title: T3BQBC06182008A_3435_CY3_STERNE_CY5_13823994_B

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

description: T3BQBC06182008A_3435_CY3_STERNE_CY5_13823994_anno_sub_95th_MDS.mev.refIsMEDB.out

hyb_protocol: Aminosaline coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 degree Celcius for 45 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in a solution of 35% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured at 95 degree Celcius prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 degree Celcius. Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature.

scan_protocol: Scanned on Axon GenePix 4000 scanner. PMT values were optimized during scanning to balance channel intensities.

data_processing:
1. Use software suite TM4 (www.tm4.org) to analyze spotted arrays.
2. Use Spotfinder with background correction to compute the spot intensities of the hybridized arrays.
3. Perform the following filtering steps:
All PFGRC arrays used in this study have 3 types of spots.
(1). Species spot: oligos designed for the species under investigation.
(2). Reserved spot or control spot: oligos designed from Arabidopsis genes as controls.
(3). Empty spots: no oligos or any DNA.
Step 1: Identify the replicates.
Sort the .mev file from Spotfinder by oligo_id.
Step 2: Identify the outliers within each set of replicates for each channel.
Outliers are identified using the Sprents method (The Handbook of Parametric and Nonparametric Statistical Procedures, Third Edition by David J. Sheskin, PP 400-402).
|Xi - M|/MAD > Max
Xi = Each intensity value from the set of replicates.
M = Median intensity value from the set of replicates.
MAD = Median absolute deviation.
Max = the critical value that the result of the inequality must exceed in order to conclude that the Xi value is an outlier. The value of 5 was used for Max.
Step 3: Replace the outliers.
Replace the outliers by the value closest to them from the tail that they occur. For example, if the outlier identified is the highest value in channel A, that value will be replaced by the next highest value of its replicate set in channel A.
Step 4: Subtract the 95th percentile of the reserved spots.
Calculate the 95th percentile of all the reserved spots and subtract that value from all the species spots and reserved spots.
Step 5: Replace zero (0) by one (1).
After subtracting the 95th percentile of the reserved spots, if one of the channel intensities is less than zero (0), replace that value by one (1); If both channels become less than zero (0), set both channels to zero (0).
Step 6. Output the filtered .mev file.
4. Use Midas X for CGH normalization:
1). Plot the histogram of the Log2 ratio data (Reference/Query) from the filtered .mev file, and identify the central peak containing oligos predicted to be shared by both the reference and query strains.
2). Fit a Gaussian curve to the central peak by 'tweaking' the log ratio mean and by shrinking or stretching the standard deviation of the curve to find the smallest least sum of squares difference.
3). Perform Log Mode Centering normalization on the channel that contains the query sample only (Either Cy3 or Cy5).
4). Output the normalized *.mev file.
5. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
1). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
2). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with the Qiaquick PCR purification kit (QIAGEN). The purified labelled DNA was then dye coupled with the appropriate cyanine dye (Cy3/Cy5).

extract_protocol: Epicentre MasterPure DNA Extraction Kit.

treatment_protocol: None.

tag: strain

organism: Bacillus anthracis str. Sterne

source_name: Sterne reference

value: Sterne


title: 244960

status: Public on Nov 20 2009

type: genomic

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

country: USA

institute: Iowa State University

description: no additional information

hyb_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)

data_processing: We used a subset of 840,289 probes that were known to have identical sequence in B73 and Mo17 (based on B73 BAC sequences and Mo17 WGS data) as a control set to obtain a best-fitting cubic spline function (Workman et al., 2002), assuming that most of these probes should have the same hybridization intensities after normalization. The spline function was then globally applied for all probes to normalize the two channels.  After within-chip normalization, linear model analyses using LIMMA (Smyth 2004; Smyth 2005) were conducted for the data from all microarrays. The linear model for each probe included effects for dyes and genotypes (B73, Mo17, RIL M0022, and RIL M0023), and p-values were calculated to test for a signal difference between Mo17 and B73 genotypes as part of each linear model analysis.

molecule: genomic DNA

organism: Zea mays

extract_protocol: Total genomic DNA of the samples were isolated using NimbleGen's standard protocols (see supplemental file: cgh_userguide_v5p1.pdf)

tag: genotype

tag: developmental stage

value: two-week-old etiolated seedlings

tag: developmental state


title: PhIP 2.5 µM sample 2

status: Public on Nov 19 2009

type: RNA

city: Maastricht

first: Kevin

last: Hochstenbach

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

molecule: total RNA

organism: Homo sapiens

source_name: control for 30_PhIP_1%

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Isolated PBMC were resuspended in tissue culture medium RPMI 1640 supplemented with L-glutamine, 10% heat inactivated foetal calf serum (FCS) (Gibco, Paisley, UK) and 100 U/ml penicillin G and 0.1 mg/ml streptomycin (PAA Laboratories GmbH, Pasching, Austria) to a final concentration of 2,4*106  cells/ml.

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: For analysis of whole genome gene expression by microarray PBMC from five independent donors per compound were exposed for 20 hours to three concentrations, i.e. the 100% and two serial ten-fold dilutions (10% and 1%), and a DMSO or PBS vehicle control. All exposures were performed in the presence of freshly prepared S9-mix.

tag: cell type

value: PBMC

tag: agent

value: control

value: PhIP

tag: dose

tag: concentration

tag: immunotoxicity

value: non-immunotoxic


title: BaP 10 µM sample 1

source_name: control for 39_BaP_10%

value: BaP

value: immunotoxic


title: BaP 10 µM sample 2

source_name: control for 40_BaP_10%


title: BaP 100 µM sample 4

source_name: control for 42_BaP_100%


title: BaP 10 µM sample 5

source_name: control for 43_BaP_10%


title: IQ 25 µM  sample 3

source_name: control for 89_IQ_10%

value: IQ


title: 270491-2

description: no additional information

scan_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)


title: PhIP 2.5 µM sample 3

source_name: control for 31_PhIP_1%


title: 270480

description: no additional information

label_protocol: See NimbleGen Array User's Guide: CGH Analysis (cgh_userguide_v5p1.pdf)


title: TCDD 10 µM sample 1

source_name: control for 34_TCDD_100%

value: TCDD


title: TCDD 10 µM sample 5

source_name: control for 38_TCDD_100%


title: TCDD 1 µM sample 2

source_name: control for 35_TCDD_10%


title: TCDD 10 µM sample 3

source_name: control for 36_TCDD_100%


title: EtOH 0.5 % sample 4

source_name: control for 55_EtOH_100%

value: EtOH


title: AA 0.5 mM sample 2

source_name: control for 65_AA_1%

value: AA


title: TCDD 1 µM sample 1

source_name: control for 34_TCDD_10%


title: AA 0.5 mM sample 3

source_name: control for 66_AA_1%


title: EtOH 0.05 % sample 5

source_name: control for 57_EtOH_10%


title: PhIP 2.5 µM sample 1

source_name: control for 28_PhIP_1%


title: PhIP 2.5 µM sample 5

source_name: control for 33_PhIP_1%


title: TCDD 1 µM sample 5

source_name: control for 38_TCDD_10%


title: BaP 10 µM sample 4

source_name: control for 42_BaP_10%


title: AA 0.5 mM sample 1

source_name: control for 64_AA_1%


title: BaP 100 µM sample 3

source_name: control for 41_BaP_100%


title: EtOH 0.05 % sample 4

source_name: control for 55_EtOH_10%


title: TCDD 10 µM sample 2

source_name: control for 35_TCDD_100%


title: TCDD 1 µM sample 3

source_name: control for 36_TCDD_10%


title: AA 0.5 mM sample 4

source_name: control for 67_AA_1%


title: TCDD 1 µM sample 4

source_name: control for 37_TCDD_10%


title: EtOH 0.5 % sample 2

source_name: control for 51_EtOH_100%


title: EtOH 0.5 % sample 3

source_name: control for 54_EtOH_100%


title: AA 0.5 mM sample 5

source_name: control for 68_AA_1%


title: EtOH 0.05 % sample 3

source_name: control for 54_EtOH_10%


title: TCDD 10 µM sample 4

source_name: control for 37_TCDD_100%


title: EtOH 0.05 % sample 2

source_name: control for 51_EtOH_10%


title: EtOH 0.5 % sample 1

source_name: control for 50_EtOH_100%


title: EtOH 0.05 % sample 1

source_name: control for 50_EtOH_10%


title: Ischemia-propranolol

city: Harbin

first: Wenliang

last: Zhu

state: Heilongjiang

address: Xuefu road 194

department: 1Institute of Clinical Pharmacology

country: China

institute: The Second Affiliated Hospital of Harbin Medical University

description: The ischemic zone of the rat left ventricle was caused by performing a surgical operation of left anterior descending coronary artery occlusion under sterie conditions. Propranolol was administered to the rat for 2 months after the surgery.

hyb_protocol: Labeled RNA samples were hybridized using Exiqon miRCURYTM Array microarray kit, Cat #208000V8.0, Corning Hybridization Chamber II, Cat #40080, and Ambion Bioarray LifterSlip coverslip.

scan_protocol: Scans were performed by using Genepix 4000B and quantified by using Genepix Pro 6.0 (Molecular Devices).

data_processing: Images were processed and quantified using Genepix Pro 6.0 software (Axon Instruments, Union City, CA). The data were filtered (or flagged) on the basis of signal levels and spot quality. Each microarray, scanned at three times were merged into one. The original values of data were amended by subtracting the measured background value and then normalized by subtracting the amended value of U6-snRNA on the same microarry.

organism: Rattus norvegicus

source_name: Ischemia-propranolol

label_protocol: RNA samples were sent to KangChen Bio-tech Inc (Shanghai, China) where they were labeled using the Exiqon mercury Array labeling kit, Cat #208032. And the labeled samples were concentrated using Qiagen RNeasy Mini Kit, Cat #74104.

