title: leaf 30%Inhibition rep2 [Populus]

city: Oak Ridge

first: David

middle: J

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

description: Gene expression data from the first fully expanded leaf of Populus trichocarpa at 30% inhibition from optimum

hyb_protocol: Hybridization was performed according to Roche protocols

scan_protocol: Dried slides were scanned using an Agilent Scanner (Agilent Technologies, Santa Clara, CA) with a PMT gain of 100% at 5 µm resolution.

data_processing: Images of all scanned slides were aligned using NimbleScan version 2.5 and pair reports were created using the slide design file provided by Roche NimbleGen. An annotation package for this array was created using the pdInfoBuilder (v.2.4) Bioconductor open access package run in the R statistical framework (R Development Core Team, 2007).

organism: Populus trichocarpa

source_name: Populus trichocarpa leaf, 30% inhibition

label_protocol: RNase A cleanup, cDNA precipitation and sample labeling were carried out according Roche provided protocol

growth_protocol: Dormant cuttings of black cottonwood (Populus trichocarpa clone 93-968) averaging ~0.5 cm diameter, 25 cm length, and 2-3 buds were rooted using 0.3% IBA and grown in a Conviron BDW80 walk-in growth chamber at 22 °C, 60% relative humidity, a 18 h photoperiod, and 350 μmol m-2s-1 light intensity. Plants were watered as needed and fertilized weekly according 250 ppm N using Jack's professional.

extract_protocol: total RNA was converted to ds cDNA using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp) according to the protocol provided by Roche for NimbleGen high-density microarrays.

treatment_protocol: For the microarray analysis, fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum). The temperature response curves were created by increasing temperature step-wise (2 °C per 10 mins) from 22 to 42 °C to the desired physiological state and waiting 20-30 mins for photosynthesis to stabilize before sampling. Each curve took 3-4 h to complete.

value: leaf, first fully expanded

tag: line

tag: treatment

value: Photosynthesis at 30% inhibition from optimum


title: leaf 30%Inhibition rep4 [Populus]

status: Public on Apr 01 2011

type: RNA

country: USA

label: biotin

molecule: total RNA

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_176

city: Seattle

first: Radu

last: Dobrin

state: WA

address: 401 Terry Ave N

institute: Merck and Co. Inc.

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Homo sapiens

source_name: liver

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: reference

value: liver

tag: ID


title: MGH_Liver_pool vs MGH_Liver_182


title: non-smoker 336D

city: Prague 2

first: Hana

last: Bruchova

address: U nemocnice 1

department: Molecular Genetics

country: Czech Republic

institute: Institute of Hematology and Transfusion

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

scan_protocol: Arrays were scanned using BeadArray Reader (Illumina), and bead level data were extracted by BeadStudio Software (Illumina).

data_processing: Bead summary data were imported into the R statistical environment (www.r-project.org) and normalized by the quantile method in the Lumi package. Only probes that reached detection P-value < 0.01 in all samples were used for further analyses. Differentially expressed genes were analysed in the Limma package. A linear model was fitted for each gene given a series of arrays using the lmFit function. Using the Benjamini and Hochberg method, P-values were corrected for multiple testing. The M, PL, and D groups were normalized separately.

source_name: cord blood, non-smoker

label_protocol: Biotinylated cRNA was prepared from 200 ng of total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). In vitro transcription (IVT) was performed at 37°C for 14 hours.

extract_protocol: Umbilical cord blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

value: cord blood

tag: smoking status

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: smoker 342D

source_name: cord blood, smoker

value: smoker


title: leaf 30%Inhibition rep1 [Populus]

tag: line


title: non-smoker 334D


title: leaf 30%Inhibition rep3 [Populus]

tag: treatment


title: smoker 337D

tag: tissue


title: leaf 20%Inhibition rep1 [Populus]

description: Gene expression data from the first fully expanded leaf of Populus trichocarpa at 20% inhibition from optimum

source_name: Populus trichocarpa leaf, 20% inhibition

value: Photosynthesis at 20% inhibition from optimum


title: leaf optimum rep4 [Populus]

description: Gene expression data from the first fully expanded leaf of Populus trichocarpa at optimum temperature

source_name: Populus trichocarpa leaf, optimum

value: Photosynthesis at optimum temperature


title: leaf 20%Inhibition rep2 [Populus]


title: leaf optimum rep2 [Populus]


title: leaf 20%Inhibition rep4 [Populus]


title: MGH_Liver_pool vs MGH_Liver_172

tag: reference


title: MGH_Liver_pool vs MGH_Liver_175

tag: ID


title: leaf optimum rep1 [Populus]


title: MGH_Liver_pool vs MGH_Liver_173


title: MGH_Liver_pool vs MGH_Liver_171


title: MGH_Liver_pool vs MGH_Liver_174


title: leaf optimum rep3 [Populus]


title: leaf baseline rep4 [Populus]

description: Gene expression data from the first fully expanded leaf of Populus trichocarpa at growth temperature

source_name: Populus trichocarpa leaf, baseline

value: Photosynthesis at growth temperature


title: leaf 20%Inhibition rep3 [Populus]


title: non-smoker 331D

tag: smoking status


title: leaf baseline rep3 [Populus]


title: smoker 328D

tag: age (years)


title: 13912822 - wt vs. fwa

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Impact of loss of DNA methylation and small interference RNAs (siRNAs) on gene expression.

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

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 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: fwa

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

growth_protocol: Rosette. Media=soil. Hygrometry=65%/75%. Temperature=22.5°C/18°C. Light=16h light/8h dark (8000 lux).

extract_protocol: fwa:10ug. Qiagen RNeasy kit.

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: genotype

value: mutant (fwa)

value: rosette

tag: developmental stage

value: Boyes 1.10 (Boyes et al. Plant Cell 2001)

source_name: wt

extract_protocol: wt:10ug. Qiagen RNeasy kit.

value: wt


title: leaf baseline rep2 [Populus]


title: non-smoker 330D

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 327D

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: miRNA expression profiles of L02 and 16HBE cell lines

city: Guangzhou

first: chen

last: wen

address: 74 Zhongshan Road 2

department: Department of Toxicology

country: China

institute: Sun Yat-sen University

description: 16HBE cells which are immortalized by expressing SV40 LT and hTERT in primary human bronchial epithelial cells

hyb_protocol: Hybridization was performed overnight on a μParaflo™ microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequnces/) or control RNA and then labeled with tag-specific dendrimer Cy3 and Cy5 fluorescent dyes. Dye switching was performed to eliminate the dye bias. The melting temperature of the detection probes was balanced by incorporation of varying numbers of modified nucleotides with increased binding affinities.

scan_protocol: Hybridization images were collected using a GenePix 4000B laser scanner (Molecular Devices, Sunnyvale, CA) and digitized using Array-Pro image analysis software (Media Cybernetics, Silver Spring, MD).

data_processing: Raw data were normalized by the LOWESS method using the background-subtracted data.

source_name: L02 cell line

label_protocol: the assay started from 2 to 5 μg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3＇-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly (A) tail for later fluorescent dye staining

extract_protocol: Total RNA was extracted from L02 cells using TRIzol reagent.

tag: cell line

extract_protocol: Total RNA was extracted from 16HBE cells using TRIzol reagent.

value: human bronchus


title: miRNA expression profiles of 16HBER and 16HBERST cell lines

description: 16HBER cells which are created by introduction of an oncogenic version of H-Ras into 16HBE cells. 16HBERST cells which are generated by the additional introduction of SV40 ST into 16HBER cells

source_name: 16HBER cell line

extract_protocol: Total RNA was extracted from 16HBER cells using TRIzol reagent.

source_name: 16HBERST cell line

extract_protocol: Total RNA was extracted from 16HBERST cells using TRIzol reagent.

