title: CH34_MM284-iron+basalt_rep3_2

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

description: For analysis, three biological repeats were used and each oligonucleotide array contained three technical repeats.

hyb_protocol: Labelled cDNA from both conditions were hybridized to the spotted slides on an automatic hybridization station (HS4800, Tecan) for 16h at 42°C with medium agitation.

scan_protocol: The arrays were scanned (at 532 and 635 nm) using the Genepix4100A from Axon Instruments.

data_processing: Median intensity values and background values of each spot were extracted for both the test samples (Cy5) and the reference samples (Cy3). Quality check of the data was performed for each microarray using the arrayQuality package in R from Bioconductor. Data was normalized to correct experimental biases in microarray data with limma package by using normexp background processing, printing tip Lowess normalization and between arrays scale normalization. Differential gene expression FC=ratio Cy5/Cy3, VALUE=log2(Cy5/Cy3) and P-value were calculated using the limma package. P-values were corrected for multiple testing using the Benjamin and Hochberg's method to control the false discovery rate.

organism: Cupriavidus metallidurans CH34

source_name: Cupriavidus metallidurans CH34, MM284, mid-log phase

label_protocol: Ten µg total RNA of high quality was reverse-transcribed by random priming according to the instructions provided with the Pronto kit (Corning-Promega, USA) and labeled by incorporation of Cy3-dCTP nucleotides (Amersham Bioscience, UK).

growth_protocol: CH34 was grown in a Tris buffered medium containing 0.2% gluconate (MM284) at 125 rpm, 30°C

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Midi Kit according to the manufacturer's instructions. The quality control of total RNA was monitored using the BioAnalyser 2100 (Agilent).

source_name: Cupriavidus metallidurans CH34, MM284-iron+basalt, mid-log phase

growth_protocol: CH34 was grown in a Tris buffered medium containing 0.2% gluconate (MM284) without iron, in the presence of basalt, at 125 rpm, 30°C. To ensure there was no external contamination of iron, cultures were grown in acid-washed Polymethylpentene flasks. The basalt rocks were crushed to a 2-5 mm diameter by placing them in a sterilized hollow metal cylinder and crushing them with a heavy metal plunger. The rocks were washed in dH2O and then sonicated in acetone, at 3 hHz, for 1 minute, prior to autoclaving. 5g of basalt was added to 50 ml of medium when required.


title: CH34_MM284-iron_rep3_2

status: Public on Dec 31 2009

type: RNA

molecule: total RNA

tag: strain

source_name: Cupriavidus metallidurans CH34, MM284-iron, mid-log phase

growth_protocol: CH34 was grown in a Tris buffered medium containing 0.2% gluconate (MM284) without iron at 125 rpm, 30°C.


title: Whole oocyte rep2

city: Iowa City

first: Douglas

middle: W.

last: Houston

state: IA

department: Department of Biology

country: USA

institute: The University of Iowa

description:
Sample Number: 2
Replicate Number: 2
Experimental condition: Control

hyb_protocol: Labelled cRNA was hybridized to Xenopus laevis Genome Arrays (Affymetrix) at 45˚C using Model 640 hyb ovens, processed using the Model 450 GeneChip fluidics station (Affymetrix).

scan_protocol: Image files were captured on a Model 3000 GeneArray scanner and processed using Affymetrix micorarray analysis software.

data_processing: Quality control included standard Affymetrix internal controls. GeneChip Operating software was used to generate data files (CEL), and MAS 5 for calculating expression signals.

label: Biotin

organism: Xenopus laevis

source_name: stage VI oocyte

label_protocol: 100 ng of total RNA was used to make complementary RNA (cRNA)d, which was amplified using the GeneChip® Two-Cycle cDNA Synthesis Kit (Invitrogen/Affymetrix). cRNA labeling, hybridization and data acquisition were performed by The University of Iowa, Carver College of Medicine DNA Core Facility, using standard Affymetrix protocols and reagents.

extract_protocol: Total RNA was prepared by proteinase K digestion followed by phenol extraction and ethanol precipitation. Purified RNA was treated with DNase prior to cDNA synthesis. RNA quality was verified using the Experion System (BioRad) for automated electrophoresis.

tag: developmental stage

value: full-grown stage VI oocyte

tag: isolation

value: collagenase treatment

tag: cell type

value: oocyte


title: EBPR sludge_AN/AE_1

city: Madison

first: Shaomei

last: He

state: WI

address: 1550 Linden Drive

institute: University of Wisconsin-Madison

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb1_Slide1_Sample AN" and "Hyb2_Slide1_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.

