title: 561856A01 - 43_WATER_24H_REP1 vs 44_ADJ_24H_REP1

hyb_protocol: 44_ADJ_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: herbaceous grape cutting


title: MCF7-B, ethanol treated, replicate 2

status: Public on Sep 01 2014

type: RNA

city: Columbus

first: Craig

middle: Joseph

last: Burd

state: OH

address: 460 W. 12th Ave. Rm 920 BRT

department: Molecular Genetics

country: USA

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, acetylated BSA , BioArray Eukaryotic Hybridization Controls (ENZO Life Sciences). 65 C for 5 minutes, 99 C for 5 min, 45 C for 5 minutes. Centrifuge top speed for 5 minutes. Hybridize 16 h at 45C at 60 rpm.  Fluidics washing is FS450_001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC

data_processing: Data was normalized using the Expression Console Software

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MCF7 cells chronically cultured in BPA

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit

growth_protocol: Cells were grown in phenol-red free DMEM containing 5% charcoal/dextran treadted FBS for 72 hours

extract_protocol: RNA was isolated using Total RNA isolation Nucleospin® RNA II kit (Macherey-Nagel

treatment_protocol: Cells were treated with either ethanol of 10 nM estradiol for 3 hours.

tag: cell type

tag: treatment

value: ethanol treated


title: 534330A10 - 8_WATER_48H_REP1 vs 13_TREATMENT4_48H_REP1

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 13_TREATMENT4_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Vitis vinifera

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

growth_protocol: caulin leaf - Growth conditions (Media/hygrometry/Temperature/Light) -peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:T4_48H - compound based treatment - pathogen infection,water inoculation:.

tag: variety

value: cv. Marselan

tag: age

tag: tissue

treatment_protocol: Name:WATER_48H - compound based treatment - pathogen infection,water:.


title: MEFs_uv2.25_t2880

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's)  the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

organism: Mus musculus

source_name: MEFs treated uv (2.25j/s) RNA harvest 2880 minutes

label_protocol: Per test sample, 5 µg total RNA combined with 1 µg random octamers (Biolegio) in 4.5 µl was heated to 65°C for 10 min to denature the RNA and was allowed to cool in an ice-waterbath for 10 min. This 4.5 µl was made to 10 µl with a first strand mastermix containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, 1.5 µl of 2.5M NaOH was added to hydrolyze the remaining RNA by heating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 10 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled as the test samples with Cy5 incorporation.

growth_protocol: Primary MEFs were isolated from E13.5 embryos in a C57BL/6 background (backcrossed for more than F8 generations). MEFs were cultured in Dulbecco's modified Eagle medium (Invitrogen, Breda, The Netherlands) containing 10% fetal bovine serum (Biocell, Rancho Dominguez, CA), 1% nonessential amino acids (Invitrogen, Breda, The Netherlands), penicillin (0.6 μg/ml), and streptomycin (1 μg/ml) at 37°C and under 5% CO2, 3% O2 conditions. The experiment was performed with early-passage MEFs (prior to passage five). FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA). RNA was assessed for quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: MEFs (p53 +/+) were expanded and plated at 3.5x105 cells per 6-cm plate. Six hours later , cells were washed with phosphate-buffered saline and exposed to UV-C light at different doses (0.25, 0.75, 2.25, 6.7, 20.0 J/m2). Control samples were mock treated. At several time points after treatment (10 min, 30 min, 1 hr, 3 hr, 6 hr, 12 hr, 24 hr, 48 hr), MEFs were rinsed with phosphate-buffered saline and collected in 350 μl RLT buffer (enclosed in the RNeasy mini kit; see “RNA isolation”).

value: MEFs

tag: strain


title: MEFs_uv0_t0

source_name: MEFs treated uv (0j/s) RNA harvest 0 minutes


title: MEFs_uv0_t360

source_name: MEFs treated uv (0j/s) RNA harvest 360 minutes


title: 534330A11 - 14_TREATMENT5_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 14_TREATMENT5_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T5_48H - compound based treatment - pathogen infection,water inoculation:.


title: MCF7-B, estradiol treated, replicate 1

value: estradiol treated


title: MEFs_uv20_t1440

source_name: MEFs treated uv (20j/s) RNA harvest 1440 minutes


title: 534330A09 - 13_TREATMENT4_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 13_TREATMENT4_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534330A12 - 8_WATER_48H_REP1 vs 14_TREATMENT5_48H_REP1

hyb_protocol: 14_TREATMENT5_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MCF7-B, estradiol treated, replicate 2


title: MEFs_uv0.75_t720

source_name: MEFs treated uv (0.75j/s) RNA harvest 720 minutes


title: MEFs_uv20_t720

source_name: MEFs treated uv (20j/s) RNA harvest 720 minutes


title: 534330A08 - 8_WATER_48H_REP1 vs 12_TREATMENT3_48H_REP1

hyb_protocol: 12_TREATMENT3_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T3_48H - compound based treatment - pathogen infection,water inoculation:.


