title: Year1 day8 10% sewage rep3

data_processing: Image TIFF files from the scanned microarrays were imported into ImaGene software version 6.1 (BioDiscovery Inc.).  ImaGene output files were imported into GeneSpring software version 7.3.1 (Agilent Technologies Inc.) for statistical analysis.  Each timepoint for each experiment was treated as a unique block and analyzed independently of other timepoints.  The data were normalized to the 50th percentile of the median values for all genes across the microarrays within each timepoint.  Statistical analysis of this normalized data was performed using one-way ANOVA, and then Welch t-tests (variances not assumed equal) were performed to compare the gene expressions in a sewage treatment versus the control with significant differences noted when p < 0.05.  NOTE: Extracted GeneSpring v7 files into GeneSpring v11 in 2012 to obtain data for each slide (in contrast, for thesis and manuscript data analysis, data was exported from GS by treatment).

source_name: liver, 10% sewage, Yr1d8

treatment_protocol: Two experiments were conducted in the month of June but exactly one year apart (called Yr 1 and Yr 2), using untreated sewage from the Capital Regional District in Victoria, British Columbia, Canada.  Juvenile chinook salmon were exposed to seawater negative control, or sewage concentrations made in seawater of 0.05%, 0.1%, 0.7%, 2% and 5/10% for 8 days (with sampling events at days 1, 4 and 8), and then a portion of fish were transferred to clean seawater to recover for 8 days and sampled at the day 16 timepoint.

tag: treatment

value: 10% sewage

tag: time

value: year 1 day 8

tag: tissue

tag: sample type

value: liver, mixture of Universal DNA Reference (UDR) material


title: SchuS4_Mono_22h_5

status: Public on Dec 01 2012

type: RNA

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours

scan_protocol: scanned using the Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and data was extracted using GenePix® pro 6.1

data_processing: 75th percentile normalisation using GeneSpring GX v 11.5.1

molecule: total RNA

organism: Homo sapiens

source_name: SchuS4 Infected, Monolayer A549s, 22 hour post infection

label_protocol: RNA was labelled with Cy3 using the Quick Amp Labelling kit (Agilent) as per the manufacturer’s instructions.

growth_protocol: Grown in RWVs in Dulbeccos modified eagle's media with 10% foetal calf serum and 4mM l-glutamine

extract_protocol: Qiagen Rneasy Mini Kit

treatment_protocol: Cells infected with F. tularensis SchuS4 for 3 hours MOI 100. RNA extracted from RWVs or Monolayers at 2, 6 and 22 hours postin infection and placed into Qiagen RLT (lysis buffer) containing B-mercaptoethanol

tag: gender

value: Male

tag: cell line

value: A549 epithelial cells

tag: culture condition

value: monolayer

tag: infection

value: SchuS4 Infected

value: 22 hour


title: vastus 13wk FRG1 rep1

city: Santa Cruz

first: Lily

last: Shiue

state: CA

address: 1156 High Street

department: MCD Biology

country: USA

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
probe group file: GPL13185_mjay.pgf
meta-probeset file: GPL13185_mjay.clf

label: biotin

organism: Mus musculus

source_name: vastus lateralis

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

growth_protocol: Vastus lateralis and biceps brachii dissected from 4wk and 13wk wild type and FRG1 mice into RNAlater (Ambion).

extract_protocol: RNA was isolated using Rneasy Fibrous Tissue Mini kit (Qiagen), and treated with Dnase I.

tag: muscle

value: vastus lateralis

tag: time point

tag: genotype/variation

value: FRG1 over-expressing

tag: background mouse strain


title: SchuS4_Mono_22h_6


title: 14162906 - col T0 BR2 vs col T10 BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Short term nitrate induction kinetics in wildtype, nlp7-1, nlp7-3 and nlp6nlp7

hyb_protocol: col T10 BR2 Cy5 / col T0 BR2 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: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: col T10 BR2

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: whole plant - Media: modified Hoagland  hygrometry: 80  Temperature: 22  Light: 100

extract_protocol: col T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 10min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 10min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.

tag: ecotype

value: Columbia

tag: age

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col

source_name: col T0 BR2

extract_protocol: col T0 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 00min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 0min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: SchuS4_RWV_2h_1

source_name: SchuS4 Infected, RWV A549s, 2 hour post infection

value: RWV

value: 2 hour


title: Year1 day8 10% sewage rep4

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

country: Canada

institute: Simon Fraser University

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

scan_protocol: Slides were scanned at 10 um resolution on a PerkinElmer ScanArray Express or PerkinElmer ProScanArray.

organism: Oncorhynchus tshawytscha

label_protocol: 25 ug of liver total RNA was labelled with Cy5-dUTP using Superscript Direct cDNA Labeling System kits (Invitrogen), as per the manufacturer's instructions.  Cy3-labelled UDR cDNA sample was made from 600 ng of UDR stock material using 1 nmol of Cy3-dCTP dye (Amersham) and Ready-To-Go beads (Amersham) as per the manufacturer’s protocol, except a 2 h incubation at 37 degree Celcius was used to maximize yield.