extract_protocol: Total cellular RNA was isolated from rat left ventricle using TRIzol (Invitrogen) followed by phase seperation purification, according to manufacturers' instructions. RNA quality was assessed using a Genepix 4000B.

value: Winstar

tag: group

value: ischemia-propranolol


title: Non-ischemia-propranolol

description: one of four chambers (two atria and two ventricles) in the rat heart. It receives oxygenated blood from the left atrium via the mitral valve, and pumps it into the aorta via the aortic valve. The rats were administered with propranolol for 2 months, which underwent open chest procedures without coronary artery occlusion.

source_name: Non-ischemia-propranolol

value: non-ischemia-propranolol


title: NDMA 67.5 mM sample 5

source_name: control for 73_DMNA_100%

value: DMNA


title: Ischemia

description: The ischemic zone of the rat left ventricle was caused by performing a surgical operation of left anterior descending coronary artery occlusion under sterie condition.

source_name: Ischemia

value: ischemia


title: NDMA 67.5 mM sample 1

source_name: control for 69_DMNA_100%


title: EtOH 0.5 % sample 5

source_name: control for 57_EtOH_100%


title: NDMA 6.75 mM sample 3

source_name: control for 71_DMNA_10%


title: NDMA 6.75 mM sample 1

source_name: control for 69_DMNA_10%


title: NDMA 6.75 mM sample 2

source_name: control for 70_DMNA_10%


title: NDMA 67.5 mM sample 2

source_name: control for 70_DMNA_100%


title: NDMA 67.5 mM sample 3

source_name: control for 71_DMNA_100%


title: NDMA 6.75 mM sample 4

source_name: control for 73_DMNA_10%


title: Control

description: one of four chambers (two atria and two ventricles) in the rat heart. It receives oxygenated blood from the left atrium via the mitral valve, and pumps it into the aorta via the aortic valve.

source_name: Control


title: NDMA 67.5 mM sample 4

source_name: control for 72_DMNA_100%


title: DON 12.5 µM sample 4

source_name: control for 52_DON_1%

value: DON


title: DON 12.5 µM sample 3

source_name: control for 49_DON_1%


title: DON 12.5 µM sample 2

source_name: control for 48_DON_1%


title: Patient 33 Tumor

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

description: Patient 33 Tumore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Bead Studio without any background subtraction.

label: biotin

source_name: Oral Tongue Tumor

label_protocol: Standard Illumina labeling protocol

extract_protocol: Qiagen Rneasy extraction kit

tag: tissue

value: Oral Tongue


title: DON 12.5 µM sample 5

source_name: control for 53_DON_1%

value: PBMC


title: Patient 8 Tumor

description: Patient 8 Tumore


title: PCB153 250 µM sample 2

source_name: control for 75_PCB_100%

value: control

value: PCB


title: Patient 51 Tumor

description: Patient 51 Tumore


title: Patient 33 Normal

description: Adjacent Normal from Patient 33

source_name: Negative Margin Oral Tongue


title: DON 12.5 µM sample 1

source_name: control for 47_DON_1%


title: PCB153 250 µM sample 4

source_name: control for 77_PCB_100%


title: PCB153 250 µM sample 5

source_name: control for 78_PCB_100%


title: Patient 8 Normal

description: Adjacent Normal from Patient 8


title: PCB153 250 µM sample 3

source_name: control for 76_PCB_100%


title: Patient 51 Normal

description: Adjacent Normal from Patient 51


title: 4T1_rep2

city: lyon

first: didier

last: auboeuf

address: 28 rue Laenec

country: France

institute: inserm

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.
Probe group file used in analysys: MoEx-1_0-st-v1.r2.pgf

organism: Mus musculus

source_name: 4T1 breast primary tumor

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

growth_protocol: 67NR, 168FARN, 4T07, and 4T1 cells were cultured in medium supplemented with 10% FBS (Fetal Bovine Serum) in a CO2 humidified chamber at 37 °C. Three-month-old female BALB/c mice from Janvier Laboratory were used for cell line injection. 67NR, 168FARN, 4T07, and 4T1 cells (5 × 105) were harvested, rinsed in FBS-free medium, and injected into the fourth mammary fat pad in 100 µl of PBS. 8 mice were injected with 67NR cells, 11 mice were injected with 168FARN cells, 15 mice were injected with 4T07 cells, and 13 were injected mice with 4T1 cells. Primary tumors were excised once the average primary tumor size in each group reached 1- to 2-cm in size (measured at the largest dimension).

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: not applicable

tag: tissue type

value: primary breast tumor

tag: tumor stage


title: 4T1_rep1


title: 4T1_rep3


title: PCB153 250 µM sample 1

source_name: control for 74_PCB_100%


title: PCB153 25 µM sample 3

source_name: control for 76_PCB_10%


title: AFB1 1.25 mM sample 5

source_name: control for 83_AFB1_1%


title: PCB153 25 µM sample 5

source_name: control for 78_PCB_10%


title: PCB153 25 µM sample 2

source_name: control for 75_PCB_10%


title: 4T07_rep2

source_name: 4T07 breast primary tumor


title: 168FARN_rep1

source_name: 168FARN breast primary tumor


title: AFB1 1.25 mM sample 3

source_name: control for 81_AFB1_1%


title: 4T07_rep3


title: AFB1 1.25 mM sample 4

source_name: control for 82_AFB1_1%


title: PCB153 25 µM sample 1

source_name: control for 74_PCB_10%


title: 168FARN_rep3


title: 67NR_rep2

source_name: 67NR breast primary tumor


title: Adipocytes Suz12 ChIP-chip

city: Boston

first: Peter

last: Kharchenko

state: MA

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: Adipocytes, Suz12 ChIP-chip

hyb_protocol: Standard Nimblegen Hybridization protocol

scan_protocol: Standard Nimblegen Scan protocol

data_processing: Calculated log2 intensity ratios from raw intensity values

source_name: Adipocytes Suz12 ChIP

label_protocol: Standard Nimblegen ChIP labelling protocol

extract_protocol: Cells were either pretreated with detergent for pre-extraction of proteins from the chromatin or directly crosslinked with 1% formaldehyde for 10 min at room temperature. The ChIP protocol by Agilent was followed. After purification, the DNA was amplified with the Whole Genome Amplification Kit (Sigma) for 2 rounds.

value: Adipocytes

tag: sample type

value: Adipocytes Suz12 ChIP

source_name: Adipocytes Input chromatin

value: Adipocytes Input chromatin


title: 4T07_rep1


title: 67NR_rep3


title: IFN-gamma 1ng/ml 2h + IL-6 50U/ml 1h CT Exp15

city: Edmonton

first: Branko

last: Braam

department: Medicine / Nephrology

country: Canada

institute: Univ. of Alberta

hyb_protocol: According to Beadchip array manufacturer's protocol.

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472449_MRa16.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IFN-gamma+IL6

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: 1 day before the experiment, MCDB-131 medium supplemented with pen/strep 1%, hEGF 0.1%, hydrocortisone 0.1%, L-glutamine 5% and 10% FCS was replaced with MCDB-131 containing 0.5% FCS and pen/strep 1%.

extract_protocol: mRNA was isolated from monocytes using Trizol reagent (Invitrogen/Gibco, USA) according to the manufacturer’s instruction. Subsequently, mRNA was purified with NucleoSpin® RNA II (Macherey-Nagel, Düren, Germany).

treatment_protocol: Cells were exposed to: IFNγ (1 ng/ml ) for 3 h; IFNγ (1 ng/ml) for 2 h followed by IL6 (50 U/ml) for 1 h; IL6 only (50 U/ml); or neither IFNγ nor IL6.

tag: cell line

tag: treatment

tag: experiment

tag: chip

tag: array

value: H


title: IFN-gamma 1ng/ml 2h + IL-6 0U/ml 1h CT Exp15

scan_protocol: According to Beadchip array manufacturer's protocol.

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472448_MRa15.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IFN-gamma

value: IFN-gamma

value: G


title: MSC H3K27me3 ChIP-chip

description: hESc-derived mesenchymal stem cells, H3K27me3 ChIP

source_name: MSC H3K27me3 ChIP

value: hESc-derived mesenchymal stem cell

source_name: MSC Input chromatin

value: hESc-derived mesenchymal stem cells, input chromatin


title: Adipocytes H3K27me3 ChIP-chip

description: Adipocytes, H3K27me3 ChIP-chip

source_name: Adipocytes H3K27me3 ChIP

value: Adipocytes H3K27me3 ChIP

value: Adipocytes, input chromatin


title: AFB1 1.25 mM sample 2

source_name: control for 80_AFB1_1%

value: immunotoxic


title: AFB1 1.25 mM sample 1

source_name: control for 79_AFB1_1%


title: Adipocytes MNase-digested chromatin vs. bare genomic DNA

description: MNase-digested mononucleosomal fragments from MSC cells

source_name: Adipocytes MNase-digested mononucleosomal fragments

extract_protocol: standard Nimblegen protocol

value: MNase digested chromatin

source_name: MNase-digested bare genomic DNA

value: MNase-digested bare genomic DNA


title: MSC Bmi1 ChIP-chip

description: hESc-derived mesenchymal stem cells, Bmi1 ChIP

source_name: MSC Bmi1 ChIP


title: 67NR_rep1


title: MSC MNase-digested chromatin vs. bare genomic DNA

source_name: MSC MNase-digested mononucleosomal fragments

value: MSC


title: IFN-gamma 0ng/ml 2h + IL-6 50U/ml 1h CT Exp15

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472447_MRa14.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IL6

