title: MBEC_PTX_rep1

status: Public on Apr 29 2009

type: RNA

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

country: USA

institute: University of Vermont

hyb_protocol: Biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

scan_protocol: The GeneChip array was stained with Streptavidin-Phycoerythrin according to the Affymetrix Technical Manual, and scanned with the GeneChip Scanner GS3000-76.

data_processing: Probe statistics were background-corrected, normalized and summarized using the rma method and affy package of Speed and coworkers.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: endothelial cells from mouse brain

label_protocol: Double-stranded cDNA was then synthesized followed by an in vitro transcription reaction and fragmentation reaction to produce biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr

extract_protocol: Total RNA was isolated from MBEC using a RNeasy Total RNA Isolation Kit(QIAgen, Valencia, CA).

tag: Strain

tag: Gender

value: male

tag: Age

value: 6-9 months


title: MBEC_PTX_rep2


title: hepatocellular carcinoma T6

status: Public on Apr 24 2009

city: Beijing

first: Hongsong

last: Chen

address: 11 Xizhimen S St

department: People's Hospital

country: China

institute: Peking university

description: We profiled HCC patients with different recurrent-free survival time after resection of tumor.

hyb_protocol: Labeled samples and reference pool were hybridized to the microarray at 42°C overnight and washed with washing solutions.

scan_protocol: Arrays were scanned with a LuxScan 10KA microarray scanner (CapitalBio Corporation), and the obtained images were analyzed with LuxScan 3.0 image analysis software (CapitalBio Corporation).

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

organism: Homo sapiens

source_name: hepatocellular carcinoma

label_protocol: Two micrograms of cRNA was labeled with Cy5（Amersham Pharmacia Biotech, Inc., Piscataway, NJ, USA）in a reverse transcription reaction. The labeled cDNA probes were purified using PCR NucleoSpin Extract II Kit (MN).

extract_protocol: Total RNA was extracted from each sample using TRIzol (Invitrogen, Carlsbad, California) according to the manufacturer’s instructions and followed by NucleoSpin® RNA clean-up Kit（MACHEREY-NAGEL, Germany）to purify the total RNA.

tag: Total RNA from hepatocellular carcinoma tissue

source_name: Adjacent nontumor tissue pool

label_protocol: Two micrograms of cRNA was labeled with Cy3（Amersham Pharmacia Biotech, Inc., Piscataway, NJ, USA）in a reverse transcription reaction. The labeled cDNA probes were purified using PCR NucleoSpin Extract II Kit (MN).

tag: Total RNA of adjacent nontumr tissue from 9 HCC patients was mixed to get a common reference.


title: MBEC_B-oligomer_rep2


title: hepatocellular carcinoma T5


title: Rat S6_bone marrow derived mesenchymal stromal cells_rep3

status: Public on Apr 26 2009

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

description: Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats

hyb_protocol: After precipitation with 4 M Lithium Chloride, 20µg of cRNA was fragmented in fragmentation buffer (40 mM Tris-Acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 35 minutes at 94o C and then 12µg of fragmented cRNA was hybridized to Arrays for 16 hours at 45o C and 60 rpm in an Affymetrix Hybridization Oven 640.

scan_protocol: The arrays were washed and stained with streptavidin phycoerythrin in Affymetrix Fluidics Station 450 using the Affymetrix GeneChip protocol and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis was performed using DNA-Chip Analyzer (Li and Wong, 2001) with CEL file. The tab-delimited format of CHP files were used for present and absent call information. PM-MM model was employed to estimate gene expression level and the invariant set approach for data normalization. The gene expression values were log2 -transformed.

organism: Rattus norvegicus

source_name: Bone marrow derived mesenchymal stromal cells

label_protocol: 10 µg of total RNA was used to synthesize double-stranded cDNA using the Superscript Choice System (Life Technologies). First strand cDNA synthesis was primed with a T7-(dT24) oligonucleotide. From the phase-log gel-purified cDNA, biotin-labelled antisense cRNA was synthesized using BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Farmingdale, NY, USA).

growth_protocol: Both blood and marrow were subject to density gradient centrifugation (1840 rpm at room temperature for 30 min) over LymphoprepTM (1.077g/ml; AXIS-SHIELD PoC AS, Oslo, Norway) to obtain the mononuclear cells. Both peripheral blood-derived mononuclear cells (PBMNCs) and bone marrow-derived mononuclear cells (BMMNCs) were washed in PBS, counted and then plated at a density of 1-3 × 105/cm2 on T-75 flasks (Iwaki) in standard culture medium containing α-MEM (MEM Alpha Medium), 15% fetal bovine serum (FBS，EU Approved Origin, Heat inactivated, REF:10108-165; LOT: 06F8144F), 2mM L-glutamine, 2.5 μg/ml Amphotericin B, 100 IU penicillin and 100 μg /ml streptomycin (all from Invitrogen Life Technologies, Paisley, UK). The flasks were incubated in a humidified atmosphere at 37℃ with 5% CO2. The medium was first changed on the seventh day of culture to remove the non-adherent cells and thereafter twice a week. When the adherent colonies formed and were nearly confluent in the primary culture, the confluent cultures were trypsinized and reseeded at 1×104/cm2 in standard culture medium, and were called passage1 cells. When passage 1 cells were confluent, cells were trypsinized and reseeded again, and became the passage 2 cells. In this study, passage 2 cells were used for the RNA extraction.

extract_protocol: Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit (Qiagen Ltd, West Sussex, UK) according to the manufacturer’s recommendations. Integrity of RNA was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). The purity/concentration was determined using a GeneSpec III (Miraibio). All RNA samples used for hybridization had an OD260/280 and OD260/230 ratio >1.8 and total RNA concentration > 1µg/ml.

