description: 105g 21_5_c YLK522 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:40:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 103E 21_3_d YLK515 1% eth

description: 103E 21_3_d YLK515 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 15:19:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 21g 4_4_d YLK183 2% glucose

description: 21g 4_4_d YLK183 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 13:18:51 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1

source_name: 21g 4_4_d YLK183 2% glucose


title: 104g 21_4_d YLK519 2% glucose

description: 104g 21_4_d YLK519 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:17:23 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 16g 3_4_d YLK163 2% glucose

description: 16g 3_4_d YLK163 2% glucose

source_name: 16g 3_4_d YLK163 2% glucose


title: 103g 21_3_d YLK515 2% glucose

description: 103g 21_3_d YLK515 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-10 Scan Time : 12:28:55 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 116g 26_1_d YLK583 2% glucose

description: 116g 26_1_d YLK583 2% glucose


title: 112g 24_1_d YLK563 2% glucose

description: 112g 24_1_d YLK563 2% glucose


title: 15g 3_3_d YLK159 2% glucose

description: 15g 3_3_d YLK159 2% glucose

source_name: 15g 3_3_d YLK159 2% glucose


title: 102g 21_2_d YLK511 2% glucose

description: 102g 21_2_d YLK511 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 12:48:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: HIGK cells infected with Porphyromonas gingivalis, biological rep3

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

description:
Gene expression data from Porphyromonas gingivalis-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)

hyb_protocol: Following fragmentation,  human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).

scan_protocol: GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.

data_processing: The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Homo sapiens

label_protocol: cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted, DNAse-treated, purified and quantified according to standard  methods (Qiagen and Affymetrix).

treatment_protocol: Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 100 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.

tag: HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).

tag: HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.


title: 101E 21_1_d YLK507 1% eth

description: 101E 21_1_d YLK507 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 14:16:18 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 101g 21_1_d YLK507 2% glucose

description: 101g 21_1_d YLK507 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 15:41:06 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 109E 22_5_d YLK543 1% ethanol

description: 109E 22_5_d YLK543 1% ethanol


title: 102E 21_2_d YLK511 1% eth

description: 102E 21_2_d YLK511 1% eth

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-13 Scan Time : 13:05:03 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 100E 20_4_c YLK498 1% ethanol

description: 100E 20_4_c YLK498 1% ethanol

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-09 Scan Time : 14:53:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: 100g 20_4_c YLK498 2% glucose

description: 100g 20_4_c YLK498 2% glucose

scan_protocol: Pixel Size : 10 Scan Date : 2005-12-11 Scan Time : 14:39:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.6.3.1


title: HIGK cells infected with Porphyromonas gingivalis, biological rep2

source_name: Human Immortalized Gingival Keratinocyte


title: HIGK cells infected with Porphyromonas gingivalis, biological rep1


title: HIGK cells infected with Porphyromonas gingivalis, biological rep4


title: Tra2-U74Av2

status: Public on Apr 12 2008

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: E11.5 FVB/N mouse trachea

hyb_protocol: The cRNA was then hybridized to the murine genome MGU74Av1 chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: raw data processed by Affymetrix Microarray Suite 5.0 is provided

organism: Mus musculus

source_name: E11.5 trachea

label_protocol: based on Affymetrix protocols

extract_protocol: GITC

tag: E11.5 FVB/N mouse trachea


title: Lg2-U74Av2

description: E11.5 FVB/N mouse lung

source_name: E11.5 Lung

tag: E11.5 FVB/N mouse lung


title: BreastStroma_Tumor_E1084_replicate2

status: Public on Apr 11 2008

city: Montreal

first: Greg

last: Finak

state: QC

address: 3775 University

department: Mcgill Center For Bioinformatics

description: No additional description

hyb_protocol: Whole Human Genome 44K arrays (Agilent Technologies, product G4112A) were used for all experiments. RNA samples (500 ng) were subjected to fragmentation followed by 18 h hybridization, washing, and scanning (Agilent Technologies, model G2505B) according to the manufacturer’s protocol (manual ID #G4140-90030). Samples were hybridized against Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA). Duplicate hybridizations were performed for all samples using reverse-dye labeling.

scan_protocol: Microarray data were feature extracted using Feature Extraction Software (v. 9.5.3) from Agilent with the default parameters.

data_processing:
Outlier features on arrays were flagged by the software. Arrays were required to have an average raw signal intensity of 800 in each channel, and a signal to noise ratio above 16 per channel. MvA plots were examined for signs of hybridization or labeling problems. Replicate arrays were required to have a concordance above 0.90. This level was established empirically using sets of known good replicate arrays in our database.
Data preprocessing and normalization were automated using the BIAS system. Raw feature intensities were background corrected using the RMA background correction algorithm. Resulting expression estimates were converted to log2-ratios. Within array normalization was performed using spatial and intensity-dependent loess. Median absolute deviation scale normalization was used to normalize between arrays.

source_name: Breast tumor-associated stroma (laser capture microdissected)

label_protocol: 2 to 4 ng of total RNA was subjected to two rounds of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and labeled with Cy3 and Cy5 dyes according to the manufacturer’s procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: Tissue specimens were microdissected into epithelium and stroma using a PixCell IIe LCM system (Arcturus). All microdissections were performed within three hours following tissue staining. Total RNA was extracted from each population of microdissected cells using a GITC (guanidinium isothiocyanate) extraction protocol. Briefly, LCM caps were incubated for 5 minutes (room temperature) in 200 μl GITC extraction buffer (4 M GITC, 25 mM sodium citrate pH 7.0, 0.1 M β-mercaptoethanol, 0.5% N-lauroylsarcosine) supplemented with 1.6 μl β-mercaptoethanol. Subsequently, 20 μl of 2 M NaOAc, pH 4.0, 220 μl of water-saturated phenol and 60 μl of chloroform-isoamyl alcohol (23:1) were added to the extraction buffer. Following 15 minutes incubation on ice and centrifugation (12,000 rpm, 15 minutes) the aqueous phase was removed and RNA was precipitated with 2 μl glycogen (GenHunter, Nashville, Tennessee, USA) and 200 μl isopropanol. Samples were placed at -80°C for 30 minutes and centrifuged at 4°C (12,000 rpm) for 30 minutes to pellet RNA. Pellets were washed with 70% ethanol, air dried and subjected to DNAseI treatment (Roche, Basel, Switzerland). DNAseI treatment was performed in the presence of an RNase inhibitor (Invitrogen, Carlsbad, California, USA). Subsequently, samples were re-extracted as described above and re-suspended in 10 μl of diethylpyrocarbonate-treated water. RNA was quantified using a RiboGreen assay (Molecular Probes, Carlsbad, California, USA).

tag: GRADE

value: III

tag: Node Status

value: Negative

tag: ER

tag: PR

tag: Age

tag: Last Follow-Up

value: Alive Without Disease

source_name: Reference

label_protocol: RNA was subjected to one round of T7 linear amplification using Ambion Amino Allyl MessageAmp kit (Ambion, Austin, Texas, USA) and labeled with Cy3 and Cy5 dyes according to the manufacturer’s procedure. Prior to microarray hybridizations, amplified products were quantified using a spectrophotometer (Nanodrop, Wilmington, Delaware, USA) and subjected to BioAnalyzer to assay for quality (Agilent Technologies, Santa Clara, California, USA).

extract_protocol: No special procedures were required to extract this material


title: BreastStroma_Tumor_E1056_replicate2

description: No additional description

value: II

value: Positive

value: Dead of Disease

tag: Universal Human Reference RNA (Stratagene, ID #740000, La Jolla, California, USA)