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_169

tag: reference


title: smoker 324D

tag: cord blood cotinine (ng/ml)

tag: individual


title: Barley_germination_stage S5_rep 1

city: St. Louis,

first: Yong-qiang

last: An

state: MO

address: 975 N. Warson Road,

department: UD Department of Agriculture

institute: USDA-ARS-Plant Genetics Research Unit, Donald Danforth Plant Science Center

description: gene expression data from germinating grains and seedlings

hyb_protocol: Staining and scanning of the hybridized GeneChips were performed as described by Chen and An (Chen and An, 2006b) and the manufacturer’s recommended protocols (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GC 3000 G7 Scanner

data_processing: GC-RMA

label: Biotin

organism: Hordeum vulgare

source_name: germination grains at S5 stage

label_protocol: Preparations of cDNA and biotin-labeled cRNA were performed and analyzed as recommended by Affymetrix, Inc. (Santa Clara, CA). According to the manufacturer’s protocol, 7.5 to 15 mg of total RNA was used in a reverse transcription reaction to generate first-strand cDNA using Reverse transcriptase SuperScript II (Invitrogen, Carlsbad, CA). After second-strand synthesis, double-strand cDNAs were used in an in vitro transcription reaction to generate biotinylated cRNA. Ten mg of fragmented cRNA was used for each hybridization.

growth_protocol: Plump and healthy barley grains (Hordeum vulgare L. cv. Morex L.) were imbibed in water for three hours at 22oC with three changes of water and were then germinated on water-saturated germination pack in the dark at 22oC. Twenty grains were planted in each 15 cm diameter Petri-dish and spaced evenly to reduce the variation of seed germination caused by grain density.

extract_protocol: Total RNA extraction was conducted as described by Chen and An with minor modifications (Chen and An, 2006b). Two grams of plant tissue was ground in liquid nitrogen followed by the addition of 10 ml extract buffer (4% p-aminosalicylic disodium, 1% 1,5-napthalenedisulfonic acid) and 10 ml phenol. The mixture was inverted several times, and polytroned for 45 seconds after the addition of 10 ml chloroform. After centrifuging, the aqueous phase was transferred into a new tube, to which 60 ml of 10% Calcoflur White was added (Skadsen, 1993). The mixture was mixed thoroughly and centrifuged for 15 min at 4°C, 12,000 rpm. Precipitate RNA from the supernatant was formed by using 1/10 volume of 3M NaOAc, and 2 volume of 100% ethanol. After centrifuging, the RNA pellet was first dissolved in 8 ml water, then 5 ml of 8M LiCl was added, and the tubes were left on ice overnight. After centrifuging, the resulting RNA pellet was dissolved in water. The RNA quality and quantity was checked by using Nano-Drop (Nano-Drop, Wilmington, DE) and Aglient 2100 Bioanalyzer (Aglient, Palo Alto, CA).

treatment_protocol: The germinating grains/developing seedlings with typical morphologies at 0 (dry), 3, 9, 18, 33, and 71 hours of germination were harvested and pooled for RNA purification.

tag: stage

tag: cultivar

value: Morex L.


title: non-smoker 332D

tag: smoking status

tag: age (years)


title: Barley_germination_stage S3_rep 2

source_name: germination grains at S3 stage


title: Barley_germination_stage S4_rep 1

source_name: germination grains at S4 stage


title: Barley_germination_stage S4_rep 2


title: Barley_germination_stage S5_rep 2


title: MGH_Liver_pool vs MGH_Liver_165

tag: ID


title: Barley_germination_stage S3_rep 3


title: leaf baseline rep1 [Populus]

value: leaf, first fully expanded

tag: line

tag: treatment


title: MGH_Liver_pool vs MGH_Liver_166


title: MGH_Liver_pool vs MGH_Liver_167


title: MGH_Liver_pool vs MGH_Liver_164


title: Barley_germination_stage S5_rep 3


title: Barley_germination_stage S4_rep 3


title: MGH_Liver_pool vs MGH_Liver_168


title: Barley_germination_stage S3_rep 1


title: smoker 322D

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 335D

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)


title: MGH_Liver_pool vs MGH_Liver_170

tag: reference

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_163


title: Barley_germination_stage S2_rep 1

source_name: germination grains at S2 stage

tag: stage


title: Barley_germination_stage S2_rep 3

tag: cultivar


title: non-smoker 320D

tag: smoking status

tag: cord blood cotinine (ng/ml)

tag: individual


title: non-smoker 318D

tag: age (years)


title: Barley_germination_stage S1_rep 3

source_name: germination grains at S1 stage


title: Barley_germination_stage S2_rep 2


title: Barley_germination_stage S0_rep 2

source_name: germination grains at S0 stage


title: Barley_germination_stage S0_rep 1


title: Barley_germination_stage S0_rep 3


title: Barley_germination_stage S1_rep 1


title: MGH_Liver_pool vs MGH_Liver_161

source_name: liver

tag: ID


title: non-smoker 314D

source_name: cord blood, non-smoker

tag: maternal bmi


title: WT / DeltaSub1 - 4NQO - Replicate - DyeSwap

city: Gif-sur-Yvette cedex

first: Christine

last: Conesa

address: CEA Saclay

department: iBiTeC-S

institute: CEA

description: Wild-type (yPH500) and sub1Δ cells were grown to exponential phase (OD600 = 1) in YPD medium at 30°C and an aliquot of cells was collected to serve as the time-zero reference. Total RNA extraction and microarray hybridization were performed as previously described (Conesa et al., 2005).

hyb_protocol: Labeled cDNAs were synthesized from 20 to 30μg total RNA using an indirect labeling protocol adapted from P.Brown (http://cmgm.stanford.edu/pbrown/protocols/aadUTPCouplingProcedure.htm) with the Superscript II reverse transcription kit (Gibco-BRL) and amino-allyl dUTP. The labeled cDNAs were purified on Microcon filters (Amicon) (http://brownlab.stanford.edu/protocols.html) then competitively hybridized to DNA microarrays harbouring S. cerevisiae open reading frames (ORF), reamplified using a pair of universal primers from 6144 full-length ORFs (1 ng) amplified from genomic DNA by Research Genetics. The PCR products were purified by ethanol precipitation, and their size and concentration were measured by agarose gel electrophoresis. 92.4% of the ORFs were correctly amplified and purified. The purified DNAs were spotted onto poly-L-lysine-coated slides (Menzel Gläser) using an automated arrayer (Genetic Micro Systems). Prehybridization and hybridization conditions were those described by P. Brown and colleagues (http://brownlab.stanford.edu/protocols.html) with few minor modifications.

scan_protocol: Hybridized arrays were scanned using a GenePix 4000A scanner (Axon Instruments, Inc.) and fluorescence ratio measurements were determined with the GenePix Pro 6.0 software (Axon Instruments, Inc.).

data_processing: Analyses were undertaken using the Limma package version 2.12.0 (Smyth, 2005) from the R/Bioconductor software version 2.6.1 (R-Development-Core-Team, 2007). spot intensities have been normalized using the 'loess' method as implemented in the 'normalizeWithinArrays' function of the Limma package. Normalized measures served to compute the log2-ratios for each probe.

organism: Saccharomyces cerevisiae

source_name: Wild-Type, 4NQO treated

label_protocol: indirect via aa-dUTP

growth_protocol: Cells were grown to exponential phase (OD600 = 1) in YPD medium at 30°C and an aliquot of cells was collected to serve as the time-zero reference. After the addition of 4NQO (1 µg/µl), the cells were further incubated for 1h.