tag: GFP transgenic Sprague-Dawley rat, 3 months old, male


title: Rat S6_peripheral blood derived mesenchymal stromal cells_rep3

source_name: Peripheral blood derived mesenchymal stromal cells


title: hepatocellular carcinoma T3


title: Rat S4_peripheral blood derived mesenchymal stromal cells_rep1

tag: GFP transgenic Sprague-Dawley rat, 3 months old, female


title: Rat S5_peripheral blood derived mesenchymal stromal cells_rep2


title: hepatocellular carcinoma T7


title: hepatocellular carcinoma GLN02


title: Rat S5_bone marrow derived mesenchymal stromal cells_rep2


title: hepatocellular carcinoma T2


title: Rat S4_bone marrow derived mesenchymal stromal cells_rep1


title: hepatocellular carcinoma GL106


title: hepatocellular carcinoma T4


title: hepatocellular carcinoma T1


title: MBEC_PBS_rep1


title: MBEC_PBS_rep2


title: MBEC_B-oligomer_rep1


title: hepatocellular carcinoma GL124


title: hepatocellular carcinoma GL116


title: hepatocellular carcinoma GL044


title: hepatocellular carcinoma GL107


title: hepatocellular carcinoma GL069


title: hepatocellular carcinoma GL095


title: hepatocellular carcinoma GL016


title: hepatocellular carcinoma GLN01


title: hepatocellular carcinoma GL079


title: hepatocellular carcinoma GL129


title: hepatocellular carcinoma GL077


title: hepatocellular carcinoma GD002


title: hepatocellular carcinoma GD001


title: hepatocellular carcinoma GL067


title: hepatocellular carcinoma GL078


title: hepatocellular carcinoma GL063


title: hepatocellular carcinoma GL036


title: 453_dmso_6hr_rep2

status: Public on Apr 15 2009

city: New York

first: Linda

middle: Saxe

last: Einbond

state: NY

address: 701 West 168Th St.

department: Rehabilitation Medicine

institute: Columbia University

description: MDA-MB-453 human breast cancer cell line treated with dmso control for 6 hours.

hyb_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture's protocol with minor modifications, and then purified twice with Qiagen's RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen). After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the BioArray high yield RNA transcript labeling kit (Enzo Life Sciences; Farmingdale, NY), according to a modified Affymetrix protocol. cRNA (15 μg) was fragmented into the final probe and hybridized to human U 133A 2.0 gene chips (Affymetrix, Inc.; Santa Clara, CA), comprised of more than 22,000 probe sets.

scan_protocol: canning was performed on an Affymetrix 3000-7G Scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm. Only 6 hour 20 or 40 microgram/ml actein data and the corresponding DMSO controls were included in the normalization (2 treated samples and 2 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.

label: biotin

source_name: Sigma

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s medium (DMEM) (Gibco BRL Life Technologies, Inc., Rockville, MD) containing 10% (v/v) fetal bovine serum (FBS) (Gibco BRL) at 37 °C, 5% C02

extract_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture’s protocol with minor modifications, and then purified twice with Qiagen’s RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen).

treatment_protocol: Dimethylsulfoxide (DMSO) (Sigma; St. Louis, MO) was added to the cell cultures as a control for the effect of the addition of actein. Cells were seeded in 15 cm plates and allowed to attach for 6h. The medium was replaced with fresh medium containing dmso. The cells were treated for 6h after which the cells were collected for microarray analysis.


title: 453_actein20microg_ml_24hr_rep3

description: MDA-MB-453 human breast cancer cell line treated with 20 microgram/ml actein for 24 hours.

scan_protocol: Scanning was performed on an Affymetrix 3000-7G Scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm. Only 24 hour 20microgram/ml actein data and the corresponding DMSO controls were included in the normalization (3 treated samples and 3 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.

source_name: MDA-MB-453 cell line treated with actein 20 micrograms/ml 24 hours

label_protocol: After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the BioArray high yield RNA transcript labeling kit (Enzo Life Sciences; Farmingdale, NY), according to a modified Affymetrix protocol.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s medium (DMEM) (Gibco BRL Life Technologies, Inc., Rockville, MD) containing 10% (v/v) fetal bovine serum (FBS) (Gibco BRL) at 37 °C, 5% C02.

treatment_protocol: Actein was obtained from ChromaDex (Laguna Hills, CA, lot number 01355-101), purity 89% by HPLC. Actein was dissolved in dimethylsulfoxide (DMSO) (Sigma; St. Louis, MO) prior to addition to the cell cultures. Cells were seeded in 15 cm plates and allowed to attach for 24 h. The medium was replaced with fresh medium containing actein. The cells were treated for 24 h after which the cells were collected for microarray analysis.


title: 453_actein40microg_ml_6hr_rep1

description: MDA-MB-453 human breast cancer cell line treated with 40 microgram/ml actein for 6 hours.

data_processing: Data was normalized using the GCRMA algorithm. Only 6 hour 40microgram/ml actein data and the corresponding DMSO controls were included in the normalization (2 treated samples and 2 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.

source_name: MDA-MB-453 cell line treated with actein 40 micrograms/ml 6 hours

extract_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture’s protocol with minor modifications, and then purified twice with Qiagen’s RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen). After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the BioArray high yield RNA transcript labeling kit (Enzo Life Sciences; Farmingdale, NY), according to a modified Affymetrix protocol.


title: 453_dmso_6hr_rep1

description: MDA-MB-453 human breast cancer cell line treated with dmso control for 6hours.


title: 453_actein20microg_ml_6hr_rep1

description: MDA-MB-453 human breast cancer cell line treated with 20 microgram/ml actein for 6 hours.

data_processing: Data was normalized using the GCRMA algorithm. Only 6 hour 20microgram/ml actein data and the corresponding DMSO controls were included in the normalization (2 treated samples and 2 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.

source_name: MDA-MB-453 cell line treated with actein 20 micrograms/ml 6 hours


title: hepatocellular carcinoma GL035


title: 453_actein40microg_ml_6hr_rep2

tag: MDA-MB-453 human breast cancer cell line


title: 453_dmso_24hr_rep4

description: MDA-MB-453 human breast cancer cell line treated with dmso control for 24 hours.

data_processing: Data was normalized using the GCRMA algorithm. Only 24 hour 40microgram/ml actein data and the corresponding DMSO controls were included in the normalization (3 treated samples and 3 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.