title: BreastStroma_Tumor_E1116_replicate2

description: No additional description


title: BreastStroma_Tumor_E1188_replicate1

description: No additional description


title: BreastStroma_Tumor_E1125_replicate2

description: No additional description

value: Alive With Disease


title: BreastStroma_Tumor_E1174_replicate2

description: No additional description


title: BreastStroma_Tumor_E1188_replicate2

description: No additional description


title: BreastStroma_Tumor_E1125_replicate1

description: No additional description


title: BreastStroma_Tumor_E1174_replicate1

description: No additional description


title: BreastStroma_Tumor_E1197_replicate2

description: No additional description

value: I


title: BreastStroma_Tumor_E1056_replicate1

description: No additional description


title: BreastStroma_Tumor_E1197_replicate1

description: No additional description


title: MIA_2_MOE430_2

description: E18.5 FVB/N mouse embryos, SP-C/MIA control

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

source_name: MIA_SS: MIA, single transgenic


title: MIA_5_MOE430_2

description: E18.5 FVB/N mouse embryos, SP-C/MIA overexpressor

source_name: MIA_DS: MIA, double transgenic


title: BreastStroma_Tumor_E1084_replicate1

description: No additional description


title: BreastStroma_Tumor_E1223_replicate3

description: No additional description


title: BreastStroma_Tumor_E1227_replicate1

description: No additional description


title: BreastStroma_Tumor_E1217_replicate2

description: No additional description


title: BreastStroma_Tumor_E1227_replicate2

description: No additional description


title: BreastStroma_Tumor_E1199_replicate1

description: No additional description


title: BreastStroma_Tumor_E1223_replicate1

description: No additional description


title: BreastStroma_Tumor_E1217_replicate1

description: No additional description


title: BreastStroma_Tumor_E1228_replicate1

description: No additional description


title: BreastStroma_Tumor_E1239_replicate4

description: No additional description


title: BreastStroma_Tumor_E1239_replicate1

description: No additional description


title: BreastStroma_Tumor_E1223_replicate2

description: No additional description


title: BreastStroma_Tumor_E1239_replicate3

description: No additional description


title: BreastStroma_Tumor_E1223_replicate4

description: No additional description


title: BreastStroma_Tumor_E1317_replicate2

description: No additional description


title: BreastStroma_Tumor_E1199_replicate2

description: No additional description


title: BreastStroma_Tumor_E1314_replicate1

description: No additional description


title: BreastStroma_Tumor_E1257_replicate2

description: No additional description


title: BreastStroma_Tumor_E1277_replicate2

description: No additional description


title: BreastStroma_Tumor_E1314_replicate2

description: No additional description


title: BreastStroma_Tumor_E1228_replicate2

description: No additional description


title: BreastStroma_Tumor_E1292_replicate1

description: No additional description


title: BreastStroma_Tumor_E1317_replicate1

description: No additional description


title: BreastStroma_Tumor_E1292_replicate2

description: No additional description


title: BreastStroma_Tumor_E1383_replicate2

description: No additional description


title: BreastStroma_Tumor_E1383_replicate1

description: No additional description


title: BreastStroma_Tumor_E1277_replicate1

description: No additional description


title: BreastStroma_Tumor_E1417_replicate1

description: No additional description


title: BreastStroma_Tumor_E1257_replicate1

description: No additional description


title: BreastStroma_Tumor_E1239_replicate2

description: No additional description


title: BreastStroma_Tumor_E1417_replicate2

description: No additional description


title: BreastStroma_Tumor_E1469_replicate2

description: No additional description


title: BreastStroma_Tumor_E1467_replicate1

description: No additional description


title: BreastStroma_Tumor_E1467_replicate2

description: No additional description


title: BreastStroma_Tumor_E1423_replicate2

description: No additional description


title: BreastStroma_Tumor_E1527_replicate2

description: No additional description


title: BreastStroma_Tumor_E1423_replicate1

description: No additional description


title: BreastStroma_Tumor_E1469_replicate1

description: No additional description


title: BreastStroma_Tumor_E1525_replicate1

description: No additional description

value: ND


title: BreastStroma_Tumor_E1529_replicate2

description: No additional description


title: BreastStroma_Tumor_E1116_replicate1

description: No additional description


title: BreastStroma_Tumor_E1529_replicate1

description: No additional description


title: BreastStroma_Tumor_E1525_replicate2

description: No additional description


title: BreastStroma_Tumor_E1527_replicate1

description: No additional description


title: BreastStroma_Tumor_E1531_replicate1

description: No additional description


title: BreastStroma_Tumor_E1551_replicate1

description: No additional description


title: BreastStroma_Tumor_E1542_replicate1

description: No additional description


title: BreastStroma_Tumor_E1542_replicate2

description: No additional description


title: BreastStroma_Tumor_E1551_replicate2

description: No additional description


title: BreastStroma_Tumor_E1634_replicate1

description: No additional description


title: BreastStroma_Tumor_E1647_replicate2

description: No additional description


title: BreastStroma_Tumor_E1659_replicate2

description: No additional description


title: BreastStroma_Tumor_E1634_replicate2

description: No additional description


title: BreastStroma_Tumor_E1531_replicate2

description: No additional description


title: BreastStroma_Tumor_E1659_replicate1

description: No additional description


title: BreastStroma_Tumor_E1647_replicate1

description: No additional description


title: F1v_Seedling_78h_exp_rep4

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description:
accession: Van(f) x Col(m)
tissue: whole seedling
stage: 78 hour on MS plate
growth condition: Percival chamber, 12h light/12h dark, 20 degree

hyb_protocol: standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Probes selected were perfect match probes. Probes were megablasted against arabidopsis genome sequence to remove probes that cross-hybridize. For the expression study, probes were selected that were within annotated genes. Data were analyzed with the bioconductor package by Affy

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: F1v whole seedling at 78 hour

label_protocol: Invitrogen Bioprime random labeling

extract_protocol:
total RNA extracted by Qiagen RNeasy Plant Mini Kit
mRNA enriched by Qiagen Oligotex Kit
double-stranded cDNA synthesis by Invitrogen cDNA synthesis system
double-stranded cDNA purified by Qiagen Quick PCR Cleanup Kit

tag: Bioprime random labeling


title: F1v_Seedling_78h_exp_rep1


title: F1v_Seedling_78h_exp_rep2


title: Col_Seedling_78h_exp_rep4

description:
accession: Col
tissue: whole seedling
stage: 78 hour on MS plate
growth condition: Percival chamber, 12h light/12h dark, 20 degree

source_name: Col whole seedling at 78 hour


title: BreastStroma_Tumor_E1668_replicate2

description: No additional description


title: F1c_Seedling_78h_exp_rep3

description:
accession: Col(f) x Van(m)
tissue: whole seedling
stage: 78 hour on MS plate
growth condition: Percival chamber, 12h light/12h dark, 20 degree

source_name: F1c whole seedling at 78 hour


title: F1c_Seedling_78h_exp_rep2


title: Van_Seedling_78h_exp_rep4

description:
accession: Van
tissue: whole seedling
stage: 78 hour on MS plate
growth condition: Percival chamber, 12h light/12h dark, 20 degree

source_name: Van whole seedling at 78 hour


title: Col_Seedling_78h_exp_rep1

type: genomic

description:
accession: Columbia
tissue: whole seedling
stage: 78 hour on MS plate
growth condition: Percival chamber, 12h light/12h dark, 20 degree

molecule: genomic DNA


title: BreastStroma_Tumor_E1668_replicate1

description: No additional description


title: Col_Seedling_78h_exp_rep3


title: Van_Seedling_78h_exp_rep1


title: F1v_Seedling_78h_exp_rep3


title: F1c_Seedling_78h_exp_rep4


title: F1c_Seedling_78h_HpaII_rep4

data_processing: Probes selected were perfect match probes. Probes were megablasted against arabidopsis genome sequence to remove those that cross-hybridize. Data were calculated using the bioconductor package by Affy.