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

value: liver

value: juvenile

organism: Oncorhynchus mykiss

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: 14162905 - col T10 BR1 vs col T0 BR1

hyb_protocol: col T0 BR1 Cy5 / col T10 BR1 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.

source_name: col T0 BR1

extract_protocol: col T0 BR1:5ug. (Extraction_ARN_au_Trizol.doc)

source_name: col T10 BR1

extract_protocol: col T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: vastus 13wk FRG1 rep2


title: Year1 day16 Control rep1

source_name: liver, neg control, Yr1d16

value: neg control

value: year 1 day 16


title: Year1 day8 10% sewage rep2

value: 10% sewage

value: year 1 day 8

value: liver, mixture of Universal DNA Reference (UDR) material


title: SchuS4_Mono_22h_4

value: Male

value: A549 epithelial cells

value: monolayer


title: 14162903 - nlp7-3 T20 BR2 vs col T20 BR2

hyb_protocol: col T20 BR2 Cy5 / nlp7-3 T20 BR2 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.

source_name: col T20 BR2

extract_protocol: col T20 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 20min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 20min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.

source_name: nlp7-3 T20 BR2

extract_protocol: nlp7-3 T20 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 20min - mut - time course study - gene disruption,nitrate:quantity 3mM time 20min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: 14162904 - col T0 BR1 vs col T10 BR1

hyb_protocol: col T10 BR1 Cy5 / col T0 BR1 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: Year1 day8 10% sewage rep1


title: SchuS4_Mono_22h_3

value: SchuS4 Infected

value: 22 hour


title: Year1 day8 2% sewage rep5

source_name: liver, 2% sewage, Yr1d8

value: 2% sewage


title: Year1 day8 2% sewage rep4


title: vastus 4wk FRG1 rep1

value: vastus lateralis

value: FRG1 over-expressing


title: vastus 4wk FRG1 rep3


title: vastus 4wk FRG1 rep2


title: vastus 13wk WT rep3

value: wild type


title: Year1 day8 2% sewage rep3


title: Year1 day16 0.1% sewage rep1

source_name: liver, 0.1% sewage, Yr1d16

value: 0.1% sewage


title: 46,XY 5mC immunoprecipitated DNA Sample 1 IF

type: genomic

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

country: Sweden

institute: Lund University

description: Methylation array

hyb_protocol: by the NimbleGen Service Group (Reykjavik, Iceland), which performed the quality control, labeling, hybridization, and scanning.

scan_protocol: standard NimbleGen protocol

data_processing: Signal intensity data were extracted from the scanned images, with each feature on the array having a corresponding log2 ratio, i.e, the ratio of the input signals for the precipitated and the input fraction DNAs. PCA and HCA were performed as above. In addition, the log2 ratio was scaled to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. A modified ACME algorithm,{Scacheri, 2006 #280} where a fixed-length window (750 bp) is placed around each consecutive probe, and the one-sided Kolmogorov-Smirnov test were then applied on the scaled log2 ratio data to determine whether the probes were drawn from a significantly more positive distribution (peak) of intensity log2 ratios than the other probes in the array. The resulting score for each probe is the -log10 p value from the windowed Kolmogorov-Smirnov test around that probe.

molecule: genomic DNA

source_name: 5mC immunoprecipitated DNA

label_protocol: Of the methylated and input fraction DNAs, 1.5 µg was differentially labeled with Cy3 and Cy5, respectively

growth_protocol: cells were maintained and passaged in RPMI 1640 medium (Invitrogen) containing 10% FBS (Sigma-Aldrich) in 250 ml cell culture flasks (BD Falcon) for 8 weeks.