treatment_protocol: Dimethylsulfoxide (DMSO) (Sigma; St. Louis, MO) was added to the cell cultures as a control for the effect of the addition of actein. Cells were seeded in 15 cm plates and allowed to attach for 24 h. The medium was replaced with fresh medium containing dmso. The cells were treated for 24 h after which the cells were collected for microarray analysis.


title: 453_actein20microg_ml_6hr_rep2


title: 453_actein40microg_ml_24hr_rep2

description: MDA-MB-453 human breast cancer cell line treated with 40 microgram/ml actein for 24 hours.

hyb_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture's protocol with minor modifications, and then purified twice with Qiagen's RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen). After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix, Inc.; Santa Clara, CA), according to the Affymetrix protocol. cRNA (15 μg) was fragmented into the final probe and hybridized to human U 133A 2.0 gene chips (Affymetrix, Inc.; Santa Clara, CA), comprised of more than 22,000 probe sets.

source_name: MDA-MB-453 cell line treated with actein 40 micrograms/ml 24 hours


title: hepatocellular carcinoma GL040


title: hepatocellular carcinoma GL037


title: hepatocellular carcinoma GL019


title: hepatocellular carcinoma GL026


title: 453_dmso_24hr_rep1


title: 453_actein40microg_ml_24hr_rep3

treatment_protocol: Planta Analytica (Danbury, CT, lot number PA-A-037), purity was over 95% by HPLC. Actein was dissolved in dimethylsulfoxide (DMSO) (Sigma; St. Louis, MO) prior to addition to the cell cultures. Cells were seeded in 15 cm plates and allowed to attach for 24 h. The medium was replaced with fresh medium containing actein. The cells were treated for 24 h after which the cells were collected for microarray analysis.


title: 13689634 - fry2-1_1 vs RD29ALuc_1

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Compare the transcriptome of 2 mutants affected in FRY2 (fry2-1 and 14-5sep) to control plants.

hyb_protocol: RD29ALuc_1 Cy5 / fry2-1_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

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

growth_protocol: whole plant - Media : MS x 0.5		 Temperature : 18°C	 Light : 110 µE m-2 s-2

treatment_protocol: no treatment

tag: Arabidopsis thaliana ( c24 )  mutant (RD29A::LUC) - harvest date:04-02-08

tag: Arabidopsis thaliana ( c24 )  mutant (fry2-1) - harvest date:04-02-08


title: 13688915 - NiiLuc_1 vs 14-5_1

hyb_protocol: 14-5_1 Cy5 / NiiLuc_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (14-5sep) - harvest date:04-02-08

tag: Arabidopsis thaliana (columbia)  mutant (NII::LUC) - harvest date:04-02-08


title: 13689646 - WT_green vs T-DNA_green

status: Public on Apr 11 2009

description: Identify the target genes of the bZIP transcriptional regulator AtbZIP9

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

growth_protocol: whole plant - media : MS/2 - 0,03% Glicose (glicose starvation) temperature : 22°C light : dim light-constant

tag: Arabidopsis thaliana (columbia)  mutant (atbzip9-1) - harvest date:23-11-07

tag: Arabidopsis thaliana (columbia)  - harvest date:23-11-07


title: 13689648 - T-DNA_red vs 18-1_red

hyb_protocol: 18-1_red Cy5 / T-DNA_red Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (VP16::atbzip9) - harvest date:23-11-07


title: 13689647 - T-DNA_green vs WT_green

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


title: 453_actein20microg_ml_24hr_rep2


title: 453_actein20microg_ml_24hr_rep1


title: 453_dmso_24hr_rep3

hyb_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture's protocol with minor modifications, and then purified twice with Qiagen's RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen). After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with with the GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix, Inc.; Santa Clara, CA), according to the Affymetrix kit protocol. cRNA (15 μg) was fragmented into the final probe and hybridized to human U 133A 2.0 gene chips (Affymetrix, Inc.; Santa Clara, CA), comprised of more than 22,000 probe sets.

label_protocol: After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix, Inc.; Santa Clara, CA), according to the Affymetrix kit protocol.


title: 13689637 - RD29ALuc_2 vs fry2-1_2

hyb_protocol: fry2-1_2 Cy5 / RD29ALuc_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana ( c24 )  mutant (fry2-1) - harvest date:07-02-08

tag: Arabidopsis thaliana ( c24 )  mutant (RD29A::LUC) - harvest date:07-02-08


title: 13689158 - RD29ALuc_1 vs fry2-1_1

hyb_protocol: fry2-1_1 Cy5 / RD29ALuc_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689636 - fry2-1_2 vs RD29ALuc_2

hyb_protocol: RD29ALuc_2 Cy5 / fry2-1_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 453_actein40microg_ml_24hr_rep1

description:
MDA-MB-453 human breast cancer cell line treated with 40 microgram/ml actein for
24 hours.

data_processing:
Data was normalized using the GCRMA algorithm. Only 24 hour 40microgram/ml
actein data and the corresponding DMSO controls were included in the normalization
(3 treated samples and 3 controls). Differential expression and its statistical significance was obtained using the LIMMA algorithm.


title: 13689645 - 18-1_blue vs T-DNA_blue

hyb_protocol: T-DNA_blue Cy5 / 18-1_blue Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689508 - WT_green vs 18-1_green

hyb_protocol: 18-1_green Cy5 / WT_green Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689644 - T-DNA_blue vs 18-1_blue

hyb_protocol: 18-1_blue Cy5 / T-DNA_blue Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689639 - 18-1_blue vs WT_blue

hyb_protocol: WT_blue Cy5 / 18-1_blue Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689156 - 14-5_2 vs NiiLuc_2

hyb_protocol: NiiLuc_2 Cy5 / 14-5_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (NII::LUC) - harvest date:07-02-08

tag: Arabidopsis thaliana (columbia)  mutant (14-5sep) - harvest date:07-02-08


title: 13689157 - NiiLuc_2 vs 14-5_2

hyb_protocol: 14-5_2 Cy5 / NiiLuc_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689650 - 18-1_red vs T-DNA_red

hyb_protocol: T-DNA_red Cy5 / 18-1_red Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689509 - 18-1_green vs WT_green

hyb_protocol: WT_green Cy5 / 18-1_green Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688914 - 14-5_1 vs NiiLuc_1

hyb_protocol: NiiLuc_1 Cy5 / 14-5_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689142 - T-DNA_red vs WT_red