source_name: F1c whole seedling at 78 hour with hpaII digestion

label_protocol: Invitrogen  Bioprime random labeling

extract_protocol: Qiagen DNeasy Plant Mini Kit


title: Van_Seedling_78h_exp_rep2


title: Col_Seedling_78h_exp_rep2


title: BreastStroma_Tumor_E1672_replicate1

description: No additional description

value: Dead of other causes


title: BreastStroma_Tumor_E1677_replicate2

description: No additional description


title: BreastStroma_Tumor_E1672_replicate2

description: No additional description


title: F1c_Seedling_78h_HpaII_rep3


title: F1c_Seedling_78h_exp_rep1


title: BreastStroma_Tumor_E1715_replicate1

description: No additional description


title: Van_Seedling_78h_exp_rep3


title: BreastStroma_Tumor_E1696_replicate1

description: No additional description


title: F1c_Seedling_78h_MspI_rep4

source_name: F1c whole seedling at 78 hour with MspI digestion


title: BreastStroma_Tumor_E1677_replicate1

description: No additional description


title: BreastStroma_Tumor_E1696_replicate2

description: No additional description


title: BreastStroma_Tumor_E1745_replicate2

description: No additional description


title: F1c_Seedling_78h_MspI_rep3


title: BreastStroma_Tumor_E1715_replicate2

description: No additional description


title: BreastStroma_Tumor_E1751_replicate2

description: No additional description


title: F1c_Seedling_78h_HpaII_rep1


title: BreastStroma_Tumor_E1745_replicate1

description: No additional description


title: BreastStroma_Tumor_E1752_replicate1

description: No additional description


title: BreastStroma_Tumor_E1752_replicate2

description: No additional description


title: F1c_Seedling_78h_HpaII_rep2


title: F1v_Seedling_78h_MspI_rep3

source_name: F1v whole seedling at 78 hour with MspI digestion


title: BreastStroma_Tumor_E1751_replicate1

description: No additional description


title: BreastStroma_Tumor_E1808_replicate2

description: No additional description


title: F1v_Seedling_78h_MspI_rep4


title: BreastStroma_Tumor_E1808_replicate1

description: No additional description

tag: Extracted molecule


title: BreastStroma_Tumor_E1830_replicate2

description: No additional description


title: BreastStroma_Tumor_E1792_replicate2

description: No additional description


title: F1v_Seedling_78h_MspI_rep2


title: BreastStroma_Tumor_E1830_replicate1

description: No additional description


title: BreastStroma_Tumor_E1843_replicate1

description: No additional description


title: BreastStroma_Tumor_E1859_replicate2

description: No additional description


title: BreastStroma_Tumor_E1859_replicate1

description: No additional description


title: F1v_Seedling_78h_HpaII_rep4

source_name: F1v whole seedling at 78 hour with hpaII digestion


title: BreastStroma_Tumor_E1897_replicate1

description: No additional description


title: BreastStroma_Tumor_E1897_replicate2

description: No additional description


title: BreastStroma_Tumor_E1900_replicate2

description: No additional description


title: BreastStroma_Tumor_E1843_replicate2

description: No additional description


title: Van_Seedling_78h_MspI_rep2

source_name: Van whole seedling at 78 hour with MspI digestion


title: BreastStroma_Tumor_E1900_replicate1

description: No additional description


title: BreastStroma_Tumor_E1792_replicate1

description: No additional description


title: Van_Seedling_78h_MspI_rep3


title: BreastStroma_Tumor_E1901_replicate3

description: No additional description


title: F1v_Seedling_78h_MspI_rep1


title: Van_Seedling_78h_HpaII_rep4

source_name: Van whole seedling at 78 hour with hpaII digestion


title: F1c_Seedling_78h_MspI_rep2


title: F1v_Seedling_78h_HpaII_rep1


title: F1c_Seedling_78h_MspI_rep1


title: BreastStroma_Tumor_E1901_replicate2

description: No additional description


title: Col_Seedling_78h_HpaII_rep4

source_name: Col whole seedling at 78 hour with hpaII digestion

extract_protocol: Invitrogen Qiagen DNeasy Plant Mini Kit


title: F1v_Seedling_78h_HpaII_rep2


title: BreastStroma_Tumor_E1902_replicate2

description: No additional description

value: Negative:


title: BreastStroma_Tumor_E1902_replicate1

description: No additional description


title: BreastStroma_Tumor_E1901_replicate1

description: No additional description


title: Col_Seedling_78h_MspI_rep4

source_name: Col whole seedling at 78 hour with MspI digestion


title: BreastStroma_Tumor_E1957_replicate1

description: No additional description


title: Van_Seedling_78h_MspI_rep4


title: BreastStroma_Tumor_E1957_replicate2

description: No additional description


title: BreastStroma_Tumor_E1973_replicate1

description: No additional description


title: BreastStroma_Tumor_E1973_replicate2

description: No additional description


title: Van_Seedling_78h_HpaII_rep3


title: BreastStroma_Tumor_E1998_replicate2

description: No additional description


title: Control_10kXba_#8

status: Public on Apr 10 2008

city: London

first: Kajsa

last: Paulsson

address: John Vane Science Centre, Charterhouse Square

department: Medical Oncology Centre

country: United Kingdom

institute: Cancer Research UK

description: SNP genotype data from non-leukemic controls

hyb_protocol: Affymetrix 10K 2.0 mapping assay protocol and Affymetrix 500K mapping assay protocol

scan_protocol: Affymetrix GeneChip scanner 3000-7G

data_processing: GCOS, GTYPE. Gene calling algorithms MPALM and BRLLM, respectively.

source_name: ALL blood/bone marrow

growth_protocol: Not applicable

extract_protocol: DNA was prepared using standard proteinase K digestion and phenol/chloroform extraction

treatment_protocol: Mononuclear cells were harvested from peripheral blood or bone marrow of patients with ALL at presentation and cryopreserved in liquid nitrogen.

tag: non-leukemic control


title: Control_10kXba_#10

label_protocol: Affymetrix 10K 2.0 mapping assay protocol and Affymetrix 500K mapping assay protocol


title: Control_10kXba_#9


title: Control_10kXba_#7


title: Control_10kXba_#4


title: Van_Seedling_78h_HpaII_rep1


title: Control_10kXba_#6


title: BreastStroma_Tumor_E1998_replicate1

description: No additional description

source_name: Breast tumor-associated stroma (laser capture microdissected)


title: Control_10kXba_#5


title: Control_10kXba_#3


title: Van_Seedling_78h_HpaII_rep2


title: BreastStroma_Tumor_E1923_replicate2

description: No additional description

source_name: Reference


title: Col_Seedling_78h_MspI_rep2


title: Control_10kXba_#1


title: ALL_10kXba_#40

description: SNP genotype data from ALL patient at diagnosis

tag: ALL patient


title: ALL_10kXba_#42


title: ALL_10kXba_#39


title: ALL_10kXba_#44


title: ALL_10kXba_#41


title: Control_10kXba_#2


title: ALL_10kXba_#45


title: ALL_10kXba_#37


title: F1v_Seedling_78h_HpaII_rep3


title: ALL_10kXba_#36


title: ALL_10kXba_#43


title: Col_Seedling_78h_HpaII_rep2


title: Col_Seedling_78h_HpaII_rep3


title: ALL_10kXba_#38


title: ALL_10kXba_#33


title: ALL_10kXba_#32


title: ALL_10kXba_#30


title: ALL_10kXba_#29


title: ALL_10kXba_#34


title: ALL_10kXba_#28


title: ALL_10kXba_#31


title: ALL_10kXba_#27


title: ALL_10kXba_#23


title: ALL_10kXba_#24


title: ALL_10kXba_#25


title: BreastStroma_Tumor_E1923_replicate1

description: No additional description


title: Van_Seedling_78h_MspI_rep1


title: Col_Seedling_78h_MspI_rep3


title: ALL_10kXba_#21


title: ALL_10kXba_#22


title: ALL_10kXba_#35


title: Col_Seedling_78h_MspI_rep1


title: ALL_10kXba_#15


title: ALL_10kXba_#5


title: ALL_10kXba_#7


title: ALL_10kXba_#10


title: ALL_10kXba_#6


title: ALL_10kXba_#9


title: ALL_10kXba_#16


title: ALL_10kXba_#8


title: ALL_10kXba_#3


title: Col_Seedling_78h_HpaII_rep1

description: starting DNA for labeling is ~300ng


title: ALL_10kXba_#4


title: ALL_10kXba_#13


title: ALL_10kXba_#12


title: ALL_10kXba_#1


title: ALL_10kXba_#20


title: ALL_10kXba_#2


title: ALL_10kXba_#19


title: ALL_10kXba_#18


title: ALL_10kXba_#11


title: Control_250kSty_#9


title: Control_250kSty_#8


title: ALL_10kXba_#14


title: ALL_10kXba_#26


title: ALL_10kXba_#17


title: Control_250kSty_#4


title: Control_250kSty_#6


title: ALL_250kSty_#45


title: Control_250kSty_#10


title: Control_250kSty_#3


title: Control_250kSty_#5


title: ALL_250kSty_#42


title: Control_250kSty_#1


title: Control_250kSty_#7


title: Control_250kNsp_#9


title: ALL_250kSty_#41


title: Control_250kNsp_#10


title: ALL_250kSty_#40


title: Control_250kNsp_#5


title: ALL_250kSty_#38


title: Control_250kNsp_#4


title: Control_250kNsp_#8


title: Control_250kSty_#2


title: Control_250kNsp_#6


title: ALL_250kSty_#44


title: Control_250kNsp_#7


title: ALL_250kSty_#43


title: ALL_250kSty_#39


title: Control_250kNsp_#2


title: Control_250kNsp_#1


title: ALL_250kSty_#35


title: ALL_250kSty_#37


title: ALL_250kNsp_#45


title: ALL_250kNsp_#44


title: Control_250kNsp_#3


title: ALL_250kSty_#36


title: ALL_250kNsp_#43


title: ALL_250kSty_#30


title: ALL_250kNsp_#39


title: ALL_250kSty_#27


title: ALL_250kSty_#31


title: ALL_250kSty_#26


title: ALL_250kSty_#28


title: ALL_250kNsp_#36


title: ALL_250kSty_#32


title: ALL_250kSty_#29


title: ALL_250kSty_#34


title: ALL_250kSty_#25


title: ALL_250kNsp_#35


title: ALL_250kSty_#23


title: ALL_250kNsp_#40


title: ALL_250kNsp_#38


title: ALL_250kNsp_#41


title: ALL_250kSty_#33


title: ALL_250kNsp_#32


title: ALL_250kNsp_#42


title: ALL_250kNsp_#33


title: ALL_250kNsp_#37


title: ALL_250kNsp_#34


title: ALL_250kSty_#24


title: ALL_250kSty_#20


title: ALL_250kSty_#19


title: ALL_250kSty_#21


title: ALL_250kSty_#16


title: ALL_250kNsp_#28


title: ALL_250kSty_#22


title: ALL_250kNsp_#30


title: ALL_250kSty_#15


title: ALL_250kNsp_#29


title: ALL_250kSty_#12


title: ALL_250kNsp_#31


title: ALL_250kSty_#9


title: ALL_250kSty_#13


title: ALL_250kNsp_#23


title: ALL_250kNsp_#26


title: ALL_250kNsp_#24


title: ALL_250kNsp_#20


title: ALL_250kNsp_#27


title: ALL_250kSty_#7


title: ALL_250kSty_#8


title: ALL_250kNsp_#21


title: ALL_250kNsp_#19


title: ALL_250kNsp_#18


title: ALL_250kSty_#5


title: ALL_250kSty_#11


title: ALL_250kSty_#4


title: ALL_250kNsp_#17


title: ALL_250kNsp_#15


title: ALL_250kSty_#17


title: ALL_250kSty_#6


title: ALL_250kSty_#14


title: ALL_250kNsp_#22


title: WCE fraction of Ino80Myc expression cells for Ino80Myc_random1 ChIP

city: Sendai

first: Yukako

last: Oma

address: Tsutsumidori-Amamiyamachi 1-1, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