extract_protocol: From each sample (fibroblasts from the CT8M patient and the references), 12 µg of DNA was diluted in standard TE buffer to a concentration of 75 ng/μl. The DNA was sonicated for 90 s with a Covaris S220 (Covaris, Woburn, MA) set to a 5% duty cycle, intensity value 3, and 200 cycles per burst to generate fragments ranging from 200-1,000 bp, as verified by gel electrophoresis. The fragmented DNA was then diluted to a concentration of 13.4 ng/μl and denatured for 10 min at 95°C, after which two input fractions (approximately 250 ng each), serving as references in subsequent microarray hybridizations (see below), were collected and stored at -80°C. The remaining DNA aliquots were immunoprecipitated overnight with monoclonal antibodies against either 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) using magnetic bead-based MeDIP and hMeDIP kits (Diagenode, Liège, Belgium) to purify and isolate the precipitated DNA. Both the input fraction and the immunoprecipitated DNAs were then amplified using the WGA2 kit (Sigma-Aldrich), generating sufficient amounts (approximately 6 µg) for the various microarray hybridizations

treatment_protocol: Single-cell cloned fibroblasts

tag: genotype

tag: cell type

value: fibroblast

tag: antibody

tag: antibody manufacturer

value: Diagenode

source_name: Input untreated DNA


title: 47,XY,+8 5mC immunoprecipitated DNA Sample 5 IF

description: Methylation array


title: 14162902 - col T20 BR2 vs nlp7-3 T20 BR2

hyb_protocol: nlp7-3 T20 BR2 Cy5 / col T20 BR2 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: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

tag: time

value: col


title: vastus 13wk WT rep1


title: 14162899 - nlp7-3 T10 BR2 vs col T10 BR2

hyb_protocol: col T10 BR2 Cy5 / nlp7-3 T10 BR2 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.

source_name: nlp7-3 T10 BR2

extract_protocol: nlp7-3 T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 10min - mut - time course study - gene disruption,nitrate:quantity 3mM time 10min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: SchuS4_Mono_6h_5

source_name: SchuS4 Infected, Monolayer A549s, 6 hour post infection

value: 6 hour


title: mRNA profiling in HIV-1 infected cells

city: Hangzhou

first: Jin

last: Yang

address: Qingchun Road 79

country: China

institute: Zhejiang University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

source_name: H9/IIIB_HIV-1 replication

label_protocol: ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: Cells were cultured in DMEM medium with 10% FBS and 1x Antibiotic-Antimycotic (GIBCO).

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen).

treatment_protocol: The low-passage (3rd) cells (1×10^7) were used to isolate total RNA .

value: lymphocyte

value: HIV-1 LAI persistent infection


title: Year1 day8 2% sewage rep1

tag: treatment

value: year 1 day 8

tag: tissue

value: liver

value: juvenile

tag: sample type

value: liver, mixture of Universal DNA Reference (UDR) material


title: 14162898 - col T10 BR2 vs nlp7-3 T10 BR2

hyb_protocol: nlp7-3 T10 BR2 Cy5 / col T10 BR2 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: SchuS4_Mono_22h_2

source_name: SchuS4 Infected, Monolayer A549s, 22 hour post infection

tag: gender

value: Male

tag: cell line

value: A549 epithelial cells

tag: culture condition

value: monolayer

value: SchuS4 Infected

value: 22 hour


title: vastus 13wk WT rep2

source_name: vastus lateralis

tag: muscle

value: vastus lateralis

tag: time point

value: wild type


title: SchuS4_Mono_6h_4

tag: infection


title: 14162900 - col T20 BR2 vs nlp7-1 T20 BR2

hyb_protocol: nlp7-1 T20 BR2 Cy5 / col T20 BR2 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.

source_name: nlp7-1 T20 BR2

extract_protocol: nlp7-1 T20 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

tag: ecotype

value: Columbia

tag: genotype/variation


title: 14162901 - nlp7-1 T20 BR2 vs col T20 BR2

hyb_protocol: col T20 BR2 Cy5 / nlp7-1 T20 BR2 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.

tag: age

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:1.02


title: SchuS4_Mono_22h_1


title: Year1 day8 2% sewage rep2

value: 2% sewage


title: vastus 4wk WT rep2

tag: background mouse strain


title: mRNA profiling in HIV-1 latently infected cells

source_name: CEM-SS_HIV-1 latency

tag: cell type

value: CEM-SS

value: HIV-1 Bru latently infected


title: Year1 day8 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr1d8

value: 0.7% sewage

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: mRNA profiling in CEM-SS cells

source_name: CEM-SS_uninfected control

value: lymphocyte

value: uninfected


title: Year1 day8 0.7% sewage rep3

value: year 1 day 8

value: liver

value: juvenile


title: SchuS4_Mono_6h_3

value: Male

value: A549 epithelial cells

value: 6 hour


title: Year1 day8 0.7% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day8 0.7% sewage rep1


title: Year1 day8 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr1d8

value: 0.1% sewage


title: SchuS4_Mono_6h_6

value: monolayer

value: SchuS4 Infected


title: Uri_iPS1

city: Guanghou

first: Guangjin

last: Pan

state: China

address: Kaiyuan Street, Guangzhou Science district

institute: Guangzhou Institute of Biomedicine and Health, CAS

description: iPS cells derived from human urine cells_replicate1

hyb_protocol: Array hybridization, wash were performed according to NimbleGen’s recommended protocol

scan_protocol: Arrays were scanned using a GenePix 4000B scanner and the PMT settings were followed by NimbleGen array manual