extract_protocol: Total RNA was isolated by heating and freezing the cells in the presence of SDS and phenol as described (Schmitt et al., 1990).

treatment_protocol: 4NQO (1 µg/µl)

tag: Strain YPH500

source_name: Delta SUB1, 4NQO treated

tag: Strain YPH500 Delta Sub1


title: non-smoker 316D

tag: parity

tag: gestational age (weeks)

tag: mode of delivery


title: WT / DeltaSub1 - 4NQO - DyeSwap


title: WT / DeltaSub1 - 4NQO


title: WT / DeltaSub1 - 4NQO - Replicate


title: non-smoker 315D

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: WT / DeltaSub1 - NO 4NQO - Replicate - DyeSwap

source_name: Wild-Type, 4NQO untreated

growth_protocol: YPD to OD600=1

treatment_protocol: No Treatment

source_name: Delta SUB1, 4NQO untreated


title: MGH_Liver_pool vs MGH_Liver_159

tag: reference

tag: tissue


title: WT / DeltaSub1 - NO 4NQO - Replicate


title: Barley_germination_stage S1_rep 2

tag: stage

tag: cultivar


title: non-smoker 311D

tag: smoking status

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: smoker 313D

source_name: cord blood, smoker

tag: age (years)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_158

tag: ID


title: MGH_Liver_pool vs MGH_Liver_156


title: MGH_Liver_pool vs MGH_Liver_162


title: MGH_Liver_pool vs MGH_Liver_160


title: 13688247 - dcl2-1,dcl3-1 repet1 vs. ddm1-2,dcl2-1,dcl3-1 repet1

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet1 Cy5 / dcl2-1,dcl3-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 650V, laser power 100%. Cy5: 635nm, pmt voltage 650V, laser power 100%.

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 was subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

growth_protocol: Seedling. Media=liquid MS. Hygrometry=65%/75%. Temperature=22.5°C/18°C. Light=16h light/8h dark (8000 lux).

extract_protocol: ddm1-2,dcl2-1,dcl3-1 repet1:10ug. Qiagen RNeasy kit.

tag: ecotype

tag: genotype

value: mutant (ddm1-2,dcl2-1,dcl3-1)

value: seedling

tag: developmental stage

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

value: mutant (dcl2-1,dcl3-1)


title: MGH_Liver_pool vs MGH_Liver_155

value: liver


title: WT / DeltaSub1 - NO 4NQO - DyeSwap

tag: Strain YPH500

tag: Strain YPH500 Delta Sub1


title: smoker 312D

value: cord blood

value: smoker

tag: maternal bmi

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

value: vaginal

tag: placental weight (g)

tag: newborn weight (g)


title: WT / DeltaSub1 - NO 4NQO


title: MGH_Liver_pool vs MGH_Liver_157

tag: reference

tag: tissue


title: non-smoker 308D

tag: smoking status

value: non-smoker

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: 13688250 - ddm1-2,dcl2-1,dcl3-1 repet1 vs. dcl2-1,dcl3-1 repet1

hyb_protocol: dcl2-1,dcl3-1 repet1 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dcl2-1,dcl3-1 repet1:10ug. Qiagen RNeasy kit.

tag: ecotype

value: Columbia


title: 13688249 - ddm1-2 repet1 vs. ddm1-2,dcl2-1,dcl3-1 repet1

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet1 Cy5 / ddm1-2 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype

extract_protocol: ddm1-2 repet1:10ug. Qiagen RNeasy kit.

value: mutant (ddm1-2)


title: 13688246 - ddm1-2,dcl2-1,dcl3-1 repet2 vs. ddm1-2,rdr2-1 repet2

hyb_protocol: ddm1-2,rdr2-1 repet2 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: ddm1-2,rdr2-1 repet2:10ug. Qiagen RNeasy kit.

value: mutant (ddm1-2,rdr2-1)

tag: developmental stage

extract_protocol: ddm1-2,dcl2-1,dcl3-1 repet2:10ug. Qiagen RNeasy kit.


title: non-smoker 305D

tag: age (years)

tag: individual


title: 13688243 - ddm1-2,dcl2-1,dcl3-1 repet2 vs. dcl2-1,dcl3-1 repet2

hyb_protocol: dcl2-1,dcl3-1 repet2 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: dcl2-1,dcl3-1 repet2:10ug. Qiagen RNeasy kit.


title: 13688244 - ddm1-2,dcl2-1,dcl3-1 repet1 vs. ddm1-2 repet1

hyb_protocol: ddm1-2 repet1 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688245 - dcl2-1,dcl3-1 repet2 vs. ddm1-2,dcl2-1,dcl3-1 repet2

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet2 Cy5 / dcl2-1,dcl3-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688510 - ddm1-2,rdr2-1 repet2 vs. ddm1-2,dcl2-1,dcl3-1 repet2

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet2 Cy5 / ddm1-2,rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688515 - ddm1-2,rdr2-1 repet1 vs. ddm1-2,dcl2-1,dcl3-1 repet1

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet1 Cy5 / ddm1-2,rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: ddm1-2,rdr2-1 repet1:10ug. Qiagen RNeasy kit.


title: MGH_Liver_pool vs MGH_Liver_152

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: ID


title: non-smoker 307D

extract_protocol: Umbilical cord blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

tag: maternal bmi

tag: parity


title: MGH_Liver_pool vs MGH_Liver_150


title: non-smoker 302D

tag: gestational age (weeks)

tag: mode of delivery


title: non-smoker 306D

tag: placental weight (g)

tag: newborn weight (g)


title: MGH_Liver_pool vs MGH_Liver_153

tag: reference

tag: tissue


title: smoker 303D

tag: smoking status

tag: apgar score (5s)


title: MGH_Liver_pool vs MGH_Liver_154


title: MGH_Liver_pool vs MGH_Liver_149


title: MGH_Liver_pool vs MGH_Liver_151


title: 13688147 - ddm1-2 repet2 vs. ddm1-2,rdr2-1 repet2

hyb_protocol: ddm1-2,rdr2-1 repet2 Cy5 / ddm1-2 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: ddm1-2 repet2:10ug. Qiagen RNeasy kit.


title: 13688153 - ddm1-2,dcl2-1,dcl3-1 repet2 vs. ddm1-2 repet2

hyb_protocol: ddm1-2 repet2 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688150 - ddm1-2,rdr2-1 repet1 vs. ddm1-2 repet1

hyb_protocol: ddm1-2 repet1 Cy5 / ddm1-2,rdr2-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688242 - ddm1-2 repet2 vs. ddm1-2,dcl2-1,dcl3-1 repet2

hyb_protocol: ddm1-2,dcl2-1,dcl3-1 repet2 Cy5 / ddm1-2 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688151 - ddm1-2 repet1 vs. ddm1-2,rdr2-1 repet1

hyb_protocol: ddm1-2,rdr2-1 repet1 Cy5 / ddm1-2 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688143 - ddm1-2,rdr2-1 repet2 vs. ddm1-2 repet2

hyb_protocol: ddm1-2 repet2 Cy5 / ddm1-2,rdr2-1 repet2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Control 1-TM2

city: Tehran

first: hassan

last: paylakhi

address: Jalale aleahmad

country: Iran

institute: Tarbiat Modares University

description: Control 1-TM2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using a quantile based algorithm available in the Beadarray VI software.