description:
WCE fraction used for the nomalization of Ino80Myc_random1 ChIP fraction
Baseline for Ino80-Myc distribution of randomly cultured Ino80-Myc expressing cells

hyb_protocol: Following denaturation at 100 C for 10 minutes, cooling, and spin-down, 200 micro liter of hybridization mixuter was hybridized for 16 hours at 42 C on GeneChip SC3456a520015F using hybridization oven 640 (Affymetrix). Each hybridization mixture contains the end-labbeled DNA, 6xSSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 (Affymetrix) and hybridization control (Affymetrix).

scan_protocol: Washing and scanning protocol (EukGE-WS1v3) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix). Arrays were scanned by Hewlett-Packard GeneArray Scanner at an emission wavelength of 560 nm at 7.5 microM resolution.

data_processing:
Data analyses were performed as previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol.409,chapter 23,389-410 in “DNA Repair” (edited by J.Campbell) (2006).
Primary data analyses were carried out with GeneChip Operating Software (GCOS 1.4) using default settings to obtain signal and detection p-value.
To discriminate significant signals for binding to DNA, signals from the ChIP fraction scan were compared to the WCE fraction scan with GCOS 1.4 using default settings.

source_name: Fragmented whole genomic DNA

label_protocol: End labeling by terminal transferase

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown in 200 ml of YPD to 1x10e7 cells/ml at 30C.

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
0.7% of the WCE was used for a preparation of WCE fraction (input).
The WCE fraction were incubated overnight at 37C with proteinase K, incubated for 6 hours at 65C, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in TE and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, Nature). The amplified DNA was digested with DNase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.

treatment_protocol:
2x10e9 cells from 200ml culture were fixed by 1% formaldehyde for 15min at 30C.
The cells were washed with sterilized water. The cells were washed with ice-cold TBS, freezed in liquid nitrogen, and stored at -80C.

tag: W303 background cells expressing Myc-tagged Ino80

tag: Strain


title: ALL_250kNsp_#25


title: ALL_250kSty_#2


title: WCE fraction of Ino80Myc expression cells for Ino80Myc_alpha1 and _alpha2 ChIP

description:
WCE fraction used for the nomalization of Ino80Myc_alpha1 and_alpha2 ChIP fraction
Baseline for Ino80-Myc distribution of Ino80-Myc expressing cells arrested by alpha-factor

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown in 200 ml of YPD to 0.5x10e7 cells/ml at 30C. Cells were washed twice with sterile water and grown in 200 ml of YPD pH4.5 containing 2.5 ug/ml of alpha-factor for 90min at 30C.


title: ALL_250kSty_#10


title: ALL_250kNsp_#14


title: WCE fraction of WT cells for Ino80_nontag_random1 ChIP

description:
WCE fraction used for the nomalization of Ino80_nontag_random1 ChIP fraction
Baseline for ChIP fraction of randomly cultured non-tagged WT cell

tag: W303 background cells


title: ALL_250kNsp_#12


title: ALL_250kSty_#1


title: ALL_250kNsp_#13


title: ALL_250kNsp_#16


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_08Ino80Myc_alpha2_ip

description:
ChIP-chip data used for the mapping of Ino80 distribution on chromosome III-VIR
Used baseline: WCE fraction of Ino80-Myc expressing cells arrested by alpha-factor

scan_protocol: Washing and scanning protocol (EukGE-WS1v3) provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 400, Affymetrix). Arrays were scanned by GeneChip Scanner 3000 7G.

source_name: Chromatin-immunoprecipitated DNA

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
The WCE was immunoprecipitated with anti-Myc monoclonal antibody 9E11 (abcam, ab56) coupled to Dynabeads (Invitrogen, protein A Dynabeads).
The chromatin immunoprecipitated sample was incubated overnight at 65ºC, incubated with proteinase K, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in TE and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, Nature). The amplified DNA was digested with DNase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_10Ino80Myc_HU1_ip

description: Used baseline: WCE fraction of Ino80-Myc expressing cells arrested by hydroxyures

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown in 200 ml of YPD to 0.5x10e7 cells/ml at 30C. Cells were washed twice with sterile water and grown in 200 ml of YPD pH4.5 containing 2.5 ug/ml of alpha-factor for 90min at 30C. Cells arrested in G1 phase were washed twice with sterile water and grown in 200 ml of YPD contining 0.2M of hydroxyurea for 60min at 30C.


title: ALL_250kSty_#18


title: ALL_250kSty_#3


title: WCE fraction of Ino80Myc expression cells for Arp5 ChIP 2

description:
WCE fraction used for the nomalization of ChIP fraction
Baseline of Arp5 distribition

hyb_protocol: Following denaturation at 100 C for 10 minutes, cooling, and spin-down, 200 micro liter of hybridization mixuter was hybridized for 16 hours at 42 C on GeneChip SC3456a520015F using hybridization oven 640 (affymetrix). Each hybridization mixture contains the end-labbeled DNA, 6xSSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 (affymetrix) and hybridization control (affymetrix).

growth_protocol: Cells were grown on a YPD plate for 2 days at 30C. The cells were grown in 200ml of YPD to a density of 1x10e7 cells/ml at 30C.

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Whole cell extract was sonicated to obtain average 500 bp genomic DNA fragments.
The WCE was immunoprecipitated with anti-Myc monoclonal antibody 9E11 (abcam, ab56) coupled to Dynabeads (Invitrogen, protein A Dynabeads).
The chromatin immunoprecipitated sample was incubated overnight at 65ºC, incubated with proteinase K, extracted with phenol/chloroform/isoamylalcohol, precipitated, and resuspended in TE and incubated with RNaseA.
The DNA was amplified by PCR after random priming as previously described (Katou et al., 2003, nature). The amplified DNA was digested with Dnase I to a mean size of 100 bp. After DNase I inactivation at 95ºC, fragments were labelled with indicated label protocol.

treatment_protocol:
2x10e9 cells from 200ml culture were fixed by 1% formaldehyde for 15min at 30C.
The cells were washed with sterilized water. The cells were washed with ice-cold TBS, freezed with liquid nitrogen, and stored at -80C.

tag: W303 background cells expressing Myc tagged Ino80

tag: Cultrue:


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_05Ino80Myc_random2_ip

description:
ChIP-chip data used for the mapping of Ino80 distribution on chromosome III-VIR
Used baseline: WCE fraction of randumly cultured Ino80Myc expression cells for Ino80Myc ChIP


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_02Ino80_nontag_random1_ip

description:
ChIP-chip data to check the non-specific binding of Myc antibody on chromosome III-VIR
Used baseline: WCE fraction of randomly cultured non-tagged WT cells


title: ALL_250kNsp_#7


title: WCE fraction of Ino80Myc expression cells for Ino80Myc_HU1 and _HU ChIP

description: Baseline for Ino80-Myc distribution of Ino80-Myc expressing cells arrested by hydroxyures

label: Biotin


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_07Ino80Myc_alpha1_ip


title: WCE fraction of Ino80Myc expression cells for Ino80Myc ChIP 1

description:
WCE fraction used for the nomalization of ChIP fraction
Baseline of Ino80-Myc distribution


title: INO80 chromatin remodeling complex promotes the restart of DNA replication 2

description:
ChIP-chip data used for the mapping of Arp5 distribution on chromosome III-VIR
Used baseline: WCE fraction of Ino80Myc expression cells for Arp5 ChIP


title: ALL_250kNsp_#6


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_03Ino80Myc_random1_ip


title: ALL_250kNsp_#8


title: ALL_250kNsp_#9


title: ALL_250kNsp_#5


title: 30d lead-exposed (replicate C) vs. non-exposed fathead minnows

status: Public on Apr 07 2008

city: Miami

first: Edward

last: Mager

address: 4600 Rickenbacker Cswy.