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


title: 15 day_loo1_wild type_all samples

status: Public on Apr 12 2009

city: Urbana

first: Yun

last: Lin

state: IL

address: 183 NSRC, 1101 W. Peabody Dr.

department: Crop Sciences

institute: University of Illinois

description: None.

hyb_protocol: Hybridization and wash conditions are as described by Hegde et al. (2003), Biotechniques 29, 548-562

scan_protocol: GenePix 4000 scanner and GenePix Pro 3.0 software (Molecular Device Corp., Sunnyvale, CA) were used following manufacture's instruction

data_processing: The GenePix raw data files were converted to MEV format using ExpressConverter and data normalization was subsequently conducted using MIDIA. Both softwares were downloaded from the TIGR-M4 package (http://www.tm4.org). Total intensity normalization, Lowess normalization, and standard deviation regulation were conducted with each slide. Ratios of normalized signals of the two channels (loo1 to wild type) were calculated before log transformation. Student t-test was conducted to test the null hypothesis: log2 (loo1/wt) = 0. Rejection of the hypothesis indicates differential gene expression between loo1 and the wild type.

source_name: 15 day old wild type or loo1 seedlings

label_protocol: aminoallyl-cDNA (aa-cDNA) was synthesized by including aa-dUTP in the reverse transcription reaction. THe aa-cDNA was then labeled with Cy3.

growth_protocol: Seedlings were grown for 15 days on 0.5 x MS salt with 2% sucrose

extract_protocol: Trizol kit (invitrogen)

tag: 15-day-old wild type or loo1 seedlings with roots removed. Channel 1 characteristics for each hybridization

value: hybridization 1A - wild type, hybridization 1B - loo1, hybridization 2A - wild type, hybridization 2B - loo1.

label_protocol: aminoallyl-cDNA (aa-cDNA) was synthesized by including aa-dUTP in the reverse transcription reaction. THe aa-cDNA was then labeled with Cy5.

extract_protocol: Trizol kit (Invitrogen)

tag: 15-day-old wild type or loo1 seedlings with roots removed. Channel 2 characteristics for each hybridization

value: hybridization 1A - loo1, hybridization 1B - wild type, hybridization 2A - loo1, hybridization 2B - wild type.


title: 13689136 - WT_red vs 18-1_red

hyb_protocol: 18-1_red Cy5 / WT_red Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689139 - Ler_T0_2 vs pop2-1_T0_2

description: The analysis aims at identifying genes that are differentially regulated by the over-accumulation of GABA observed in the mutant pop2-1 in response to treatment with exogenous GABA and that may explain the singular phenotype of the mutant in this condition.

hyb_protocol: pop2-1_T0_2 Cy5 / Ler_T0_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3: 532nm, pmt voltage, 500V, laser power 35%, Cy5:635nm, pmt voltage 500V, laser power 30%

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

growth_protocol: whole plant - media : 1 % agar medium, nutrition solution was based on a half strength Hoagland's solution for macronutrients, full strength for micronutrients excepted a two-fold concentration of Iron. Medium contains 5 mM MES, pH was adjusted at 5.7 with Tris hygrometry : 50% temperature : 22°C light : 12h-light (100 µEinstein.cm-2.min-1)

tag: Arabidopsis thaliana (landsberg erecta) mutant (pop2) - harvest date:14-01-08

tag: Arabidopsis thaliana (landsberg erecta) - harvest date:14-01-08


title: 13689150 - pop2-1_T0_1 vs Ler_T0_1

hyb_protocol: Ler_T0_1 Cy5 / pop2-1_T0_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689642 - 18-1_green vs T-DNA_green

hyb_protocol: T-DNA_green Cy5 / 18-1_green Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689641 - WT_blue vs T-DNA_blue

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


title: 13689643 - T-DNA_green vs 18-1_green

hyb_protocol: 18-1_green Cy5 / T-DNA_green Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689640 - T-DNA_blue vs WT_blue

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


title: 13689141 - pop2-1_GABA1_2 vs Ler_GABA1_2

hyb_protocol: Ler_GABA1_2 Cy5 / pop2-1_GABA1_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

organism: Populus x canadensis

growth_protocol: stem - Plants were grown in a greenhouse, in 10 liter pots filled with peat/sand mix(50/50 v/v amended with 60g/60l CaMg(CO2)3 and fertilised with Nutricote T100(13-13-13-2,N-P-K-Mg+trace elements). In the greehouse, temperature oscillated with rayonnement but kept in the range 15-27 °C, and air humidity in the range 50-70%. Light dependend on natural and varied in the range. During the 3 days preceeding harvest, temperature was, humidity was and light was

extract_protocol: Pool of extract, 117-C-Tem:1ug, 134-C-Tem:1ug, Ler_GABA1_2:4.8ug.

treatment_protocol: Name:AU05-03_GABA_1 - compound based treatment - compound addition,gaba:quantity 1mM time 1day .

tag: Poplar (populus deltoides x populus nigra) - harvest date:06-06-06

tag: Arabidopsis thaliana (landsberg erecta) mutant (pop2) - harvest date:15-01-08


title: 13689638 - WT_blue vs 18-1_blue

hyb_protocol: 18-1_blue Cy5 / WT_blue Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689143 - Ler_GABA4_1 vs pop2-1_GABA4_1

hyb_protocol: pop2-1_GABA4_1 Cy5 / Ler_GABA4_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:AU05-03_GABA_4 - compound based treatment - compound addition,gaba:quantity 1mM time 4day .

tag: Arabidopsis thaliana (landsberg erecta) mutant (pop2) - harvest date:18-01-08

extract_protocol: Pool of extract, 103-S-Tem:1ug, 104-S-Tem:1ug, Ler_GABA4_1:4ug.