hyb_protocol: The hybridization and wash steps were according to Combimatrix’s instructions. Briefly, a pre-hybridization step was performed to block non-specific binding of targets. Subsequently, a total of 5 ug aRNA was loaded on each array, and hybridized at 45 oC with a hybridization buffer containing 15% of formamide for 14-16 hours, followed by five washes with increasing stringency in wash buffers as instructed by Combimatrix.

scan_protocol: The hybridized array was imaged using a Molecular Devices Axon4000B scanner (Molecular Devices Corporation, Sunnyvale, CA), with a resolution of 5 um, excitation wavelength of 635 nm and PMT gain of 550.

data_processing: To identify differentially expressed genes between the anaerobic and aerobic samples, Lowess normalization without background subtraction was applied to remove signal intensity-dependent and array-dependent variations. The log2 ratio of Anaerobic to Aerobic samples (AN/AE) using normalized signal intensities was calculated and reported in the VALUE column.

organism:
uncultured bacterium
Candidatus Accumulibacter phosphatis

source_name: Anaerobic EBPR sludge (AN)

label_protocol:
The mRNA was enriched by removing 16S and 23S rRNA from 4-7 μg of total RNA, with the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion, Austin, TX) and then poly(A)-tailed using mRNA-ONLY™ Prokaryotic mRNA Poly(A)-Tailing Kit (EPICENTRE, Madison, WI). The double-strand cDNA was synthesized and further in vitro transcribed, with 5-(3-aminoallyl)-UTP incorporated into the resulting antisense RNA (aRNA), using TargetAmp™ 1-Round aRNA Amplification Kit (EPICENTRE).
Alexa Fluor 647 (Invitrogen, Carlsbad, CA) was coupled to the 5-(3-aminoallyl)-UTP in aRNA according to the manufacture’s instructions. The dye-incorporated aRNA was purified by using the RNeasy mini kit (QIAGEN) and fragmented by incubation in a fragmentation solution (Ambion) at 70 oC for 15 min to generate fragments sized 50-200 nucleotides.

extract_protocol: RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA), including a 2 min bead-beating step with a spherical ceramic bead. An on-column DNase I digestion with RNase-free DNase set (Qiagen) was performed according to manufacture’s instruction to remove DNA contamination.

tag: sampling stage

value: early anaerobic phase

tag: sampling time

value: 15 min after acetate addition

source_name: Aerobic EBPR sludge (AE)

value: early aerobic phase

value: 15 min after switching to aeration


title: CH34_MM284-iron+basalt_rep3

data_processing: Median intensity values and background values of each spot were extracted for both the test samples (Cy5) and the reference samples (Cy3). Quality check of the data was performed for each microarray using the arrayQuality package in R from Bioconductor. Data was normalized to correct experimental biases in microarray data with limma package using background subtraction, printing tip Lowess normalization and Aquantile normalization. Differential gene expression FC=ratio Cy5/Cy3, VALUE=log2(Cy5/Cy3) and P-value were calculated using the limma package. P-values were corrected for multiple testing using the Benjamin and Hochberg's method to control the false discovery rate.

label_protocol: Ten µg total RNA of high quality was reverse-transcribed by random priming according to the instructions provided with the Pronto kit (Corning-Promega, USA) and labeled by incorporation of Cy5-dCTP nucleotides (Amersham Bioscience, UK).


title: EBPR sludge_AN/AE_6

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb7_Slide2_Sample AN" and "Hyb8_Slide2_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.

label: Alexa Fluor 647 (Invitrogen, Carlsbad, CA)


title: EBPR sludge_AN/AE_2

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb3_Slide1_Sample AN" and "Hyb2_Slide1_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.


title: H240 111707

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: ped Healthy, Gender=M, Age=6

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13  (This information is in the .XML file)

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

label: biotin

organism: Homo sapiens

source_name: Whole blood

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: Tempus RNA extraction kit and GlobinClear kit

tag: age

tag: gender

value: male

tag: illness

value: ped Healthy

tag: treatment

tag: time point


title: Vegetal cortex rep2

description:
Sample Number: 3
Replicate Number: 1
Experimental condition: Experimental sample

treatment_protocol: Manual isolation of vegetal cortices was performed using the methods of Elinson et al. (1993), with modifications. Briefly, collagenased stage VI oocytes were transferred to 1x MEM (100 mM MOPS pH 7.4, 2 mM EGTA, 1 mM MgSO4,) in a clean glass dish and bisected into animal and vegetal halves using a new scalpel blade. The vegetal halves were placed cortex side down onto a nitrocellulose filter, and a cover slip was used to compress away the yolky cytoplasm. After the cover slips were removed, gentle agitation was used to free the cortex from the membrane and to dislodge any additional yolk. Isolated cortices were rinsed in fresh MEM and frozen in batches of ten on dry ice. Intact stage VI oocytes from the same female were frozen as controls.