department: MBF

institute: University of Miami, RSMAS

description: Equal amounts of RNA from all no lead controls were pooled (12 fish total) for hybridization with each of 3 replicate pools (4 fish total) of RNA from age-matched, lead-exposed fish.

hyb_protocol: All hybridizations were performed using the 3DNA Array 900 detection kit (Genisphere) as follows: cDNA Hybridization 1. Thaw and resuspend the 2X Hybridization Buffer by heating to 65-70°C for at least 10 minutes or until completely resuspended. Vortex to ensure that the components are resuspended evenly. If necessary, repeat heating and vortexing until all the material has been resuspended. Microfuge for 1 minute. 2. For each array, prepare the following cDNA Hybridization Mix for use with a 24x60 glass coverslip and 2X Enhanced Hybridization Buffer: 12.7 μl cDNA Synthesis #1 12.7 μl cDNA Synthesis #2 29 μl 2X Enhanced Hybridization Buffer 1.6 μl Nuclease Free Water 2 μl LNA dT Blocker 58μl total volume 3. Gently vortex and briefly microfuge the cDNA Hybridization Mix after addition of all components.  Incubate the Hybridization Mix first at 75-80°C for 10 minutes, and then at 53°C until loading the array.  Pre-warm the microarrays to 53°C. 4. Gently vortex and briefly microfuge the cDNA Hybridization Mix. Add the cDNA Hybridization Mix to a pre-warmed microarray, taking care to leave behind any precipitate at the bottom of the tube. 5. Apply the glass coverslip to the array. Incubate the array overnight in a dark humidified chamber at 53°C. Post cDNA Hybridization Wash 1. Prewarm the 2X SSC, 0.2%SDS wash buffer to 42°C. 2. Remove the coverslip by washing the array in prewarmed 2X SSC, 0.2% SDS for 2-5 minutes or until the coverslip floats off. 3. Wash for 10-15 minutes in prewarmed 2X SSC, 0.2%SDS. 4. Wash for 10-15 minutes in 2X SSC at room temperature. 5. Wash for 10-15 minutes in 0.2X SSC at room temperature. 6. Transfer the array to a dry 50 mL centrifuge tube, orienting the slide so that any label is at the bottom of the tube. Immediately centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide. 3DNA Hybridization 1. Prepare the 3DNA Capture Reagent to break up aggregates that may form during the freezing process. a. Thaw the 3DNA Capture Reagent in the dark at room temperature for 20 minutes. b. Vortex at the maximum setting for 3 seconds and microfuge briefly. c. Incubate at 50-55°C for 10 minutes. d. Vortex at the maximum setting for 3-5 seconds. e. Microfuge the tube briefly to collect the contents at the bottom.  Check the sample for aggregates and repeat vortexing if necessary. Repeat steps a-e if necessary. 2. Thaw and resuspend the 2X Hybridization Buffer by heating to 70°C for at least 10 minutes or until completely resuspended. Vortex to ensure that the components are resuspended evenly. If necessary, repeat heating and vortexing until all the material has been resuspended. Microfuge for 1 minute. 3. Prepare a stock solution of Anti-Fade Reagent by combining 1 μl of Anti-Fade with 100 μl of the 2X Hybridization Buffer to be used in the 3DNA hybridization. 4. For each array, prepare a 3DNA Hybridization Mix as follows: 2.5 μl 3DNA Capture Reagent #1 2.5 μl 3DNA Capture Reagent #2 20 μl Nuclease Free Water 25 μl 2X Hybridization Buffer (with Anti-Fade Reagent from step 3) Add 1.0μl Cot-1 DNA (denatured at 95-100°C for 10 minutes prior to use) to the cDNA Hybridization Mix. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. Incubate the 3DNA Hybridization Mix first at 75-80°C for 10 minutes, and then at the hybridization temperature until loading the array.  Pre-warm the microarrays to 62°C. 6. Gently vortex and briefly microfuge the 3DNA Hybridization Mix. Add the 3DNA Hybridization Mix to a prewarmed microarray, taking care to leave behind any precipitate at the bottom of the tube. 7. Apply a glass coverslip to the array. Incubate the array for 4 hours in a dark humidified chamber at 62°C. Post 3DNA Hybridization Wash 1. Prewarm the 2X SSC, 0.2%SDS wash buffer at 65°C. 2. Remove the coverslip by washing the array in prewarmed 2X SSC, 0.2% SDS for 2-5 minutes or until the coverslip floats off. 3. Wash for 10-15 minutes in prewarmed 2X SSC, 0.2%SDS. 4. Wash for 10-15 minutes in 2X SSC at room temperature. 5. Wash for 10-15 minutes in 0.2X SSC at room temperature. 6. Transfer the array to a dry 50mL centrifuge tube, orienting the slide so that any label is at the bottom of the tube.  Immediately centrifuge without the tube cap for 2 minutes at 800-1000 RPM to dry the slide.

scan_protocol: An ArrayWoRx Biochip Reader (Applied Precision) and GenePix software version 3.01 (Molecular Devices) were used to scan and quantify hybridization signals, respectively.

data_processing: An in-house, α-outlier-generating model approach was employed for determination of statistically-significant changes in gene expression as previously described (Loguinov AV, Mian IS, Vulpe CD. 2004. Exploratory differential gene expression analysis in microarray experiments with no or limited replication. Genome Biol 5(3):R18).

organism: Pimephales promelas

source_name: Pool of 12 control fathead minnows not exposed to lead (Pb)

label_protocol: Synthesis of Cy5-labeled cDNA was performed using the 3DNA Array 900 detection kit (Genisphere) and SuperScript II reverse transcriptase (Invitrogen) with 1 μg total RNA at 42°C for 2 h.

growth_protocol: Fathead minnows were obtained at <24h post-hatch on arrival and distributed evenly among 18 1 L plastic beakers (~70 fish per beaker, 3 replicates per treatment).  Fish were fed freshly hatched Artemia nauplii once daily.  Prior to feeding, any fish that had perished were removed, the mortality was recorded and leftover food and feces were siphoned out. Average water temperature throughout the exposures was 22°C ±1.

extract_protocol: Total RNA was isolated from whole fish using RNA STAT-60 solution (Tel-Test) and a Polytron homogenizer following the manufacturer’s recommended procedure. From each isolate 10 µg was subsequently treated with DNase I to remove any traces of genomic DNA using the Turbo DNA-free kit (Ambion). DNase-treated RNA was quantified spectrophotometrically and integrity confirmed by gel electrophoresis prior to cDNA synthesis.

treatment_protocol: Control treatment (no Pb) fish were reared in 2:1 deionized water:dechlorinated Virginia Key tap water. Fish were collected and euthanized 30 days after initiation of exposures to age-matched Pb treatments and immediately snap-frozen in liquid nitrogen for future processing.

tag: 4 whole body control fish from each of 3 replicate beakers (A, B, & C).  Age

value: 37 days.

source_name: 30d lead-exposed fathead minnows, replicate beaker C

label_protocol: Synthesis of Cy3-labeled cDNA was performed using the 3DNA Array 900 detection kit (Genisphere) and SuperScript II reverse transcriptase (Invitrogen) with 1 μg total RNA at 42°C for 2 h.

treatment_protocol: Following one week of acclimation, Pb exposures were carried by dispensing concentrated PbNO3 solutions to 2:1 deionized water:dechlorinated Virginia Key tap water, maintaining final concentrations of approximately 170 nM Pb. Fish were collected and euthanized following 30 days of exposure and immediately snap-frozen in liquid nitrogen for future processing.

tag: Pool of 4 whole body fish exposed to lead (Pb) for 30d from replicate beaker C. Age


title: 30d lead-exposed (replicate C) vs. non-exposed fathead minnows (repeat)


title: INO80 chromatin remodeling complex promotes the restart of DNA replication 1

description:
ChIP-chip data used for the mapping of Ino80 and Arp5 distribution on chromosome III-VIR.
Used baseline: WCE fraction of Myc tagged-Ino80 expressing cells

hyb_protocol: The hybridization mixture (End-labelled DNA, 6x SSPE, 0.005% Triton X-100, 0.1 mg/ml herring sperm DNA, oligo B2 and hybridization control (Affymetrix) ) was denatured at 100C for 10 min and hybridized to GeneChip SC3456a520015F for 16 hr at 42C using hybridization oven 640 (Affymetrix).

scan_protocol: Washing and scanning protocol EukGE-WS1v3 was performed automatically on a GeneChip fluidics station 400 (Affymetrix). Microarrays were scanned by GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data analyses were performed as previously described in Methods in Enzymology, Elsevier Life Sciences (CA), vol. 409, Chapter 23, 389-410 in “DNA repair” (edited by J. Campbell, 2006). Initial data of each single chip was provided with GeneChip Operating Softwere (GCOS 1.4) using default parameters to obtain signal intensity value and detection p-value. To discriminate significant signals for protein binding profile, signal intensity values of the ChIP fraction were compared to that of WCE fraction with GCOS 1.4 using default setting.