value: F


title: Osteoblast MNase-digested chromatin vs. bare genomic DNA

source_name: Osteoblasts MNase-digested mononucleosomal fragments

value: Osteoblasts

value: MNase-digested chromatin


title: H9 ES MNase-digested chromatin vs. bare genomic DNA

source_name: H9 ES MNase-digested mononucleosomal fragments

value: H9 ES

source_name: MNase digested bare genomic

value: MNase-degested bare genomic DNA


title: 168FARN_rep2

source_name: 168FARN breast primary tumor

value: primary breast tumor


title: MDA 30.5 mM sample 4

source_name: control for 62_MDA_100%

value: PBMC

value: control

value: MDA


title: MSC Suz12 ChIP-chip

description: hESc-derived mesenchymal stem cells, Suz12 ChIP

source_name: MSC Suz12 ChIP

value: hESc-derived mesenchymal stem cell


title: IFN-gamma 0ng/ml 2h + IL-6 0U/ml 1h CT Exp15

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472446_MRa13.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, no treatment

value: E


title: MDA 30.5 mM sample 3

source_name: control for 59_MDA_100%


title: IFN-gamma 1ng/ml 2h + IL-6 0U/ml 1h CT Exp14

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472444_MRa11.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IFN-gamma

value: IFN-gamma

value: C


title: IFN-gamma 1ng/ml 2h + IL-6 50U/ml 1h CT Exp14

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472445_MRa12.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IFN-gamma+IL6

value: D


title: IFN-gamma 0ng/ml 2h + IL-6 50U/ml 1h CT Exp14

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472443_MRa10.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

value: B


title: MDA 3.05 mM sample 5

source_name: control for 63_MDA_10%

value: immunotoxic


title: IFN-gamma 1ng/ml 2h + IL-6 0U/ml 1h CT Exp4

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472440_MRa07.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

value: G


title: Adipocytes Bmi1 ChIP-chip

description: Adipocytes, Bmi1 ChIP-chip

source_name: Adipocytes Bmi1 ChIP

value: Adipocytes

value: Adipocytes Bmi1 ChIP

source_name: Adipocytes Input chromatin

value: Adipocytes, input chromatin


title: IFN-gamma 0ng/ml 2h + IL-6 0U/ml 1h CT Exp14

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472442_MRa09.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

value: A


title: MDA 30.5 mM sample 2

source_name: control for 58_MDA_100%


title: MDA 3.05 mM sample 3

source_name: control for 59_MDA_10%


title: IFN-gamma 0ng/ml 2h + IL-6 50U/ml 1h CT Exp4

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472439_MRa06.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

value: F


title: MDA 3.05 mM sample 4

source_name: control for 62_MDA_10%


title: IFN-gamma 1ng/ml 2h + IL-6 50U/ml 1h CT Exp4

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472441_MRa08.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

value: H


title: IFN-gamma 0ng/ml 2h + IL-6 0U/ml 1h CT Exp4

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472438_MRa05.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.


title: PCB153 25 µM sample 4

data_processing: Data preparations were performed in GeneSight software (BioDiscovery) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of test compound versus respective vehicle control.

source_name: control for 77_PCB_10%

value: PBMC

value: PCB


title: IFN-gamma 1ng/ml 2h + IL-6 50U/ml 1h CT ExpC05

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472437_MRa04.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.


title: MDA 3.05 mM sample 2

source_name: control for 58_MDA_10%

value: control

value: MDA


title: MDA 30.5 mM sample 5

source_name: control for 63_MDA_100%


title: 4-HNE 32.05 µM sample 5

source_name: control for 88_4-HNE_10%


title: IFN-gamma 0ng/ml 2h + IL-6 50U/ml 1h CT ExpC05

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472435_MRa02.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IL6


title: IFN-gamma 0ng/ml 2h + IL-6 0U/ml 1h CT ExpC05

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472434_MRa01.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.


title: 4-HNE 32.05 µM sample 1

source_name: control for 84_4-HNE_10%


title: 4-HNE 32.05 µM sample 4

source_name: control for 87_4-HNE_10%


title: 4-HNE 32.05 µM sample 2

source_name: control for 85_4-HNE_10%


title: 4-HNE 32.05 µM sample 3

source_name: control for 86_4-HNE_10%


title: Schuller_1-7_amino-acid-substitution_Rep1_ATH1

status: Public on Nov 18 2009

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Seeds were sterilized by incubating them at RT with 1 mL 70% EtOH/0.05% TritonX-100 for 20 min with continuous shaking, followed by incubation for 20 min in 1 mL 100% EtOH. Plants were grown on MS plates for 35 days at 21ºC. 6 autoclaved 21 ºC average, 21 ºC day, 21 ºC night 53 % average, 53 % day, 53 % night Murashige & Skoog basal salt mixture Constant light

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

extract_protocol: Qiagen RNeasy kit protocol

value: whole plant

tag: strain

tag: genome/variation

value: EMS induced mutation mutation in HDA6


title: Schuller_1-8_amino-acid-substitution_Rep2_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Schuller_1-3_double-transformant_Rep3_ATH1

source_name: Columbia


title: Schuller_1-9_amino-acid-substitution_Rep3_ATH1_rpt


title: IFN-gamma 1ng/ml 2h + IL-6 0U/ml 1h CT ExpC05

data_processing:
Raw array data were extracted using Illumina's BeadStudio software. Individual bead outliers were removed from raw bead data if signal intensity was higher or lower than median intensity plus or minus 2x median absolute deviation, respectively (T4Illumina). After outlier removal, average bead intensities were log2-transformed and quantile normalized using FlexArray version 1.2. Genes that were expressed (i.e., mean of gene intensity significant above mean of negative control intensities, T4Illumina) in at least 1 of the compared groups were subjected to Cyber t-test (FlexArray). P-value <0.05 was considered significant.

The supplementary 'GSM472436_MRa03.txt' file contains the original bead intensities as outputted by BeadArray.
Non-normalized signal intensities are available in the 'GSE19082_non-normalized_data.txt' file, which is linked to the Series GSE19082 record as a supplementary file.

source_name: HMEC-1 culture, IFN-gamma

value: IFN-gamma

value: C


title: Tatematsu_2-4_axillary-shoots-at-24-h-after-decapitation_Rep2_ATH1

description: Growth Room Commercial soil 22ºC 55%

growth_protocol: Plants were grown under continuous light at 22°C. Nonsterilized plants were grown in pots containing a 1:1 mixture of vermiculite:Jiffy mix (Sakatanotane).

value: axillary shoots


title: Tatematsu_2-2_axillary-buds-before-decapitation_Rep2_ATH1

description: Growth Room Commercial soil 22ºC 55%

growth_protocol: Under continuous light at 22°C. Nonsterilized plants were grown in pots containing a 1:1 mixture of vermiculite:Jiffy mix (Sakatanotane).

value: axillary buds


title: Schuller_1-1_double-transformant_Rep1_ATH1_rpt

description: Seeds were sterilized by incubating them at RT with 1 mL 70% EtOH/0.05% TritonX-100 for 20 min with continuous shaking, followed by incubation for 20 min in 1 mL 100% EtOH. Plants were grown on MS plates for 35 days at 21ºC. 6 autoclaved 21 ºC average, 21 ºC day, 21 ºC night 53 % average, 53 % day, 35 % night Murashige & Skoog basal salt mixture Constant light


title: Schuller_1-5_null-mutant_Rep2_ATH1


title: Schuller_1-2_double-transformant_Rep2_ATH1


title: Schuller_1-4_null-mutant_Rep1_ATH1_rpt


title: Schuller_1-6_null-mutant_Rep3_ATH1


title: Tatematsu_2-1_axillary-buds-before-decapitation_Rep1_ATH1

description: Growth Room Commercial soil 22ºC 55%


title: Synek_1-4_exo70A1-2_Rep2_ATH1

description: Sterilized seeds are stored for 3 days in water at 4ºC. 3 min in 70% ethanol; 2x 5 min in 10% commercial bleach under shaking; 3x rinse in sterile distilled water Seedlings were grown vertically on 1.6% agar in square plates (12x12 cm). Plants were grown in a climate chamber at 22ºC under constant light. 1.6 75 seeds per plate (12x12 cm) in 3 rows 22 ºC average, 22 ºC day, 22 ºC night 65 % average, 65 % day, 65 % night Murashige & Skoog basal salt mixture Constant light

tag: developmental stage

value: 1.0 week

value: exo70A1 mutant


title: Synek_1-3_exo70A1-2_Rep1_ATH1


title: Synek_1-1_Col-0_Rep1_ATH1


title: Tatematsu_2-3_axillary-shoots-at-24-h-after-decapitation_Rep1_ATH1

description: Growth Room Commercial soil 22ºC 55%


title: Wang_1-7_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep2_ATH1

description: Seeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood. Individual component stock autoclaved separately; FeEDTA filter-sterilized

growth_protocol: Arabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.

value: 10 days

value: shoots


title: Wang_1-8_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep2_ATH1


title: Wang_1-6_Wild-type-Col-250-micromolar-KNO3-20-min-shoots_Rep1_ATH1


title: Rylott_1-6_DMF-treated-control-seedlings_Rep3_ATH1

description: Seeds were stratified for three days at 4 ºC in the dark on agar plates containing half strength Murashige and Skoog medium with 20 mM sucrose. Seeds were sterilized using Conclor disinfectant tablets. One tablet was dissolved in 14 ml of dH20 with 2-3 drops of 1% Tween 20, then 5 ml of this solution added to 45 ml of 95% ethanol. Any precipitate was allowed to settle, then 1 ml of the ethanol/ Conchlor solution was added to each Eppendorf tube of seeds. The tubes were shaken for five minutes then the Conchlor solution removed and the seeds washed six times with 95% ethanol and the seeds air-dried. Gandia-Herrero F, Lorenz A, Larson T, Graham I, Bowles D, Rylott E, Bruce N. Detoxification of the explosive 2,4,6-trinitrotoluene in Arabidopsis- discovery of bifunctional O- and C-glucosyltransferases 2008, The Plant Journal (In Press). Growth Room Agar 20ºC 75% Murashige & Skoog basal salt mixture 20 mM Sucrose (pre autoclave) and 1 x filter-sterilized Gamborg's vitamin solution (post autoclave) added.