value: full-grown, stage VI oocyte

value: manual dissection of vegetal cortex

tag: cell part

value: vegetal cortex


title: Whole oocyte rep1

description:
Sample Number: 1
Replicate Number: 1
Experimental condition: Control


title: EBPR sludge_AN/AE_3

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb3_Slide1_Sample AN" and "Hyb4_Slide1_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.


title: EBPR sludge_AN/AE_4

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb5_Slide2_Sample AN" and "Hyb6_Slide2_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.


title: EBPR sludge_AN/AE_5

description: Although submitted as dual channel, both the anaerobic and aerobic samples were labeled with Alexa Fluor 647. One sample was first hybridized on the microarray slide. After scanning, the hybridized sequences were stripped off, allowing the hybridization of the second sample on the same slide. The comparison of gene expression profiles between the two samples was performed on two consecutive hybridizations on the same slide. The two raw data files for this pair of comparison were submitted to GEO as "Hyb7_Slide2_Sample AN" and "Hyb6_Slide2_Sample AE". See Overall design under Series GSE17857 for more detailed explanation.


title: Control preadipocyte C2 Cy5 slide 786

city: Maastricht

first: Florence

last: van Tienen

address: Universiteitssingel 50

department: Genetics and Cell biology

country: Netherlands

institute: Maastricht University

description: Array-Pro analyzer software (MediaCybernetics, Bethesda, USA).

hyb_protocol: Hybridization was performed using the Operon Human oligo collection V2 (21521 features) spotted on CodeLink slides (Amersham Biosciences) printed by the Microarray Facility (University Medical Center Utrecht, The Netherlands). T2DM patients and controls were paired on each slide based on respectively gender, age and BMI. Two-color microarray hybridizations were performed including dye-swap for technical replication. Hybridizations, washings, and slide drying were performed on a Tecan HS4800 hybridization station. Slides were blocked in 5xSSC, 25% Formamide, 0.1% SDS, 1% BSA (Sigma, St Louis, USA) for 1 hour. 120 pmol of each dye-labeled aRNA sample (2% - 4.5% dye incorporation) was fragmented using RNA fragmentation buffer (Ambion), mixed with 100 ug tRNA (Roche, Mannheim, Germany) and 50 ug Herring sperm DNA (Invitrogen) in 120 ul hybridization solution [5xSSC, 25% Formamide, 0.1% SDS], denaturated for 5 minutes at 95 degrees C, hybridized for 16 hours at 42 degrees C and washed 3 times with decreasing concentrations of SSC and SDS (1xSSC, 0.2%SDS; 0.1xSSC, 0.2%SDS; 0.1xSSC).

scan_protocol: Array scanning was performed on an Axon 4000B scanner with laser power 100% for both channels and three photo multiplier settings for respectively the red and the green channel (1000 and 888 to detect low expressed probes, 756 and 671 to detect highly expressed probes (around 0.05% of all spots saturated) and an intermediate setting of 878 and 779).

data_processing: First, bad and missing spots were excluded from further analysis. Secondly, the number of missing data and spots with intensities below background was computed for each gene for all three scanning powers. For each gene, the intensities obtained from the scanning power with the least missing and most values above background were kept. If more than one scan setting was suitable for a spot, then the scanning at medium power was preferred over high power, which was itself preferred over the low setting. The foreground intensities of the remaining genes were analyzed using a Gaussian linear regression model including labeling efficiency, dye swap, hybridization days, background level, sex, age, BMI and a random effect to take into account multiple observations on the same subject. The inference criterion used for comparing the models is their ability to predict the observed data, i.e., models are compared directly through their minimized minus log-likelihood. When the numbers of parameters in models differ, they are penalized by adding the number of estimated parameters, a form of the Akaike information criterion (AIC). For each gene, the group was then added to the model. A gene was found to be differentially expressed if the AIC decreased compared to the model not containing the group.