growth_protocol: Cells were grown in 200 ml of YPD to a density of 1x10e7 cells/ml at 30C. For synchronous culture, precultured cells were washed twice and resuspended at 0.7x10e7 cell/ml in YPD (pH4.5) containing 2.5 ug/ml of alpha-factor. For G1-arrest, the cells were treated for 90 min at 30C and then fixed with 1% formaldehyde. For early S phase arrest, the cells treated with alpha-factor treated were washed twice, treated with YPD containing 0.2 M of hydroxyurea for 60 min at 30C, and then fixed with 1 % formaldehyde.

extract_protocol: Chromatin immunoprecipitations were performed as previously described (Katou et al. 2003, Nature). Cells were disrupted by Multi-Beads Shocker (Yasui KIKAI, Osaka) with 0.5 mm zirconia beads. Whole cell extract was sonicated to produce an average DNA fragment size of 500 bp. Protein-DNA complexes were immunoprecipitated with 3 ul of the anti-Myc monoclonal antibody 9E11 (Abcam, ab56) or 3ul of an anti-Arp5 polyclonal antibody (Kitayama et al., submitted) bound to Dynabeads protein A (DYNAL). Precipitated complexes were eluted in 50 mM Tris-HCl (pH8.0), 10 mM EDTA, 1% SDS and in TE containing 0.67% of SDS at 65C, treated by proteinase K for 8hr at 37C, and incuvated for 6hr at 65C for reverse crosslink. The eluted fraction was subjected to phenol/chloroform/isoamylalcohol extraction twice and to ethanol precipitation. Purified DNA was suspended in TE containing RNaseA and incubated for 1 hr at 37C. DNA was amplified by PCR after random priming and digested by DNase I to an average size of 100 bp. After the inactivation of DNase I at 95C, the ends of DNA fragments were labeled with Biotin-11-ddATP (Perkin Elmer, P/N NEL548).

treatment_protocol: 2x10e9 cells from 200 ml were fixed by 1% formaldehyde for 15 min at 30C. Cells were washed with ice-cold TBS and stored at -80C.

tag: W303 background cells expressing Myc tagged-Ino80.

tag: Cultrue

value: YPD


title: 30d lead-exposed (replicate A) vs. non-exposed fathead minnows (repeat)

source_name: 30d lead-exposed fathead minnows, replicate beaker A

tag: Pool of 4 whole body fish exposed to lead (Pb) for 30d from replicate beaker A. Age


title: 30d lead-exposed (replicate B) vs. non-exposed fathead minnows

source_name: 30d lead-exposed fathead minnows, replicate beaker B

tag: Pool of 4 whole body fish exposed to lead (Pb) for 30d from replicate beaker B. Age


title: ALL_250kNsp_#4


title: 30d lead-exposed (replicate C) vs. non-exposed fathead minnows (dye swap)


title: ALL_250kNsp_#3


title: 30d lead-exposed (replicate A) vs. non-exposed fathead minnows (dye swap)


title: 30d lead-exposed (replicate A) vs. non-exposed fathead minnows


title: 30d lead-exposed (replicate A) vs. non-exposed fathead minnows (dye swap-repeat)


title: 10d lead-exposed (replicate C) vs. non-exposed fathead minnows

treatment_protocol: Control treatment (no Pb) fish were reared in 2:1 deionized water:dechlorinated Virginia Key tap water. Fish were collected and euthanized 10 days after initiation of exposures to age-matched Pb treatments and immediately snap-frozen in liquid nitrogen for future processing.

value: 17 days.

source_name: 10d lead-exposed fathead minnows, replicate beaker C

treatment_protocol: Following one week of acclimation, Pb exposures were carried by dispensing concentrated PbNO3 solutions to 2:1 deionized water:dechlorinated Virginia Key tap water, maintaining final concentrations of approximately 170 nM Pb. Fish were collected and euthanized following 10 days of exposure and immediately snap-frozen in liquid nitrogen for future processing.

tag: Pool of 4 whole body fish exposed to lead (Pb) for 10d from replicate beaker C. Age


title: 10d lead-exposed (replicate A) vs. non-exposed fathead minnows (dye swap)

source_name: 10d lead-exposed fathead minnows, replicate beaker A

tag: Pool of 4 whole body fish exposed to lead (Pb) for 10d from replicate beaker A. Age


title: ALL_250kNsp_#11


title: INO80 chromatin remodeling complex promotes the restart of DNA replication_11Ino80Myc_HU2_ip


title: 10d lead-exposed (replicate C) vs. non-exposed fathead minnows (dye swap)


title: ALL_250kNsp_#2


title: 10d lead-exposed (replicate A) vs. non-exposed fathead minnows


title: 4d lead-exposed (replicate C) vs. non-exposed fathead minnows

description: Equal amounts of RNA from all no lead controls were pooled (18 fish total) for hybridization with each of 3 replicate pools (6 fish total) of RNA from age-matched, lead-exposed fish.

source_name: Pool of 18 control fathead minnows not exposed to lead (Pb)

treatment_protocol: Control treatment (no Pb) fish were reared in 2:1 deionized water:dechlorinated Virginia Key tap water. Fish were collected and euthanized 4 days after initiation of exposures to age-matched Pb treatments and immediately snap-frozen in liquid nitrogen for future processing.

tag: 6 whole body control fish from each of 3 replicate beakers (A, B, & C).  Age

value: 11 days.

source_name: 4d lead-exposed fathead minnows, replicate beaker C

treatment_protocol: Following one week of acclimation, Pb exposures were carried by dispensing concentrated PbNO3 solutions to 2:1 deionized water:dechlorinated Virginia Key tap water, maintaining final concentrations of approximately 170 nM Pb. Fish were collected and euthanized following 4 days of exposure and immediately snap-frozen in liquid nitrogen for future processing.

tag: Pool of 6 whole body fish exposed to lead (Pb) for 4d from replicate beaker C. Age


title: ALL_250kNsp_#10


title: ALL_250kNsp_#1


title: 10d lead-exposed (replicate B) vs. non-exposed fathead minnows

source_name: 10d lead-exposed fathead minnows, replicate beaker B

tag: Pool of 4 whole body fish exposed to lead (Pb) for 10d from replicate beaker B. Age


title: 4d lead-exposed (replicate B) vs. non-exposed fathead minnows (repeat)

source_name: 4d lead-exposed fathead minnows, replicate beaker B

tag: Pool of 6 whole body fish exposed to lead (Pb) for 4d from replicate beaker B. Age


title: 4d lead-exposed (replicate B) vs. non-exposed fathead minnows


title: 30d lead-exposed (replicate B) vs. non-exposed fathead minnows (dye swap)


title: 4d lead-exposed (replicate A) vs. non-exposed fathead minnows

source_name: 4d lead-exposed fathead minnows, replicate beaker A

tag: Pool of 6 whole body fish exposed to lead (Pb) for 4d from replicate beaker A. Age


title: 4d lead-exposed (replicate C) vs. non-exposed fathead minnows (dye swap)


title: 10d lead-exposed (replicate B) vs. non-exposed fathead minnows (dye swap)


title: histidine kinase (apsS) with5ug/ml indolicidin biological rep 1

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_histidine kinase (apsS) with 5ug/ml indolicidin biological rep 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Se genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

source_name: apsS treated rep 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: For microarray experiments, overnight cultures were diluted 1:100 into 50 ml of TSB and incubated at 37C with shaking at 180rpm until grown to an OD600 of 2.5-3.0 (mid-logarithmic growth phase). Cultures were then split in two equal volumes and cells were washed twice in 10 mM sodium phosphate buffer (pH 6.5) with 100 mM NaCl and resuspended in the same buffer.