tag: Poplar (populus deltoides x populus nigra) - harvest date:06-06-07


title: hepatocellular carcinoma GL006

hyb_protocol: Labeled samples and reference pool were hybridized to the microarray at 42°C overnight and washed with washing solutions.

tag: Total RNA from hepatocellular carcinoma tissue

tag: Total RNA of adjacent nontumr tissue from 9 HCC patients was mixed to get a common reference.


title: 13689506 - WT_red vs T-DNA_red

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

tag: Arabidopsis thaliana (columbia)  mutant (atbzip9-1) - harvest date:23-11-07


title: MRC5_16 hours_UVB exposure_M06_24C/16H

status: Public on Apr 10 2009

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description:
PMTGain=700	650
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.9	3.09
Temperature=30.76
ScanPower=100	100

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 350 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Control samples corresponding to 24H

label_protocol: 3DNA Array 350 kit was used for fluorescence labeling on cDNA. Each total RNA (5μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column and was blocked by addictive 0.5μg of Cot1 human DNA.

growth_protocol: The MRC-5 cell, obtained from the American Type Culture Collection (ATCC, MA, USA) was grown in the complete growth medium and was incubated at 37 oC and 5 % CO2 in air atmosphere. The complete growth medium was the α-MEM medium supplemented with antibiotic (100 U/ml penicillin plus 10ug/ml streptomycin), and 10% heat-inactivated fetal bovine serum. The medium was replenished every 48 h after cell passage. Cells were routinely subcultivated in cell culture petri dishes of 100 mm2 every 3-4 days with 1:3 subcultivation ratio. In the beginning of subcultivation, the cell layer was briefly rinsed with 2 ml of 0.25% (w/v) trypsin-0.53 mM EDTA in 15 ~ 20 seconds after removal of whole medium with serum. Then we incubated the culture dish at 37 oC to facilitate dispersal in 1.5~2 min. We add fresh complete growth medium 10 ml per petri dish and aspirate cells by gently pipeting. Finally we add appropriate aliquots of the cell suspension to new petri dishes. The entire experiments were performed at passages 21 to 28.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 1.0 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: No

tag: Cell strain, Gender

value: male, Age:14 weeks, Tissue: hung fibroblast,

source_name: Sample harvested at 16 hours after UVB irradiation


title: MRC5_24 hours_UVB exposure_M07_24H/24C

description:
PMTGain=700	520
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.9	3.09
Temperature=29.3
ScanPower=100	100

source_name: Sample harvested at 24 hours after UVB irradiation


title: 13689149 - Ler_T0_1 vs pop2-1_T0_1

hyb_protocol: pop2-1_T0_1 Cy5 / Ler_T0_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689146 - pop2-1_T0_2 vs Ler_T0_2

hyb_protocol: Ler_T0_2 Cy5 / pop2-1_T0_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MRC5_UVB exposure_M09_24H/8H

description:
PMTGain=710	600
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.87	3.09
Temperature=31.25
ScanPower=100	100

treatment_protocol: Sample harvested at 24 hours after UVB irradiation

source_name: Sample harvested at 8 hours after UVB irradiation


title: 13689153 - pop2-1_GABA1_1 vs Ler_GABA1_1

hyb_protocol: Ler_GABA1_1 Cy5 / pop2-1_GABA1_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, 87-C-Tem:1ug, 105-C-Tem:1ug, Ler_GABA1_1:4ug.

tag: Poplar(populus deltoides x populus nigra) - harvest date:06-06-07


title: 13689148 - pop2-1_GABA4_2 vs Ler_GABA4_2

hyb_protocol: Ler_GABA4_2 Cy5 / pop2-1_GABA4_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: Pool of extract, 118-S-Tem:1ug, 111-S-Tem:1ug, Ler_GABA4_2:5ug.


title: 13689134 - 18-1_red vs WT_red

hyb_protocol: WT_red Cy5 / 18-1_red Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  - harvest date:23-11-07

tag: Arabidopsis thaliana (columbia)  mutant (VP16::atbzip9) - harvest date:23-11-07


title: 13689152 - Ler_GABA1_1 vs pop2-1_GABA1_1

hyb_protocol: pop2-1_GABA1_1 Cy5 / Ler_GABA1_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Erythrocyte RNA, HbSS 10

status: Public on Apr 04 2009

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive, DUMC 3382

department: Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: The fluorescently labeled microRNAs were mixed with 3x microRNA Hybridization Buffer (Ambion) and heated at 95°C for 3 min before hybridizing with the printed microRNA microarrays for 12–16 h in a 42°C water bath in sealed cassettes.

scan_protocol: Following hybridization, the slides were washed, dried and scanned on a GenePix 4000B Array Scanner (Axon, CA).

data_processing: Array images were analyzed using the GenePix Pro 5.0 software (Axon) and submitted into and Lowess normalized the Duke Microarray Database (DMD).  For the accompanying publication, hierarchical clustering was performed using the data contained in these Sample records.

source_name: Erythrocyte RNA, HbSS 10

label_protocol: 10 total RNA samples were size-fractionated and cleaned with the flashPAGE Fractionator (Ambion, TX) to collect RNAs smaller than 40 nucleotides. These samples then were labeled with the mirVana microRNA Labeling Kit (Ambion) according to the manufacture’s instructions.

extract_protocol: Total RNA extracted using Ambion miRVana kits

treatment_protocol: RNA isolated from purified erythrocytes

tag: Erythrocyte RNA, HbSS 10

source_name: Total RNA from one unit of whole blood

tag: Total RNA from one unit of whole blood


title: 453_dmso_24hr_rep2

hyb_protocol: Total cellular RNA was extracted using Trizol (Invitrogen; Carlsbad, CA) according to the manufacture's protocol with minor modifications, and then purified twice with Qiagen's RNeasy column. High quality total RNA (8 μg) was reverse transcribed with T7-(dT)24 primer and Super Script III reverse transcriptase (Invitrogen). After purification, cDNA was in vitro transcribed into biotin labeled antisense cRNA with the BioArray high yield RNA transcript labeling kit (Enzo Life Sciences; Farmingdale, NY), according to a modified Affymetrix protocol. cRNA (15 μg) was fragmented into the final probe and hybridized to human U 133A 2.0 gene chips (Affymetrix, Inc.; Santa Clara, CA), comprised of more than 22,000 probe sets.