source_name: preadipocytes

label_protocol: 1 ug RNA from each sample with a RIN>7, was amplified using the Amino-Allyl MessageAmp II aRNA kit (Ambion, Austin, USA) to generate amino-allyl aRNA (AA-aRNA). AA-aRNA was generated according to manufacturer’s protocol with a modification in the ratio UTP: AA-UTP, which was changed from 1:1 to 7:3. RNA integrity was assessed by determining the aRNA size. Each amino AA-aRNA sample was coupled to Cy3 or Cy5 (Amersham Biosciences, GE healthcare, Little Chalfont, UK) and purified with the RNeasy Minelute clean-up kit (Qiagen).

growth_protocol: Preadipocytes were suspended in 5 ml DMEM medium containing 10% fetal calf serum (Gibco-Invitrogen, Carlsbad, USA) and 1% glutamax/ penecillin/streptomycin (Gibco-Invitrogen), grown for 2 passages and frozen. Control and T2DM preadipocytes were taken into culture in parallel and cultured for 3 passages till a 90% confluent 162cm2 culture flask was obtained per sample (passage 5 - 9) for RNA isolation.

extract_protocol: Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, USA) and purified with the RNeasy clean-up kit (Qiagen, Valencia, USA), according to manufacturer’s protocol.

treatment_protocol: At fasted state, subcutaneous adipose tissue biopsy samples were taken caudal from the umbilicus via liposuction under local anesthesia and subsequently treated with collagenase. The cell suspension was filtered through 500µm nylon mesh and spun at 220 × g for 1 min to separate preadipocytes from mature adipocytes.

value: preadipocyte

tag: age (yr)