growth_protocol: Seeds on plates were transferred to 125 uM.m-1.s-2 light, 16 h photoperiod, at 20 - 18 oC day and night temperature for 24 h, then ten seedlings transferred to a 500 ml conical flask containing 100 ml 1/2MS medium, 20 mM sucrose and 1 x Gamborg's vitamin solution with 130 rpm, 20 uM.m-1.s-2 light for 13 days. The flask was dosed with 60 ul dimethyl formamide (DMF). After 6 h, RNA was extracted.

tag: treatment group

value: DMF-treated-control-seedlings

value: 1.05 weeks

tag: stock code


title: Wang_1-3_WT-Col-250-micromolar-KCl-20-min-roots_Rep2_ATH1

value: Roots


title: Rylott_1-5_DMF-treated-control-seedlings_Rep2_ATH1


title: Wang_1-2_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep1_ATH1


title: Wang_1-5_Wild-type-Col-250-micromolar-KCL-20-min-shoots_Rep1_ATH1


title: Rylott_1-3_TNT-treated-seedlings_Rep3_ATH1

growth_protocol: Seeds on plates were transferred to 125 uM.m-1.s-2 light, 16 h photoperiod, at 20 - 18 oC day and night temperature for 24 h, then ten seedlings transferred to a 500 ml conical flask containing 100 ml 1/2MS medium, 20 mM sucrose and 1 x Gamborg's vitamin solution with 130 rpm, 20 uM.m-1.s-2 light for 13 days. The flask was dosed with 60 uM TNT dissolved in 60 ul dimethyl formamide (DMF). After 6 h, RNA was extracted.

value: TNT-treated-seedlings


title: Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep2_ATH1


title: Wang_1-1_WT-Col-250-micromolar-KCl-20-min-roots_Rep1_ATH1


title: Xoconostle_2-5_rli-2_Rep2_ATH1

description: We sterilized the seeds using ethanol 50% for 10 minutes. Growth chamber Commercial soil 4 plants/pot 4in2 70% 26ðC Hoagland's No.2 basal salt mixture We used the whole plant. Once extracted carefully from the soil, the root was rinsed with distilled water in order to remove the soil.

growth_protocol: Seeds were sterilized, mixed with agarose 0.01% and dropped onto prewet sunshine mix soil. Trays were covered until plantelets appeared.

value: 1.14 weeks

value: RLI T-DNA insertion mutant


title: Xoconostle_2-6_rli-3_Rep3_ATH1


title: Rylott_1-1_TNT-treated-seedlings


title: Rylott_1-2_TNT-treated-seedlings_Rep2_ATH1


title: Xoconostle_2-4_rli-1_Rep1_ATH1


title: Mugford_1-6_ab-double-knockout_Rep3_ATH1

description: Seeds were kept at 4 degrees centigrade in water for 3 days prior to sowing Growth Room Commercial soil Grown in P40 trays, each cell was occupied 60% 22ðC Total RNA was extracted from whole rosettes from 5 week old ab mutant plants grown in 10h day (before bolting). Each sample was a pool of 10 rosettes.

source_name: salk_053427 crossed with salk_093072

growth_protocol: The seeds were kept in water for 3 days at 4 degrees centigrade prior to sowing. Seeds were placed individually on compost and placed in a controlled environment room (CER). The growth regime was 10h light 14h dark, 22 degrees centigrade with 60% humidity. The plants were watered every day. After 5 weeks growth in the CER, the rosettes were harvested by cutting the plant at the top of the root and freezing immediately in liquid nitrogen. Harvesting was done at 12 noon, 4 hours after the lights had come on. Ten rosettes were pooled for each replicate, and three replicates were harvested.

value: 35 days

value: whole rosette

value: N55347 crossed with N593072

value: double mutant APK1/APK2


title: Xoconostle_2-2_WT2_Rep2_ATH1

value: 3.20 weeks

value: whole plant


title: Rylott_1-4_DMF-treated-control-seedlings_Rep1_ATH1

description: seeds were stratified for three days at 4 ºC in the dark on agar plates containing half strength Murashige and Skoog medium with 20 mM sucrose. Seeds were sterilized using Conclor disinfectant tablets. One tablet was dissolved in 14 ml of dH20 with 2-3 drops of 1% Tween 20, then 5 ml of this solution added to 45 ml of 95% ethanol. Any precipitate was allowed to settle, then 1 ml of the ethanol/ Conchlor solution was added to each Eppendorf tube of seeds. The tubes were shaken for five minutes then the Conchlor solution removed and the seeds washed six times with 95% ethanol and the seeds air-dried. Gandia-Herrero F, Lorenz A, Larson T, Graham I, Bowles D, Rylott E, Bruce N. Detoxification of the explosive 2,4,6-trinitrotoluene in Arabidopsis- discovery of bifunctional O- and C-glucosyltransferases 2008, The Plant Journal (In Press). Growth Room Agar 20ºC 75% Murashige & Skoog basal salt mixture 20 mM Sucrose (pre autoclave) and 1 x filter-sterilized Gamborg's vitamin solution (post autoclave) added.


title: MDA 3.05 mM sample 1

source_name: control for 56_MDA_10%

tag: cell type

value: PBMC

tag: agent

value: control

value: MDA

tag: dose

tag: concentration

value: immunotoxic


title: Mugford_1-4_ab-double-knockout_Rep1_ATH1

tag: tissue


title: Xoconostle_2-3_WT3_Rep3_ATH1


title: Mugford_1-1_Col0-control_Rep1_ATH1

description: Seeds were kept at 4 degrees centigrade in water for 3 days prior to sowing Growth Room Commercial soil Grown in P40 trays, each cell was occupied 60% 22ðC Total RNA was extracted from whole rosettes from 5 week old plants grown in 10h day (before bolting). Each sample was a pool of 10 rosettes. There are three replicates, and two genotypes WT and ab.


title: Mugford_1-2_Col0-control_Rep2_ATH1


title: Mugford_1-5_ab-double-knockout_Rep2_ATH1


title: Xoconostle_2-1_WT1_Rep1_ATH1


title: Riha_1-3_pad4-1-mutant_Rep2_ATH1

description:
4ðC 24 hrs  1. Seeds were stratified at 4ðC for 24 hrs at wet filter paper
2. Seeds were transferred to the soil and grown under high humidity (~95%) at 16/8 light/dark photoperiod for two weeks.
3. Humidity was decreased to ~70% and plants were grown for additional three weeks before RNA was extracted (16/8 dark/light, 22ðC).  5 plants per 100 sq cms 22 ðC average, 22 ðC day, 22 ðC night 70% % average, 75% % day, 65% % night

source_name: phytoalexin deficient

extract_protocol: Qiagen RNAeasy kit protocol

value: 3.90 weeks

value: leaves

value: Col


title: MDA 30.5 mM sample 1

source_name: control for 56_MDA_100%

tag: immunotoxicity


title: Mugford_1-3_Col0-control_Rep3_ATH1


title: Riha_1-4_pad4-1-mutant_Rep3_ATH1


title: Riha_1-2_pad4-1-est1b-1-doublemutant_Rep1_ATH1

source_name: SALK_073354 pad4-1 double mutant

value: 5.10 weeks

value: developed rosette leaves

value: knock out mutation in At5g19400,At3g52430


title: Riha_1-5_pad4-1-est1b-1-doublemutant_Rep2_ATH1


title: Baubec_1-8_mutant-line1135_Rep2_ATH1

description:
Seeds were dried after harvesting and cold-treated for minimum 7 days at 4°C  6 minutes shaking in 5% hypochloric acid, 0.05% Tween-80 solution. Subsequent washes with ddH2O (3x) and over night drying.  Cold treated seeds were surface-sterilized in 5% hypochloric acid and 0,05% Tween-80 for 6 minutes, washed and air-dried overnight. 50 seeds were sawn in a regular matrix on petri dishes containing semisolid germination medium with 0.8% agar and grown for 17 days in Percival growth chambers at 16h light/8h dark cycles and 21°C.  8 50/plate 21 °C average, 21 °C day, 21 °C night ~100% % average, ~100% % day, ~100% % night
Own medium: MS macro 50ml; B5 micro 1ml; ammonium iron citrate 50mg; sucrose 10g; MES 350mg; 8% Agar 450ml

value: T-DNA knock out mutation


title: Baubec_1-1_WT-control_Rep1_ATH1


title: Baubec_1-4_mutant-line774_Rep1_ATH1


title: Baubec_1-6_mutant-line774_Rep3_ATH1


title: Control 2 (127.Control2)

status: Public on Nov 17 2009

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

data_processing: Standard Illumina processing protocol

label: Cy3, Cy5

source_name: Control 2 (127.Control2)