title: MEFs_uv0.75_t2880

source_name: MEFs treated uv (0.75j/s) RNA harvest 2880 minutes


title: MCF7-B, ethanol treated, replicate 1


title: MCF7-F, estradiol treated, replicate 2

source_name: MCF7 cells cultured in normal FBS


title: Mm_Mouse_5t_9

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Gene id's) the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

growth_protocol: Wild-type (WT; p53+/+) mice were used for UV exposure studies. All mice used were males of 7-10 weeks of age and at least 10 times backcrossed in SKH hairless strain. Mice received normal feed and water ad libitum.

extract_protocol: At different time points after UV-B exposure, both treated and untreated mice were anaesthetized by isoflurane. 1.5mm biopsies were sampled from the back.  by punching a half moon shape on folded skin. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C until further processing. Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA). RNA was assessed for quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All mouse treatments have been approved by the institute's Experimental Animal Ethical Committee and carried out in accordance with national legislation. Mice were UVB irradiated at different doses (90, 180, 360, 450, 720 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated.

value: 0 UV-B J/m2

value: skin

tag: genotype

value: Wild-type (WT; p53+/+)

tag: time (hours)

tag: mouse


title: IML1_1

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Leaf at the floral initiation stage, non-transgenic, biological replicate 1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa Japonica Group

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Seeds of non-transgenic (Oriza sativa L. japonica cultivar Ilmi) and over-expression line were geminated on soil and grown in greenhouse (16-hr-light/ 8-hr-dark cycle). At the age of 1-month, plants were transferred to pot and grown outside of greenhouse under natural conditions.

extract_protocol: Total RNAs were extracted using TriReagent (Molecular Research Center, Inc.).

treatment_protocol: Panicles were collected based on size i.e. 1-3, 8-15, and 20.5-22 cm as P1, P8 and P21; respectively. Moreover, panicles at 5-day-after-pollination 5DAP, was also collected to analyze the developing seed. Leaves (L) at the stage of 4-week before heading which was around the date of panicle initiation was used at reference.

tag: cultivar

value: Oryza sativa L. cv. Ilmi

value: Leaf at the floral initiation stage

value: non-transgenic


title: MCF7-F, estradiol treated, replicate 1


title: MEFs_uv2.25_t360

source_name: MEFs treated uv (2.25j/s) RNA harvest 360 minutes


title: 534330A07 - 12_TREATMENT3_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 12_TREATMENT3_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv6.7_t10

source_name: MEFs treated uv (6.7j/s) RNA harvest 10 minutes


title: 561856A08 - 47_TREATMENT3_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 47_TREATMENT3_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: caulin leaf - peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:. Name: - compound based treatment - plant defense activation ,water:.


title: MEFs_uv6.7_t360

source_name: MEFs treated uv (6.7j/s) RNA harvest 360 minutes


title: 534330A06 - 8_WATER_48H_REP1 vs 11_TREATMENT2_48H_REP1

hyb_protocol: 11_TREATMENT2_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T2_48H - compound based treatment - pathogen infection,water inoculation:.


title: MEFs_uv0.25_t30

source_name: MEFs treated uv (0.25j/s) RNA harvest 30 minutes


title: MCF7-F, ethanol treated, replicate 2


title: MCF7-F, ethanol treated, replicate 1


title: 534330A04 - 8_WATER_48H_REP1 vs 10_TREATMENT1_48H_REP1

hyb_protocol: 10_TREATMENT1_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T1_48H - compound based treatment - pathogen infection,water inoculation:.


title: WT grown in BG11C-Cu untreated rep4

city: Sevilla

first: Luis

last: Lopez Maury

address: Av Americo Vespucio 49

country: Spain

institute: IBVF

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505C US91803681).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1_105_Dec08  extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Limma

organism: Synechocystis sp. PCC 6803

source_name: 30 ml sample

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cRNA probe preparation using 200ng of total RNA.

growth_protocol: cells were grown to exponetial phase (3-5 µg chlorophyll mL-1) in BG11C-Cu

extract_protocol: cells were resuspended in 400 µl STET and vortexedin the presence of phenol chloroform and glass beads; RNA was precipitated with ClLi treated with Turbo DNAse (Ambion) and further purified by phenol chloroform extraction.

treatment_protocol: cultures were supplemented  with 0.3 µM or 3µM CuSO4 for 1h.

value: WT

value: untreated


title: MEFs_uv0.25_t180

source_name: MEFs treated uv (0.25j/s) RNA harvest 180 minutes


title: WT grown in BG11C-Cu untreated rep2


title: 534330A03 - 10_TREATMENT1_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 10_TREATMENT1_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv0_t10

source_name: MEFs treated uv (0j/s) RNA harvest 10 minutes


title: 561856A09 - 43_WATER_24H_REP1 vs 48_TREATMENT4_24H_REP1

hyb_protocol: 48_TREATMENT4_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T4_24H - compound based treatment - plant defense activation ,water:.