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software

label_protocol: Amino Allyl labeling method,  About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit

growth_protocol: The primary urine cells were cultured in urine cell medium consisting of a 1:1 mixture of DMEM/F12 culture medium supplemented with 10% of fetal bovine serum (FBS, PAA), 0.1 mM nonessential amino acids (NEAA), 1 mM L-glutamax, 0.1 mM ß-mercaptoethanol and SingleQuot Kit CC-4127 REGM (Lonza). Neural stem cells were dissociated to small cluster or single cells to suspend in flasks containing neural growth medium as neural spheres(1:1 of DMEM/F12 supplemented with 1% N2 (Invitrogen) and Neurobasal medium supplemented with 2% B27 (Invitrogen) supplemented with 20ng/ml bFGF, 20ng/ml EGF). iPS cell maintained on matrigel by defined medium_TeSR.

extract_protocol: Total RNA was prepared with RNeasy Mini Kit (Qiagen, Inc., Valencia, CA)  and subjected to on-column DNase treatment. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: no treatments

value: pluripotent stem cells (iPSCs)


title: vastus 4wk WT rep3

value: vastus lateralis

value: wild type


title: 14162893 - col T0 BR2 vs nlp7-3 T0 BR2

hyb_protocol: nlp7-3 T0 BR2 Cy5 / col T0 BR2 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.

source_name: nlp7-3 T0 BR2

extract_protocol: nlp7-3 T0 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 00min - mut - time course study - gene disruption,nitrate:quantity 3mM time 0min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.

value: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

source_name: col T0 BR2

value: col


title: SchuS4_Mono_2h_5

source_name: SchuS4 Infected, Monolayer A549s, 2 hour post infection

value: 2 hour


title: SchuS4_Mono_6h_2


title: 14162892 - nlp7-1 T0 BR2 vs col T0 BR2

hyb_protocol: col T0 BR2 Cy5 / nlp7-1 T0 BR2 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.

source_name: nlp7-1 T0 BR2

extract_protocol: nlp7-1 T0 BR2:5ug. (Extraction_ARN_au_Trizol.doc)


title: UiNSC2

description: neral stem cells derived from human urine cells_replicate2

source_name: neural stem cells derived from human urine cells

value: neural stem cells (NSCs)


title: Uri_iPS2

description: iPS cells derived from human urine cells_replicate2


title: SchuS4_Mono_2h_4

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours


title: SchuS4_Mono_6h_1


title: Year1 day8 0.1% sewage rep2

value: year 1 day 8

value: liver


title: SchuS4_Mono_2h_6

value: Male


title: UrC2

description: cells isolated from human urine_replicate2

source_name: epithelial-like cells isolated from human urine

value: epithelial-like


title: 14162896 - col T10 BR2 vs nlp7-1 T10 BR2

hyb_protocol: nlp7-1 T10 BR2 Cy5 / col T10 BR2 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.

source_name: nlp7-1 T10 BR2

extract_protocol: nlp7-1 T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

source_name: col T10 BR2


title: 14162863 - col T0 BR2 vs nlp7-1 T0 BR2

hyb_protocol: nlp7-1 T0 BR2 Cy5 / col T0 BR2 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: 14162895 - nlp7-3 T0 BR2 vs col T0 BR2

hyb_protocol: col T0 BR2 Cy5 / nlp7-3 T0 BR2 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: 14163070 - col T20 BR2 vs col T10 BR2

hyb_protocol: col T10 BR2 Cy5 / col T20 BR2 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.

source_name: col T20 BR2


title: UrC1

description: cells isolated from human urine_replicate1


title: UiNSC1

description: neral stem cells derived from human urine cells_replicate1


title: SchuS4_Mono_2h_3

extract_protocol: Qiagen Rneasy Mini Kit

value: A549 epithelial cells


title: vastus 4wk WT rep1

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

extract_protocol: RNA was isolated using Rneasy Fibrous Tissue Mini kit (Qiagen), and treated with Dnase I.


title: Grape control 96 hr rep2

city: Geisenheim

first: Alicia

middle: Eva

last: Timm

address: Vone-Lade-Str 1

department: Phytomedicine

country: Germany

institute: Forschungsanstalt Geisenheim

hyb_protocol: Samples were hybridised to slides using a NimbleGen hybridization system.

scan_protocol: The slide was scanned using an Axon GenePix® 4000A scanner, after which resulting images were imported into NimbleScan software for grid alignment and expression data analyses.