tag: sample type

value: control

tag: bmi


title: H256 111707

description: ped Healthy, Gender=F, Age=9

value: female


title: Vegetal cortex rep1


title: H244 111707

description: ped Healthy, Gender=M, Age=12


title: FR-SYS23-M6

description: SoJIA, Gender=F, Age=12

value: SoJIA

value: Anakinra

value: Month 6


title: FR-SYS23-M1

description: SoJIA, Gender=F, Age=11

value: Placebo

value: Month 1


title: H257 111707

description: ped Healthy, Gender=M, Age=13


title: H228 100507

description: ped Healthy, Gender=F, Age=8


title: H225 100507

description: ped Healthy, Gender=F, Age=10


title: H219 100507

description: ped Healthy, Gender=M, Age=9


title: FR-SYS17-J1

description: SoJIA, Gender=F, Age=7

value: Day 1


title: FR-SYS22-M6

description: SoJIA, Gender=F, Age=17


title: FR-SYS17-M1

description: SoJIA, Gender=F, Age=7


title: H216 100507

description: ped Healthy, Gender=M, Age=14


title: H199 021207

description: ped Healthy, Gender=F, Age=19


title: FR-SYS23-J1

description: SoJIA, Gender=F, Age=11


title: FR-SYS10-J1

description: SoJIA, Gender=M, Age=3


title: FR-SYS22-M1

description: SoJIA, Gender=F, Age=16


title: FR-SYS22-J1

description: SoJIA, Gender=F, Age=16


title: FR-SYS17-M6

description: SoJIA, Gender=F, Age=8


title: FR-SYS02-J1

description: SoJIA, Gender=M, Age=3


title: FR-SYS02-M6

description: SoJIA, Gender=M, Age=3


title: H200 042507

description: ped Healthy, Gender=F, Age=15


title: FR-SYS10-M6

description: SoJIA, Gender=M, Age=3


title: FR-SYS02-M1

description: SoJIA, Gender=M, Age=3


title: H37 112706

description: ped Healthy, Gender=F, Age=14


title: FR-SYS10-M1

description: SoJIA, Gender=M, Age=3


title: FR-SYS09-J1

description: SoJIA, Gender=M, Age=4


title: FR-SYS09-M1

description: SoJIA, Gender=M, Age=4


title: FR-SYS12-M1

description: SoJIA, Gender=F, Age=10


title: FR-SYS12-J1

description: SoJIA, Gender=F, Age=10


title: FR-SYS07-J1

description: SoJIA, Gender=F, Age=7


title: H-PID-646

description: ped Healthy, Gender=F, Age=4


title: FR-SYS20-J15

description: SoJIA, Gender=F, Age=10

value: Day 15


title: FR-SYS25-J1

description: SoJIA, Gender=M, Age=14


title: FR-SYS09-M6

description: SoJIA, Gender=M, Age=4


title: FR-SYS21-M1

description: SoJIA, Gender=F, Age=15


title: FR-SYS21-M6

description: SoJIA, Gender=F, Age=15


title: FR-SYS07-M3

description: SoJIA, Gender=F, Age=7

value: Month 3


title: FR-SYS15-J1

description: SoJIA, Gender=F, Age=4


title: FR-SYS15-M1

description: SoJIA, Gender=F, Age=4


title: FR-SYS15-M9

description: SoJIA, Gender=F, Age=5

value: Month 9


title: FR-SYS21-J1

description: SoJIA, Gender=F, Age=15


title: H-PID-645

description: ped Healthy, Gender=M, Age=10M

value: male


title: FR-SYS25-M6

description: SoJIA, Gender=M, Age=14


title: FR-SYS25-M1

description: SoJIA, Gender=M, Age=14


title: FR-SYS16-M1

description: SoJIA, Gender=F, Age=7


title: FR-SYS16-M2

description: SoJIA, Gender=F, Age=7

value: Month 2


title: FR-SYS20-J1

description: SoJIA, Gender=F, Age=10


title: H155 030507

description: ped Healthy, Gender=M, Age=14

value: ped Healthy


title: H159 011907

description: ped Healthy, Gender=F, Age=19


title: FR-SYS07-M1

description: SoJIA, Gender=F, Age=7


title: FR-SYS14-J1

description: SoJIA, Gender=F, Age=7


title: FR-SYS11-M1

description: SoJIA, Gender=M, Age=7


title: FR-SYS14-M6

description: SoJIA, Gender=F, Age=7


title: FR-SYS14-M1

description: SoJIA, Gender=F, Age=7


title: FR-SYS08-J1

description: SoJIA, Gender=F, Age=4


title: FR-SYS16-J1

description: SoJIA, Gender=F, Age=7


title: FR-SYS13-M6

description: SoJIA, Gender=M, Age=6


title: FR-SYS08-M1

description: SoJIA, Gender=F, Age=4


title: FR-SYS11-J1

description: SoJIA, Gender=M, Age=7


title: FR-SYS03-M6

description: SoJIA, Gender=M, Age=10


title: FR-SYS03-M1

description: SoJIA, Gender=M, Age=10


title: FR-SYS08-M6

description: SoJIA, Gender=F, Age=4


title: FR-SYS11-M6

description: SoJIA, Gender=M, Age=7


title: FR-SYS24-J1

description: SoJIA, Gender=F, Age=15


title: FR-SYS06-J1

description: SoJIA, Gender=F, Age=7


title: H201 050207

description: ped Healthy, Gender=F, Age=4


title: H184 031907

description: ped Healthy, Gender=F, Age=11


title: FR-SYS03-J1

description: SoJIA, Gender=M, Age=10


title: FR-SYS13-M1

description: SoJIA, Gender=M, Age=6


title: FR-SYS13-J1

description: SoJIA, Gender=M, Age=5


title: FR-SYS24-M1

description: SoJIA, Gender=F, Age=15


title: FR-SYS24-M3

description: SoJIA, Gender=F, Age=15


title: H164 112206

description: ped Healthy, Gender=F, Age=10


title: D_H3K27me3_rep3

status: Public on Dec 30 2009

type: genomic

city: New Haven

first: Hang

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

hyb_protocol: DNA was hybridized according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.

scan_protocol: Whole Genome Tiling array were scanned on Affymetrix scanner G7

data_processing: Raw microarray data were quantile normalized and modified regions were detected with TileMap using the Hidden Markov model option and the Unbalanced Mixture Subtraction (UMS) method (Ji and Wong, 2005) to provide an approximate estimate of model parameters for HMM (false discovery rate).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 5 day-old dark grow seedlings (D).

label_protocol: DNA was labeled according to Affymetrix’ Chromatin Immunoprecipitation Assay Protocol Rev.3.

growth_protocol: 5 day-old dark grow seedlings (D).

extract_protocol: Chromatin isolation was performed with 10 g of whole seedlings tissue according to Bowler et al. (2004). The resuspended chromatin pellet was sonicated at 4°C with a Diagenode Bioruptor (Diagenode, Sparta, NJ) set at high intensity for 10 min (30 sec on, 30 sec off intervals). The DNA was sheared to approximatively 0.3-0.8 kb fragments.Three μl of the following antibodies were used for immunoprecipitation: anti-H3K9ac (Upstate 06-942), anti-H3K9me3 (Upstate 07-442), anti-H3K27ac (Upstate 07-360), anti-H3K27me3 (Upstate 07-449), and anti-H3 (Upstate 07-690).