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: To one sample,  indolicidin was added to a final concentration of 5ug /ml. Samples were incubated at 37°C for 3 h.


title: 2d lead-exposed (replicate C) vs. non-exposed fathead minnows (dye swap-repeat)

source_name: 2d lead-exposed fathead minnows, replicate beaker C

treatment_protocol: Following one week of acclimation, Pb exposures were carried by dispensing concentrated PbNO3 solutions to 2:1 deionized water:dechlorinated Virginia Key tap water, maintaining final concentrations of approximately 170 nM Pb. Fish were collected and euthanized following 2 days of exposure and immediately snap-frozen in liquid nitrogen for future processing.

tag: Pool of 6 whole body fish exposed to lead (Pb) for 2d from replicate beaker C. Age

value: 9 days.

treatment_protocol: Control treatment (no Pb) fish were reared in 2:1 deionized water:dechlorinated Virginia Key tap water. Fish were collected and euthanized 2 days after initiation of exposures to age-matched Pb treatments and immediately snap-frozen in liquid nitrogen for future processing.


description: Gene expression data from_histidine kinase (apsS) with 5ug/ml indolicidin biological rep 3

source_name: apsS treated rep 3


description: Gene expression data from_histidine kinase (apsS) without indolicidin biological rep 1

source_name: apsS untreated rep 1


description: Gene expression data from_histidine kinase (apsS) without indolicidin biological rep 3

source_name: apsS untreated rep 3


description: Gene expression data from_histidine kinase (apsS) with 5ug/ml indolicidin biological rep 2

source_name: apsS treated rep 2


description: Gene expression data from_wt with 5ug/ml indolicidin biological rep 3

source_name: wt treated rep 3


description: Gene expression data from_histidine kinase (apsS) without indolicidin biological rep 2

source_name: apsS untreated rep 2


description: Gene expression data from_wt with 5ug/ml indolicidin biological rep 1

source_name: wt treated rep 1


title: 4d lead-exposed (replicate A) vs. non-exposed fathead minnows (dye swap)


title: 2d lead-exposed (replicate C) vs non-exposed fathead minnows


description: Gene expression data from_wt with 5ug/ml indolicidin biological rep 2

source_name: wt treated rep 2


title: 2d lead-exposed (replicate C) vs. non-exposed fathead minnows (dye swap)


title: 2d lead-exposed (replicate B) vs. non-exposed fathead minnows

source_name: 2d lead-exposed fathead minnows, replicate beaker B

tag: Pool of 6 whole body fish exposed to lead (Pb) for 2d from replicate beaker B. Age


title: 2d lead-exposed (replicate A) vs. non-exposed fathead minnows

value: 9 days

source_name: 2d lead-exposed fathead minnows, replicate beaker A

tag: Pool of 6 whole body fish exposed to lead (Pb) for 2d from replicate beaker A. Age


title: 2d lead-exposed (replicate A) vs. non-exposed fathead minnows (dye swap)

source_name: Pool of 18 control fathead minnows not exposed to lead (Pb)


title: 2d lead-exposed (replicate B) vs. non-exposed fathead minnows (repeat)


title: 2d lead-exposed (replicate B) vs. non-exposed fathead minnows (dye swap)


title: wt without indolicidin biological rep 1

description: Gene expression data from_wt without indolicidin biological rep 1

source_name: wild type untreated rep 1


title: Mammary Gland_QSi5_Lactation day 9_rep2

status: Public on Apr 03 2008

city: Camperdown

first: Peter

last: Williamson

state: NSW

address: RMC Gunn Building, B19

department: Faculty of Veterinary Science

country: Australia

institute: University of Sydney

description: 3 replicates from each strain were hybridised to MOE 430 v2 Genechip (45,101 probesets) while another 2 replicates from each strain were hybridised to MOE 430 A v2 Genechip(22,690 probesets). So normalisation was done using the data from 22,690 probesets common to both chip types using "matchprobes" package available from http://www.bioconductor.org in R

hyb_protocol: Samples that pass QC were then prepared for hybridisation to the Mouse 430 A version 2.0 GeneChip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul was prepared for each sample and 200ul loaded into a Mouse 430 A version 2.0 GeneChip.  The chip was hybridised at 45C for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip was washed using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: Upon completion of the washing, the chips are then scanned using the Affymetrix GeneChip Scanner 3000.  The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL and CHP files for analysis.

data_processing: Quantile normalisation and calculation of probe-set intensity was performed using the robust-multi array average (RMA) function available from the “affy” package in R (Gautier et al., 2004). Data filtering removed low intensity probesets close to background noise by selecting probesets having an un-logged intensity of over 20 in at least one of the conditions. Differential expression was assessed by ranked penalised t-statistics on the logged data using lm.series and e-bayes function in the “limma” package in R (Smyth, 2004).

source_name: Mammary gland excised from lactating day 9 QSi5 strain of mice

label_protocol: A total of 7ug was labelled using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  The subsequent cDNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cDNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  A total of 20ug of labelled cRNA was then fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.

extract_protocol: Total RNA was extracted from 20 mg of mammary tissue by using Qiagen RNeasy Minipreps according to the manufacturer’s instructions.Mouse total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

treatment_protocol: Mammary glands were immediately snap frozen in Liquid Nitrogen and stored at -80 degree C.

tag: Strain-QSi5; Female; RNA isolated from inguinal mammary glands collected from Day 9 lactating mice


title: Mammary Gland_CBA_Lactation day 9_rep2

source_name: Mammary gland excised from lactating day 9 CBA strain of mice

tag: Strain-CBA/CaH; Female; RNA isolated from inguinal mammary glands collected from Day 9 lactating mice


title: Mammary Gland_QSi5_Lactation day 9_rep1


title: wt without indolicidin biological rep 3

description: Gene expression data from_wt without indolicidin biological rep 3

source_name: wild type untreated rep 3


title: wt without indolicidin biological rep 2

description: Gene expression data from_wt without indolicidin biological rep 2

source_name: wild type untreated rep 2


title: 4d lead-exposed (replicate B) vs. non-exposed fathead minnows (dye swap)

source_name: 4d lead-exposed fathead minnows, replicate beaker B


title: Mammary Gland_CBA_Lactation day 9_rep3


title: Striatum from saline treated mutant animal, biological rep. 3

city: Heidelberg

first: Jan

last: Rodriguez Parkitna

address: Im Neuenheimer Feld 581

country: Germany

institute: German Cancer Research Center

description: Gene expression data from mutant animals treated with cocaine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on mouse 430A 2.0 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Analysis of array data was performed using the R 2.4.1/Bioconductor 1.9 (Gentleman et al. 2004) . Data was normalized and expression values were computed using the gcrma method.

source_name: The striatum including nucleus accumbens from saline treated mutant animal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 to 6 week-old littermate female mice were single-caged and handled for 5 days

extract_protocol: Whole brains were removed and placed in RNAlater (Ambion) overnight. Brains were sliced into 150 μm-thick vibratome sections and the striatum including the nucleus accumbens was excised with thin needles. Total RNA was prepared with Rneasy RNA Mini kit (Qiagen) and its quality was assessed on RNA LabChips (Agilent).

treatment_protocol: Intra peritoneal injection of 25 mg/kg cocaine, animals were sacrificed one hour after the injection

tag: Female, mixed background C57Bl6 and 129, Cre+, Creb1 flox/flox, Crem -/-


title: Striatum from cocaine treated control animal, biological rep. 5

description: Gene expression data from control animals treated with cocaine

source_name: The striatum including nucleus accumbens from cocaine treated control animal

tag: Female, mixed background C57Bl6 and 129, Cre-, Creb1 flox/flox, Crem +/-


title: Striatum from cocaine treated mutant animal, biological rep. 2

source_name: The striatum including nucleus accumbens from cocaine treated mutant animal


title: Striatum from cocaine treated control animal, biological rep. 4


title: Striatum from cocaine treated mutant animal, biological rep. 3


title: Striatum from saline treated mutant animal, biological rep. 1


title: tumor_vegf_14d

status: Public on Apr 04 2008

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Stress Science

institute: Institue for Health Biosciences, The University of Tokushima Graduate School

description: The gene expression level was presented as ratio of sample intensity against reference intensity.

hyb_protocol: 750ng of Cy3 and Cy5-labeled cRNA were mixed and hybridized on an Agilent 22k human 1A array in a hybridization oven (Agilent G2545A) as rotating at 65oC for 17 h. Array slide was washed according to Agilent protocol instructions.

scan_protocol: Fluorescence images of the hybridized microarrays were obtained with 10 micro meter resoluion using an Agilent microarray scanner (G2565BA).

data_processing: Signal intensities of Cy5 and Cy3 were quantified and analyzed by subtracting the backgrounds using feature extraction software (Agilent, version 9.5). Cy5/Cy3 ratios of 12,178 genes having a higher fluorescence value than 100 for both Cy5 and Cy3 signals were transformed to logarithms. We selected genes whose mRNA levels differed by > 2 fold between vegf 5’-G5 and mut-D5 tumors.

source_name: reference RNA

label_protocol: 500 ng of reference RNA purified from vegf 5'mut-D5 clone-injected tumor was converted to cDNA with oligo dT conjugated T7 promoter primer and reverse transcriptase, then amplified using T7 RNA polymerase while labeling with Cy3-CTP (Low RNA Fluorescent Linear Amplification Kit, Agilent Technologies).

extract_protocol: total RNA was extracted from vegf 5'mut-D5 clone-derived tumor sample using RNeasy mini (Qiagen) and contaminated DNA was removed by treating with DNaseI (Qiagen) acoording to manufacture's protocol.