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated from white blood cells by standard procedures

tag: gender

value: female

tag: age

tag: ethnicity

value: White

value: white blood cell


title: DM twin (129.DM)

source_name: DM twin (129.DM)


title: Baubec_1-5_mutant-line774_Rep2_ATH1


title: Riha_1-1_pad4-1-mutant_Rep1_ATH1


title: Baubec_1-2_WT-control_Rep2_ATH1


title: Control 2 (129.Control2)

source_name: Control 2 (129.Control2)


title: Baubec_1-9_mutant-line1135_Rep3_ATH1


title: Control 2 (103.Control2)

source_name: Control 2 (103.Control2)


title: DM twin (127.DM)

source_name: DM twin (127.DM)


title: Baubec_1-7_mutant-line1135_Rep1_ATH1


title: Riha_1-6_pad4-1-est1b-1-doublemutant_Rep3_ATH1


title: Healthy twin (129.Healthy)

source_name: Healthy twin (129.Healthy)


title: Control 1 (129.Control1)

source_name: Control 1 (129.Control1)


title: Control 1 (103.Control1)

source_name: Control 1 (103.Control1)


title: Healthy twin (103.Healthy)

source_name: Healthy twin (103.Healthy)


title: DM twin (103.DM)

source_name: DM twin (103.DM)


title: Baubec_1-3_WT-control_Rep3_ATH1


title: Control 1 (127.Control1)

source_name: Control 1 (127.Control1)


title: Healthy twin (127.Healthy)

source_name: Healthy twin (127.Healthy)


title: Control 2 (33.Control2)

source_name: Control 2 (33.Control2)

value: male


title: Control 1 (33.Control1)

source_name: Control 1 (33.Control1)


title: DM twin (33.DM)

source_name: DM twin (33.DM)


title: Healthy twin (33.Healthy)

source_name: Healthy twin (33.Healthy)


title: Control 2 (16.Control2)

source_name: Control 2 (16.Control2)

value: Black/AA


title: Control 1 (16.Control1)

source_name: Control 1 (16.Control1)


title: Healthy twin (16.Healthy)

source_name: Healthy twin (16.Healthy)


title: DM twin (16.DM)

source_name: DM twin (16.DM)


title: RA twin (80.RA)

source_name: RA twin (80.RA)


title: Healthy twin (80.Healthy)

source_name: Healthy twin (80.Healthy)


title: RA twin (85.RA)

source_name: RA twin (85.RA)


title: Control 2 (80.Control2)

source_name: Control 2 (80.Control2)


title: Control 1 (80.Control1)

source_name: Control 1 (80.Control1)


title: Healthy twin (85.Healthy)

source_name: Healthy twin (85.Healthy)


title: Control 1 (12.Control1)

source_name: Control 1 (12.Control1)


title: Control 2 (12.Control2)

source_name: Control 2 (12.Control2)


title: RA twin (12.RA)

source_name: RA twin (12.RA)


title: Control 2 (4.Control2)

source_name: Control 2 (4.Control2)


title: Healthy twin (12.Healthy)

source_name: Healthy twin (12.Healthy)


title: Healthy twin (86.Healthy)

source_name: Healthy twin (86.Healthy)


title: Control 2 (85.Control2)

source_name: Control 2 (85.Control2)


title: RA twin (86.RA)

source_name: RA twin (86.RA)


title: Control 1 (85.Control1)

source_name: Control 1 (85.Control1)


title: Control 1 (86.Control1)

source_name: Control 1 (86.Control1)


title: Healthy twin (4.Healthy)

source_name: Healthy twin (4.Healthy)


title: Control 1 (4.Control1)

source_name: Control 1 (4.Control1)


title: Control 2 (86.Control2)

source_name: Control 2 (86.Control2)


title: Control 1 (20.2.Control1)

source_name: Control 1 (20.2.Control1)


title: Control 2 (20.2.Control2)

source_name: Control 2 (20.2.Control2)


title: Healthy twin (20.2.Healthy)

source_name: Healthy twin (20.2.Healthy)


title: RA twin (4.RA)

source_name: RA twin (4.RA)


title: Synek_1-2_Col-0_Rep2_ATH1

value: 1.0 week

value: whole plant


title: SLE twin (20.2.SLE)

source_name: SLE twin (20.2.SLE)


title: Control 2 (29.Control2)

source_name: Control 2 (29.Control2)


title: Control 1 (29.Control1)

source_name: Control 1 (29.Control1)


title: Healthy twin (29.Healthy)

source_name: Healthy twin (29.Healthy)


title: SLE twin (11.SLE)

source_name: SLE twin (11.SLE)


title: Control 1 (11.Control1)

source_name: Control 1 (11.Control1)


title: Control 2 (34.Control2)

source_name: Control 2 (34.Control2)


title: SLE twin (20.1.SLE)

source_name: SLE twin (20.1.SLE)

value: Hispanic


title: Control 1 (20.1.Control1)

source_name: Control 1 (20.1.Control1)


title: Control 2 (20.1.Control2)

source_name: Control 2 (20.1.Control2)


title: Control 1 (34.Control1)

source_name: Control 1 (34.Control1)


title: Healthy twin (11.Healthy)

source_name: Healthy twin (11.Healthy)


title: SLE twin (29.SLE)

source_name: SLE twin (29.SLE)


title: Substantia Nigra left animal 6

type: other

city: Roskilde

first: Thomas

last: Werge

address: Boserupvej 2

department: Institute of biological Psychiatry

country: Denmark

institute: Psychiatric Center, Sct. Hans Hospital

description: Biological replicate 1 of 4.

hyb_protocol: Samples were hybridized against the reference overnight to NCode™ Multi-Species miRNA Microarrays (Invitrogen, Carlsbad, CA, USA) using the NCode™ Multi-Species miRNA Microarrays Kit (Invitrogen, Carlsbad, CA, USA) following the instructions given by the manufacturer. Arrays were then hybridized on a MAUI hybridization station (BioMicro Systems, Inc, Salt Lake City, UT, USA) with Alexa Fluor® 3 and Alexa Fluor® 5 capture reagents and washed.

scan_protocol: Scanned using an Agilent DNA microarray scanner. Images were processed using GenePix Pro software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: Background adjusted using “normexp” with an offset of 50. Print-tip-loess normalization was used to adjust data within each array and subsequent Gquantile normalization to allow comparisons between arrays. Thelimma package from BioConductor was used in R.

label: Alexa Fluor® 5 fluorophor

molecule: other

source_name: Substantia Nigra left hand side

label_protocol: 600 ng microRNA sample were poly-A tailed and tagged with the sequence tag for the Alexa Fluor® 5 fluorophor using the NCode™ miRNA Labeling System (Invitrogen). Universal reference were labeled with Alexa Fluor® 3.

growth_protocol: Animals were kept under normal day/night and dairy conditions with unlimited access to food and water.

extract_protocol: RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's instructions

value: Sprague-Dawley

value: Adult

value: substantia Nigra

tag: hemisphere

value: Left

tag: molecule

value: microRNA

source_name: universal brain reference

tag: sample type

value: Invitrogen universal brain reference small RNA (>200 nt in length)


title: Substantia Nigra left animal 10

description: Biological replicate 3 of 4

tag: strain


title: Substantia Nigra left animal 8

description: Biological replicate 2 of 4.


title: Substantia Nigra right animal 8

description: Biological replicate 2 of 4.

source_name: Substantia Nigra right hand side

value: Right


title: Substantia Nigra right animal 11

description: Biological replicate 4 of 4.


title: Substantia Nigra right animal 6

description: Biological replicate 1 of 4.


title: Healthy twin (34.Healthy)

source_name: Healthy twin (34.Healthy)


title: Substantia Nigra right animal 10

description: Biological replicate 3 of 4


title: Substantia Nigra left animal 11

description: Biological replicate 4 of 4.


title: Healthy twin (20.1.Healthy)

source_name: Healthy twin (20.1.Healthy)


title: Hypothalamus left animal 8

description: Biological replicate 3 of 4

source_name: Hypothalamus left hand side

value: hypothalamus


title: Hypothalamus right animal 11

description: Biological replicate 4 of 4.

source_name: Hypothalamus right hand side


title: Hypothalamus right animal 8

description: Biological replicate 3 of 4


title: Hypothalamus left animal 10

description: Biological replicate 2 of 4.


title: Hypothalamus left animal 6

description: Biological replicate 1 of 4.


title: Hippocampus left animal 5

description: Biological replicate 4 of 4.

source_name: Hippocampus left hand side

value: hippocampus


title: SLE twin (34.SLE)

source_name: SLE twin (34.SLE)

value: female


title: Hypothalamus right animal 6

description: Biological replicate 1 of 4.


title: Hippocampus right animal 5

description: Biological replicate 4 of 4.

source_name: Hippocampus right hand side


title: Hippocampus right animal 2

description: Biological replicate 1 of 4.


title: Hippocampus left animal 3

description: Biological replicate 2 of 4.


title: Hypothalamus left animal 11

description: Biological replicate 4 of 4.


title: Hippocampus right animal 4

description: Biological replicate 3 of 4


title: Hippocampus right animal 3

description: Biological replicate 2 of 4.


title: Hippocampus left animal 4

description: Biological replicate 3 of 4


title: Cerebellum right animal 4

description: Biological replicate 3 of 4

source_name: Cerebellum right hand side

value: cerebellum


title: Cerebellum left animal 4

description: Biological replicate 3 of 4

source_name: Cerebellum left hand side


title: Cerebellum left animal 3

description: Biological replicate 2 of 4.


title: Cerebellum right animal 3

description: Biological replicate 2 of 4.


title: Hypothalamus right animal 10

description: Biological replicate 2 of 4.


title: Cerebellum right animal 2

description: Biological replicate 1 of 4.


title: Cerebellum right animal 5

description: Biological replicate 4 of 4.


title: Amygdala right animal 11

description: Biological replicate 4 of 4.

source_name: Amygdala right hand side

value: amygdala


title: Amygdala left animal 11

description: Biological replicate 4 of 4.

source_name: Amygdala left hand side

value: male


title: Amygdala left animal 8

description: Biological replicate 3 of 4


title: Amygdala left animal 7

description: Biological replicate 2 of 4.


title: Cerebellum left animal 5

description: Biological replicate 4 of 4.


title: Hippocampus left animal 2

description: Biological replicate 1 of 4.


title: Cerebellum left animal 2

description: Biological replicate 1 of 4.


title: Amygdala right animal 8

description: Biological replicate 3 of 4


title: Amygdala right animal 7

description: Biological replicate 2 of 4.


title: Amygdala right animal 6

description: Biological replicate 1 of 4.


title: Amygdala left animal 6

description: Biological replicate 1 of 4.

growth_protocol: Animals were kept under normal day/night and dairy conditions with unlimited access to food and water. Animals were not exposed to experimental manipulations.


