title: Mature reactor biofilm [Biofilm vs. Batch-Planktonic]

type: mixed

city: Bozeman

first: Matthew

middle: W

last: Fields

state: MT

address: 366 EPS Bldg

department: Center for Biofilm Engineering

institute: Montana State University

hyb_protocol: He, Z., L. Wu, X. Li, M.W. Fields, and J. Zhou.  2005.  Empirical establishment of oligonucleotide probe design critieria.  Appl. Environ. Microbiol.  71:3753-3760.

scan_protocol: ImaGene software

data_processing: Lowess intensity-based normalization was done within the MicrobesOnline (microbesonline.org) workbench as previously described with a statistical model that incorporated both per-gene variance (z values) and operon structure (OpWise) to compute the posterior probability that the expression level of each gene changed in the direction indicated by the mean value.     J Bacteriol  2006, 188:4068-4078.

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: lactate/sulfate mature bioiflm

growth_protocol: Biofilm was grown in CDC biofilm reactor with LS4D medium at 30 degrees C and a dilution rate of 0.09/h.

treatment_protocol: Biofilm was allowed to reach steady-state as determined by stable protein and carbohydrate levels.

tag: physiology state

value: biofilm

source_name: Batch planktonic

tag: physiological state

value: planktonic


title: Mature reactor biofilm [Biofilm vs. Reactor-Planktonic]

status: Public on Apr 01 2012

country: USA

molecule: total RNA

label_protocol: He, Z., L. Wu, X. Li, M.W. Fields, and J. Zhou.  2005.  Empirical establishment of oligonucleotide probe design critieria.  Appl. Environ. Microbiol.  71:3753-3760.

molecule: genomic DNA

source_name: Reactor planktonic


title: 581T

type: genomic

city: Bronx

first: Miao

last: Shi

state: NY

address: 1301 Morris Park ave

institute: Albert einstein College of Medicine

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
581T_B1.S

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

scan_protocol: see manufacturer's web site www.nimblegen.com

data_processing: HELP assay data analysis was performed using the published pipeline (Thompson, Reimers, Khulan, Gissot, Richmond, Chen, Zheng, Kim and Greally 2008), an open source resource available through BioConductor (HELP package). Quantile normalized, log2 HpaII/MspI ratio data is available on a Series records [Final_Qnormalized_ratio.txt]

organism: Homo sapiens

source_name: LM-PCR products from HpaII digested DNA

label_protocol: The HELP samples were labeled for microarray analysis as described previously [Selzer, Genes Chromosomes Cancer 44:305–319] using Cy3 or Cy5-conjugated oligonucleotides and random primers.

extract_protocol: DNA was isolated using proteinase K digestion, phenol-chloroform extraction, dialysis against 0.2X SSC and concentration by surrounding the dialysis bag with PEG 20,000 to reduce water content by osmosis.  The quality of the DNA was checked by gel electrophoresis and spectrophotometry.

tag: tissue

value: Lung

tag: phenotype

value: tumor

tag: gender

value: female

tag: tumor histology

value: squamous cell carcinoma (Sq)

tag: smoking status

value: Former

tag: restriction enzyme

value: HpaII

source_name: LM-PCR products from MspI digested DNA

value: MspI


title: 14268656 - Col0 Generation11 infectedFA Repet2 vs Col0 Generation11 infected Repet2

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process?

hyb_protocol: Col0 Generation11 infected Repet2 Cy5 / Col0 Generation11 infectedFA Repet2 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: Col0 Generation11 infected Repet2

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: rosette - Media hygrometry Temperature=22ºC Light=Long day

extract_protocol: Col0 Generation11 infected Repet2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:TCV - biotic stress - pathogen infection,tcv virus infection:time 10day . Col-0 and dcl2/3/4 were grown until rosette state and inoculated with TCV virus. Ten days post-inoculation, leaves and flowers were harvested and frozen with liquid nitrogen. They were kept at -80 until the TRNA was extracted. The same was made for Fisrt, Last generations and Fitness experiment.

tag: ecotype

value: columbia

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

tag: generation

tag: disease state

value: infected

source_name: Col0 Generation11 infectedFA Repet2

extract_protocol: Col0 Generation11 infectedFA Repet2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:TCV FA - biotic stress - pathogen infection,tcv virus infection:time 10day . A.ColO and dcl234 were grown until resette state and innoculated with TCV. Ten days postinnoculation, leaves were harvested. TCV from these tissues were used to innoculate next set of plants. The process was done 10 times. B. TCV from dcl234 G10 was inoculated on ColO plants (FA).


title: 14268652 - Col0 Generation11 infected Repet1 vs Col0 Generation11 infectedFA Repet1

hyb_protocol: Col0 Generation11 infectedFA Repet1 Cy5 / Col0 Generation11 infected Repet1 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: Col0 Generation11 infectedFA Repet1

extract_protocol: Col0 Generation11 infectedFA Repet1:10ug. (Qiagen_RNeasy.pdf)

source_name: Col0 Generation11 infected Repet1

extract_protocol: Col0 Generation11 infected Repet1:10ug. (Qiagen_RNeasy.pdf)


title: Lame 61 Cy 3 Ptv Cy5 Vivo 4

city: Quebec

first: Claude

last: Robert

state: Quebec

address: Pavillon Comtois

department: Animal Sciences

country: Canada

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Slides were scan on Agilent G2505 B Micro Array Scanner.