tag: MDA-MB-453 human breast cancer cell line


title: 13689140 - Ler_GABA1_2 vs pop2-1_GABA1_2

hyb_protocol: pop2-1_GABA1_2 Cy5 / Ler_GABA1_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13689147 - Ler_GABA4_2 vs pop2-1_GABA4_2

hyb_protocol: pop2-1_GABA4_2 Cy5 / Ler_GABA4_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MRC5_4 hours_UVB exposure_M02_8C/4H

description:
PMTGain=650	600
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.88	3.11
Temperature=30.76
ScanPower=100	100

source_name: Control samples corresponding to 8H

source_name: Sample harvested at 4 hours after UVB irradiation


title: PS43_30,MEF(+/+), 3hrs 643-EJ-31

status: Public on Apr 09 2009

city: Nashville

first: Josh

middle: T

last: Beckham

state: TN

address: 5824 Stevenson Center

department: Biomedical Engineering

institute: Vanderbilt University

description: PS43_30,MEF(+/+), 3hrs 643-EJ-31

hyb_protocol: The biotinylated cRNA (20 µg) was fragmented and hybridized to an Affymetrix GeneChip Mouse Genome 430 2.0 Array containing 45,000 sets of 11 to 25-mer oligomers, representing 39,000 mouse transcripts (34,000 are annotated as well-defined genes). Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

data_processing: CEL files (raw Affymetrix data) were imported in GeneSpring 7.3 (Agilent Technologies) and transformed by Mas5. The "Value" column shows this normalized signal intensity value.

source_name: MEF(+/+) cells, pretreated

label_protocol: Following quality control, the RNA was prepared for microarray analysis using the GeneChip® One-Cycle Target Labeling and Control Reagents kit (Affymetrix Inc, Santa Clara, CA). Briefly, 1.5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.

growth_protocol: Maintained in DMEM with 10% Fetal Bovine Serum, and 2ul/ml of Normocin(Invivogen). Wells were covered with a gas permeable membrane to prevent water influx during thermal treatment.

extract_protocol: At 3 hours after thermal treatment, cell lysates from 144 individual wells were pooled and total RNA was harvested to make each sample. Approximately 4-6 ug of RNA was isolated with the RNeasy Micro Kit (Qiagen, Valencia, CA) along with on column DNAse treatment (Qiagen). RLT buffer in the RNeasy Kit was used without adding β- mercaptoethanol in order to reduce background noise on the microarrays. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.

treatment_protocol: Cells were plate in 96 well plates at 3k/well, incubated 20hrs, Preshocked in a constant temperature water bath for 30 minutes, then returned to incubator for 3 hours before harvesting RNA

tag: Murine Embryo Fibroblast hsp70 knockout cells of both isoforms:hsp70.1 and hsp70.3 that have hsp70.1 gene reintroduced to restore some hsp70 function


title: Ctrl MEF(+/+), 3hrs 643-EJ-44

description: Ctrl MEF(+/+), 3hrs 643-EJ-44

source_name: MEF(+/+) cells, unheated control

extract_protocol: Cell lysates from 144 individual wells were pooled and total RNA was harvested to make each sample. Approximately 4-6 ug of RNA was isolated with the RNeasy Micro Kit (Qiagen, Valencia, CA) along with on column DNAse treatment (Qiagen). RLT buffer in the RNeasy Kit was used without adding β- mercaptoethanol in order to reduce background noise on the microarrays. Agilent’s Bioanalyzer microfluidic assay (Agilent Technologies, Palo Alto CA) was used to assay RNA integrity. Spectrophotometric and fluorometric methods were combined to quantitate protein and nucleic acids present in the sample, and to ensure quality control of each sample.

treatment_protocol: Cells were plate in 96 well plates at 3k/well, incubated 23 hrs before harvesting RNA


title: PS43_30,MEF(+/+), 3hrs 643-EJ-43

description: PS43_30,MEF(+/+), 3hrs 643-EJ-43


title: Erythrocyte RNA, HbSS 11

source_name: Erythrocyte RNA, HbSS 11

tag: Erythrocyte RNA, HbSS 11


title: MRC5_UVB exposure_M10_4H/16H

description:
PMTGain=710	600
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.89	3.09
Temperature=31.25
ScanPower=100	100

source_name: Sample harvested at 4 hours after UV irradiation

treatment_protocol: Sample harvested at 4 hours after UVB irradiation

treatment_protocol: Sample harvested at 16 hours after UVB irradiation


title: Erythrocyte RNA, HbSS 4

source_name: Erythrocyte RNA, HbSS 4

tag: Erythrocyte RNA, HbSS 4


title: Erythrocyte RNA, HbSS 6

source_name: Erythrocyte RNA, HbSS 6

tag: Erythrocyte RNA, HbSS 6


title: 13689144 - pop2-1_GABA4_1 vs Ler_GABA4_1

hyb_protocol: Ler_GABA4_1 Cy5 / pop2-1_GABA4_1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Erythrocyte RNA, HbSS 3

source_name: Erythrocyte RNA, HbSS 3

tag: Erythrocyte RNA, HbSS 3


title: Erythrocyte RNA, HbSS 1

source_name: Erythrocyte RNA, HbSS 1

tag: Erythrocyte RNA, HbSS 1


title: Erythroycte RNA, Normal 6

description: Biological replicate 2 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.