title: leaf root loop 12_nzr vs chl

city: Palmerston North

first: Claudia

last: Voelckel

address: Riddet Road

department: Allan Wilson Centre for Molecular Ecology and Evolution

country: New Zealand

institute: Massey University

description: leaf root loop 12_nzr vs chl

hyb_protocol: According to Janssen B, Thodey K, Schaffer R, Alba R, Balakrishnan L, Bishop R, Bowen J, Crowhurst R, Gleave A, Ledger S et al: Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biology 2008, 8(1):16. Labelled samples were hybridised to the microarray slides in an Amersham Lucidea Automated Slide Processor. Slides were pre-washed with 2 × SSC, 0.3% SDS. Samples were injected into the slide chamber together in 3 × SSC, 0.2% SDS, 6% liquid blocking reagent (RPN3601, GE Healthcare, Chalfont St Giles, United Kingdom). Chambers were heated to 45°C and mixed overnight. After hybridisation, arrays were washed with 2 × SSC, 0.3% SDS for 1.2 min and cooled to 30°C, then washed again with 2 × SSC, 0.3% SDS for 1.2 min, 2 × SSC, 0.3% SDS for 2.4 minutes, 0.5 × SSC, 0.2% SDS for 2.4 min (twice) and then once with 0.5 × SSC.

scan_protocol: According to Janssen B, Thodey K, Schaffer R, Alba R, Balakrishnan L, Bishop R, Bowen J, Crowhurst R, Gleave A, Ledger S et al: Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biology 2008, 8(1):16. Slides were dried by centrifugation and scanned on a GenePix 4000 B Scanner (Axon Instruments). Raw data from scanning of the array slides were captured using GenePix4 (Axon Instruments) and automated spot alignment was augmented with manual checking of each slide to remove substandard spots.

data_processing: Data analysis was done with R-based package limma. Background correction was done using 'method=mormexp' and 'offset=50', within array normalization was done using 'method=printtiploess'. Between array normalization was done using 'method=quantile'. Linear models were fitted to normalized log2 cy5/cy3 ratios for 'contrasts of interest' using a design and contrast matrix as required by the 'limma' procedure. We were interested in comparing a) aboveground tissues of the three fruiting species (contrasts: chl vs exl, chl vs nzl, exl vs nzl, chl vs exl+nzl, exl vs chl+nzl, nzl vs chl+exl), b) aboveground tissues of the two rosette stage species (contrast: fal vs enl) and c) roots of all five species (contrasts: chr vs exr, chr vs nzr, chr vs far, chr vs enr, exr vs nzr, exr vs far, exr vs enr, nzr vs far, nzr vs enr, far vs enr). Results for a) are part of a manuscript prepared for submission to BMC Evolutionary Biology. Results for b) and c) are currently being written up.

organism: Pachycladon novaezelandiae

label_protocol: According to Janssen B, Thodey K, Schaffer R, Alba R, Balakrishnan L, Bishop R, Bowen J, Crowhurst R, Gleave A, Ledger S et al: Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biology 2008, 8(1):16. Reverse transcription (RT) of mRNA was performed using an oligodT23V primer and with the incorporation of amino-allyl deoxyuridine (aadU, Sigma-Aldrich, Milwaulke, WI). Each RT reaction contained 50 μg total RNA and 10 units Transcriptor Reverse Transcriptase (Roche, Indianapolis, IN) together with 10 μM oligodT23V, 1× first strand buffer (Roche, Indianapolis, IN), 6.6 μM DTT, and nucleotides at 0.5 mM for dA, dG, dC and 0.25 mM for dT and aadU in a total volume of 30 μL. The RNA and oligodT23V were incubated at 70°C for 10 min and cooled to 4°C for 5min. First strand buffer, DTT, nucleotides and enzyme were added and the reaction was incubated for 30 min at 42°C. 1 μL of 20 mM EDTA was added to stop the reaction, and RNA degraded by addition of 1 μL 500 mM NaOH and the sample heated to 70°C for 10 min then neutralised with 1 μL 500 mM HCl. The cDNA was ethanol precipitated and resuspended in 5 μL 100 mM Na2CO3 (pH 9.0). 5 μL Cy3 or Cy5 (Amersham Biosciences, Buckinghamshire, England) in DMSO was added and the sample incubated at room temperature for 2 hr in the dark. Unreacted dye was quenched by addition of 10 μL 4 M hydroxylamine (Sigma, St Louis, MO) and incubation for 10 min at room temperature in the dark. Labelled DNA was purified on PCR Clean-up Columns (Qiagen, Hilden, Germany) and paired samples were pooled. Sample absorbance at 260 nm, 550 nm and 650 nm was measured to determine the amount of labelled DNA and efficiency of Cy3 and Cy5 labelling, respectively. The PCR Clean-up Column purification was repeated once more after pooling to reduce background fluorescence.

growth_protocol: Five Pachycladon species were sampled (P. cheesemanii: accession Bob’s cove, CH; P. exile: accession: Awahokomo, EX; P. novae-zelandiae: accession Old man range, NZ; P. fastigiatum, accession Serpentine creek, FA; P. enysii, accession: Avalanche peak, PE). Seeds were stratified at 4⁰C for a week and then germinated on potting soil in early July 2007. Plants were grown in shade houses at Landcare Research (Lincoln, NZ) for seven months.

extract_protocol: RNA was isolated from approximately 200mg of aboveground tissues and root tissue of each plant using the Rneasy kit (Qiagen, Hilden, Germany). Extracted RNA was quantified and quality checked on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: In February 2008, roots and above-ground plant tissues of each plant were separately flash frozen and ground in liquid nitrogen. Ground material was partially allocated to RNA analysis and partially freeze-dried for protein and metabolite analysis. Replicate plant numbers were as follows: CH, n=12; EX, n=13; NZ, n=12; FA, n=8; EN, n=8. P. cheesemanii, P. exile and P. novae-zelandiae were grown until all three species started producing their first seeds. By sampling leaves, flowers and siliques we expected to increase the probability of capturing expression differences. P. fastigiatum and P. enysii were harvested in rosette stage to enable a valid comparison with a previous field study.

value: roots

organism: Pachycladon cheesemanii

source_name: ch_entire plant except roots

value: all above ground tissues (leaves, stems, flowers, siliques)


title: leaf root loop 8_enr vs nzl

description: leaf root loop 8_enr vs nzl

organism: Pachycladon enysii

source_name: nz_entire plant except roots


title: leaf root loop 6_exr vs enl

description: leaf root loop 6_exr vs enl

organism: Pachycladon exile

source_name: en_entire plant except roots


title: leaf root loop 5_chl vs exr

description: leaf root loop 5_chl vs exr


title: CAM E7 replicate 3

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

institute: University Hospital of Montpellier

description: We investigated vascular development and maturation in vivo by determining global gene regulation throughout the formation of the chick chorio-allantoic membrane (CAM).

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Chicken Genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

organism: Gallus gallus

source_name: chick embryo (day7) chorioallantoic membrane (CAM), replicate 3

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol'.

growth_protocol: Chick embryos were incubated at 37.8ºC and 75% humidity.

extract_protocol: CAMs were immediately snap-frozen in liquid nitrogen after excision. Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

tag: CAMs were isolated from normal embryos at developmental day E7 (= HH30)


title: leaf root loop 10_nzl vs nzr

description: leaf root loop 10_nzl vs nzr


title: CAM E5 replicate 3

source_name: chick embryo (day5) chorioallantoic membrane (CAM), replicate 3

tag: CAMs were isolated from normal embryos at developmental day E5 (= HH26)


title: CAM E7 replicate 1

source_name: chick embryo (day7) chorioallantoic membrane (CAM), replicate 1


title: CAM E5 replicate 2

source_name: chick embryo (day5) chorioallantoic membrane (CAM), replicate 2


title: leaf root loop 4_far vs chl

description: leaf root loop 4_far vs chl

organism: Pachycladon fastigiatum


title: GIST-T1 cells treated with 10 microM IM for 48 hours, Third Replicate

city: Baltimore

first: Michael

middle: F

last: Ochs

state: MD

address: 550 North Broadway, Ste 1103

department: Oncology Biostatistics

institute: Johns Hopkins University

hyb_protocol: Fragmented targets were placed on the 4xG4112a slides, assembled into a hybridization chamber (Agilent Technologies) and hybridized at 65ºC for 17 hours in a hybridization oven with rotation. Hybridized microarrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Microarrays were scanned using an Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction 9.5.3.1 software.

data_processing: Data were extracted with Agilent Feature Extraction 9.5.3.1 software.  The Agilent summary files were read into R/Bioconductor (version 2.4.1).  LOESS normalization was performed with width 0.7 and no background correction.  MA plots were reviewed together with Agilent summary files to confirm the quality of all arrays.

source_name: GIST-T1 Cell Line

label_protocol: 0.4 microgram of total RNA was reverse transcribed into first strand and second strand cDNA by MMLV-RT using an oligo dT primer (System Biosciences) that incorporated a T7 promoter sequence. The cDNA was then used as a template for in vitro transcription in the presence of T7 RNA polymerase and Cyanine labeled CTPs. The labeled cRNA was purified using RNeasy mini kit (Qiagen) and dye labeled. RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to the manufacturer's protocol.  0.828 microgram of each sample labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies).