data_processing: Images were quantified using Feature extraction software

organism: Bos taurus

source_name: In vivo

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol:
In vitro production
In vivo production

extract_protocol:
Total RNA was extract using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA.
Amplification of RNA was done using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). Quantity of produce aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: For in-vitro: bovine ovaries were obtained from a slaughterhouse, cumulus-oocyte complexes aspiration were aspirated from 2 to 6 mm follicles. Healthy COCs with at least five layers of cumulus were selected for in vitro maturation, in vitro fertilization and in vitro culture. For In-vivo: On Day 8 to 12 post-oestrus, follicles with a diameter larger than 8 mm from Holstein heifers cows were aspirated. Thirty-six hours later, 8 injections of  FSH were given for a total of 400 mg of FSH were administered in doses decreasing from 60 mg to 20 mg (two injections per day). A 500-µg dose of prostaglandin F2α analogue was administered with each of the two final FSH injections. The animals exhibited oestrus about 36 h after the final injection and were inseminated twice, 12 and 24 h post-estrus with the pooled semen used for in vitro fertilization. Embryos were recovered by uterine flushing 7.5 days after the first insemination.

tag: sample type

value: in vivo embryos

tag: time of embryo collection

value: 7 dpi (days post-in-vivo insemination)

tag: in vitro production

value: No

source_name: Embryo produced in vitro after OPU

value: in vitro embryos

value: 168 hpf (hours post-in-vitro fertilization)

value: Yes


title: 14268654 - Col0 Generation11 infectedFA Repet1 vs dcl234 Generation11 not infected Repet1

hyb_protocol: dcl234 Generation11 not infected Repet1 Cy5 / Col0 Generation11 infectedFA Repet1 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: dcl234 Generation11 not infected Repet1

extract_protocol: dcl234 Generation11 not infected Repet1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: genotype

value: mutant (dcl2/3/4)

value: not infected


title: 14268649 - Col0 Generation11 not infected Repet1 vs Col0 Generation11 infectedFA Repet1

hyb_protocol: Col0 Generation11 infectedFA Repet1 Cy5 / Col0 Generation11 not infected Repet1 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: Col0 Generation11 not infected Repet1

extract_protocol: Col0 Generation11 not infected Repet1:10ug. (Qiagen_RNeasy.pdf)


title: 14268651 - Col0 Generation11 not infected Repet3 vs Col0 Generation11 infectedFA Repet3

hyb_protocol: Col0 Generation11 infectedFA Repet3 Cy5 / Col0 Generation11 not infected Repet3 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: Col0 Generation11 infectedFA Repet3

extract_protocol: Col0 Generation11 infectedFA Repet3:10ug. (Qiagen_RNeasy.pdf)

source_name: Col0 Generation11 not infected Repet3

extract_protocol: Col0 Generation11 not infected Repet3:10ug. (Qiagen_RNeasy.pdf)


title: 581NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
581NT_B1.S

value: Lung

value: non-tumor


title: 14268648 - Col0 Generation11 infectedFA Repet1 vs Col0 Generation11 not infected Repet1

hyb_protocol: Col0 Generation11 not infected Repet1 Cy5 / Col0 Generation11 infectedFA Repet1 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: Lame 58 Cy 3 Vivo Cy5 Ptv 3


title: Lame 61 Cy 3 Ptv Cy5 Vivo 2


title: Lame 58 Cy 3 Vivo Cy5 Ptv 1


title: Lame 58 Cy 3 Vivo Cy5 Ptv 2


title: Lame 61 Cy 3 Ptv Cy5 Vivo 1


title: Lame 61 Cy 3 Ptv Cy5 Vivo 3


title: Lame 58 Cy 3 Vivo Cy5 Ptv 4


title: 14268653 - Col0 Generation11 infectedFA Repet1 vs Col0 Generation11 infected Repet1

hyb_protocol: Col0 Generation11 infected Repet1 Cy5 / Col0 Generation11 infectedFA Repet1 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: 14268647 - Col0 Generation11 infected Repet2 vs Col0 Generation11 not infected Repet2

hyb_protocol: Col0 Generation11 not infected Repet2 Cy5 / Col0 Generation11 infected Repet2 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: Col0 Generation11 not infected Repet2

extract_protocol: Col0 Generation11 not infected Repet2:10ug. (Qiagen_RNeasy.pdf)


title: 14268650 - Col0 Generation11 infectedFA Repet3 vs Col0 Generation11 not infected Repet3

hyb_protocol: Col0 Generation11 not infected Repet3 Cy5 / Col0 Generation11 infectedFA Repet3 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: 566NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
566NT_B6.S

value: female

value: Current


title: 561Tr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
561Tr_B7.S

value: tumor

value: male

value: squamous cell carcinoma (Sq)


title: 566T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
566T_B6.S

value: HpaII

value: MspI


title: 14268645 - Col0 Generation11 infected Repet3 vs Col0 Generation1 infected Repet3

hyb_protocol: Col0 Generation1 infected Repet3 Cy5 / Col0 Generation11 infected Repet3 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: Col0 Generation1 infected Repet3

extract_protocol: Col0 Generation1 infected Repet3:10ug. (Qiagen_RNeasy.pdf)

value: columbia

value: infected

source_name: Col0 Generation11 infected Repet3

extract_protocol: Col0 Generation11 infected Repet3:10ug. (Qiagen_RNeasy.pdf)


title: 14268646 - Col0 Generation11 not infected Repet2 vs Col0 Generation11 infected Repet2

hyb_protocol: Col0 Generation11 infected Repet2 Cy5 / Col0 Generation11 not infected Repet2 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: In_vitro_site_B vs In_vitro_site_A rep 3

treatment_protocol: Bovine ovaries were obtained from a slaughterhouse, cumulus-oocyte complexes aspiration were aspirated from 2 to 6 mm follicles. Healthy COCs with at least five layers of cumulus were selected for in vitro maturation, in vitro fertilization and in vitro culture.