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:.


title: 534108A10 - 27_TREATMENT4_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 27_TREATMENT4_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534108A11 - 22_WATER_48H_REP2 vs 28_TREATMENT5_48H_REP2

hyb_protocol: 28_TREATMENT5_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534330A05 - 11_TREATMENT2_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 11_TREATMENT2_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv20_t2880

source_name: MEFs treated uv (20j/s) RNA harvest 2880 minutes


title: MEFs_uv6.7_t720

source_name: MEFs treated uv (6.7j/s) RNA harvest 720 minutes


title: WT grown in BG11C-Cu treated with 0.3 µM Cu rep1

value: treated with 0.3 µM Cu


title: WT grown in BG11C-Cu untreated rep1


title: Cortex PD rep5

city: South San Francisco

first: Brigit

middle: Erin

last: Riley

state: CA

address: 180 Oyster Point Blvd.

institute: Elan Pharmaceuticals

description:
X201274
Sydney Brain Bank at Neuroscience Research Australia

hyb_protocol: Expression Analysis (Durham, NC) performed the microarray according to their standard protocols, hybridation was with Affymetrix hybridation cocktail.

scan_protocol: Expression Analysis (Durham, NC) performed the microarray according to their standard protocols, scanning was on the Affymetrix GeneChip scanner and data extraction using Expression Console.

data_processing: Software:  ‘affy’ package of Bioconductor (‘just.rma’ function)

source_name: Cortex, PD

label_protocol: Expression Analysis (Durham, NC) performed the microarray according to their standard protocols, labeling was with the Affymetrix GeneChip WT Terminal Labeling Kit.

extract_protocol: RNA extraction was performed by Expression Analysis (Durham, NC) using the Qiagen miRNAeasy Mini Kit.

tag: disease state

value: PD

value: Cortex

tag: gender

value: M


title: Striatum PD rep6

description:
X201273
Sydney Brain Bank at Neuroscience Research Australia

source_name: Striatum, PD

value: Striatum


title: MEFs_uv0.25_t1440

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

source_name: MEFs treated uv (0.25j/s) RNA harvest 1440 minutes


title: 534108A12 - 28_TREATMENT5_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 28_TREATMENT5_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: herbaceous grape cutting


title: WT grown in BG11C-Cu treated with 3 µM Cu rep2

value: treated with 3 µM Cu


title: 534108A08 - 26_TREATMENT3_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 26_TREATMENT3_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: cv. Marselan


title: WT grown in BG11C-Cu untreated rep3


title: Cortex PD rep4

description:
X201272
Sydney Brain Bank at Neuroscience Research Australia


title: WT grown in BG11C-Cu treated with 0.3 µM Cu rep2


title: MEFs_uv0.75_t60

source_name: MEFs treated uv (0.75j/s) RNA harvest 60 minutes

value: MEFs


title: 534108A09 - 22_WATER_48H_REP2 vs 27_TREATMENT4_48H_REP2

hyb_protocol: 27_TREATMENT4_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Striatum PD rep5

description:
X201271
Sydney Brain Bank at Neuroscience Research Australia


title: 534108A07 - 22_WATER_48H_REP2 vs 26_TREATMENT3_48H_REP2

hyb_protocol: 26_TREATMENT3_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv0_t720

source_name: MEFs treated uv (0j/s) RNA harvest 720 minutes


title: 534108A06 - 25_TREATMENT2_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 25_TREATMENT2_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: COPR grown in BG11C-Cu untreated rep4

value: COPR


title: COPR grown in BG11C-Cu untreated rep3


title: MEFs_uv6.7_t2880

source_name: MEFs treated uv (6.7j/s) RNA harvest 2880 minutes


title: WT grown in BG11C-Cu treated with 3 µM Cu rep1


title: COPR grown in BG11C-Cu untreated rep2


title: 534108A05 - 22_WATER_48H_REP2 vs 25_TREATMENT2_48H_REP2

hyb_protocol: 25_TREATMENT2_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv2.25_t180

source_name: MEFs treated uv (2.25j/s) RNA harvest 180 minutes


title: MEFs_uv0.75_t360

source_name: MEFs treated uv (0.75j/s) RNA harvest 360 minutes


title: 534108A03 - 22_WATER_48H_REP2 vs 24_TREATMENT1_48H_REP2

hyb_protocol: 24_TREATMENT1_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:ADJUVANT_48H - compound based treatment - pathogen infection,adjuvant:.


title: Striatum normal rep6

description:
X201267
Sydney Brain Bank at Neuroscience Research Australia

source_name: Striatum, normal

value: normal

value: F


title: Cortex normal rep5

description:
X201268
Sydney Brain Bank at Neuroscience Research Australia

source_name: Cortex, normal


title: COPR grown in BG11C-Cu untreated rep1


title: Cortex PD rep3

description:
X201270
Sydney Brain Bank at Neuroscience Research Australia


title: Striatum normal rep5

description:
X201265
Sydney Brain Bank at Neuroscience Research Australia


title: Striatum PD rep4

description:
X201269
Sydney Brain Bank at Neuroscience Research Australia


title: 534105A12 - 42_TREATMENT5_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 42_TREATMENT5_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534105A11 - 36_WATER_48H_REP3 vs 42_TREATMENT5_48H_REP3

hyb_protocol: 42_TREATMENT5_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cortex normal rep4

description:
X201266
Sydney Brain Bank at Neuroscience Research Australia


title: 534108A04 - 24_TREATMENT1_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 24_TREATMENT1_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv20_t30

source_name: MEFs treated uv (20j/s) RNA harvest 30 minutes


title: COPR grown in BG11C-Cu treated with 0.3 µM Cu rep2

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.