data_processing:
The data were normalized using quantile normalization and gene calls generated using a robust multi-chip average (RMA) algorithm (Irizarry).  Analysis of differentially expressed genes was performed using linear modelling and empirical Bayes methods, as implemented in the Limma R package (Smyth 2005). P-values were adjusted for multiple testing with the Benjamini and Hochberg method (Benjamini & Hochberg).
NimbleScan software computed signal intensities.

organism: Vitis vinifera

source_name: Grapevine leaf control 96 hours

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit

extract_protocol: Spectrum™ Plant Total RNA Kit (Sigma-Aldrich)

treatment_protocol: Grapevine (cv Riesling plants) were exposed to 10-15 P. ficus indivduals by enclosing insects within a clip cage attached to the leaf for periods of 6 or 96 hours

value: leaf

value: control

tag: cultivar

value: Riesling


title: Year1 day8 0.1% sewage rep1

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

value: 0.1% sewage

tag: time

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day8 0.05% sewage rep5

source_name: liver, 0.05% sewage, Yr1d8

tag: treatment

value: 0.05% sewage


title: Year1 day8 0.1% sewage rep3

tag: tissue


title: SchuS4_Mono_2h_2

value: monolayer

value: SchuS4 Infected


title: 14163069 - col T10 BR2 vs col T20 BR2

hyb_protocol: col T20 BR2 Cy5 / col T10 BR2 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: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col

extract_protocol: col T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)


title: Year1 day8 0.05% sewage rep3

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

value: year 1 day 8

tag: sample type


title: 14163068 - col T10 BR2 vs col T5 BR2

hyb_protocol: col T5 BR2 Cy5 / col T10 BR2 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.

source_name: col T5 BR2

extract_protocol: col T5 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 05min - Wt - time course study - nitrogen concentration,nitrate:quantity 3mM time 5min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: Year1 day8 0.05% sewage rep4

value: liver


title: Year1 day8 0.05% sewage rep2


title: Grape treated 96 hr rep2

source_name: Grapevine leaf attacked by P. ficus, 96 hours

value: 96 hrs

value: attacked by P. ficus


title: SchuS4_Mono_2h_1

tag: gender

value: Male

value: A549 epithelial cells

value: 2 hour


title: Naïve_RWV_22h_6

source_name: Uninfected, RWV A549s, 22 hour post infection

tag: cell line

value: RWV

value: Uninfected

value: 22 hour


title: Naïve_RWV_22h_5

tag: culture condition


title: Grape control 6 hr rep2

source_name: Grapevine leaf control 6 hours

value: leaf

value: control

value: Riesling


title: Year1 day8 0.05% sewage rep1

value: 0.05% sewage

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day8 Control rep4

source_name: liver, neg control, Yr1d8

value: neg control

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day8 Control rep3

value: year 1 day 8


title: 14163066 - col T5 BR2 vs col T0 BR2

hyb_protocol: col T0 BR2 Cy5 / col T5 BR2 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.

extract_protocol: col T0 BR2:5ug. (Extraction_ARN_au_Trizol.doc)

value: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col


title: 14163065 - col T0 BR2 vs col T5 BR2

hyb_protocol: col T5 BR2 Cy5 / col T0 BR2 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: 14163067 - col T5 BR2 vs col T10 BR2

hyb_protocol: col T10 BR2 Cy5 / col T5 BR2 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: Naïve_RWV_22h_2

value: Male


title: Grape control 96 hr rep1


title: Naïve_RWV_22h_4

value: A549 epithelial cells


title: Naïve_RWV_22h_1


title: Year1 day8 Control rep2

value: liver


title: Grape treated 96 hr rep1

value: 96 hrs

value: attacked by P. ficus


title: Year1 day8 Control rep1


title: Grape treated 6 hr rep2

source_name: Grapevine leaf attacked by P. ficus, 6 hours

value: 6 hrs


title: Grape control 6 hr rep1

value: leaf


title: Grape treated 6 hr rep1


title: Naïve_RWV_6h_6

source_name: Uninfected, RWV A549s, 6 hour post infection

value: RWV

value: Uninfected

value: 6 hour


title: Year1 day4 2% sewage rep3

source_name: liver, 2% sewage, Yr1d4

value: 2% sewage

value: year 1 day 4

value: juvenile


title: Naïve_RWV_22h_3

value: 22 hour


title: Year1 day4 2% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day4 2% sewage rep1


title: Year1 day4 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr1d4

value: 0.7% sewage


title: 14163062 - col T10 BR1 vs col T20 BR1

hyb_protocol: col T20 BR1 Cy5 / col T10 BR1 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.