value: blastocysts

tag: embryo quality score (iets codes)

value: not scored


title: P1090 AN

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

hyb_protocol: All hybridizations were done for 40 hours at 20 rpm and 65C

scan_protocol: Microarray slides were scanned using an Agilent 2565C DNA scanner and images were analyzed with Agilent Feature Extraction version 10.5 using default settings

data_processing: The aCGH data from each sorted sample that passed our QC metrics were analyzed in Agilent Genomics Workbench 5.0 using the ADM2 step gram algorithm to identify genomic intervals that were significantly aberrant relative to a normal diploid genome.11 We then ranked the aberrant intervals in each cancer genome based on the relative fold change and the number of annotated genes in each interval.

source_name: tumors

label_protocol: 1 ug of amplified sample and 1 ug of amplified reference template were digested with DNaseI then labeled with Cy-5 dUTP and Cy-3 dUTP respectively, using a BioPrime labeling kit (Invitrogen, Carlsbad, CA).

extract_protocol: DNAs were extracted using Qiagen micro kits (Qiagen, Valencia, CA). For each hybridization, 100 ng of genomic DNA from each sample and of pooled commercial 46XX reference DNA (Promega, Madison, WI) were amplified using the GenomiPhi amplification kit (G.E. Healthcare, Piscataway, NJ).

value: Pancreatic Neuroendocrine

source_name: Reference pooled 46XX

value: Normal female genome


title: In_vitro_site_B vs In_vitro_site_A rep 1


title: In_vitro_site_A vs. In_vitro_site_B rep 3


title: In_vitro_site_B vs In_vitro_site_A rep 2


title: 14268644 - Col0 Generation1 infected Repet3 vs Col0 Generation11 infected Repet3

hyb_protocol: Col0 Generation11 infected Repet3 Cy5 / Col0 Generation1 infected Repet3 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: 560NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
560NT_B2.A

source_name: LM-PCR products from HpaII digested DNA

value: adenocarcinoma (Ad)


title: 560T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
560T_B2.A

source_name: LM-PCR products from MspI digested DNA


title: 558Tr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
558Tr_B8.A

value: Former


title: 561NTo

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
561NTo_B4.S

value: Lung


title: 558NTr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
558NTr_B8.A

value: non-tumor


title: Non-FAP 38

city: Leiden

first: Els

last: Robanus-Maandag

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

scan_protocol: Scanned on an Genepix 4100A scanner. Images were quantified using Genepix Pro 4.1 software.

data_processing: Within this software, spots in which the reference DNA intensity was either below five times the average of the background or presented more than 3% saturated pixels were excluded from further analyses. The test/reference ratios were normalized for the median of the ratios of all features. The triplicates of the features were averaged in a homemade routine developed in Microsoft Excel 2000, and spots outside the 20% confidence interval of the average of the replicate were excluded. Only those targets presenting at least two spots within 20% confidence interval of their average were used. Unbalances of the targets were determined based on log2 ratios of the average of their replicates, and we considered sequences as amplified or deleted when outside the ±0.3 range.

label_protocol: Overnight random prime labelling reaction (BioPrime Random Prime labelling Kit, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA was isolated from 25 x 20 uM frozen sections using the Genomic-tips 20/G kit (Qiagen, Hilden, Germany), yielding 10-60 ug genomic DNA.

value: F

tag: group

value: Non-FAP

tag: mutationapc

tag: location

value: intra-abd small bowel

tag: genomeprofile

value: Gender matched DNA


title: 2.0N 11

value: Cholangiocarcinoma

tag: tissue

value: tumor


title: 3.4N (4)


title: 3.4N (11)


title: 4.0N 11


title: In_vitro_site_A vs. In_vitro_site_B rep 2


title: 552Tr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
552Tr_B6.S

tag: phenotype

tag: gender

value: male

tag: tumor histology

value: squamous cell carcinoma (Sq)

tag: smoking status

value: Current

value: HpaII

value: MspI


title: Placenta female, litter P76

city: Paris

first: Jean-Philippe

last: Jais

address: 149 rue de Sevres

institute: Université Paris Descartes - Hopital Necker-Enfants Malades

description: RMA expression value derived from Affymetrix power tools software; core-gene analysis

hyb_protocol: The samples were hybridized onto Affymetrix Mouse Exon 1.0 ST microarray and revealed with phycoerythrine-Streptavidin (GeneChip 450 fluidic station).

scan_protocol: Fluorescence was read with a GeneChip 3000 scanner with the GCOS software (v1.4) according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the apt-probeset-summarize program from the Affymetrix Power Tools (v1.6) for background correction and normalization. RMA algorithm with full quantile normalization was applied using the array design library files V1 release 2 and core-gene probesets definition file based on mouse genome release mm8. Transcripts and genes were annotated with the Affymetrix release 23 annotation file. Data analysis and statistical evaluations was performed with R Bioconductor LIMMA package. LIMMA and Bioconductor were not used for the normalization steps, only for the statistical analysis. RMA normalized data generated by APT were used for LIMMA analysis (contained in data table below).

label: biotin

organism: Mus musculus

source_name: litter P76

label_protocol: Five µg of RNA per sample from the same litter were pooled together according to the foetus sex. RNA concentrations were normalized to 100ng/µl. Microarray hybridization was performed by PartnerChip (Evry, France) with the following protocol. Total RNA concentration, quality and protein contamination were determined by Nanodrop measurements and RNA integrity number (RIN) and 28S/18S ratio were determined by the Agilent chip (Bioanalyser 2100). An enrichment in mRNA was performed with oligo-d(T) magnetic beads and a second quality control on Agilent chip was done to assess the 18S and 28S decrease. cDNA were synthesized with SuperScriptII (Invitrogen), purified and fragmented. Agilent chip quality control was performed to verify the size of the cDNA fragments (40-70bp). The cDNA samples were labelled with biotin.