source_name: Trabecular meshwork tissue from eye

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with RNXTM-plus  reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: age

tag: gender

value: Male

tag: condition

value: Control 1

tag: cell type


title: 13688512 - ddm1-2,dcl2-1,dcl3-1 repet1 vs. ddm1-2,rdr2-1 repet1

hyb_protocol: ddm1-2,rdr2-1 repet1 Cy5 / ddm1-2,dcl2-1,dcl3-1 repet1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: genotype

tag: developmental stage


title: non-smoker 317D

hyb_protocol: 750 ng of biotinylated cRNA was hybridized to the array for 17 hours according to the manufacturer manual. Final staining was performed with streptavidin conjugated to Cy-3 fluorescent dye.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Control 2-TM2

description: Control 2-TM2

value: Control 2


title: MGH_Liver_pool vs MGH_Liver_148

hyb_protocol: Microarrays are incubated at 40?C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

tag: ID


title: MGH_Liver_pool vs MGH_Liver_147

tag: reference


title: MGH_Liver_pool vs MGH_Liver_146

tag: tissue


title: Mucin Bio3 Tech3 Column3

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: biological replicate 3 of 3, technical replicate 9 of 9

hyb_protocol: Fluorescent indocarbocyanine- and indodicarbocyanine-labeled cDNAs were combined and purified with Qiaquick PCR spin columns according to the manufacturer's instructions (Qiagen, Valencia, Calif.). The fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 μl of water, to which was added 2.5 μl of salmon sperm DNA (10 mg/ml), 9 μl of 20× SSC (1× SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7), 0.36 μl of 10% sodium dodecyl sulfate (SDS), and 9 μl of formamide. Prior to hybridization, microarray slides were prehybridized at 42°C for 45 min in prehybridization buffer (25% formamide, 5× SSC buffer, 0.1% SDS, and 1% bovine serum albumin), rinsed with water, and dried by spinning. The probe was denatured by boiling for 2 min, followed by cooling to 42°C. The probe was then applied to the microarray slide under a coverslip (Grace Bio-labs), placed in a humidified chamber (ArrayIt), and incubated at 42°C overnight. Following hybridization, slides were washed in 2× SSC-0.1% SDS for 5 min at 42°C, 0.1× SSC-0.1% SDS for 10 min at room temperature, and four times in 0.1× SSC for 1 min at room temperature. Slides were then rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: Spots within regions of printing or hybridization anomalies were excluded from the analysis. The raw fluorescence intensity values were background subtracted, and spots with background-subtracted values less than three times the standard deviation of the local background in both channels were also excluded from further analysis. Subsequently, the background-subtracted fluorescent intensity in each wavelength (channel 1 for indocarbocyanine [Cy3] and channel 2 for indodicarbocyanine [Cy5]) was normalized using the MIDAS software (available from TIGR, http://www.tigr.org/software/) and by applying a locally weighted linear regression (Lowess).

organism: Campylobacter jejuni

source_name: MEMα control sample

label_protocol: Total RNA from each growth condition was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 μg of total RNA was combined with 10 μg of random hexamers in a 34.35-μl reaction mixture containing 8 μl of 5× Superscript II reverse transcriptase buffer and 2 μl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 μl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 μl of Superscript II and incubated at 42°C for 120 min.  At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 μl of 50 mM EDTA and 2 μl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 μl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 μl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 × g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 μl under vacuum in a SpeedVac and adjusted to a final volume of 10 μl by adding 1 μl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 μl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 45 min at room temperature in the dark. This reaction was quenched by adding 4.5 μl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: C. jejuni strain NCTC11168 was grown routinely on Mueller-Hinton (MH) agar plates.  Overnight MH biphasic cultures were adjusted to an  OD at 600nm of 1.0 and used to inoculate 20ml of MEMα to an O.D. of 0.01.

extract_protocol: Cultures were grown to an O.D. at  of 0.2, representing mid-log phase, at which point the RNA quality was preserved by adding a 1/1 volume of RNAlater (Ambion).  Cultures were pelleted by centrifugation (6000rpm for 5min) and resuspended and lysed in a denaturing solution of 4M guanidinium thiocyanate, 25mM sodium citrate, 0.5% Sarkosyl and 1% N acetyl-cysteine.  RNA was extracted using a hot phenol method.  Briefly, 0.5 ml of phenol was added to 0.5 ml of lysate and heated at 64°C for 10 minutes.  1 ml of chloroform was added, mixed thoroughly, incubated on ice for 15 minutes, then centrifuged for 30 minutes, 13000rpm at 4°C.  The aqueous layer was removed to a fresh tube and RNA was precipitated out with 60 μl 3M sodium acetate, 1.2 μl 0.5 mM EDTA and 1 ml of ethanol, and an overnight incubation at -80°C.  The precipitated RNA was washed four times in 70% ethanol and resuspended in 50μl DEPC treated dH2O.  DNA was removed by 4 DNAse treatements, and quality and quantity were ascertained using Biorad's experion system using manufacturer protocols.

treatment_protocol: Control cultures consisted of 20ml MEMα medium (Gibco 41061) containing no phenol red and supplemented with 20mM sodium pyruvate.  The experimental culture was 20ml MEMα supplemented 2mg/ml porcine gastric mucin (Sigma)

tag: strain

tag: culture optical density

tag: treatment

value: control

source_name: MEMα + 2mg/ml Pocine gastric mucin

value: porcine gastric mucin


title: Mucin Bio3 Tech3 Column1

description: biological replicate 3 of 3, technical replicate 7 of 9


title: Mucin Bio3 Tech2 Column3

description: biological replicate 3 of 3, technical replicate 6 of 9


title: Mucin Bio3 Tech2 Column2

description: biological replicate 3 of 3, technical replicate 5 of 9


title: Mucin Bio3 Tech2 Column1

description: biological replicate 3 of 3, technical replicate 4 of 9


title: Mucin Bio3 Tech1 Column3

description: biological replicate 3 of 3, technical replicate 3 of 9


title: MGH_Liver_pool vs MGH_Liver_145


title: Mucin Bio2 Tech2 Column3

description: biological replicate 2 of 3, technical replicate 6 of 9


title: Control 2-TM1

description: Control 2-TM1

tag: age

tag: gender


title: Mucin Bio2 Tech3 Column2

description: biological replicate 2 of 3, technical replicate 8 of 9


title: Mucin Bio3 Tech1 Column1

description: biological replicate 3 of 3, technical replicate 1 of 9


title: Mucin Bio3 Tech3 Column2

description: biological replicate 3 of 3, technical replicate 8 of 9


title: Mucin Bio2 Tech3 Column1

description: biological replicate 2 of 3, technical replicate 7 of 9


title: Mucin Bio2 Tech2 Column1

description: biological replicate 2 of 3, technical replicate 4 of 9


title: Mucin Bio2 Tech3 Column3

description: biological replicate 2 of 3, technical replicate 9 of 9


title: Mucin Bio3 Tech1 Column2

description: biological replicate 3 of 3, technical replicate 2 of 9


title: MGH_Liver_pool vs MGH_Liver_143

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.