title: MEFs_uv2.25_t1440

source_name: MEFs treated uv (2.25j/s) RNA harvest 1440 minutes


title: Cortex normal rep3

description:
X201264
Sydney Brain Bank at Neuroscience Research Australia


title: 534105A10 - 41_TREATMENT4_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 41_TREATMENT4_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: COPR grown in BG11C-Cu treated with 3 µM Cu rep2

source_name: 30 ml sample


title: MEFs_uv0_t30

source_name: MEFs treated uv (0j/s) RNA harvest 30 minutes


title: Striatum normal rep4

description:
X201263
Sydney Brain Bank at Neuroscience Research Australia


title: COPR grown in BG11C-Cu treated with 3 µM Cu rep1


title: MEFs_uv0.25_t10

source_name: MEFs treated uv (0.25j/s) RNA harvest 10 minutes


title: MEFs_uv0.75_t1440

source_name: MEFs treated uv (0.75j/s) RNA harvest 1440 minutes


title: 534105A07 - 36_WATER_48H_REP3 vs 40_TREATMENT3_48H_REP3

hyb_protocol: 40_TREATMENT3_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534105A08 - 40_TREATMENT3_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 40_TREATMENT3_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E.est_deltamethrin 0.32ug/kg_replicate 3

city: Moncton

first: Paula

last: Jackman

state: NB

address: 443 University ave

country: Canada

institute: Environment Canada

description: SAMPLE 21

hyb_protocol: Microarray hybridizations were performed using Agilent’s 4 x 44K Eohaustorius estuarius microarray slides containing 4 grids with the same ~ 44 000 features (Design ID 029660), using a one-color approach.  All hybridizations, including washes and drying steps were carried out on a HS4800 automated hybridization station using quad chambers (Tecan, Männedorf, Switzerland). Briefly, slides were initially washed with Agilent’s aOligo aCGH Prehybridization buffer for 1 min at 65°C and injected with a 60 µl of hybridization mix containing 30 µl of fragmentation mix and 30 µl of Agilent’s 2x GEx hybridization Buffer Hi-RPM per chamber.  The injected material was hybridized for 17 hour at 65°C.  Following hybridization slides were washed twice with Agilent’s gene expression wash buffer 1 at 23°C for 1 min, twice with Agilent’s gene expression wash buffer 2 with 0.01 wash buffer additive at 37°C for 1 min and then dried under nitrogen

scan_protocol: Microarray slides were scanned at a resolution of 5 µm using Agilent’s High Resolution Microarray Scanner (Agilent, CA, USA) using a 20-bit data format and automatic PMT adjustment.

data_processing: The resulting TIFF images were quantified using Agilent’s Feature Extraction software (Agilent, CA, USA). Numerical intensities, descriptive statistics and flag value were computed for each spot and exported in a text file. Spots were considered flagged it they were saturated, not uniform, below background levels and if the background was not uniform. Genes that had a flag on more than 1/3 of the slides used for a particular statistical analysis were filtered out.  The gProcessedSignal values (foreground value minus background value) for each spot were then log2 transformed and normalized between arrays using a shift to 75e percentile ans a baseline transformation of the median of all samples approach found in Genespring version 12.6.  Statistical analysis was performed on log2 transformed and normalized gProcessedSignal value.

organism: Eohaustorius estuarius

source_name: E.est_deltamethrin 0.32ug/kg

label_protocol: RNA amplification and labeling for microarray was performed using the one-color Low Input Quick Amp Labeling kit (Agilent, CA, USA) and following the manufacturer’s recommendations. Briefly, 50 ng of each RNA sample was reverse transcribed, amplified and labeled using Cy3 dyes resulting in Cy3 labeled amplified RNA (aRNA). Purification of the labeled aRNA was performed using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s recommendations. Following purification, labeled aRNA samples were then quantified using the NanoDrop 8000 to verify the yield of aRNA and the labeling efficiency. 1.65 µg of each purified aRNA was prepared for hybridization using the fragmentation step described in Agilent’s Low Input Quick Amp labeling kit protocol. Briefly each aRNA was fragmented by mixing 1.65 µg of aRNA in a volume of 22.8 µl, with 6 µl of 10X blocking agent and 1.2 µl of 25X fragmentation buffer and heating the mix at 60°C for 30 min.

extract_protocol: Total RNA from RNAlater preserved E.estuarius samples was extracted using the RNeasy MIcro kit (Quiagen, Venlo, Netherlands) and following the manufacturer’s protocol.  An the column DNase digestion step was performed on each sample.  RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA).  RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

value: deltamethrin

tag: concentration


title: COPR grown in BG11C-Cu treated with 0.3 µM Cu rep1


title: MEFs_uv0_t60

source_name: MEFs treated uv (0j/s) RNA harvest 60 minutes


title: Cortex nonPD normal rep1

description:
X201261
Sydney Brain Bank at Neuroscience Research Australia

hyb_protocol: Expression Analysis (Durham, NC) performed the microarray according to their standard protocols, hybridation was with Affymetrix hybridation cocktail.