source_name: col T20 BR1

extract_protocol: col T20 BR1:5ug. (Extraction_ARN_au_Trizol.doc)

value: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col

source_name: col T10 BR1

extract_protocol: col T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_RWV_6h_5

value: Male

value: A549 epithelial cells


title: 14163034 - col T10 BR1 vs col T5 BR1

hyb_protocol: col T5 BR1 Cy5 / col T10 BR1 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.

source_name: col T5 BR1

extract_protocol: col T5 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Year1 day4 0.7% sewage rep3

value: liver


title: Year1 day4 0.7% sewage rep2


title: 14163063 - col T20 BR1 vs col T10 BR1

hyb_protocol: col T10 BR1 Cy5 / col T20 BR1 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: 14163031 - col T0 BR1 vs col T5 BR1

hyb_protocol: col T5 BR1 Cy5 / col T0 BR1 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.

source_name: col T0 BR1

extract_protocol: col T0 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: 14163030 - nlp6nlp7 T5 BR1 vs col T5 BR1

hyb_protocol: col T5 BR1 Cy5 / nlp6nlp7 T5 BR1 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.

source_name: nlp6nlp7 T5 BR1

extract_protocol: nlp6nlp7 T5 BR1:5ug. (Extraction_ARN_au_Trizol.doc)

treatment_protocol: Name:Nitrate induction kinetics - 05min - mut - time course study - gene disruption,nitrate:quantity 3mM time 5min . Addition of nitrate (final concentration of 3mM) to 13 days old seedlings growing in vitro for 10 days with 3mM nitrate and for 3 days without N, harvest after 0, 5, 10 and 20 minutes.


title: 14163033 - col T5 BR1 vs col T10 BR1

hyb_protocol: col T10 BR1 Cy5 / col T5 BR1 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: Year1 day4 0.7% sewage rep1


title: Naïve_RWV_6h_3

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours


title: Naïve_RWV_6h_1


title: 14163029 - col T5 BR1 vs nlp6nlp7 T5 BR1

hyb_protocol: nlp6nlp7 T5 BR1 Cy5 / col T5 BR1 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: Naïve_RWV_6h_4


title: Naïve_RWV_6h_2


title: 14163028 - nlp7-3 T5 BR1 vs col T5 BR1

hyb_protocol: col T5 BR1 Cy5 / nlp7-3 T5 BR1 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.

source_name: nlp7-3 T5 BR1

extract_protocol: nlp7-3 T5 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: 14163027 - col T5 BR1 vs nlp7-3 T5 BR1

hyb_protocol: nlp7-3 T5 BR1 Cy5 / col T5 BR1 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: Naïve_RWV_2h_4

source_name: Uninfected, RWV A549s, 2 hour post infection

value: 2 hour


title: Year1 day4 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr1d4

value: 0.1% sewage


title: 14163032 - col T5 BR1 vs col T0 BR1

hyb_protocol: col T0 BR1 Cy5 / col T5 BR1 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: 14163025 - nlp7-1 T5 BR1 vs col T5 BR1

hyb_protocol: col T5 BR1 Cy5 / nlp7-1 T5 BR1 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.

source_name: nlp7-1 T5 BR1

extract_protocol: nlp7-1 T5 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_RWV_2h_5

value: RWV


title: Year1 day4 0.1% sewage rep2

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.


title: Naïve_RWV_2h_2

value: Uninfected


title: 14163024 - col T5 BR1 vs nlp7-1 T5 BR1

hyb_protocol: nlp7-1 T5 BR1 Cy5 / col T5 BR1 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: Year1 day4 Control rep8

source_name: liver, neg control, Yr1d4

value: neg control


title: Year1 day4 0.1% sewage rep1


title: Year1 day4 Control rep7


title: 14163022 - col T0 BR1 vs nlp6nlp7 T0 BR1

hyb_protocol: nlp6nlp7 T0 BR1 Cy5 / col T0 BR1 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.

source_name: nlp6nlp7 T0 BR1

extract_protocol: nlp6nlp7 T0 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Year1 day4 Control rep6

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Naïve_RWV_2h_3


title: 14163023 - nlp6nlp7 T0 BR1 vs col T0 BR1

hyb_protocol: col T0 BR1 Cy5 / nlp6nlp7 T0 BR1 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: Naïve_RWV_2h_6


title: 14163017 - col T0 BR1 vs nlp7-1 T0 BR1

hyb_protocol: nlp7-1 T0 BR1 Cy5 / col T0 BR1 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.