source_name: Erythroycte RNA, Normal 6

tag: Erythroycte RNA, Normal 6


title: Erythrocyte RNA, HbSS 9

source_name: Erythrocyte RNA, HbSS 9

tag: Erythrocyte RNA, HbSS 9


title: Erythrocyte RNA, HbSS 12

source_name: Erythrocyte RNA, HbSS 12

tag: Erythrocyte RNA, HbSS 12


title: Erythroycte RNA, Normal 2

description: Biological replicate 2 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: Erythroycte RNA, Normal 2

tag: Erythroycte RNA, Normal 2


title: Erythrocyte RNA, HbSS 8

source_name: Erythrocyte RNA, HbSS 8

tag: Erythrocyte RNA, HbSS 8


title: MRC5_8 hours_UVB exposure_M04_16C/8H

description:
PMTGain=630	600
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.91	3.07
Temperature=30.76
ScanPower=100	100

source_name: Control samples corresponding to 16H

tag: Cell strain, Gender

source_name: Sample harvested at 8 hours after UVB irradiation


title: MRC5_8 hours_UVB exposure_M03_8H/8C

description:
PMTGain=700	540
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.94	3.05
Temperature=29.3
ScanPower=100	100

treatment_protocol: Sample harvested at 8 hours after UVB irradiation

source_name: Control samples corresponding to 8H


title: MRC5_4 hours_UVB exposure_M01_4H/4C

description:
PMTGain=700	500
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.91	3.12
Temperature=29.79
ScanPower=100	100

source_name: Sample harvested at 4 hours after UVB irradiation

source_name: Control samples corresponding to 4H


title: Erythrocyte RNA, HbSS 7

source_name: Erythrocyte RNA, HbSS 7

tag: Erythrocyte RNA, HbSS 7

source_name: Total RNA from one unit of whole blood


title: MRC5_16 hours_UVB exposure_M05_16H/16C

description:
PMTGain=750	560
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.94	3.06
Temperature=29.3
ScanPower=100	100

source_name: Sample harvested at 16 hours after UVB irradiation


title: Erythrocyte RNA, HbSS 2

source_name: Erythrocyte RNA, HbSS 2

tag: Erythrocyte RNA, HbSS 2


title: Erythroycte RNA, Normal 3

description: Biological replicate 3 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: Erythroycte RNA, Normal 3

tag: Erythroycte RNA, Normal 3


title: Erythroycte RNA, Normal 4

description: Biological replicate 4 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: Erythroycte RNA, Normal 4

tag: Erythroycte RNA, Normal 4

tag: Total RNA from one unit of whole blood


title: Erythrocyte RNA, HbSS 5

source_name: Erythrocyte RNA, HbSS 5

tag: Erythrocyte RNA, HbSS 5


title: Erythroycte RNA, Normal 7

description: Biological replicate 3 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.

source_name: Erythroycte RNA, Normal 7

tag: Erythroycte RNA, Normal 7


title: Ctrl MEF(+/+), 3hrs 643-EJ-32

description: Ctrl MEF(+/+), 3hrs 643-EJ-32

source_name: MEF(+/+) cells, unheated control

tag: Murine Embryo Fibroblast hsp70 knockout cells of both isoforms:hsp70.1 and hsp70.3 that have hsp70.1 gene reintroduced to restore some hsp70 function


title: Erythroycte RNA, Normal 5

description: Biological replicate 1 of 3. Stable triple-fusion-reporter-gene transfected embryonic stem cells, harvested after several passages.

source_name: Erythroycte RNA, Normal 5

tag: Erythroycte RNA, Normal 5


title: MRC5_24 hours_UVB exposure_Mo8_4C/24H

description:
PMTGain=690	640
Scanner=GenePix 4100A 01 [100641]
LaserPower=2.88	3.1
Temperature=30.76
ScanPower=100	100

source_name: Sample harvested at 24 hours after UVB irradiation


title: KT95-418-non-infected,  biological rep3

status: Public on Apr 02 2009

city: Fuzhou

first: Xiaoting

last: Zhang

state: Fujian

address: Jinshan

department: Plant Protection Department

institute: Fujian Agriculture and Forestry University

description: Gene expression data from non-innoculated KT95-418

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

organism: Oryza sativa

source_name: Tissue: aerial parts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol 5 ug total RNA.

growth_protocol: RSV-innoculated or non-innoculated WuYun3 or KT95-418 rice plants were grown in greenhouse at 25±3C with a daily photoperiodic cycle of 16 hours light and 8 hours.

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

treatment_protocol: Untreated

tag: Age

value: 32th day after germination


title: KT95-418-non-infected,  biological rep2


title: Erythroycte RNA, Normal 1

description: Biological replicate 1 of 4. Control embryonic stem cells, untreated, harvested after several passages.

source_name: Erythroycte RNA, Normal 1

tag: Erythroycte RNA, Normal 1


title: KT95-418-RSV infected,biological rep2

description: Gene expression data from RSV-innoculated KT95-418


title: Control (APMM-024A)

status: Public on Apr 01 2009

first: Huan

last: Meng

address: Mailbox 918, Yuquan Road 19

institute: Lab of Bioeffects of Nanosized Materials, Institute of High Energy Physics

hyb_protocol: Ensure that you do not contaminate the 2X real-time PCR cocktail by dividing into aliquots containing the amount of cocktail necessary for the number of reactions you are preparing each day. The rest of the cocktail should be kept in storage away from any sources of template DNA. When using RT² Real-Time™ Master Mixes with RT²Profiler™ PCR Arrays or RT2 PCR Primer Sets, refer to the appropriate User Manuals. For general PCR purposes, mix the following components in a PCR tube: 12.5 µl RT² Real-Time™ SYBR Green / ROX PCR Master Mix 10.5 µl ddH2O 1.0 µl template cDNA (up to 250 ng) 1.0 µl gene-specific 10 µM PCR primer pair stock 25.0 µl final volume Recommended real-time thermal cycler program: 95 ºC, 10 min; 40 cycles of (95 ºC, 15 sec; 60 ºC, 60 sec). NOTE: The 10 min step at 95 ºC is required to activate the HotStart Taq DNA polymerase.

scan_protocol: Program the real-time thermal cycler to detect and record the SYBR® Green I signal from every reaction at the end of the annealing step of each cycle.