treatment_protocol: Chromatin immunoprecipitated with anti-H3K27me3

tag: ecotype

tag: modification and growth condition

value: H3K27me3 D

tag: antibody


title: D_H3K27me3_rep1


title: D_H3K27me3_rep4


title: D_H3K9me3_rep3

treatment_protocol: Chromatin immunoprecipitated with anti-H3K9me3

value: H3K9me3 D


title: FR-SYS05-M6

description: SoJIA, Gender=F, Age=2


title: FR-SYS04-M1

description: SoJIA, Gender=M, Age=9


title: FR-SYS06-M1

description: SoJIA, Gender=F, Age=7


title: FR-SYS04-M6

description: SoJIA, Gender=M, Age=9


title: FR-SYS05-J1

description: SoJIA, Gender=F, Age=2


title: H202 062707

description: ped Healthy, Gender=F, Age=5


title: FR-SYS04-J1

description: SoJIA, Gender=M, Age=9


title: H192 071906

description: ped Healthy, Gender=F, Age=9


title: D_H3K27ac_rep2

treatment_protocol: Chromatin immunoprecipitated with anti-H3K27ac

value: H3K27ac D


title: D_H3K27ac_rep4


title: D_H3K27ac_rep3


title: FR-SYS06-M4

description: SoJIA, Gender=F, Age=7

value: Month 4


title: D_H3K27ac_rep1


title: D_H3K9me3_rep4


title: D_H3K9ac_rep3

treatment_protocol: Chromatin immunoprecipitated with anti-H3K9ac

value: H3K9ac D


title: D_H3K9me3_rep2


title: D_H3K9ac_rep4


title: D_H3K9me3_rep1


title: D_H3K9ac_rep1


title: D_H3_rep3

treatment_protocol: Chromatin immunoprecipitated with anti-H3

value: H3 D


title: D_H3_rep2


title: D_H3_rep1


title: D to L_H3K27me3_rep4

source_name: 5 day-old dark grow seedlings transfered to white light for 6 hours (D to L).

value: H3K27me3 D to L


title: D to L_H3K27me3_rep3

growth_protocol: 5 day-old dark grow seedlings transfered to white light for 6 hours (D to L).


title: D to L_H3K27ac_rep3

value: H3K27ac D to L


title: D to L_H3K27me3_rep2


title: D to L_H3K27ac_rep4


title: D_H3K9ac_rep2


title: D to L_H3K27ac_rep2


title: D to L_H3K27ac_rep1


title: D to L_H3K9me3_rep2

value: H3K9me3 D to L


title: D_H3_rep4


title: D to L_H3K9ac_rep4

value: H3K9ac D to L


title: D to L_H3K9me3_rep4


title: D to L_H3K9me3_rep1


title: D to L_H3K9me3_rep3


title: D to L_H3K9ac_rep3


title: D to L_H3K9ac_rep2


title: D to L_H3K27me3_rep1


title: D to L_H3K9ac_rep1


title: D to L_H3_rep2

value: H3 D to L


title: D to L_H3_rep4


title: D to L_H3_rep1


title: D to L_H3_rep3


title: Stroma_Endo_cAMP_rep5

status: Public on Dec 19 2009

city: Valencia

first: Jose

middle: Antonio

last: Martinez-Conejero

address: C/ Guadassuar 1, bajo

country: Spain

institute: iGenomix

description: No additional information

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007).

scan_protocol: According to manufacturer's instruction.

data_processing: To minimize technical (non-biological) variability among arrays, densitometry values between arrays were normalized using the RMA function and further transformed to the logarithmic scale (log2). Probes with a corresponding GenBank accession ID were selected for functional analysis. Statistically significant differences between groups were determined using SAM and RankProd methods using the Bioconductor (http://www.bioconductor.org/) packages Siggene and RankProd, respectively, both run under R software (http://www.r-project.org/).

source_name: Stromal culture, endometriosis, cAMP

label_protocol: Hybridization was performed using Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Inc, Santa Clara, CA). Briefly, for each sample 100 ng of total RNA were reverse transcribed to cDNA using 500 ng of T7-(N6) primers and SuperScript II. A second strand of DNA was generated using DNA Polymerase, followed by overnight in vitro transcription to generate cRNA. After processing through cRNA cleanup spin columns, 10 μg of cRNA was reverse transcribed using random primers and SuperScript II. Mixtures were digested with RNase H, and the cDNA purified by the cDNA clean-up spin columns. Finally, 5.5 μg of sense cDNA was fragmented and labeled using the geneChip WT terminal labeling kit. Quality of cDNA and fragmented cDNA was assessed using an Agilent bioanalyzer.