title: Mucin Bio2 Tech2 Column2

description: biological replicate 2 of 3, technical replicate 5 of 9


title: siRNA 1 PITX2-TM2

description: siRNA 1 PITX2-TM2

tag: condition

value: siRNA 1 PITX2

tag: cell type


title: Control 1-TM1

description: Control 1-TM1


title: siRNA 1 PITX2-TM1

description: siRNA 1 PITX2-TM1


title: non-smoker 411PL

description:
411PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

source_name: term placenta, non-smoker

extract_protocol: The middle parts of placenta sections were frozen in RNA Later solution (Ambion) and stored at –20°C until RNA isolation. Placental total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

value: term placenta

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: siRNA 2 PITX2-TM1

description: siRNA 2 PITX2-TM1

value: siRNA 2 PITX2


title: siRNA 2 PITX2-TM2

description: siRNA 2 PITX2-TM2


title: MGH_Liver_pool vs MGH_Liver_142

tag: ID


title: MGH_Liver_pool vs MGH_Liver_139

tag: reference


title: MGH_Liver_pool vs MGH_Liver_141

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_144


title: Mucin Bio2 Tech1 Column3

description: biological replicate 2 of 3, technical replicate 3 of 9

tag: strain


title: MGH_Liver_pool vs MGH_Liver_140


title: non-smoker 410PL

description:
410PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Mucin Bio2 Tech1 Column2

description: biological replicate 2 of 3, technical replicate 2 of 9

tag: culture optical density

tag: treatment


title: Fucose Bio3 Tech3 Column3

description: biological replicate 3 of 3, technical replicate 9 of 9

label_protocol: Total RNA from each growth condition was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 μg of total RNA was combined with 10 μg of random hexamers in a 34.35-μl reaction mixture containing 8 μl of 5× Superscript II reverse transcriptase buffer and 2 μl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 μl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 μl of Superscript II and incubated at 42°C for 120 min.  At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 μl of 50 mM EDTA and 2 μl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 μl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 μl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 × g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 μl under vacuum in a SpeedVac and adjusted to a final volume of 10 μl by adding 1 μl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 μl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 1 hour at room temperature in the dark. This reaction was quenched by adding 4.5 μl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: C. jejuni strain NCTC11168 was grown routinely on Mueller-Hinton (MH) agar plates.  Overnight MH biphasic cultures were adjusted to an OD at 600nm of 1.0 and used to inoculate 20ml of MEMα to an O.D. of 0.01.

extract_protocol: Cultures were grown to an O.D. at  of 0.2, representing mid-log phase, at which point the RNA quality was preserved by adding a 1/10-volume stop solution of 10% buffer saturated phenol (pH4.3) and ethanol.  Cultures were pelleted by centrifugation (6000rpm for 5min) and resuspended and lysed in a denaturing solution of 4M guanidinium thiocyanate, 25mM sodium citrate, 0.5% Sarkosyl and 1% N acetyl-cysteine.  RNA was extracted using a hot phenol method.  Briefly, 0.5ml of phenol was added to 0.5ml of lysate and heated at 64°C for 10minutes.  1ml of chloroform was added, mixed thoroughly, incubated on ice for 15 minutes, then centrifuged for 30 minutes, 13000rpm at 4°C.  The aqueous layer was removed to a fresh tube and RNA was precipitated out with 60μl 3M sodium acetate, 1.2μl 0.5mM EDTA and 1ml of ethanol, and an overnight incubation at -80°C.  The precipitated RNA was washed four times in 70% ethanol and resuspended in 50μl DEPC treated dH2O.  DNA was removed by 4 DNAse treatements, and quality and quantity were ascertained using biorad's experion system using manufacturer protocols.

treatment_protocol: Control cultures consisted of 20ml MEMα medium (Gibco 41061) containing no phenol red and supplemented with 20μM FeSO4 and 20mM sodium pyruvate.  The experimental culture was 20ml MEMα supplemented with  20μM FeSO4 and 25mM L-fucose.

source_name: MEMα + 25mM L-Fucose

value: fucose


title: non-smoker 403PL

description:
403PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity


title: non-smoker 401PL

description:
401PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: gestational age (weeks)

tag: mode of delivery


title: Fucose Bio3 Tech3 Column2


title: Fucose Bio3 Tech3 Column1

description: biological replicate 3 of 3, technical replicate 7 of 9


title: Mucin Bio1 Tech2 Column1

description: biological replicate 1 of 3, technical replicate 4 of 9


title: Mucin Bio1 Tech1 Column1

description: biological replicate 1 of 3, technical replicate 1 of 9


title: Mucin Bio1 Tech3 Column1

description: biological replicate 1 of 3, technical replicate 7 of 9


title: Mucin Bio1 Tech1 Column2

description: biological replicate 1 of 3, technical replicate 2 of 9


title: Mucin Bio1 Tech1 Column3

description: biological replicate 1 of 3, technical replicate 3 of 9


title: Mucin Bio1 Tech3 Column2

description: biological replicate 1 of 3, technical replicate 8 of 9


title: Mucin Bio1 Tech2 Column3

description: biological replicate 1 of 3, technical replicate 6 of 9


title: Mucin Bio1 Tech3 Column3

description: biological replicate 1 of 3, technical replicate 9 of 9


title: Mucin Bio1 Tech2 Column2

description: biological replicate 1 of 3, technical replicate 5 of 9


title: smoker 400PL

description:
400PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

source_name: term placenta, smoker

tag: placental weight (g)

tag: newborn weight (g)


title: MGH_Liver_pool vs MGH_Liver_138

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

value: liver

tag: ID


title: Mucin Bio2 Tech1 Column1

description: biological replicate 2 of 3, technical replicate 1 of 9


title: Fucose Bio3 Tech2 Column2

description: biological replicate 3 of 3, technical replicate 5 of 9


title: Fucose Bio3 Tech2 Column3

description: biological replicate 3 of 3, technical replicate 6 of 9


title: non-smoker 399PL

description:
399PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: apgar score (5s)


title: smoker 408PL

description:
408PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue


title: non-smoker 407PL

description:
407PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: non-smoker 398PL

description:
398PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: MGH_Liver_pool vs MGH_Liver_132

tag: reference


title: MGH_Liver_pool vs MGH_Liver_134


title: MGH_Liver_pool vs MGH_Liver_137


title: MGH_Liver_pool vs MGH_Liver_135


title: MGH_Liver_pool vs MGH_Liver_133


title: MGH_Liver_pool vs MGH_Liver_136


title: Fucose Bio3 Tech1 Column1

description: biological replicate 3 of 3, technical replicate 1 of 9

tag: strain


title: Fucose Bio3 Tech2 Column1

description: biological replicate 3 of 3, technical replicate 4 of 9


title: MGH_Liver_pool vs MGH_Liver_131


title: Fucose Bio2 Tech3 Column3

description: biological replicate 2 of 3, technical replicate 9 of 9


title: Fucose Bio2 Tech3 Column1

description: biological replicate 2 of 3, technical replicate 7 of 9


title: Fucose Bio3 Tech1 Column2

description: biological replicate 3 of 3, technical replicate 2 of 9


title: Fucose Bio2 Tech2 Column3

description: biological replicate 2 of 3, technical replicate 6 of 9


title: smoker 395PL

description:
395PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi


title: Fucose Bio2 Tech2 Column2

description: biological replicate 2 of 3, technical replicate 5 of 9


title: Fucose Bio2 Tech3 Column2

description: biological replicate 2 of 3, technical replicate 8 of 9


title: MGH_Liver_pool vs MGH_Liver_130

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.