source_name: nlp7-1 T0 BR1

extract_protocol: nlp7-1 T0 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_Mono_22h_4

source_name: Uninfected, monolayer A549s, 22 hour post infection

value: monolayer


title: Naïve_Mono_22h_6


title: 14163018 - nlp7-1 T0 BR1 vs col T0 BR1

hyb_protocol: col T0 BR1 Cy5 / nlp7-1 T0 BR1 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: Year1 day4 0.1% sewage rep3

value: year 1 day 4


title: 14162897 - nlp7-1 T10 BR2 vs col T10 BR2

hyb_protocol: col T10 BR2 Cy5 / nlp7-1 T10 BR2 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.

source_name: col T10 BR2

source_name: nlp7-1 T10 BR2

extract_protocol: nlp7-1 T10 BR2:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_Mono_22h_5

extract_protocol: Qiagen Rneasy Mini Kit


title: Year1 day4 Control rep5

value: juvenile


title: 14163016 - nlp6nlp7 T20 BR1 vs col T20 BR1

hyb_protocol: col T20 BR1 Cy5 / nlp6nlp7 T20 BR1 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.

source_name: nlp6nlp7 T20 BR1

extract_protocol: nlp6nlp7 T20 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: 14163020 - nlp7-3 T0 BR1 vs col T0 BR1

hyb_protocol: col T0 BR1 Cy5 / nlp7-3 T0 BR1 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.

source_name: nlp7-3 T0 BR1

extract_protocol: nlp7-3 T0 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: 14163012 - col T20 BR1 vs nlp6nlp7 T20 BR1

hyb_protocol: nlp6nlp7 T20 BR1 Cy5 / col T20 BR1 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.

source_name: col T20 BR1


title: Naïve_RWV_2h_1


title: 14163011 - nlp7-3 T20 BR1 vs col T20 BR1

hyb_protocol: col T20 BR1 Cy5 / nlp7-3 T20 BR1 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.

source_name: nlp7-3 T20 BR1

extract_protocol: nlp7-3 T20 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Year1 day4 10% sewage rep4

source_name: liver, 10% sewage, Yr1d4

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

value: 10% sewage


title: 14163019 - col T0 BR1 vs nlp7-3 T0 BR1

hyb_protocol: nlp7-3 T0 BR1 Cy5 / col T0 BR1 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.

source_name: col T0 BR1


title: 14163010 - col T20 BR1 vs nlp7-3 T20 BR1

hyb_protocol: nlp7-3 T20 BR1 Cy5 / col T20 BR1 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: Year1 day4 10% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day4 10% sewage rep3


title: Year1 day4 10% sewage rep1


title: Naïve_Mono_6h_5

hyb_protocol: Hybridised as per manufacturers instructions for 17 hours

source_name: Uninfected, monolayer A549s, 6 hour post infection

value: 6 hour


title: Year1 day4 0.05% sewage rep2

source_name: liver, 0.05% sewage, Yr1d4

value: 0.05% sewage


title: Naïve_Mono_6h_4


title: Naïve_Mono_22h_2

value: 22 hour


title: Year1 day4 0.05% sewage rep4


title: Naïve_Mono_22h_1


title: Naïve_Mono_6h_6


title: 14163008 - nlp7-1 T20 BR1 vs col T20 BR1

hyb_protocol: col T20 BR1 Cy5 / nlp7-1 T20 BR1 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: Columbia

value: (Boyes et al. Plant Cell 2001):boyes:1.02

value: col

source_name: nlp7-1 T20 BR1

extract_protocol: nlp7-1 T20 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_Mono_6h_2

value: Male

value: A549 epithelial cells


title: Naïve_Mono_22h_3


title: 14163006 - nlp6nlp7 T10 BR1 vs col T10 BR1

hyb_protocol: col T10 BR1 Cy5 / nlp6nlp7 T10 BR1 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.

source_name: col T10 BR1

source_name: nlp6nlp7 T10 BR1

extract_protocol: nlp6nlp7 T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: 14163005 - col T10 BR1 vs nlp6nlp7 T10 BR1

hyb_protocol: nlp6nlp7 T10 BR1 Cy5 / col T10 BR1 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: 14162917 - nlp7-3 T10 BR1 vs col T10 BR1

hyb_protocol: col T10 BR1 Cy5 / nlp7-3 T10 BR1 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.

source_name: nlp7-3 T10 BR1

extract_protocol: nlp7-3 T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: B. canis, broth culture, rep2 (set 2)

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description: This sample is of B.canis from broth culture. It is the second of two  biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled samples (1.5 µg) were hybridized at 42ºC to Brucella ovis custom designed array (Nimblegen), using a 1X mixing chamber (Nimblegen) and Maui hybridization system (BioMicro).  After 18-20 h, chambers were removed and slides were washed according to the manufacturer’s protocol.