growth_protocol: Four-week-old pathogen-free male and female C57BL/6J and DBA/2 mice were obtained from Harlan® and housed in groups until mating. All animals were maintained under controlled light (12 h light/12 h dark cycle, light on at 07:00) and temperature (22 ± 2 °C) conditions. The mice were allowed access to water and the control diet ad libitum. After two weeks of adaptation, DBA/2 male mice were mated with C57BL/6J female mice in the evening. The following day (day 0), if a vaginal plug was observed, females were fed either a HFD (60% of calories from fat, 20% from carbohydrates and 20% from proteins) or a CD (10% of calories from fat, 70% carbohydrates, 20% proteins) ad libitum for 15 days. Diets were supplied in pellet form by Research Diets (New Brunswick, USA: CD: D12450B, HFD: D12492). At E15.5, placentae and foetuses were collected, dried, weighed and frozen in liquid nitrogen before storage at -80°C.

extract_protocol: Total RNA was extracted from rodent placenta with the RNeasy Mini kit according to the manufacturer’s instructions (Qiagen). Concentrations were estimated by measuring absorbance at 260 nm with a spectophotometer (Nanodrop).

tag: strain

value: mixed C57BL/6J and DBA/2

value: placenta

tag: Sex

value: female

tag: diet

value: control


title: Placenta male, litter P62

source_name: litter P62

value: high fat


title: Placenta male, litter P76


title: 14268640 - Col0 Generation1 infected Repet1 vs Col0 Generation11 infected Repet1

hyb_protocol: Col0 Generation11 infected Repet1 Cy5 / Col0 Generation1 infected Repet1 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

value: columbia

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

tag: generation

tag: disease state

value: infected

source_name: Col0 Generation1 infected Repet1

extract_protocol: Col0 Generation1 infected Repet1:10ug. (Qiagen_RNeasy.pdf)


title: Non-FAP 37

value: M

tag: group

value: Non-FAP

value: yes

value: no

value: extra-abd thoracic wall

tag: sample type


title: 552NTr

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
552NTr_B6.S

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

extract_protocol: DNA was isolated using proteinase K digestion, phenol-chloroform extraction, dialysis against 0.2X SSC and concentration by surrounding the dialysis bag with PEG 20,000 to reduce water content by osmosis.  The quality of the DNA was checked by gel electrophoresis and spectrophotometry.

value: Lung

value: non-tumor

value: male

tag: restriction enzyme


title: 14268641 - Col0 Generation11 infected Repet1 vs Col0 Generation1 infected Repet1

hyb_protocol: Col0 Generation1 infected Repet1 Cy5 / Col0 Generation11 infected Repet1 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: Col0 Generation11 infected Repet1


title: 14268642 - Col0 Generation1 infected Repet2 vs Col0 Generation11 infected Repet2

hyb_protocol: Col0 Generation11 infected Repet2 Cy5 / Col0 Generation1 infected Repet2 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: Col0 Generation11 infected Repet2

extract_protocol: Col0 Generation11 infected Repet2:10ug. (Qiagen_RNeasy.pdf)

source_name: Col0 Generation1 infected Repet2

extract_protocol: Col0 Generation1 infected Repet2:10ug. (Qiagen_RNeasy.pdf)


title: Non-FAP 36

value: F

tag: mutationapc

tag: location

value: abd wall recurrence

tag: genomeprofile

value: Gender matched DNA


title: 14268637 - Col0 Generation11 not infected Repet1 vs Col0 Generation11 infected Repet1

hyb_protocol: Col0 Generation11 infected Repet1 Cy5 / Col0 Generation11 not infected Repet1 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: not infected


title: 3.4N (5)

value: Cholangiocarcinoma

tag: tissue

value: tumor

value: Normal female genome


title: Non-FAP 35

tag: gender

value: abd wall


title: 14268638 - Col0 Generation11 infected Repet1 vs Col0 Generation11 not infected Repet1

hyb_protocol: Col0 Generation11 not infected Repet1 Cy5 / Col0 Generation11 infected Repet1 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: infected


title: Placenta female, litter P62

value: mixed C57BL/6J and DBA/2

value: placenta

value: female

value: high fat


title: 14268643 - Col0 Generation11 infected Repet2 vs Col0 Generation1 infected Repet2

hyb_protocol: Col0 Generation1 infected Repet2 Cy5 / Col0 Generation11 infected Repet2 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: In_vitro_site_A vs. In_vitro_site_B rep 1

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

value: blastocysts

tag: embryo quality score (iets codes)

value: not scored


title: Placenta male, litter P52

source_name: litter P52

tag: strain

value: male


title: 551T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
551T_B2.S

value: Lung

tag: phenotype

tag: tumor histology

value: squamous cell carcinoma (Sq)

tag: smoking status

value: Current

value: HpaII

value: MspI


title: 14268635 - Col0 Generation11 infectedFA Repet1 vs dcl234 Generation11 infected Repet1

hyb_protocol: dcl234 Generation11 infected Repet1 Cy5 / Col0 Generation11 infectedFA Repet1 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: dcl234 Generation11 infected Repet1

extract_protocol: dcl234 Generation11 infected Repet1:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

tag: genotype

value: mutant (dcl2/3/4)

tag: age

source_name: Col0 Generation11 infectedFA Repet1

extract_protocol: Col0 Generation11 infectedFA Repet1:10ug. (Qiagen_RNeasy.pdf)