title: Fucose Bio2 Tech2 Column1

description: biological replicate 2 of 3, technical replicate 4 of 9


title: non-smoker 378PL

description:
378PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: non-smoker 389PL

description:
389PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: individual


title: smoker 374PL

description:
374PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: Fucose Bio2 Tech1 Column2

description: biological replicate 2 of 3, technical replicate 2 of 9

tag: culture optical density

tag: treatment


title: MGH_Liver_pool vs MGH_Liver_129


title: smoker 377PL

description:
377PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity


title: MGH_Liver_pool vs MGH_Liver_127


title: MGH_Liver_pool vs MGH_Liver_128


title: non-smoker 372PL

description:
372PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: gestational age (weeks)

tag: mode of delivery


title: Fucose Bio2 Tech1 Column1

description: biological replicate 2 of 3, technical replicate 1 of 9


title: Fucose Bio1 Tech2 Column3

description: biological replicate 1 of 3, technical replicate 6 of 6


title: MGH_Liver_pool vs MGH_Liver_125


title: MGH_Liver_pool vs MGH_Liver_124


title: smoker 369PL

description:
369PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: placental weight (g)

tag: newborn weight (g)


title: MGH_Liver_pool vs MGH_Liver_126

tag: ID


title: Fucose Bio1 Tech2 Column2

description: biological replicate 1 of 3, technical replicate 5 of 6


title: MGH_Liver_pool vs MGH_Liver_123

tag: tissue


title: Fucose Bio1 Tech2 Column1

description: biological replicate 1 of 3, technical replicate 4 of 6


title: Fucose Bio1 Tech1 Column1

description: biological replicate 1 of 3, technical replicate 1 of 6


title: non-smoker 368PL

description:
368PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: apgar score (5s)


title: Fucose Bio1 Tech1 Column2

description: biological replicate 1 of 3, technical replicate 2 of 6

tag: strain


title: Fucose Bio1 Tech1 Column3

description: biological replicate 1 of 3, technical replicate 3 of 6


title: smoker 356PL

description:
356PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)


title: MGH_Liver_pool vs MGH_Liver_122

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

tag: reference


title: Fucose Bio3 Tech1 Column3

description: biological replicate 3 of 3, technical replicate 3 of 9


title: non-smoker 353PL

description:
353PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)


title: MGH_Liver_pool vs MGH_Liver_121


title: non-smoker 354PL

description:
354PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: cord blood cotinine (ng/ml)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_119


title: Nociceptor differentiation using 5 inhibitors for 15 days C

city: New York

first: Stuart

middle: M

last: Chambers

state: NY

address: 1270 York Ave

institute: Sloan-Kettering Institute

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Quantile normalization using Illumina Genome Studio Data Analysis Software 2010.v3

source_name: WI-09 Embryonic Stem Cell

label_protocol: Biotinlylation

growth_protocol: hESC cell (WA-09; passages 32-50) were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. hESC cells were grown in DMEM:F12 hESC media containing 6ng/mL FGF2 and passaged using dispase or accutase.

extract_protocol: Trizol LS

treatment_protocol: hESC were plated on matrigel for differentiation and grown in the presence of LDN-193189 (Stemgent) and SB431542 (Tocris) for LSB, or grown in the presence of LDN-193189, SB431542, CHIR 99021 (Stemgent), DAPT (Tocris), and SU5402 (BioVision) for 3I.

tag: cell line

tag: treatment

tag: time

value: 15 days


title: Nociceptor differentiation using 5 inhibitors for 15 days A


title: MGH_Liver_pool vs MGH_Liver_117


title: MGH_Liver_pool vs MGH_Liver_120


title: MGH_Liver_pool vs MGH_Liver_118


title: Nociceptor differentiation using 5 inhibitors for 9 days A

value: 9 days


title: non-smoker 355PL

description:
355PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: gestational age (weeks)

value: vaginal


title: non-smoker 352PL

description:
352PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

value: non-smoker

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)


title: smoker 349PL

description:
349PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

value: smoker

tag: apgar score (5s)


title: 9937deltaropB_2

city: Houston

first: Samuel

last: Shelburne

state: TX

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

hyb_protocol: Per Affymetrix protocol

scan_protocol: Per Affymetrix protocol

data_processing: Probes corresponding to the serotype M3 strains used were extracted from the total data set.  The total intensity of the array for each sample was then calculated by adding the values for each of the probe sets.  The probe set values were then normalized such that the total intensity derived from each sample was equivalent.

organism: Streptococcus pyogenes

source_name: 9937deltaropB grown to early stationary phase in THY

label_protocol: Per Affymetrix protocol

extract_protocol: Strain was grown to early stationary phase in THY.  2x RNAprotect (Qiagen) was added for 5 mins and cells were pelleted.  Total RNA was extracted with RNeasy (Qiagen) and reverse transcribed to cDNA with SuperScriptIII (Invitrogen).  cDNA was labeled and hybridized following Affymetrix instructions.

tag: strain

tag: genotype/variation

value: deltaropB

tag: growth

value: early stationary phase in THY


title: MGH_Liver_pool vs MGH_Liver_115

tag: reference

tag: ID


title: Nociceptor differentiation using 5 inhibitors for 15 days B


title: smoker 350PL

description:
350PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Nociceptor differentiation using 5 inhibitors for 7 days C

tag: cell line

tag: treatment

tag: time

value: 7 days


title: smoker 351PL

description:
351PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: 9937deltaropB_1

tag: strain

tag: genotype/variation


title: Nociceptor differentiation using 5 inhibitors for 7 days B


title: MGAS9937_2

source_name: MGAS9937 grown to early stationary phase in THY

value: RopB allele containing a C85Y polymorphism

tag: growth


title: Nociceptor differentiation using 5 inhibitors for 7 days A


title: non-smoker 347PL

description:
347PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

tag: newborn weight (g)

tag: apgar score (5s)


title: Nociceptor differentiation using 5 inhibitors for 9 days B


title: MGH_Liver_pool vs MGH_Liver_116

tag: reference

tag: ID


title: Fucose Bio2 Tech1 Column3

description: biological replicate 2 of 3, technical replicate 3 of 9

tag: culture optical density


title: non-smoker 343PL

description:
343PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Nociceptor differentiation using 5 inhibitors for 9 days C

tag: cell line

tag: treatment

tag: time


title: MGAS9937_1

tag: strain


title: Nociceptor differentiation using 5 inhibitors for 5 days C

value: 5 days


title: Nociceptor differentiation using 5 inhibitors for 5 days B


title: 10870deltaropB_2

source_name: 10870deltaropB grown to early stationary phase in THY

tag: genotype/variation


title: MGH_Liver_pool vs MGH_Liver_114

source_name: liver


title: MGH_Liver_pool vs MGH_Liver_113


title: smoker 342PL

description:
342PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: non-smoker 340PL

description:
340PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

tag: newborn weight (g)

tag: apgar score (5s)


title: Nociceptor differentiation using 5 inhibitors for 5 days A


title: MGH_Liver_pool vs MGH_Liver_111

tag: reference

tag: ID


title: MGH_Liver_pool vs MGH_Liver_110


title: 10870deltaropB_1

tag: growth


title: Nociceptor differentiation using 5 inhibitors for 3 days C

value: 3 days


title: MGAS10870_1

source_name: Strain MGAS10870 grown to early stationary phase in THY

value: wild-type RopB allele


title: smoker 337PL

description:
337PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Nociceptor differentiation using 5 inhibitors for 3 days B

tag: cell line

tag: treatment

tag: time


title: MGAS10870_2

source_name: MGAS10870 grown to early stationary phase in THY

tag: strain

tag: genotype/variation


title: non-smoker 338PL

description:
338PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: Neural differentiation using Dual SMAD inhibition for 15 days C


title: non-smoker 335PL

description:
335PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

tag: newborn weight (g)

tag: apgar score (5s)


title: Neural differentiation using Dual SMAD inhibition for 15 days A


title: MGH_Liver_pool vs MGH_Liver_112

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.