source_name: Cortex, nonPD normal

value: nonPD normal


title: 534105A09 - 36_WATER_48H_REP3 vs 41_TREATMENT4_48H_REP3

hyb_protocol: 41_TREATMENT4_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534105A06 - 39_TREATMENT2_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 39_TREATMENT2_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cortex nonPD rep2

description:
X201259
Sydney Brain Bank at Neuroscience Research Australia

source_name: Cortex, nonPD

value: nonPD


title: MEFs_uv2.25_t10

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

source_name: MEFs treated uv (2.25j/s) RNA harvest 10 minutes


title: E.est_deltamethrin 0.32ug/kg_replicate 2

description: SAMPLE 20


title: Cortex nonPD rep3

description:
X201260
Sydney Brain Bank at Neuroscience Research Australia


title: Cortex nonPD normal rep2

description:
X201262
Sydney Brain Bank at Neuroscience Research Australia


title: MEFs_uv0_t180

source_name: MEFs treated uv (0j/s) RNA harvest 180 minutes


title: E.est_deltamethrin 0.32ug/kg_replicate 1

description: SAMPLE 19


title: Cortex nonPD rep1

description:
X201258
Sydney Brain Bank at Neuroscience Research Australia


title: MEFs_uv6.7_t30

source_name: MEFs treated uv (6.7j/s) RNA harvest 30 minutes


title: 534105A03 - 36_WATER_48H_REP3 vs 38_TREATMENT1_48H_REP3

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 38_TREATMENT1_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E.est_deltamethrin 0.18ug/kg_replicate 3

description: SAMPLE 18

source_name: E.est_deltamethrin 0.18ug/kg


title: 534105A04 - 38_TREATMENT1_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 38_TREATMENT1_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv0.75_t10

source_name: MEFs treated uv (0.75j/s) RNA harvest 10 minutes


title: E.est_deltamethrin 0.18ug/kg_replicate 2

description: SAMPLE 17


title: Striatum normal rep3

description:
X201257
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Striatum, normal


title: E.est_deltamethrin 0.18ug/kg_replicate 1

description: SAMPLE 16


title: Cortex normal rep2

description:
X201254
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Cortex, normal


title: 534330A01 - 9_ADJ_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 9_ADJ_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534330A02 - 8_WATER_48H_REP1 vs 9_ADJ_48H_REP1

hyb_protocol: 9_ADJ_48H_REP1 Cy5 / 8_WATER_48H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MEFs_uv0.25_t2880

source_name: MEFs treated uv (0.25j/s) RNA harvest 2880 minutes


title: Substantia Nigra normal rep3

description:
X201255
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Substantia Nigra, normal

value: Substantia Nigra


title: MEFs_uv0.25_t720

source_name: MEFs treated uv (0.25j/s) RNA harvest 720 minutes


title: Striatum normal rep2

description:
X201253
UCLA Human Brain and Spinal Fluid Resource Center


title: 534105A05 - 36_WATER_48H_REP3 vs 39_TREATMENT2_48H_REP3

hyb_protocol: 39_TREATMENT2_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E.est_cypermethrin 1.0ug/kg_replicate 3

description: SAMPLE 15

source_name: E.est_cypermethrin 1.0ug/kg

value: cypermethrin

value: 1.0 ug/kg


title: 534108A02 - 23_ADJ_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 23_ADJ_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534108A01 - 22_WATER_48H_REP2 vs 23_ADJ_48H_REP2

hyb_protocol: 23_ADJ_48H_REP2 Cy5 / 22_WATER_48H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Substantia Nigra normal rep2

description:
X201251
UCLA Human Brain and Spinal Fluid Resource Center


title: MEFs_uv0_t1440

source_name: MEFs treated uv (0j/s) RNA harvest 1440 minutes


title: E.est_cypermethrin 1.0ug/kg_replicate 2

description: SAMPLE 14


title: E.est_cypermethrin 1.0ug/kg_replicate 1

description: SAMPLE 13


title: MEFs_uv6.7_t60

source_name: MEFs treated uv (6.7j/s) RNA harvest 60 minutes


title: 534105A02 - 37_ADJ_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 37_ADJ_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E.est_cypermethrin 0.56ug/kg_replicate 3

description: SAMPLE 12

source_name: E.est_cypermethrin 0.56ug/kg


title: Cortex normal rep1

description:
X201250
UCLA Human Brain and Spinal Fluid Resource Center


title: 534105A01 - 36_WATER_48H_REP3 vs 37_ADJ_48H_REP3

hyb_protocol: 37_ADJ_48H_REP3 Cy5 / 36_WATER_48H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: VSMC 1070M9C

city: Cambridge

first: Kelly

middle: Louise

last: Gray

state: Cambs

address: Addenbrookes Hospital, Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