title: 551NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
551NT_B2.S

value: non-tumor


title: 14268636 - dcl234 Generation11 infected Repet1 vs Col0 Generation11 infectedFA Repet1

hyb_protocol: Col0 Generation11 infectedFA Repet1 Cy5 / dcl234 Generation11 infected Repet1 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: dev.stage (boyes et al. plant cell 2001)

tag: generation

tag: disease state


title: 543T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
543T_B2.A

value: tumor

value: adenocarcinoma (Ad)

value: Former

tag: restriction enzyme


title: 543NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
543NT_B2.A


title: 542T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
542T_B5.A


title: 542NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
542NT_B5.A


title: Non-FAP 33

value: F

tag: group

value: Non-FAP

value: yes

tag: mutationapc

value: no

value: abd wall

tag: sample type

value: Gender matched DNA


title: Non-FAP 31

tag: location


title: Non-FAP 34

tag: gender


title: Non-FAP 30

value: M

value: extra-abd neck


title: 14249211 - Col0 Generation11 infected Repet3 vs Col0 Generation11 infectedFA Repet3

description: 1. What are the genes (including miRNA precursors) that are differentially regulated in a set of viral siRNA in A.thaliana? 2. There are also differentially regulated during an evolution and a fitness process?

hyb_protocol: Col0 Generation11 infectedFA Repet3 Cy5 / Col0 Generation11 infected Repet3 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: Col0 Generation11 infectedFA Repet3

value: columbia

value: infected


title: 14268657 - Col0 Generation11 infected Repet2 vs Col0 Generation11 infectedFA Repet2

hyb_protocol: Col0 Generation11 infectedFA Repet2 Cy5 / Col0 Generation11 infected Repet2 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: Col0 Generation11 infectedFA Repet2

extract_protocol: Col0 Generation11 infectedFA Repet2:10ug. (Qiagen_RNeasy.pdf)


title: 541T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
541T_B4.S

tag: tissue

value: Lung

value: male

value: squamous cell carcinoma (Sq)

value: Current

value: HpaII


title: Non-FAP 28

value: extra-abd paravertebral

tag: genomeprofile


title: 14249216 - Col0 Generation11 infectedFA Repet3 vs Col0 Generation11 infected Repet3

hyb_protocol: Col0 Generation11 infected Repet3 Cy5 / Col0 Generation11 infectedFA Repet3 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: Non-FAP 32


title: Non-FAP 29

value: extra-abd mandible


title: Placenta female, litter P52

tag: strain

value: mixed C57BL/6J and DBA/2

value: placenta

tag: Sex

value: female

tag: diet

value: high fat


title: Non-FAP 27

value: Non-FAP

value: yes

value: no

value: extra-abd leg


title: 14268633 - dcl234 Generation11 not infected Repet2 vs dcl234 Generation11 infected Repet2

hyb_protocol: dcl234 Generation11 infected Repet2 Cy5 / dcl234 Generation11 not infected Repet2 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: dcl234 Generation11 infected Repet2

extract_protocol: dcl234 Generation11 infected Repet2:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: columbia

value: mutant (dcl2/3/4)

source_name: dcl234 Generation11 not infected Repet2

extract_protocol: dcl234 Generation11 not infected Repet2:10ug. (Qiagen_RNeasy.pdf)

value: not infected


title: 541NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
541NT_B4.S

value: Lung

tag: phenotype

value: non-tumor

value: male

tag: tumor histology

tag: smoking status

value: MspI


title: 14268634 - dcl234 Generation11 infected Repet2 vs dcl234 Generation11 not infected Repet2

hyb_protocol: dcl234 Generation11 not infected Repet2 Cy5 / dcl234 Generation11 infected Repet2 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

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

tag: generation

value: infected


title: Placenta female, litter P46

source_name: litter P46


title: Placenta female, litter P42

source_name: litter P42


title: 14268639 - Col0 Generation11 not infected Repet3 vs Col0 Generation11 infected Repet3

hyb_protocol: Col0 Generation11 infected Repet3 Cy5 / Col0 Generation11 not infected Repet3 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: Col0 Generation11 infected Repet3

tag: disease state

source_name: Col0 Generation11 not infected Repet3


title: Placenta male, litter P42

hyb_protocol: The samples were hybridized onto Affymetrix Mouse Exon 1.0 ST microarray and revealed with phycoerythrine-Streptavidin (GeneChip 450 fluidic station).


title: Placenta male, litter P46


title: Placenta female, litter P22

source_name: litter P22

value: control


title: Placenta male, litter P22

value: mixed C57BL/6J and DBA/2


title: Placenta male, litter P19

source_name: litter P19

value: placenta


title: 14228106 - dcl234 Generation11 infected Repet1 vs dcl234 Generation11 not infected Repet1

hyb_protocol: dcl234 Generation11 not infected Repet1 Cy5 / dcl234 Generation11 infected Repet1 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: dcl234 Generation11 not infected Repet1

extract_protocol: dcl234 Generation11 not infected Repet1:10ug. (Qiagen_RNeasy.pdf)


title: Non-FAP 26

hyb_protocol: Labelled test and reference samples were pooled and precipitated in the presence of Cot1 DNA (Invitrogen, Breda, The Netherlands). DNA pellet was dissolved in hybridisation mixture. Sample was hybridized for 20 hours followed post-hybridisation washes and drying of slides by using an automated hybridisation station (Tecan Benelux BVBA, Giesen, The Netherlands).