tag: reference

tag: ID


title: Neural differentiation using Dual SMAD inhibition for 15 days B


title: non-smoker 331PL

description:
331PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)

tag: maternal bmi

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: non-smoker 339PL

description:
339PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: individual


title: non-smoker 332PL

description:
332PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: non-smoker 336PL

description:
336PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: Nociceptor differentiation using 5 inhibitors for 3 days A

tag: cell line

tag: treatment

tag: time


title: Neural differentiation using Dual SMAD inhibition for 9 days C


title: non-smoker 392PL

description:
392PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity


title: MGH_Liver_pool vs MGH_Liver_108


title: non-smoker 330PL

description:
330PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: gestational age (weeks)

tag: mode of delivery


title: MGH_Liver_pool vs MGH_Liver_109

tag: tissue


title: MGH_Liver_pool vs MGH_Liver_106


title: MGH_Liver_pool vs MGH_Liver_107


title: non-smoker 329PL

description:
329PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: placental weight (g)

tag: newborn weight (g)


title: MGH_Liver_pool vs MGH_Liver_103

tag: reference


title: immortoLEC passage 14

city: Zurich

first: benjamin

last: vigl

address: W.-Pauli-Str. 10, HCI, G490

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description: Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single stranded cDNA

hyb_protocol: Biotin-labeled cDNAs were mixed in 220 μl of Hybridization Mix (Affymetrix Inc.) containing hybridization controls and control oligonucleotide B2 (Affymetrix Inc.). Samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays for 18h at 45°C. Arrays were washed using an Affymetrix Fluidics Station 450 FS450 0004 protocol.

scan_protocol: Fluorescence intensity of the arrays was measured on an Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) as implemented in the BioConductor simpleaffy package - with default parameters, in particular the trimmed mean target intensity of each array was set to 100. The chip description file used for summarization was standard Affymetrix Mouse430_2 CDF file.

organism: Mus musculus

source_name: Mouse, skin, normal, lymphatic endothelial cells

label_protocol: Single-stranded cDNA (5 μg) was fragmented and biotin-labeled, using the FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies), following the manufacturer’s instructions.

growth_protocol: imLECs  were cultured at 33°C in dishes pre-coated with collagen (10 μg/ml, PureColTM purified collagen for tissue engineering, Inamed Biomaterials, Fremont, CA) and fibronectin (10 μg/ml, Human Plasma Fibronectin Purified Protein, Chemicon) in Immorto medium consisting of 40% DMEM low glucose (Invitrogen), 40% F12 (Heme, Invitrogen), 20% Fetal Bovine Serum (FBS, Invitrogen), and 1% antibiotics (antibiotic-antimycotic, liquid, Invitrogen). The medium also contained endothelial cell mitogen (10 μg/ml, native bovine endothelial mitogen AbD Serotec) and heparin (56 μg/ml, heparin sodium salt from porcine intestinal mucosa, Sigma). In order to further induce large T antigen expression Interferon-γ (recombinant mouse IFNγ, R&D) was added in a concentration of 1 unit/ml. Upon transfer to 37 ºC, cell were cultured for 3 days in Immorto media containing no IFNγ, in order to induce  degradation of the large T antigen.

extract_protocol: Total RNA was extracted in parallel from 3 imLEC cultures using RNeasy plus micro kit (Qiagen). gDNA eliminator column was used to eliminate genomic DNA. The Whole Transcriptome-OvationTM Pico RNA amplification kit from Nugen Technologies (San Carlos, CA) and QIAQuick PCR purification kit (Quiagen) were used for cDNA synthesis and a single round of isothermal amplification (SPIA amplification, i.e. a linear isothermal DNA amplification process, was used to prepare single-stranded cDNA in the antisense direction of the mRNA starting material). This precedure typically yielded more than 5 μg of amplified cDNA. The quantity and quality of the amplified cDNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent). Amplified cDNA gave a peak length of 300 - 900 nt.

tag: strain

value: H-2Kb-tsA58 mice; ImmortoMice

tag: cell type

value: immortalized lymphatic endothelial cells

tag: condition

value: normal, healthy

tag: cell isolation method

value: FACS

tag: passage


title: MGH_Liver_pool vs MGH_Liver_102

value: liver

tag: ID


title: MGH_Liver_pool vs MGH_Liver_104


title: Neural differentiation using Dual SMAD inhibition for 7 days C

tag: cell line


title: smoker 328PL

description:
328PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

value: term placenta

tag: age (years)

tag: maternal bmi

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: MGH_Liver_pool vs MGH_Liver_101

tag: tissue


title: immortoLEC passage 13


title: non-smoker 327PL

description:
327PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)


title: smoker 322PL

description:
322PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: newborn weight (g)


title: Neural differentiation using Dual SMAD inhibition for 7 days B

tag: treatment

tag: time


title: non-smoker 320PL

description:
320PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: non-smoker 318PL

description:
318PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.


title: Neural differentiation using Dual SMAD inhibition for 5 days B


title: Neural differentiation using Dual SMAD inhibition for 9 days A

value: 9 days


title: non-smoker 317PL

description:
317PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

value: vaginal


title: Neural differentiation using Dual SMAD inhibition for 3 days C


title: MGH_Liver_pool vs MGH_Liver_97

tag: reference

tag: ID


title: MGH_Liver_pool vs MGH_Liver_98


title: non-smoker 316PL

description:
316PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

value: non-smoker

tag: age (years)


title: Neural differentiation using Dual SMAD inhibition for 3 days B

tag: cell line


title: Neural differentiation using Dual SMAD inhibition for 5 days A


title: Neural differentiation using Dual SMAD inhibition for 5 days C


title: MGH_Liver_pool vs MGH_Liver_95


title: MGH_Liver_pool vs MGH_Liver_99


title: smoker 324PL

description:
324PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

value: smoker

tag: maternal bmi

tag: apgar score (5s)


title: Neural differentiation using Dual SMAD inhibition for 7 days A


title: MGH_Liver_pool vs MGH_Liver_96

description: Gene expression data from Human livers, biopsies taken during RY gastric bypass surgery. All individuals were compared to a common pool created from equal portions of RNA.


title: MGH_Liver_pool vs MGH_Liver_100


title: MGH_Liver_pool vs MGH_Liver_93


title: MGH_Liver_pool vs MGH_Liver_94


title: Neural differentiation using Dual SMAD inhibition for 3 days A


title: MGH_Liver_pool vs MGH_Liver_92


title: non-smoker 305PL

description:
305PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: smoker 313PL

description:
313PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

tag: individual


title: non-smoker 308PL

description:
308PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity


title: Neural differentiation using Dual SMAD inhibition for 2 days B

value: 2 days


title: CpG-ODN 3 (IGROV-1 cells)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalised using quantile normalisation with BeadStudio software

source_name: ovarian cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: CpG-ODN


title: Neural differentiation using Dual SMAD inhibition for 2 days C


title: MGH_Liver_pool vs MGH_Liver_87


title: Neural differentiation using Dual SMAD inhibition for 2 days A


title: S(Cy5)×1.2% S(Cy3)_Pooled Sample 2

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description: Dye-swap (Cy5/Cy3) of Spleen Sample 2

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scaner

data_processing: Software: Feature Extraction ver 9.5.3.1

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Animals were housed at the Animal Institution in Showa University, and maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights turned on at 8:00 AM) and had access to chow (CE-2, CLEA Japan) and tap water ad libitum.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: NP diet

tag: strain

tag: diet

value: nucleoprotein

value: spleen

source_name: Control Cy5

treatment_protocol: control diet

value: control


title: non-smoker 410M

source_name: maternal peripheral blood, non-smoker

extract_protocol: Peripheral blood was sampled and processed using the LeukoLOCK™ Total RNA Isolation System (Ambion, Austin, TX, USA) according to the manufacturer manual. The system employs filter-based leukocyte-depletion technology to isolate leukocytes from whole blood and RNAlater™ (Ambion) to stabilize the cells on the filter. By removal of red blood cells, the RNA purified from captured leukocytes is inherently depleted of globin mRNA, which improves sample quality for expression profiling and other applications. Integrity of the total RNAs was assayed by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), and only samples with RNA integrity number (RIN) above 7.0 were used for gene expression profiling.