description: plaque

data_processing:
The normalization and all the data analysis was performed according to the manufacturers instructions using their web based software package http://sabiosciences.com/pcrarraydataanalysis.php
The normalization uses the average of five housekeeping genes: B2M, HPRT, RPL13A, GAPDH, ACTB
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt= (Ct_Target-Ct_HKG)
The web-based software package automatically performs all deltadeltaCt based fold change calculations from the uploaded raw threshold cycle data

label: FAM

source_name: carotid

label_protocol: FAM

growth_protocol: cells were cultured in DMEM+10%FCS and L-glutamine from human tissue

extract_protocol:
Total RNA was isolated using the High Pure RNA Isolation Kit including Dnase treatment and reverse transcribed using the First Strand cDNA Kit
The cDNA was preamplified using the PreAmp DNA damage damage signaling primers

tag: passage

value: Low Passage VSMCs

value: vascular smooth muscle cells

value: diseased carotid plaques


title: VSMC 1159F6C

description: plaque


title: VSMC 75F25c

description: plaque


title: VSMC 1177m4c

description: plaque


title: E.est_ammonia 1000ug/g_replicate 2

description: SAMPLE 8

source_name: E.est_ammonia 1000ug/g

value: ammonia


title: MEFs_uv20_t360

source_name: MEFs treated uv (20j/s) RNA harvest 360 minutes


title: Striatum PD rep3

description:
X201246
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Striatum, PD

value: PD

value: Striatum


title: Substantia Nigra normal rep1

description:
X201247
UCLA Human Brain and Spinal Fluid Resource Center


title: Substantia Nigra PD rep3

description:
X201244
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Substantia Nigra, PD


title: E.est_ammonia 1000ug/g_replicate 3

description: SAMPLE 9


title: Striatum PD rep2

description:
X201243
UCLA Human Brain and Spinal Fluid Resource Center

value: M


title: E.est_cypermethrin 0.56ug/kg_replicate 1

description: SAMPLE 10


title: clpX/clpXspx dyeswap

city: Hannover

first: Kürsad

last: Turgay

address: Schneiderberg 50

department: Institut für Mikrobiologie

country: Germany

institute: Leibniz Universität Hannover

description: Different mRNA expression due to Spx in B. subtilis clpX vs. B. subtilis clpX spx cells

hyb_protocol: The respective cDNA's labelled with Alexa 555 or Alexa 647 were combined, concentrated and with SlideHyb Glass Array Hybridisation Buffer # 1 (Ambion) with the help of a lifter slip (22x40, IMPLEN GmbH) in a Micro-Array Hybrid Chamber (Amlab) in a water bath o/n at 55°C hybridized with an oligonucleotide Microaaray prepared and spotted on a glassslide by the Center of Applied Genomics (ICPH, UMDNJ, Newark). The array was subsequently washed with 55°C warm buffer 1 (2xSSC, 0.5%SDS), buffer 2 (0.5xSSC, 0.5%SDS)  buffer 3 (0.5 SSC, 0.03% SDS) and further washed with buffer 4 (0.2xSSC), buffer 5 (0.1xSSC) and buffer 6 (0.1xSSC) at RT

scan_protocol: The hybridzed slides were scanned with a Genepix 4100 (Molecular Devices) Laserscanner using auto PMT

data_processing: The data was analyzed with Genepix Pro 6.1 (Axon), the dye swap and further analysis was performed with Acuity (Axon) and Excel.

label: Alexa 555

organism: Bacillus subtilis

source_name: exponential LB 37°C

label_protocol: The cDNA synthesis purification and labeling was performed with Superscript SuperScript Plus Indirect cDNA Labeling Kit using random hexamer primers and Alexa Fluor R555 & 647 dyes (Invitrogen)

growth_protocol: B. subtilis cells were grown at 37°C  in 50 ml LB at 300 rpm to an OD of 0.6. The cells were harvested by centrifugation and the pellets frozen in liquid nitrogen.

extract_protocol: The total RNA was prepared using FastRNA ProBlue Kit (Qbiogene, CA) using a Retsch Mixer Mill. The total RNA was DNAseI  treated and purified using Phenol/Chloroform/Isoamyl extraction and EtOH precipitation.

value: 168 clpX spx

label: Alexa 647

source_name: exponential LB 15 min 48°C and 15 min 53°C

value: 168 clpX


title: E.est_cypermethrin 0.56ug/kg_replicate 2

description: SAMPLE 11


title: VSMC 0756M1A

description: normal

source_name: aortic

value: normal


title: VSMC 0973M3A

description: normal


title: E.est_ammonia 560ug/g_replicate 3

description: SAMPLE 6

source_name: E.est_ammonia 560ug/g


title: VSMC 0256m13a

description: normal


title: clpX/clpXspx


title: E.est_ammonia 1000ug/g_replicate 1

description: SAMPLE 7


title: E.est_control_replicate 3

description: SAMPLE 3

value: not exposed to contaminant


title: Striatum PD rep1

description:
X201238
UCLA Human Brain and Spinal Fluid Resource Center


title: Cortex PD rep2

description:
X201241
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Cortex, PD