growth_protocol: Endometrial tissue biopsies were obtained from 14 reproductive age women. Six subjects had endometriosis (n=1 minimal, n=2 mild, n=1 moderate-severe, n=2 severe),  on visualization of lesions during laparoscopy and their histologic evaluation (Table 1). Staging of endometriosis was according to the revised American Fertility Society classification system (19). Participating subjects with endometriosis were 22-46 years old (mean 33.5+/-3.0), not pregnant, and did not use hormonal medications within 3 months before surgery. Controls were eight cycling  subjects (37-49 years old, mean 44.4+/-.7) undergoing endometrial biopsy or hysterectomy for benign reasons such as fibroids, pelvic organ prolapse, pelvic pain or endometrial polyps. Controls had regular menstrual cycles (25-35 days), were documented not to be pregnant, had no history of endometriosis and no evidence of endometriosis at laparoscopy and had not been on hormonal therapies for at least 3 months before tissue sampling.

extract_protocol: Total RNA was isolated from hESF from subjects without (n=4) and with (n=4) endometriosis and purified using Qiagen RNeasy Plus Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Samples were stored in RNase-free H2O, quantified by spectroscopy, and purity was analyzed using the 260/280 absorbance ratio. RNA quality and integrity were assessed using Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA) with all samples demonstrating high quality (RIN=9.7-10).

tag: tissue

value: endometrial stromal culture cell

value: stromal cell fibroblasts

tag: disease status

value: endometriosis

tag: treatment group


title: D_H3K27me3_rep2


title: Stroma_NoEndo_control_rep3

description: No additional information

source_name: Stromal culture, no endometriosis, control

tag: cell type

value: no endometriosis

value: control


title: Stroma_NoEndo_cAMP_rep2

description: No additional information

source_name: Stromal culture, no endometriosis, cAMP


title: Stroma_Endo_control_rep3

description: No additional information

source_name: Stromal culture, endometriosis, control


title: Stroma_Endo_cAMP_rep2

description: No additional information


title: Stroma_NoEndo_control_rep1

description: No additional information


title: Stroma_Endo_control_rep5

description: No additional information


title: Stroma_NoEndo_cAMP_rep5

description: No additional information


title: Stroma_Endo_cAMP_rep4

description: No additional information


title: Stroma_NoEndo_control_rep2

description: No additional information


title: Stroma_Endo_control

description: No additional information


title: Stroma_NoEndo_cAMP_rep3

description: No additional information


title: Stroma_Endo_control_rep4

description: No additional information


title: Stroma_Endo_cAMP_rep1

description: No additional information


title: Stroma_NoEndo_control_rep5

description: No additional information


title: Stroma_NoEndo_cAMP_rep4

description: No additional information


title: Stroma_NoEndo_control_rep4

description: No additional information


title: H198 011507

description: ped Healthy, Gender=F, Age=16

value: female

value: ped Healthy


title: Stroma_Endo_control_rep2

description: No additional information

growth_protocol: Endometrial tissue biopsies were obtained from 14 reproductive age women. Six subjects had endometriosis (n=1 minimal, n=2 mild, n=1 moderate-severe, n=2 severe), based on visualization of lesions during laparoscopy and their histologic evaluation (Table 1). Staging of endometriosis was according to the revised American Fertility Society classification system (19). Participating subjects with endometriosis were 22-46 years old (mean 33.5+/-3.0), not pregnant, and did not use hormonal medications within 3 months before surgery. Controls were eight cycling premenopausal subjects (37-49 years old, mean 44.4+/-.7) undergoing endometrial biopsy or hysterectomy for benign reasons such as fibroids, pelvic organ prolapse, pelvic pain or endometrial polyps. Controls had regular menstrual cycles (25-35 days), were documented not to be pregnant, had no history of endometriosis and no evidence of endometriosis at laparoscopy and had not been on hormonal therapies for at least 3 months before tissue sampling.