value: maternal peripheral blood

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)


title: MGH_Liver_pool vs MGH_Liver_85

tag: reference

tag: ID


title: MGH_Liver_pool vs MGH_Liver_89


title: non-smoker 314PL

description:
314PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: age (years)


title: non-smoker 302PL

description:
302PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: maternal bmi


title: Neural differentiation using Dual SMAD inhibition for 9 days B

tag: cell line

tag: treatment

tag: time


title: non-smoker 315PL

description:
315PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: tissue

tag: apgar score (5s)

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)


title: Saline 3 (IGROV-1 cells)

value: saline


title: smoker 303PL

description:
303PL
Middle part of the placenta villi parenchyma sections; 5-cm away from the site of cord insertion.

tag: smoking status

tag: parity

tag: individual


title: MGH_Liver_pool vs MGH_Liver_88


title: MGH_Liver_pool vs MGH_Liver_105


title: MGH_Liver_pool vs MGH_Liver_91


title: CpG-ODN 1 (IGROV-1 cells)


title: CpG-ODN 2 (IGROV-1 cells)


title: S(Cy3)×1.2% S(Cy5)_Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Spleen Sample 1

source_name: Control Cy3

tag: strain

tag: diet


title: MGH_Liver_pool vs MGH_Liver_86


title: MGH_Liver_pool vs MGH_Liver_90


title: L(Cy5)×1.2% L(Cy3)_Pooled Sample 2

description: Dye-swap (Cy5/Cy3) of Liver Sample 2


title: non-smoker 409M

tag: gestational age (weeks)

tag: mode of delivery

tag: placental weight (g)

tag: newborn weight (g)


title: CpG-ODN 1 (tumor cells grown in mice)

source_name: tumor cells grown in mice


title: MGH_Liver_pool vs MGH_Liver_81

tag: reference

tag: ID


title: Saline 2 (tumor cells grown in mice)

tag: cell line

tag: treatment


title: MGH_Liver_pool vs MGH_Liver_84

tag: tissue


title: Saline 2 (IGROV-1 cells)


title: non-smoker 407M

tag: age (years)

tag: maternal bmi

tag: apgar score (5s)


title: immortoLEC passage 18

description: Extracted RNA was used in linear isothermal whole transcriptome amplification (SPIA amplification) that results in single stranded cDNA

value: H-2Kb-tsA58 mice; ImmortoMice

tag: cell type

tag: condition

tag: cell isolation method

tag: passage


title: L(Cy3)×1.2% L(Cy5)_Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Liver Sample 1

tag: strain

tag: diet


title: smoker 400M

source_name: maternal peripheral blood, smoker

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: mode of delivery

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: Mother Control (Cy3) Mother FD (Cy5) Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Mother Liver Sample 1

treatment_protocol: control

tag: treatment

tag: tissue

tag: subject

value: mother

source_name: FD Cy5

treatment_protocol: FD

value: food deprivation


title: Saline 4 (tumor cells grown in mice)

tag: cell line


title: non-smoker 399M

tag: age (years)

tag: maternal bmi

tag: placental weight (g)

tag: newborn weight (g)

tag: apgar score (5s)


title: CpG-ODN 3 (tumor cells grown in mice)


title: Saline 1 (IGROV-1 cells)


title: AVC control 4 vs. mutant 4

city: Salt Lake City

first: Deborah

last: Frank

state: UT

address: 15 North 2030 East

department: Pediatrics

institute: University of Utah

description: Biological replicate 4 of 4.

hyb_protocol: Agilent Two-color GE Hyb/Wash Protocol, incubated at 65 deg C for 17 hours at 10 rpm

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 um resolution.  Primary scan at 100% laser power, and secondary scan at 10% power

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

label_protocol: Agilent Two-Color Low RNA input Linear Amplification Kit, with purification using the Qiagen Rneasy mini kit.

growth_protocol: embryonic development timed with noon on the day a copulation plug identified in female mouse designated a e0.5

extract_protocol: 5 tissue pieces pooled for each sample and total RNA purified using Qiagen Rneasy micro kit.

treatment_protocol: Embryos harvested in ice cold PBS at 3pm on e10.5,  heart AVC tissue samples micro-dissected and placed in RLT buffer then frozen at -80C until all samples collected.

tag: age

value: heart AVC

tag: background strain

tag: genotype variation

value: wild type control

value: Tbx3 mutant


title: non-smoker 401M

tag: smoking status

tag: parity

tag: gestational age (weeks)


title: Fetus Control (Cy3) Fetus FD (Cy5) Pooled Sample 1

description: Dye-swap (Cy3/Cy5) of Fetus Liver Sample 1

tag: strain

value: liver

value: fetus


title: Mother Control (Cy5) Mother FD (Cy3) Pooled Sample 2

description: Dye-swap (Cy5/Cy3) of Mother Liver Sample 2

source_name: FD Cy3


title: Fetus Control (Cy5) Fetus FD (Cy3) Pooled Sample 2

description: Dye-swap (Cy5/Cy3) of Fetus Liver Sample 2


title: MGH_Liver_pool vs MGH_Liver_83

tag: reference

tag: ID


title: CpG-ODN 4 (tumor cells grown in mice)

tag: treatment


title: smoker 395M

tag: tissue

tag: mode of delivery

value: vaginal

tag: maternal blood cotinine (ng/ml)

tag: cord blood cotinine (ng/ml)

tag: individual


title: AVC control 3 vs. mutant 3

description: Biological replicate 3 of 4.


title: MGH_Liver_pool vs MGH_Liver_82


title: MGH_Liver_pool vs MGH_Liver_80


title: MGH_Liver_pool vs MGH_Liver_78


title: non-smoker 398M

value: non-smoker

tag: age (years)

tag: maternal bmi

tag: placental weight (g)

tag: newborn weight (g)


title: Saline 3 (tumor cells grown in mice)

tag: cell line


title: MGH_Liver_pool vs MGH_Liver_77


title: MGH_Liver_pool vs MGH_Liver_79


title: CpG-ODN 2 (tumor cells grown in mice)


title: AVC control 1 vs. mutant 1

description: Biological replicate 1 of 4.

tag: age

tag: background strain

tag: genotype variation


title: Saline 1 (tumor cells grown in mice)


title: MGH_Liver_pool vs MGH_Liver_76


title: d2-DMSO

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

institute: Tokyo Medical University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4121F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The scanned images was analyzed automatically in Agilent feature extraction 9.5.3 (Agilent) using default protocol (GE1-v5_95_Feb07). No interarray normalization method was employed.

source_name: 3T3-L1, d2-DMSO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 3T3-L1 preadipocytes (American Type Culture Collection, Manassas, VA) were grown to confluence in DMEM media (Sigma Aldrich, Tokyo, Japan) with 10% calf serum and penicillin (100 U/ml)/streptomycin (100 ug/ml). Adipogenesis was induced using an adipogenesis assay kit (Chemicon International, Temecula, CA). On day 0, cells were induced with initiation media (10 ug/ml insulin, 1µM dexamethasone and 0.5 uM IBMX in DMEM media supplemented with 10% fetal calf serum. On day 3, initiation media was replaced with progression media (10 µg/ml insulin in DMEM media supplemented with 10% fetal calf serum). On day 6, progression media was replaced with maintenance media (DMEM supplemented with 10% fetal calf serum). From day 6, cells were kept in maintenance media with new maintenance media being replaced by every two days. Cells are incubated at 37°C with 5% CO2 at all time.

extract_protocol: Total RNA was extracted by using ISOGEN  (Nippon gene) according to manufacturer’s instruction.

treatment_protocol: 3T3-L1 were treated for 6 days (from day0 to day6) with additives.

tag: cell type

value: adipocyte

tag: additive

value: DMSO


title: non-smoker 391M

tag: smoking status

tag: parity

tag: gestational age (weeks)

tag: apgar score (5s)