source_name: tumors

value: F

tag: group

tag: mutationapc

value: extra-abd rectus abdominus

tag: sample type

value: Gender matched DNA


title: Placenta female, litter P19

tag: tissue

value: female


title: 538T

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
538T_B2.A

hyb_protocol: The HpaII and MspI representations were co-hybridized to the microarray and scanned to quantify the 532 and 635 nm fluorescence at each oligonucleotide on the microarray.

source_name: LM-PCR products from HpaII digested DNA

value: tumor

tag: gender

value: adenocarcinoma (Ad)

value: Former

tag: restriction enzyme

value: HpaII

source_name: LM-PCR products from MspI digested DNA


title: 14228105 - dcl234 Generation11 not infected Repet1 vs dcl234 Generation11 infected Repet1

hyb_protocol: dcl234 Generation11 infected Repet1 Cy5 / dcl234 Generation11 not infected Repet1 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: mutant (dcl2/3/4)

value: not infected


title: 538NT

description:
Methylation differences between tumor and adjacent non-tumor expressed as ratios of HpaII to MspI generated fragments for the same sample using Nimbelgen HD2 whole genome array.
538NT_B2.A

value: Lung

value: non-tumor


title: Placenta male, litter P15

source_name: litter P15

tag: strain

tag: Sex

value: male


title: 14249210 - Col0 Generation11 infected Repet3 vs Col0 Generation11 not infected Repet3

hyb_protocol: Col0 Generation11 not infected Repet3 Cy5 / Col0 Generation11 infected Repet3 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: Col0 Generation11 not infected Repet3:10ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: infected


title: Non-FAP 25

value: M

value: Non-FAP

value: yes

value: no

tag: location

value: extra-abd suprapubical

tag: genomeprofile


title: Non-FAP 22

value: F

value: extra-abd rectus abdominus

value: Gender matched DNA


title: Non-FAP 23

value: abd wall anterior


title: Non-FAP 21


title: Non-FAP 19

value: abd wall post-surgery


title: 14228101 - dcl234 Generation11 infected Repet2 vs dcl234 Generation1 infected Repet2

hyb_protocol: dcl234 Generation1 infected Repet2 Cy5 / dcl234 Generation11 infected Repet2 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: dcl234 Generation1 infected Repet2

extract_protocol: dcl234 Generation1 infected Repet2:10ug. (Qiagen_RNeasy.pdf)

value: columbia


title: 14228104 - dcl234 Generation1 infected Repet2 vs dcl234 Generation11 infected Repet2

hyb_protocol: dcl234 Generation11 infected Repet2 Cy5 / dcl234 Generation1 infected Repet2 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: mutant (dcl2/3/4)


title: Non-FAP 20


title: Non-FAP 17

value: extra-abd neck


title: Placenta female, litter P15

value: mixed C57BL/6J and DBA/2

value: placenta

value: female

tag: diet

value: control


title: 14228100 - dcl234 Generation1 infected Repet1 vs dcl234 Generation11 infected Repet1

hyb_protocol: dcl234 Generation11 infected Repet1 Cy5 / dcl234 Generation1 infected Repet1 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: dcl234 Generation11 infected Repet1

tag: genotype

value: infected

source_name: dcl234 Generation1 infected Repet1

extract_protocol: dcl234 Generation1 infected Repet1:10ug. (Qiagen_RNeasy.pdf)


title: 14227756 - dcl234 Generation11 infected Repet1 vs dcl234 Generation1 infected Repet1

hyb_protocol: dcl234 Generation1 infected Repet1 Cy5 / dcl234 Generation11 infected Repet1 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


title: Non-FAP 16

value: Non-FAP

value: extra-abd paraspinal


title: 25 Spongy4 vs. pooled reference

city: Pacific Grove

first: Nishad

last: Jayasundara

state: CA

address: 120 Oceanview Blvd

institute: Stanford University

description: 25C Spongy biological replicate 4 of 4 compared to pooled reference.

hyb_protocol: Hybridization of the microarrays followed the Two-Color Microarray-Based Gene Expression Analysis protocol with reagents from the Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: Axon GenePix® 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Feature Extraction 9.5.3 image analysis software (Agilent Technologies, Santa Clara, CA, USA) was used to extract and process the raw microarray images using protocol GE2-v5_95_Feb07. After removal of flagged spots, Lowess normalization was performed to normalize the data. We used the Agilent GeneSpring program for further analysis.

organism: Thunnus orientalis

source_name: fish 4 at 25C, ventricular spongy

label_protocol: Target preparation including reverse transcription of total RNA, RNA amplification by in vitro transcription, and aRNA labeling was conducted using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Applied Biosystems, Foster City, CA, USA) according to manufacturer’s instructions.

extract_protocol:
Cardiac tissue samples were collected from PBFT caught by hook and line and temperature acclimated at the Tuna Research and Conservation Center, Stanford University. Tissues were sampled from the fish in a sterile manner and fixed immediately in RNAlater.