value: Cortex


title: MEFs_uv20_t180

source_name: MEFs treated uv (20j/s) RNA harvest 180 minutes

value: MEFs


title: Striatum normal rep1

description:
X201249
UCLA Human Brain and Spinal Fluid Resource Center

source_name: Striatum, normal

value: F


title: VSMC Ct 75F2A

description: normal


title: E.est_control_replicate 1

description: SAMPLE 1


title: E.est_ammonia 560ug/g_replicate 2

description: SAMPLE 5


title: VSMC 0663F2A

description: normal


title: WholeBlood_d30_Cs-137_rep1

status: Public on Aug 31 2014

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1_107_Sep091 and Grid: 026655_D_F_20110722) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Well Above Background were excluded

source_name: mouse blood, day 30 after Cs-137 injection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the PAXgene Blood RNA Kit (Qiagen/BD) according to manufacturer’s instructions, followed by removal of globin transcripts using the GLOBINclear kit (Ambion Inc., Austin, TX) to remove both a- and b-globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were either injected intraperitoneally with 8.0 ± 0.3 MBq 137CsCl solution in a volume of 50 μL or kept as controls. At the time of sacrifice, blood was collected by cardiac puncture and 400 ul was placed in PAXgene blood RNA solution (PreAnalytiX GmbH, USA) and kept at 4-degrees C for shipping to Columbia for RNA isolation.

value: male

tag: accrued radiation dose

value: whole blood


title: WholeBlood_d30_Cs-137_rep2


title: WholeBlood_d30_Control_rep6

source_name: mouse blood, day 30, control

value: 0 Gy


title: WholeBlood_d30_Cs-137_rep6


title: Cortex PD rep1

description:
X201239
UCLA Human Brain and Spinal Fluid Resource Center


title: E.est_ammonia 560ug/g_replicate 1

description: SAMPLE 4


title: WholeBlood_d30_Cs-137_rep3


title: WholeBlood_d30_Control_rep2


title: WholeBlood_d30_Control_rep4


title: Substantia Nigra PD rep1

description:
X201236
UCLA Human Brain and Spinal Fluid Resource Center

value: Substantia Nigra


title: WholeBlood_d5_Cs-137_rep6

source_name: mouse blood, day 5 after Cs-137 injection


title: Substantia Nigra PD rep2

description:
X201240
UCLA Human Brain and Spinal Fluid Resource Center


title: WholeBlood_d30_Control_rep5


title: WholeBlood_d5_Cs-137_rep4


title: E.est_control_replicate 2

description: SAMPLE 2


title: WholeBlood_d30_Cs-137_rep4


title: WholeBlood_d30_Cs-137_rep5


title: WholeBlood_d30_Control_rep3


title: WholeBlood_d5_Cs-137_rep3


title: WholeBlood_d30_Control_rep1


title: WholeBlood_d5_Cs-137_rep5


title: WholeBlood_d5_Cs-137_rep2


title: WholeBlood_d3_Cs-137_rep2

source_name: mouse blood, day 3 after Cs-137 injection


title: WholeBlood_d5_Control_rep1

source_name: mouse blood, day 5, control


title: WholeBlood_d3_Control_rep3

source_name: mouse blood, day 3, control


title: WholeBlood_d5_Control_rep3


title: WholeBlood_d3_Cs-137_rep5


title: WholeBlood_d2_Cs-137_rep5

source_name: mouse blood, day 2 after Cs-137 injection

value: 2 Gy


title: WholeBlood_d3_Cs-137_rep1


title: WholeBlood_d2_Cs-137_rep4


title: WholeBlood_d3_Control_rep1


title: WholeBlood_d20_Cs-137_rep4

source_name: mouse blood, day 20 after Cs-137 injection


title: WholeBlood_d5_Control_rep2


title: WholeBlood_d20_Cs-137_rep3


title: WholeBlood_d3_Control_rep2


title: WholeBlood_d2_Cs-137_rep1


title: WholeBlood_d2_Cs-137_rep3


title: WholeBlood_d20_Cs-137_rep2


title: WholeBlood_d3_Cs-137_rep6


title: WholeBlood_d20_Control_rep4

source_name: mouse blood, day 20, control


title: WholeBlood_d3_Cs-137_rep3


title: WholeBlood_d3_Cs-137_rep4


title: WholeBlood_d20_Cs-137_rep1


title: WholeBlood_d20_Cs-137_rep6


title: WholeBlood_d20_Control_rep5


title: WholeBlood_d2_Cs-137_rep2


title: WholeBlood_d2_Cs-137_rep6


title: WholeBlood_d20_Control_rep3


title: WholeBlood_d20_Cs-137_rep5


title: WholeBlood_d20_Control_rep6


title: WholeBlood_d20_Control_rep2


title: MDA-MB-231 control

status: Public on Aug 29 2014

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

country: Greece

institute: University of Crete

description: Breast cancer derived cells

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA). CEL files were loaded to Genespring V11 and normalization was performed with the RMA normalization algorithm.