scan_protocol: Slides were scanned at 5µm at a wavelength of 532 using a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).

data_processing: Fluorescent intensity levels were determined using Nimblescan (Nimblegen) software.  The acquired images were normalized using quantile normalization and gene expression signals were generated using the Robust Multichip Average (RMA) algorithm.

organism: Brucella canis

source_name: B. canis ATCC#23365

label_protocol: Samples were labeled and hybridized utilizing a Nimblegen protocol.

growth_protocol:
B. canis was grown to log phase on a shaker platform at 37ºC in Brucella broth (Difco) for 1-2 days.  Optical density (absorbance at 600nm) was determined and an appropriate aliquot was added to Brucella broth to achieve log phase within 24 h. All work performed with Brucella spp. was conducted in a BSL3 environment.
The mouse macrophage cell line, RAW 264.7 (ATCC TIB71), was maintained at 37ºC with 5% CO2 in supplemented RPMI 1640 (10% bovine growth serum and 0.2mM L-glutamine).  One day prior to infection, 1-2 x 107 RAW 264.7 cells were plated in T75 flasks.  On the day of infection, RAW cells in a sample flask were counted, and the optical density of the bacteria was determined.  Bacteria were added to the RAW cells to achieve an MOI of 100.  All work performed with Brucella spp. was conducted in a BSL3 environment.

extract_protocol:
For RNA isolation from broth cultures, 4 ml of Protect (Qiagen) was added to 2 ml of log phase bacteria.  Cultures were incubated for 5 min at room temperature and then centrifuged at 1100 x g for 10 min.  Supernatant was decanted and the pellet resuspended in 200 µl of lysis buffer (TE containing 66 µg/ml Proteinase K (Epicentre) and 0.193 KU/ml ReadyLyse (Epicentre).  Cells were incubated at room temperature for 10 min with vortexing every 2 min.  RLT buffer (700 µl) with β-mercaptoethanol (Qiagen) was added and samples were transferred to 2 ml tubes containing 30-50 mg acid washed glass beads (1.0 mm).  Bacteria were mechanically disrupted in a BeadBeater (Biospec Products, Inc) twice for 50s at 4800 rpm.  Tubes were quick-spun to pellet beads and supernatant transferred to new tubes.  RNA was isolated using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.  On-column DNase treatment was included in the isolation protocol.  Yield and quality were determined using a spectrophotometer (Nanodrop Technologies) and Agilent bioanalyzer (Agilent).
For RNA isolation from infected cells, RAW264.7 cells were infected at an MOI of 100 for 24 h.  Flasks were washed twice with supplemented RPMI 1640 to remove extracellular bacteria and 2 ml of Protect diluted 2:1 in PBS was added.  Cells were transferred to centrifuge tubes, pelleted, and resuspended in 200 µl of lysis buffer.  Cell lysis and mechanical disruption were performed as described above.  RNA was isolated using RNeasy Mini Kit (Qiagen) with DNase treatment.  Yield and quality were determined using a Nanodrop spectrophotometer and Agilent bioanalyzer, respectively. Bacterial RNA was enriched from RAW infected cells using MICROBEnrich kit (Ambion).  Oligo Magbeads were washed with nuclease-free water and equilibrated in binding buffer.  RNA was resuspended in binding buffer, mixed with capture oligo, incubated at 70ºC for 10 min and annealed at 37ºC for 1 h.  The RNA/capture oligo mix was added to the magbeads and incubated at 37ºC for 15 min.  The oligo Magbeads were removed, and the supernatant was collected.  Bacterial enriched RNA was assessed for yield and quality using a Nanodrop spectrophotometer and Agilent bioanalyzer.

tag: strain

tag: host

value: control


title: B. canis from infected cells (24h), rep2 (set 2)

description: This sample is of B.canis from RAW cells infected for 24h. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: Naïve_Mono_6h_3

tag: infection


title: 14163007 - col T20 BR1 vs nlp7-1 T20 BR1

hyb_protocol: nlp7-1 T20 BR1 Cy5 / col T20 BR1 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.

tag: ecotype

extract_protocol: col T20 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Naïve_Mono_6h_1


title: 14162916 - col T10 BR1 vs nlp7-3 T10 BR1

hyb_protocol: nlp7-3 T10 BR1 Cy5 / col T10 BR1 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.

tag: genotype/variation

extract_protocol: col T10 BR1:5ug. (Extraction_ARN_au_Trizol.doc)


title: Year1 day4 0.05% sewage rep1

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

value: liver

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: B. canis from infected cells (24h), rep1 (set 2)

description: This sample is of B.canis from RAW cells infected for 24h. It is the first of two biological replicates used in this experiment, each from separate cultures.