Total RNA was extracted using Trizol following the manufacturer's instructions.

value: ventricular spongy

tag: acclimation temperature (celsius)

source_name: Pooled reference of total RNA from all experimental samples

value: atrium, ventricular compact, ventricular spongy

value: reference


title: Non-FAP 18

value: F

value: yes

value: no

value: intra-abd mesocolon


title: SLqEPD1-stem_rep2

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

description: Gene expression of the vegetative stem in SL with Habataki qEPD1 allele, replicate 2

hyb_protocol: Fragmentation and hybridization was carried out with Agilent Gene Expression Hybridization Kit. 1650 ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505B according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities (gProcessedSignal) were normalized by variance stabilization (VSN) using R software (http://www.r-project.org/).

organism: Oryza sativa Japonica Group

source_name: Stem at 30 days after imbibition, replicate 2

label_protocol: One-color spike-mix was added to total RNA before labeling reaction. The Cy3-labeled cRNA was prepared from total RNA using Quick Amp Labeling Kit (Agilent Technologies) in accordance with the manufacturer's protocol. Then, labeled cRNA was purified using RNeasy mini kit (QIAGEN).

growth_protocol: Rice (O. sativa L. ssp. japonica cv. Koshihikari) plants were grown in a greenhouse under normal conditions.

extract_protocol: Total RNA was extracted from the vegetative stem of 1cm on the ground, using RNeasy mini kit (QIAGEN).

tag: subspecies

value: japonica

tag: cultivar

value: Chromosome segment substitution line (SL), carrying Habataki qEPD1 allele in Koshihikari background

value: stem


title: Non-FAP 15

extract_protocol: DNA was isolated from 25 x 20 uM frozen sections using the Genomic-tips 20/G kit (Qiagen, Hilden, Germany), yielding 10-60 ug genomic DNA.

value: M

tag: group

value: extra-abd foot

value: Gender matched DNA


title: Non-FAP 14

tag: mutationapc

value: intra-abd  spleen


title: 25 Spongy1 vs. pooled reference

description: 25C Spongy biological replicate 1 of 4 compared to pooled reference.

source_name: fish 1 at 25C, ventricular spongy

tag: sample type


title: 25 Spongy2 vs. pooled reference

description: 25C Spongy biological replicate 2 of 4 compared to pooled reference.

source_name: fish 2 at 25C, ventricular spongy

tag: tissue


title: Control-stem_rep2

description: Gene expression of the vegetative stem in Koshihikari, replicate 2

value: Koshihikari


title: SLqEPD1-stem_rep1

description: Gene expression of the vegetative stem in SL with Habataki qEPD1 allele, replicate 1

source_name: Stem at 30 days after imbibition, replicate 1


title: 25 Spongy3 vs. pooled reference

description: 25C Spongy biological replicate 3 of 4 compared to pooled reference.

source_name: fish 3 at 25C, ventricular spongy


title: 20 Spongy4 vs. pooled reference

description: 20C Spongy biological replicate 4 of 4 compared to pooled reference.

source_name: fish 4 at 20C, ventricular spongy


title: SLqEPD2-stem_rep3

description: Gene expression of the vegetative stem in SL with Habataki qEPD2 allele, replicate 3

source_name: Stem at 30 days after imbibition, replicate 3

value: Chromosome segment substitution line (SL), carrying Habataki qEPD2 allele in Koshihikari background


title: SLqEPD2-stem_rep2

description: Gene expression of the vegetative stem in SL with Habataki qEPD2 allele, replicate 2


title: SLqEPD1-stem_rep3

description: Gene expression of the vegetative stem in SL with Habataki qEPD1 allele, replicate 3


title: Control-stem_rep3

description: Gene expression of the vegetative stem in Koshihikari, replicate 3


title: SLqEPD2-stem_rep1

description: Gene expression of the vegetative stem in SL with Habataki qEPD2 allele, replicate 1


title: SSc fibroblasts

type: other

city: kumamoto

first: Noritoshi

last: Honda

state: kumamoto

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

institute: Kumamoto University

description: Test

data_processing:
The raw threshold cycle (Ct) was normalized using the value of housekeeping gene ; deltaCt = (Ct_Target − Ct_HKG)]
For the normalization, it uses the average of five housekeeping genes ;SNORD48,SNORD44,U6 .
Fold Change worksheet reports 1/2^ delta delta Ct

label: SYBR Green

molecule: other

source_name: Human dermal fibroblasts obtained by skin biopsy from patients with diffuse cutaneous SSc

label_protocol: For RT2 Profiler PCR Array (SABioscience), microRNAs were reverse-transcribed into first strand cDNA using RT2 miRNA First Strand Kit (SABiosciences). A mixture of equal amounts of cDNAs from 5 normal fibroblasts, 5 normal fibroblasts stimulated with exogenous TGF-β1 or 5 SSc fibroblasts was prepared. The cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix and the mixture was added into a 96-well RT2 miRNA PCR Array (SABiosciences) that included primer pairs for 88 human microRNAs.

extract_protocol: Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan). MicroRNA isolation from total RNA was performed using RT2 qPCR-Grade miRNA Isolation Kit (SA Bioscience).

tag: cell type

value: SSs fibroblasts

tag: activation agent

value: no activation


title: Normal fibroblasts + TGF-β1

description: Test

source_name: Human dermal fibroblasts obtained by skin biopsy from healthy donors

value: normal fibroblasts


title: 20 Spongy3 vs. pooled reference

description: 20C Spongy biological replicate 3 of 4 compared to pooled reference.

source_name: fish 3 at 20C, ventricular spongy

value: ventricular spongy

value: atrium, ventricular compact, ventricular spongy

value: reference


title: Non-FAP 12

source_name: tumors

tag: gender

value: F

value: Non-FAP

value: no

value: intra-abd


title: Normal fibroblasts

description: control


title: Non-FAP 13

value: yes

value: extra-abd thigh


title: Non-FAP 10

value: M

value: extra-abd foot


title: Non-FAP 11

value: extra-abd arm

value: Gender matched DNA


title: 20 Spongy2 vs. pooled reference

description: 20C Spongy biological replicate 2 of 4 compared to pooled reference.

source_name: fish 2 at 20C, ventricular spongy


title: 20 Spongy1 vs. pooled reference

description: 20C Spongy biological replicate 1 of 4 compared to pooled reference.

source_name: fish 1 at 20C, ventricular spongy


title: 14 Spongy4 vs. pooled reference

description: 14C Spongy biological replicate 4 of 4 compared to pooled reference.

source_name: fish 4 at 14C, ventricular spongy


title: Control-stem_rep1

description: Gene expression of the vegetative stem in Koshihikari, replicate 1

value: japonica

value: Koshihikari

value: stem


title: 14 Spongy3 vs. pooled reference

description: 14C Spongy biological replicate 3 of 4 compared to pooled reference.

source_name: fish 3 at 14C, ventricular spongy


title: 59A vs. 59A NADPH Bdh_100mM replicate 3

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

description: Biological replicate 3 of 3 of 59A vs. Biological replicate 3 of 3 of 59A NADPH Bdh100.