data_processing:
the date analysis was performed by program provided by superarray corp. (see SuperArray website)
Briefly,
Data Analysis: ΔΔCt Method
1. Examine the threshold cycle of the negative controls.
The No Template Control (NTC) tests for DNA contamination in your PCR system, while the No Reverse Transcription (NRT) control tests for contamination of the original RNA with genomic DNA. Both threshold cycles should be greater than 35. If the threshold cycle for either of these controls is less than 35, then the presence of DNA contamination is evident. See the Troubleshooting Guide for more information.
2. Change all Ct values reported as greater than 35 or as N/A (not detected) to 35. Any Ct value equal to 35 is considered a negative call.
3. When biological and/or technical replicates are performed, calculate the average Ct value of each gene (each well) across those replicate arrays for each treatment group.
4. Calculate the ΔCt for each pathway-focused gene in each treatment group.
ΔCt (group 1) = average Ct – average of HK genes’ Ct for group 1 array
ΔCt (group 2) = average Ct – average of HK genes’ Ct for group 2 array
NOTE: The expression level of the housekeeping genes chosen for normalization in the
ΔΔCt method must not be influenced by your experimental conditions. If one or more such genes have been previously identified by independent means and if the PCR Array reproduces those results, use the average of their Ct values in the equation above. If an appropriate housekeeping gene has not been previously identified, use the average Ct value of all five housekeeping genes, but only if the difference in the average values between the two groups to be compared is less than one (1) cycle. Otherwise, simply use zero (0) in the place of the average of HK genes’ Ct for each group to be compared,and rely on the consistency in the quantity and quality of your original input total RNA across your groups to effectively normalize your results.
5. Calculate the ΔΔCt for each gene across two PCR Arrays (or groups).
ΔΔCt = ΔCt (group 2) - ΔCt (group 1)
Where group 1 is the control and group 2 is the experimental
6. Calculate the fold-change for each gene from group 1 to group 2 as 2-ΔΔCt.
OPTIONAL: If the fold-change is greater than 1, then the result may be reported as a fold up-regulation. If the fold-change is less than 1, then the negative inverse of the result may be reported as a fold down-regulation.

label: SYBR Green

source_name: human breast cancer xenograft (MCF-7)

label_protocol:
RT² Real-Time™ SYBR Green / ROX PCR Master Mix
see SuperArray website

growth_protocol: Athymic BALB/c nu/nu mice of female (weighing 16.0±1.0g) were purchased from the Cancer Institute and Cancer Hospital Chinese Academy of Medical Sciences, and maintained under specific pathogen-free (SPF) conditions. Nude mice were acclimated in the controlled environment (22±1℃ in temperature, 60±10% in humidity and a 12 h light/dark cycle) with free access to sterile distilled water and commercial laboratory complete food without pathogen.

extract_protocol:
Total RNA was isolated using the Trizol according to the manufacturer’s instruction (Invitrogen, Carlsbad, CA). Briefly, 100mg tumor tissue was added into 1ml of Trizol reagent. Add 0.2 ml chloroform per 1 ml  Trizol reagent. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol (0.5 ml of isopropyl alcohol per 1 ml of TRIZOL reagent). Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C. The a gel-like RNA precipitate was hence produced.
After 75% ethanol washing, mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C. Air-dry the RNA pellet for 5-10 minutes (partially dissolved RNA samples have an A260/280 ratio < 1.6). Dissolve RNA in RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C. RNA can be stored at -70°C.

treatment_protocol: The small tumor tissues of xenografts were subcutaneously inoculated into left inguinal region of the ether-anesthetized nude mice, using a trocar needle. 17β-estradiol dipropionate at 5 mg/kg and 17 α-progesterone caproate at 250 mg/kg were injected intramuscularly into mice bearing MCF-7 on the day of tumor inoculation to ensure exponential tumor growth.  7 days after the inoculation, the saline (0.2ml/20g) was injected  intraperitoneally as the negative control.

tag: Gender

value: female

value: 7 weeks

tag: Tissue

value: human breast cancer xenograft (MCF-7)

tag: Location

value: groin (left)


title: Nanodrug (APMM-024A)

label_protocol:
RT² Real-Time™ SYBR Green / ROX PCR Master Mix
see SuperArray website
Ensure that you do not contaminate the 2X real-time PCR cocktail by dividing into aliquots containing the amount of cocktail necessary for the number of reactions you are preparing each day. The rest of the cocktail should be kept in storage away from any sources of template DNA.
When using RT² Real-Time™ Master Mixes with RT²Profiler™ PCR Arrays or RT2 PCR Primer Sets, refer to the appropriate User Manuals.
For general PCR purposes, mix the following components in a PCR tube:
12.5 µl RT² Real-Time™ SYBR Green / ROX PCR Master Mix
10.5 µl ddH2O
1.0 µl template cDNA (up to 250 ng)
1.0 µl gene-specific 10 µM PCR primer pair stock
25.0 µl final volume
Recommended real-time thermal cycler program:
95 ºC, 10 min; 40 cycles of (95 ºC, 15 sec; 60 ºC, 60 sec).
NOTE: The 10 min step at 95 ºC is required to activate the HotStart Taq DNA polymerase.

treatment_protocol: The small tumor tissues of xenografts were subcutaneously inoculated into left inguinal region of the ether-anesthetized nude mice, using a trocar needle. 17β-estradiol dipropionate at 5 mg/kg and 17 α-progesterone caproate at 250 mg/kg were injected intramuscularly into mice bearing MCF-7 on the day of tumor inoculation to ensure exponential tumor growth.  7 days after the inoculation, the nanodrug (2.5umol/kg) was injected intraperitoneally everyday.


title: WuYun3-non-infected, biological rep1

description: Gene expression data from non-innoculated WuYun3


title: WuYun3-RSV infected, biological rep3

description: Gene expression data from RSV-innoculated WuYun3


title: WuYun3-non-infected,  biological rep3


title: WuYun3-non-infected,  biological rep2


title: KT95-418-RSV infected, biological rep1


title: WuYun3-RSV infected, biological rep2


title: KT95-418-RSV infected, biological rep3


title: KT95-418-non-infected,  biological rep1