treatment_protocol: vegf 5'mut-D5 clone was established  by the selection of HCT116 cells after plasmid transfection which stably expressed vegf 5'UTR where partially mutated between nt 591 and nt 746.  vegf 5'mut-D5 clone (5000000 cells) were subcutaneously injected into the right flanks of nude mice, then generated tumor was removed on day 14 after injection and total RNA was extracted. The mixture from 10 micro g each of triplicate total RNA samples from 3 different mice was used as reference control for dual colour-microarray analysis.

tag: Tumor generated by injection of HCT116 human colon carcinoma cell line, which were stably expressed vegf 5'mut-D5, into the flank of nude mice

source_name: sample RNA

label_protocol: 500 ng of sample RNA purified from vegf 5'-G5 clone-injected tumor was converted to cDNA with oligo dT conjugated T7 promoter primer and reverse transcriptase, then amplified using T7 RNA polymerase while labeling with Cy5-CTP (Low RNA Fluorescent Linear Amplification Kit, Agilent Technologies).

extract_protocol: total RNA was extracted from vegf 5'-G5 clone-derived tumor sample using RNeasy mini (Qiagen) and contaminated DNA was removed by treating with DNaseI (Qiagen) acoording to manufacture's protocol.

treatment_protocol: vegf 5'-G5 clone was established  by the selection of HCT116 cells after plasmid transfection which stably expressed full length of vegf 5'UTR.  vegf 5'-G5 clone (5000000 cells) were subcutaneously injected into the left flanks of nude mice simultaneously with injection of vegf 5'mut-D5 clone to the right flanks, then generated vegf 5'-G5 clone-derived tumor was removed from the left flanks on day 14 after injection and total RNA was extracted. The mixture from 10 micro g each of triplicate total RNA samples from 3 different mice was used as sample for dual colour-microarray analysis.

tag: Tumor generated by injection of HCT116 human colon carcinoma cell line, which were stably expressed vegf 5'-G5, into the flank of nude mice


title: Striatum from cocaine treated mutant animal, biological rep. 4


title: Striatum from saline treated mutant animal, biological rep. 2


title: Striatum from cocaine treated mutant animal, biological rep. 1


title: Striatum from saline treated control animal, biological rep. 1

description: Gene expression data from control animals treated with saline

source_name: The striatum including nucleus accumbens from saline treated control animal


title: Hippocampi from kainate treated mutant animal, biological rep. 2

description: Gene expression data from mutant animals treated with kainate

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on mouse GPL81 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: Pooled hippocampi from 3 kainate treated mutant animals

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 mg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5 to 6 week-old littermate male and female mice were single-caged and handled for 5 days

extract_protocol: Hippocampi were removed and placed in RNAlater (Ambion) overnight. Total RNA was prepared with Absolutely RNA Miniprep kit (Stratagene) and its quality was assessed on RNA LabChips (Agilent). RNA samples from 3 animals were pooled before labelling.

treatment_protocol: Intra peritoneal injection of 20 mg/kg kainate, animals were sacrificed one hour after the injection

tag: Mixed background C57Bl6 and 129, Cre+, Creb1 flox/flox, Crem -/-


title: Striatum from cocaine treated control animal, biological rep. 1


title: Hippocampi from kainate treated mutant animal, biological rep. 1


title: Striatum from cocaine treated control animal, biological rep. 2


title: Hippocampi from kainate treated mutant animal, biological rep. 3


title: Striatum from saline treated control animal, biological rep. 3


title: Leaf_LCO treated_Rep 1_48 h After Treatment

first: John

middle: K

last: Lindsay

address: 21111 Lakeshore Rd

department: Plant Science

description: All steps followed Affymetrix guidelines and protocols.

hyb_protocol: The cRNA quality was determined using a 2100 BioAnalyzer equipped with an RNA Nano LabChip, overnight hybridization of the chip utilized 15 µg of fragmented cRNA and the staining and washes were performed using an Affymetrix GeneChip Fluidics Station 450 robot, following the manufacturer's protocols.

scan_protocol: The microarray chips were scanned with an Affymetrix GeneChip Scanner 3000 7G, following the manufacturer's protocols.

data_processing: Robust multi-array average (RMA) analysis was performed on the .CEL files (with normalization and suppression of background noise). The base 2 logarithm of RMA signals were median-centered so that the median log-scale expression measure for each GeneChip was zero.

source_name: First trifoliolate leaf, 48h after sprayed with lipo-chitooligosaccharide (NOD factor)

label_protocol: 3.5 µg was used to synthesize labeled target cRNA using the GeneChip HT One-Cycle Target Labeling and Controls kit (Affymetrix). cRNA were labelled with biotin, stained with Streptavidin-phycoerythrin  (SAPE) and detected with Biotinylated anti-streptavidin antibody.

growth_protocol: Soybean cultivar (cv.) Ontario Agricultural College (OAC) Bayfield seeds were surface-sterilized in 25% v/v sodium hypochlorite (Javex) for 2 min and then washed five times with distilled water (dH2O).  The seeds were then spread evenly on a 5 cm thick bed of autoclaved vermiculite in a large plastic tray (54 x 28 x 6.5 cm) with holes at the bottom, to allow drainage of excess water, and then covered with 1 cm of vermiculite. The tray, with seeds, was placed in a growth chamber with a 16 h photoperiod (25 ºC) and an 8 h period of darkness (20 ºC).  The germination/rooting medium was kept moist through regular additions of dH2O.  When the cotyledons had emerged and separated (V1 growth stage) the seedlings were transferred to 5 cm pots containing a mixture of Pro-Mix (sphagnum peat moss) and perlite, as growth media.  Each seedling was transferred to an individual pot and returned to the growth chamber under the conditions described above.  The seedlings were watered with ½ strength Hoagland’s solution every day.

extract_protocol: Frozen leaf tissue was rapidly ground with a mortar and pestle chilled with liquid N2 that had been placed in a -20 ºC freezer for 4 h prior to RNA extraction.  Total RNA was extracted from ~100 mg of finely-ground, frozen tissue using the Qiagen RNeasy® Plant Mini Kit for total RNA isolation, with an on-column DNase digestion via the RNase-free DNase Set, according to the manufacturer’s instructions. Samples were stored at -80 oC until use.

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 10-7 M LCO (lipo-chitooligosaccharide; NodBj-V (C18:1, MeFuc) from strain Bradyrhizobium japonicum strain 532C) and 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. LCO, 1 of 3 replicates.

tag: Soybean cv. OAC Bayfield, V1 stage of development, first trifoliolate leaf.


title: Leaf_Water Control_Rep 3_48 h After Treatment

source_name: First trifoliolate leaf, 48h after sprayed with water control

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. Water CONTROL, 3 of 3 replicates.


title: Leaf_LCO treated_Rep 3_48 h After Treatment

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 10-7 M LCO (lipo-chitooligosaccharide; NodBj-V (C18:1, MeFuc) from strain Bradyrhizobium japonicum strain 532C) and 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. LCO, 3 of 3 replicates.


title: Hippocampi from saline treated mutant animal, biological rep. 2

description: Gene expression data from mutant animals treated with saline

source_name: Pooled hippocampi from 3 saline treated mutant animals


title: Leaf_LCO treated_Rep 2_48 h After Treatment

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 10-7 M LCO (lipo-chitooligosaccharide; NodBj-V (C18:1, MeFuc) from strain Bradyrhizobium japonicum strain 532C) and 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. LCO, 2 of 3 replicates.


title: Hippocampi from saline treated mutant animal, biological rep. 1


title: Striatum from saline treated control animal, biological rep. 2


title: Leaf_Water Control_Rep 2_48 h After Treatment

treatment_protocol: Once the soybean plants had reached the V1 stage of development, the first trifoliolate leaf of each plant was sprayed with 2 mL of sterilized dH2O, containing 0.02% Tween 20. 48 h later, the first trifoliolate leaf was harvested, immediately submerged in liquid N2, and stored at -80 ºC until extraction. Water CONTROL, 2 of 3 replicates.


title: Hippocampi from kainate treated control animal, biological rep. 3

description: Gene expression data from control animals treated with kainate

source_name: Pooled hippocampi from 3 kainate treated animals

tag: Mixed background C57Bl6 and 129, Cre-, Creb1 flox/flox, Crem +/-


hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on mouse MG-U74Cv2 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.


title: Hippocampi from kainate treated control animal, biological rep. 2


title: Hippocampi from saline treated control animal, biological rep. 3

source_name: Pooled hippocampi from 3 saline treated animals


title: Hippocampi from kainate treated control animal, biological rep. 1


title: Hippocampi from saline treated mutant animal, biological rep. 3


title: Hippocampi from saline treated control animal, biological rep. 1


title: Hippocampi from saline treated control animal, biological rep. 2


title: Hippocampi from kainate treated mutant animal, biological rep. 3

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on mouse MG-U74Bv2 arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.


title: Hippocampi from kainate treated mutant animal, biological rep. 2


title: Hippocampi from kainate treated mutant animal, biological rep. 1


title: Striatum from cocaine treated mutant animal, biological rep. 5