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: print-tip-loess witinh-array normalization, none between-array normalization. R 2.8.0 software and limma bioconductor package used.

organism: Saccharomyces cerevisiae

source_name: Total RNA of 59A strain

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: strain

source_name: Total RNA of 59A NADPH Bdh 100 mM strain

tag: state

value: NADPH Bdh100mM


title: Non-FAP 5

tag: location

value: extra-abd back


title: 59A vs. 59A NADPH Bdh_100mM replicate 2

description: Biological replicate 2 of 3 of 59A vs. Biological replicate 2 of 3 of 59A NADPH Bdh100.


title: Non-FAP 6

tag: genomeprofile


title: endoderm, NF15, Ngn3GR mRNA, -DEX, biological rep2

city: Woods Hole

first: Marko

last: Horb

state: MA

address: 7 MBL Street

institute: Marine Biological Laboratory

description:
Xenopus SAMPLE 2 -Dex
Gene expression data from Ngn3-GR injected embryo not treated with DEX. Anterior endoderm dissected at NF15.

hyb_protocol: 10 μg of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Xenopus Genome array. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned on a GeneChip® Scanner 3000 7G. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: The data were analyzed with Flexarray using the RMA algorithm for normalization and the EB(Simon Wright)P algorithm for statistical analysis.

organism: Xenopus laevis

source_name: Endoderm of embryos not treated with DEX

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit. 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: Embryos were grown in 0.1XMMR.

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

treatment_protocol: Embryos were cultured in 30 ml of 0.1XMMR in a final concentration of 10 micromolar of dexamethasone.

value: endoderm

tag: developmental stage

tag: overexpression

tag: treatment

value: no dexamethasone (DEX)


title: Non-FAP 7

tag: age


title: Non-FAP 9

value: F


title: 59A vs. 59A NADPH Bdh_100mM replicate 1

description: Biological replicate 1 of 3 of 59A vs. Biological replicate 1 of 3 of 59A NADPH Bdh100.


title: Non-FAP 8

value: Non-FAP


title: 14 Spongy1 vs. pooled reference

description: 14C Spongy biological replicate 1 of 4 compared to pooled reference.

source_name: fish 1 at 14C, ventricular spongy

value: ventricular spongy

tag: acclimation temperature (celsius)

source_name: Pooled reference of total RNA from all experimental samples

value: atrium, ventricular compact, ventricular spongy

value: reference


title: Non-FAP 4

value: yes

value: no

value: intra-abd


title: 25 Compact2 vs. pooled reference

description: 25C Compact biological replicate 2 of 4 compared to pooled reference.

source_name: fish 2 at 25C, ventricular compact

value: ventricular compact


title: endoderm, NF15, Ngn3GR mRNA, +DEX, biological rep3

description:
Xenopus SAMPLE 3 +DEX
Gene expression data from Ngn3-GR injected embryo treated with DEX. Anterior endoderm dissected at NF15.

source_name: Endoderm of embryos treated with DEX for four hours at stage 12

value: dexamethasone (DEX)


title: 14 Spongy2 vs. pooled reference

description: 14C Spongy biological replicate 2 of 4 compared to pooled reference.

source_name: fish 2 at 14C, ventricular spongy


title: 25 Compact4 vs. pooled reference

description: 25C Compact biological replicate 4 of 4 compared to pooled reference.

source_name: fish 4 at 25C, ventricular compact


title: endoderm, NF15, Ngn3GR mRNA, +DEX, biological rep2

description:
Xenopus SAMPLE 2 +DEX
Gene expression data from Ngn3-GR injected embryo treated with DEX. Anterior endoderm dissected at NF15.


title: Non-FAP 3

value: M

value: extra-abd knee

value: Gender matched DNA


title: 25 Compact1 vs. pooled reference

description: 25C Compact biological replicate 1 of 4 compared to pooled reference.

source_name: fish 1 at 25C, ventricular compact


title: endoderm, NF15, Ngn3GR mRNA, -DEX, biological rep1

description:
Xenopus SAMPLE 1 -Dex
Gene expression data from Ngn3-GR injected embryo not treated with DEX. Anterior endoderm dissected at NF15.


title: endoderm, NF15, Ngn3GR mRNA, +DEX, biological rep1

description:
Xenopus SAMPLE 1 +DEX
Gene expression data from Ngn3-GR injected embryo treated with DEX. Anterior endoderm dissected at NF15.


title: endoderm, NF15, Ngn3GR mRNA, +DEX, biological rep4

description:
Xenopus SAMPLE 4 +DEX
Gene expression data from Ngn3-GR injected embryo treated with DEX. Anterior endoderm dissected at NF15.


title: Non-FAP 2

value: extra-abd leg


title: endoderm, NF15, Ngn3GR mRNA, -DEX, biological rep4

description:
Xenopus SAMPLE 4 -Dex
Gene expression data from Ngn3-GR injected embryo not treated with DEX. Anterior endoderm dissected at NF15.