growth_protocol: GIST T1 cells were maintained in DMEM supplemented with 10% fetal bovine serum and glutamine.  For imatinib treatment, imatinib was added directly to the cell medium at a final concentration indicated in each result.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were treated with 10 microM imatinib mesylate (IM) in growth medium

tag: cell line

value: 10 microM IM

tag: replicate

value: Third

tag: time point

value: 48 hours

source_name: Universal Human Reference RNA

tag: reference

value: Universal Human Reference RNA (Stratagene)


title: CAM E14 replicate 2

source_name: chick embryo (day14) chorioallantoic membrane (CAM), replicate 2

tag: CAMs were isolated from normal embryos at developmental day E14 (= HH40)


title: leaf root loop 7_enl vs enr

description: leaf root loop 7_enl vs enr

value: all above ground tissues (leaves)


title: leaf root loop 11_nzl vs nzr

description: leaf root loop 11_nzl vs nzr


title: CAM E10 replicate 3

source_name: chick embryo (day10) chorioallantoic membrane (CAM), replicate 3

tag: CAMs were isolated from normal embryos at developmental day E10 (=HH>35)


title: leaf root loop 9_enr vs nzl

description: leaf root loop 9_enr vs nzl

tag: tissue


title: leaf root loop 3_enl vs far

description: leaf root loop 3_enl vs far


title: CAM E14 replicate 1

source_name: chick embryo (day14) chorioallantoic membrane (CAM), replicate 1


title: CAM E5 replicate 1

source_name: chick embryo (day5) chorioallantoic membrane (CAM), replicate 1


title: CAM E14 replicate 3

source_name: chick embryo (day14) chorioallantoic membrane (CAM), replicate 3


title: GIST-T1 cells treated with 10 microM IM for 48 hours, Second Replicate

tag: agent

value: Second


title: CAM E10 replicate 2

source_name: chick embryo (day10) chorioallantoic membrane (CAM), replicate 2


title: leaf root loop 1_chl vs chr

description: leaf root loop 1_chl vs chr


title: CAM E7 replicate 2

source_name: chick embryo (day7) chorioallantoic membrane (CAM), replicate 2


title: leaf root loop 2_chr vs enl

description: leaf root loop 2_chr vs enl


title: CAM E10 replicate 1

source_name: chick embryo (day10) chorioallantoic membrane (CAM), replicate 1


title: GIST-T1 cells treated with 10 microM IM for 48 hours, First Replicate

value: First


title: root loop 10_ch vs en

description: root loop 10_ch vs en


title: root loop 5_nz vs fa

description: root loop 5_nz vs fa


title: root loop 3_ex vs nz

description: root loop 3_ex vs nz


title: root loop 6_fa vs nz

description: root loop 6_fa vs nz


title: Pichia angusta NCYC 495 leu1.1 replicate 4

city: Haren

first: Tim

last: van Zutphen

state: Groningen

address: Kerklaan 30

department: Molecular Cell Biology

institute: University of Groningen

description: Biological replicate 4 of 4. Glucose-grown Pichia angustase cells vs a shift to methanol

hyb_protocol: The agilent custom 8x15K Hansenula polymorpha (a.k.a Pichia angusta) are used for hybridization. The XDR function is used to extend the dynamic range at least with 10-fold. Agilent protocols are strictly followed for hybridization, washing, staining and scanning

scan_protocol: Agilent Technologies Scanner G2505B US23502317 Agilent feature extraction software version 9.5 protcol GE2-v5_95_Feb07 is used to generate feature extraction data.

data_processing: No background substraction and spatial detrend is used for background substraction, Linear and Lowess normalisation is applied for normalisation using default settings.

organism: Ogataea polymorpha NCYC 495 leu1.1

source_name: Glucose-grown Pichia angusta complete RNA isolate 4

label_protocol: The agilent low-input labeling kit is used to synthesize cy3 and cy5 labeled cRNA. From each RNA sample 500ng is used for the labeling experiments, 300ng labeled cRNA is used for hybridization

growth_protocol: Pichia angusta cells were extensively pre-cultivated on glucose at 37 ºC to an OD of 2.3 (660nm) prior to a shift to methanol as sole carbon source OD 0.2 for 2 hours. Four independent glucose-grown cultures were used

extract_protocol: Total RNA was extracted using phenol extracton followed by column purification

tag: carbon source

value: glucose

value: NCYC 495 leu1.1

source_name: Methanol-grown Pichia angusta complete RNA isolate 4

value: methanol


title: Pichia angusta NCYC 495 leu1.1 dye-swap of replicate 3

description: Technical replicate of 3, dye-swapped

source_name: Methanol-grown Pichia angusta complete RNA isolate 3

source_name: Glucose-grown Pichia angusta complete RNA isolate 3


title: GIST-T1 cells treated with 10 microM IM for 18 hours, Second Replicate

value: 18 hours


title: Pichia angusta NCYC 495 leu1.1 dye-swap of replicate 2

description: Technical replicate of 2, dye-swapped

source_name: Methanol-grown Pichia angusta complete RNA isolate 2

source_name: Glucose-grown Pichia angusta complete RNA isolate 2


title: Pichia angusta NCYC 495 leu1.1 replicate 3

description: Biological replicate 3 of 4. Glucose-grown Pichia angustase cells vs a shift to methanol


title: GIST-T1 cells treated with 10 microM IM for 18 hours, First Replicate


title: GIST-T1 cells treated with 10 microM IM for 12 hours, First Replicate

value: 12 hours


title: GIST-T1 cells treated with 10 microM IM for 12 hours, Third Replicate


title: root loop 2_ex vs ch

description: root loop 2_ex vs ch


title: GIST-T1 cells treated with 10 microM IM for 12 hours, Second Replicate


title: Pichia angusta NCYC 495 leu1.1 replicate 2

description: Biological replicate 2 of 4. Glucose-grown Pichia angustase cells vs a shift to methanol


title: root loop 1_ch vs ex

description: root loop 1_ch vs ex


title: root loop 8_en vs fa

description: root loop 8_en vs fa


title: GIST-T1 cells treated with 10 microM IM for 24 hours, First Replicate

value: 24 hours


title: root loop 9_en vs ch

description: root loop 9_en vs ch


title: GIST-T1 cells treated with 10 microM IM for 18 hours, Third Replicate


title: root loop 7_fa vs en

description: root loop 7_fa vs en


title: Pichia angusta NCYC 495 leu1.1 dye-swap of replicate 1

description: Technical replicate of 1, dye-swapped

source_name: Methanol-grown Pichia angusta complete RNA isolate 1

source_name: Glucose-grown Pichia angusta complete RNA isolate 1


title: GIST-T1 cells treated with 10 microM IM for 9 hours, Third Replicate

source_name: GIST-T1 Cell Line

value: 9 hours

source_name: Universal Human Reference RNA


title: GIST-T1 cells treated with 10 microM IM for 24 hours, Second Replicate


title: Pichia angusta NCYC 495 leu1.1 replicate 1

description: Biological replicate 1 of 4. Glucose-grown Pichia angustase cells vs a shift to methanol


title: Taurine vs Cysteine 1

city: Saint Paul

first: Masayuki

last: Sugawara

state: MN

address: 250 Borloug Hall, 1991 Upper Buford Circle

department: Soil, Water, and Climate

institute: University of Minnesota

hyb_protocol: Both cy3 and cy5 labeled cDNAs to be compared were mixed, dried to completion, and then resuspended in 70 ul of preheated hybridization buffer (nuclease free water:formamide:20X SSC:1% SDS = 4:2.5:2.5:1) at 42 C. After adding 0.7 ul salmon sperm DNA (10 mg/ml) to prevent non-specific binding to the array, the mixture was hybridized at 42 C for 16 to 18 h. Hybridized arrays were washed with 1X SSC, 0.2% SDS at 42 C for 6 min, and, subsequently, with 0.1X SSC, 0.2% SDS at room temperature for 6 min, and twice with 0.1X SSC at room temperature for 3 min.

scan_protocol: The arrays were scanned using an Axon GenePix 4000B scanner (Molecular Devices Corp., Sunnyvale, CA). Signal intensities were analyzed using GenePix Pro 6.0 software (Molecular Devices Corp., Sunnyvale, CA).

data_processing: All raw data GPR files produced by the scanning software, were uploaded into CARMAweb where normalization and data analysis took place. Median F635 and B635 values were used for each spot; and flagged spots were ignored. NORMEXP algorithm was used to correct background signal, LOESS for within-array normalization, and AQUANTILE for between-array standardization. For each comparison of culture growth in two different media, two replicate arrays were produced with swap-dye pattern; these were averaged as technical replicates (arithmetic mean). The normalized data set was truncated to remove control probes and those genes for which less than 33% of the data points were available. To generate lists of differentially expressed genes for each comparison, the genes with |M|≥1 and |A| ≥10% percentile range in that comparison were considered (M=log2(R/G); A =log2(R•G)). Because only two replicates were available for each comparison, statistical tests of differential expression significance were not carried out.

organism: Bradyrhizobium japonicum

source_name: B. japonicum was grown in MHM medium supplemented with 2 mM taurine.

label_protocol: 20 ug of total RNA was used for cDNA synthesis with superscript III reverse transcriptase and random hexamers (Invitrogen Corp.). After digesting the remaining RNA by RNase H (Fermentas), cDNA was purified using a Microcon YM-30 column (Millipore) and concentration was determined.

growth_protocol: Bradyrhizobium strains were grown in 100 ml AG medium (Sadowsky et al. 1987) at 30ºC to the stationary phase of growth, cells we collected by centrifugation at 10,000 xg for 10 min, and washed twice in sulfur-free minimal medium (MHM). Washed cells were resuspended in 100 ml MHM medium and incubated at 30ºC for 4 days to induce sulfur starvation.

extract_protocol: Standard hot-phenol method

treatment_protocol: Sulfur-starved Bradyrhizobium cells were inoculated into 15 ml MHM medium supplemented  with either 2 mM NaSO4, HEPES, Taurine, or cysteine to an initial OD600 nm = 0.2. Cultures were incubated at 30ºC until OD600 = 0.5 to 0.6, and 1.5 ml of cold stop solution (5 % water-saturated phenol in 95 % ethanol) was added to each culture.

value: USDA 110

source_name: B. japonicum was grown in MHM medium supplemented with 2 mM cysteine.