source_name: MDA-MB-231 cells, treated for 3 hours with 0.1% Ethanol

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)

growth_protocol: The human breast cancer cell line MDA-MB-231 was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: MDA-MB-231 cells were incubated with vehicle, E2 (10-6M) or tamoxifen (10-6M) for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS

tag: cell line

value: 3 hours with 0.1% Ethanol


title: WholeBlood_d20_Control_rep1


title: MDA-MB-231 tamoxifen

description: Breast cancer derived cells

source_name: MDA-MB-231 cells, treated for 3 hours with 10-6M tamoxifen

value: 3 hours with 10-6M tamoxifen


title: T47D control

description: Breast cancer derived cells

source_name: T47D cells, treated for 3 hours with 0.1% Ethanol

growth_protocol: The human breast cancer cell line T47D was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

treatment_protocol: T47D cells were incubated with vehicle, E2 (10-6M) or tamoxifen (10-6M) for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS


title: MDA-MB-231 estradiol

description: Breast cancer derived cells

source_name: MDA-MB-231 cells, treated for 3 hours with 10-6M estradiol

value: 3 hours with 10-6M estradiol


title: heads-dark_dark-CircadianTime36

status: Public on Aug 19 2014

city: Notre Dame

first: Matthew

last: Leming

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

description: Wh_DD_12(2) hr constant darkness

hyb_protocol: Hybridization was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, by using the Hybridization Kit, LS and Wash Buffer Kit (Roche NimbleGen, Madison, WI).

scan_protocol: Scanning was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, using a NimbleGen MS 200 Microarray Scanner at 2 μM resolution.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Aedes aegypti

source_name: Wh_DD_12 hr constant darkness

label_protocol: Labeling was performed by the Genomics and Bioinformatics Core Facility, University of Notre Dame, using the NimbleGen Single Color Labeling Kit (Roche NimbleGen, Madison, WI).

growth_protocol: ~30 mated non-blood fed female Ae. aegypti Higgs White eye (Wh) strain mosquitoes, aged 2-6 days, were placed in 24 cages, and sequestered in light controlled boxes.

extract_protocol: Heads were removed from bodies at 0C on a chilled metal plate and collected. The RNeasy RNA Isolation Kit (Qiagen, Valencia, CA) was used to isolate RNA from each sample, following manufacturer’s instructions. Genomic DNA was instead removed by using the DNA-free Kit (Applied Biosystems, Carlsbad, CA) per manufacturer instructions.

value: Higgs White Eye

value: 2-6 days

tag: Sex

value: female

tag: treatment condition

value: constant dark conditions

tag: time point


title: heads-dark_dark-CircadianTime28

description: Wh_DD_4(2) hr constant darkness

source_name: Wh_DD_4 hr constant darkness


title: heads-dark_dark-CircadianTime40

description: Wh_DD_16(2) hr constant darkness

source_name: Wh_DD_16 hr constant darkness


title: T47D tamoxifen

description: Breast cancer derived cells

source_name: T47D cells, treated for 3 hours with 10-6M tamoxifen

tag: treatment


title: heads-dark_dark-CircadianTime20

description: Wh_DD_20 hr constant darkness

source_name: Wh_DD_20 hr constant darkness

tag: age


title: T47D estradiol

description: Breast cancer derived cells

source_name: T47D cells, treated for 3 hours with 10-6M estradiol


title: heads-dark_dark-CircadianTime32

description: Wh_DD_8(2) hr constant darkness

source_name: Wh_DD_8 hr constant darkness


title: heads-dark_dark-CircadianTime8

description: Wh_DD_8 hr constant darkness


title: heads-light_dark-ZeitgeberTime16

description: Wh_LD_16 hr light/dark

source_name: Wh_LD_16 hr light/dark

value: light/dark conditions


title: heads-light_dark-ZeitgeberTime44

description: Wh_LD_20(2) hr light/dark

source_name: Wh_LD_20 hr light/dark


title: heads-light_dark-ZeitgeberTime40

description: Wh_LD_16(2) hr light/dark


title: heads-light_dark-ZeitgeberTime12

description: Wh_LD_12 hr light/dark

source_name: Wh_LD_12 hr light/dark


title: heads-light_dark-ZeitgeberTime32

description: Wh_LD_8(2) hr light/dark

source_name: Wh_LD_8 hr light/dark


title: heads-dark_dark-CircadianTime44

description: Wh_DD_20(2) hr constant darkness


title: heads-light_dark-ZeitgeberTime36

description: Wh_LD_12(2) hr light/dark


title: heads-dark_dark-CircadianTime0

description: Wh_DD_0 hr constant darkness

source_name: Wh_DD_0 hr constant darkness


title: heads-light_dark-ZeitgeberTime28

description: Wh_LD_4(2) hr light/dark

source_name: Wh_LD_4 hr light/dark


title: heads-light_dark-ZeitgeberTime20

description: Wh_LD_20 hr light/dark


title: heads-light_dark-ZeitgeberTime24

description: Wh_LD_0(2) hr light/dark

source_name: Wh_LD_0 hr light/dark


title: heads-dark_dark-CircadianTime12

description: Wh_DD_12 hr constant darkness


title: heads-dark_dark-CircadianTime16

description: Wh_DD_16 hr constant darkness


title: heads-dark_dark-CircadianTime24

description: Wh_DD_0(2) hr constant darkness


title: heads-dark_dark-CircadianTime4

description: Wh_DD_4 hr constant darkness