title: GIST-T1 cells treated with 10 microM IM for 6 hours, Third Replicate

value: 6 hours


title: GIST-T1 cells treated with 10 microM IM for 9 hours, Second Replicate


title: leaf loop 13_en vs ch

description: leaf loop 13_en vs ch

source_name: en_entire plant except roots

source_name: ch_entire plant except roots

value: all above ground tissues (leaves, stems, flowers, siliques)


title: GIST-T1 cells treated with 10 microM IM for 9 hours, First Replicate

value: 10 microM IM


title: HEPES vs Cysteine 2

source_name: B. japonicum was grown in MHM medium supplemented with 2 mM HEPES.


title: leaf loop 12_en vs fa

description: leaf loop 12_en vs fa

source_name: fa_entire plant except roots


title: GIST-T1 cells treated with 10 microM IM for 4 hours, Third Replicate

value: Third

value: 4 hours


title: leaf loop 11_fa vs en

description: leaf loop 11_fa vs en


title: HEPES vs Taurine 2


title: GIST-T1 cells treated with 10 microM IM for 6 hours, First Replicate

value: Universal Human Reference RNA (Stratagene)


title: HEPES vs Cysteine 1


title: Taurine vs Cysteine 2


title: GIST-T1 cells treated with 10 microM IM for 6 hours, Second Replicate


title: GIST-T1 cells treated with 10 microM IM for 4 hours, Second Replicate


title: Sulfate vs Cysteine 2

source_name: B. japonicum was grown in MHM medium supplemented with 2 mM sulfate.


title: HEPES vs Taurine 1


title: leaf loop 8_fa vs nz

description: leaf loop 8_fa vs nz

value: all above ground tissues (leaves)

source_name: nz_entire plant except roots


title: leaf loop 10_fa vs nz

description: leaf loop 10_fa vs nz


title: Pichia angusta NCYC 495 leu1.1 dye-swap of replicate 4

description: Technical replicate of 4 (2-3), dye-swapped

source_name: Methanol-grown Pichia angusta complete RNA isolate 4

source_name: Glucose-grown Pichia angusta complete RNA isolate 4


title: leaf loop 7_nz vs fa

description: leaf loop 7_nz vs fa


title: GIST-T1 cells treated with 10 microM IM for 4 hours, First Replicate


title: leaf loop 9_nz vs fa

description: leaf loop 9_nz vs fa


title: GIST-T1 cells treated with 10 microM IM for 2 hours, Third Replicate

value: 2 hours


title: Sulfate vs HEPES 1


title: Sulfate vs Cysteine 1


title: leaf loop 6_nz vs ex

description: leaf loop 6_nz vs ex

source_name: ex_entire plant except roots


title: Sulfate vs HEPES 2


title: Sulfate vs Taurine 1


title: leaf loop 5_ex vs nz

description: leaf loop 5_ex vs nz


title: leaf loop 3_ex vs nz

description: leaf loop 3_ex vs nz


title: leaf loop 14_ch vs en

description: leaf loop 14_ch vs en


title: Sulfate vs Taurine 2


title: leaf loop 4_nz vs ex

description: leaf loop 4_nz vs ex


title: GIST-T1 cells without IM, Third Replicate

value: 0 hours


title: GIST-T1 cells treated with 10 microM IM for 2 hours, First Replicate

value: First


title: leaf loop 1_ch vs ex

description: leaf loop 1_ch vs ex


title: leaf loop 2_ex vs ch

description: leaf loop 2_ex vs ch


title: GIST-T1 cells without IM, Second Replicate

value: Second


title: GIST-T1 cells without IM, First Replicate


title: root loop 4_nz vs ex

description: root loop 4_nz vs ex

value: roots


title: GIST-T1 cells treated with 10 microM IM for 2 hours, Second Replicate


title: Endothelial Cells, Reversing Flow, Replicate 3

status: Public on Nov 16 2009

city: Snellville

first: Marcie

middle: R

last: Williams

state: GA

address: 2300 Country Walk 3427

department: Biomedical Engineering

institute: Georgia Institute of Technology

description: Gene expression after exposure to reversing flow for 24 hours.

hyb_protocol: Cy3-labeled cRNA for each sample was hybridized to a 44k Whole Human Genome Microarray (Agilent) according to the manufacturer’s instructions.

scan_protocol: Slides were dried under nitrogen and scanned on an Agilent DNA Microarray Scanner.

data_processing: The scanned images were amalyzed with Feature Extraction Software from Agilent and data was further analyzed using Genespring GX.

label_protocol: RNA was linearly amplified to cRNA using Cy3 labeled CTP and a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacturer’s instructions.

growth_protocol: HUVEC (passage 3-5) were grown to confluence on glass slides.

extract_protocol: Immediately after exposure to shear stress total RNA was extracted using TRI-zol (Invitrogen); RNA was further purified with DNase (Qiagen) and RNeasy MinElute Cleanup Kit (Qiagen), according to manufacturers’ instructions. RNA quantity and quality were assessed by loading 1 ml of sample RNA onto a RNA 6000 Nano chip (Agilent) and analyzing with an Agilent 2100 Bioanalyzer to determine the amount and integrity of RNA recovered.  Samples having an RNA Integrity Number of 9.5 or greater were used for microarray experiments.

treatment_protocol: HUVEC were mounted in a parallel plate flow chamber and exposed to one of four conditions for 24 hours.

value: Human Umbilical Vein Endothelial Cells


title: JL00002_SDC3_YPT47_MXemb_ChIP_replicate2

city: Chapel Hill

first: Jason

middle: D

last: Lieb

state: NC

address: 408 Fordham Hall, CB# 3280

department: Biology

institute: University of North Carolina at Chapel Hill

description: SDC-3 ChIP-chip from YPT47 X-V fusion strain mixed stage embryos. An affinity purified rabbit polyclonal antibody to SDC-3 was used.

hyb_protocol: ChIP-chip_label_hyb_nimblegen_v1. DNA was labeled and hybridized to C. elegans tiling array by Roche NimbleGen according to the protocol described in chapter 3 and 4 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, Amplified IP or input DNA was either labeled with Cy5 or Cy3 in the presence of Klenow fragment. The reaction was stopped by the addition of EDTA. Labeled DNA was recovered by isopropanol precipitation, and dried. The labeled DNA was hybridized to C. elegans tiling array for 16 - 20 hours at 42?C.

scan_protocol: ChIP-chip_scanning_nimblegen_v1. Array scanning and raw data extraction were performed at Roche NimbleGen, according to the protocol described in chapter 5 and 6 of the NimbleGen Arrays User?s Guide ChIP-chip Analysis, Version 3.1, 27 May 2008. Briefly, array signal was scanned by using a GenePix 4000B Scanner with associated software and saved as .tif files of the 532nm and 635nm images individually. Raw signal intensities of the images were extracted  and saved as .pair files by using NimbleScan software according to the NimbleScan v2.4 User?s Guide.

data_processing: ChIP-chip_normalization_standard_zscore_v2. First, the ratio of intensity from sample/reference channel was transformed to log2 space. Second, z-scores were obtained by standardizing the data for each IP by subtracting the mean and dividing by the standard deviation of all probes. Z-scores were calculated or probes within each physical array and then concatenated for a full-genome dataset (where multiple physical arrays cover the full genome). Replicates were then combined by taking the median/mean probe z-score.

organism: Caenorhabditis elegans

source_name: ChIP DNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. http://www.nimblegen.com/products/lit/index.html

growth_protocol: Worm_embryo_growth_and_harvest_vSE1. Embryos were prepared by bleaching from gravid adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature. Embryos were then washed once with 100 mM Tris, twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% TritonX-100, 0.1 % sodium deoxycholate; 150 mM NaCl).  Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_v4.1. 2.2 mg extract was taken and sarkosyl was added to 1% final concentration. 0.2 mg was used for each ChIP with 10% taken as input directly into elution buffer (1% SDS in TE, 250 mM NaCl) and treated with RNAse. Antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were incubated (2hrs at 4C) with 20 uL protein A sepharose (Amersham) and washed 5 minutes with 1 mL of each of the following solutions: ChIP Buffer, ChIP Buffer+1M NaCl, ChIP Buffer+500mM NaCl, TEL Buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and 2X TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were eluted twice with 150uL elution buffer for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/.DNA was amplified with a modified ligation mediated PCR (LM-PCR) protocol derived from Ren, R et al (2000) Science 290, 2306-9.

treatment_protocol: Worm_embryo_extraction_vSE1. Embryos were resuspended in FA buffer and dounced 30 times (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: fix

value: 2% CHO, 30 minutes

tag: stage

value: Mixed Embryos

source_name: Input genomic DNA


title: JL00002_SDC3_YPT47_MXemb_ChIP_replicate1


title: Endothelial Cells, Low Shear Stress, 1 dyne/cm2, Replicate 3

description: Gene expression after exposure to low shear stress for 24 hours.


title: Endothelial Cells, High Shear Stress, 15 dyne/cm2, Replicate 3

description: Gene expression after exposure to high shear stress for 24 hours.


title: JL00001_DPY27_YPT47_MXemb_ChIP_replicate1

description: DPY-27 ChIP-chip from YPT47 X-V fusion strain mixed stage embryos. An affinity purified rabbit polyclonal antibody to DPY-27 was used.


title: Endothelial Cells, Static Culture, Replicate 3

description: Gene expression after exposure to static culture for 24 hours.


title: JL00001_DPY27_YPT47_MXemb_ChIP_replicate2


title: JL00001_DPY27_YPT47_MXemb_ChIP_replicate3


title: Endothelial Cells, High Shear Stress, 15 dyne/cm2, Replicate 2


title: Endothelial Cells, Reversing Flow, Replicate 2


title: Endothelial Cells, Static Culture, Replicate 2


title: Endothelial Cells, Static Culture, Replicate 1


title: Endothelial Cells, High Shear Stress, 15 dyne/cm2, Replicate 1


title: Endothelial Cells, Low Shear Stress, 1 dyne/cm2, Replicate 1


title: Endothelial Cells, Reversing Flow, Replicate 1


title: Endothelial Cells, Low Shear Stress, 1 dyne/cm2, Replicate 2