title: Stroma_Endo_cAMP_rep3

description: No additional information


title: Stroma_NoEndo_cAMP_rep1

description: No additional information


title: female tumor Stat3fl/fl rep15

status: Public on Dec 01 2009

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: azoxymethane/dextransulfate-induced colorectal tumor in the APCmin mouse model

hyb_protocol: Affymetrix WT kit

scan_protocol: Affymetrix WT kit

data_processing: RMA Normalization, log2 intensities

organism: Mus musculus

source_name: female tumor Stat3fl/fl

label_protocol: Affymetrix WT kit

extract_protocol: RNeasy mini kit (Qiagen)

tag: genotype

value: intestinal tumor


title: female tumor Stat3-/- rep16

description: azoxymethane/dextransulfate-induced colorectal tumor in the APCmin mouse model.

source_name: female tumor Stat3-/-


title: female tumor Stat3-/- rep17


title: FR-SYS05-M1

description: SoJIA, Gender=F, Age=2

tag: age

value: SoJIA

value: Placebo

value: Month 1


title: male tumor Stat3-/- rep10

source_name: male tumor Stat3-/-

tag: gender

value: male


title: male tumor Stat3-/- rep11


title: male tumor Stat3fl/fl rep8

source_name: male tumor Stat3fl/fl


title: male tumor Stat3-/- rep12


title: female tumor Stat3fl/fl rep13


title: IEC Stat3-/- rep6

source_name: Intestinal epithelial cells from STAT3-/- mice

value: Intestinal epithelial cell


title: IEC Stat3-/- rep4


title: IEC Stat3fl/fl rep1

source_name: Intestinal epithelial cells from STAT3fl/fl mice


title: female tumor Stat3-/- rep18

source_name: female intestinal tumor from STAT3-/- mice


title: female tumor Stat3fl/fl rep14

source_name: female intestinal tumor


title: male tumor Stat3fl/fl rep7


title: IEC Stat3fl/fl rep2


title: Primary human fetal neuronal cell culture

city: Stockholm

first: Linda

middle: Alexandra Csöregh

last: Nord

address: Karolinska University Hospital, Solna, C4:U1

department: Dept. of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

description: Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. A total of 28 tissue samples yielding 10 cell cultures were used in this experiment. The cells were harvested after 8 days of culturing for RNA extraction.

hyb_protocol: Hybridization was performed at the Cancer Centre Karolinska Microarray Core Facility at the Karolinska University Hospital in Solna according to the manufactureres protocol.

scan_protocol: Scanning was performed according to the manufacturer's recommended protocols with Agilent Probe Array Scan.

data_processing: Raw data was analysed with the MAS5 method using Affymetrix GeneChip Operating Software (GCOS). Transcripts with signal intensities <100 in both samples were excluded.

source_name: Human fetal material, 8-12 weeks, from legal abortions

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

growth_protocol: Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. Procedures were approved by the local Ethics committee at the Karolinska University Hospital, Stockholm. The cells were grown on Poly-D-lysine in Neurobasal medium supplemented with 2% B27 supplement, L-Glutamine and Antibiotic-antimycotic. The cells were grown for 8 days.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit, followed by further cleaning and concentration by using RNeasy MinElute Cleanup Kit.

value: primary human fetal neuronal cell culture


title: IEC Stat3fl/fl rep3


title: IEC Stat3-/- rep5


title: Oestrogen treated primary human fetal neuronal cell culture

description: Primary neuronal cell cultures were established from human brain tissue, which was obtained from 8-12 weeks old fetuses at legal abortion after informed consent from the patients. A total of 28 tissue samples yielding 10 cell cultures were used in this experiment. Half of the cell cultures were treated with β-oestradiol the day after seeding. The duration of the oestrogen treatment was 7 days and the cells were harvested after 8 days of culturing for RNA extraction.

treatment_protocol: The cell cultures were treated with 2µM β-oestradiol, the day after seeding. Medium was not changed during the culture period. The duration of oestrogen treatment was 7 days and then cells were harvested for RNA extraction.

tag: agent

value: oestrogen


title: male tumor Stat3fl/fl rep9


title: Female mice kidney sample No.10-4 (diseased)

city: Bronx

first: Han

last: Si

state: NY

address: 1300 Morris Park

department: Medicine/Nephrology

institute: AECOM

description: Gene expression data from diseased female mice kidney

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG133A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with ArrayAssist software using gcRMA as normalization method.

source_name: Balb/c female mice kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle target preparation protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Albuminuria and renal disease was induced in about 10-week old male and female Balb/c mice via intravenous injection 12 mg/kg doxorubicin.After 14 days, mice were sacreficed for the kidney RNA extraction.

tag: Diseased mice kidney

tag: Female


title: CLOCK KO Rep 2

first: Aaron

middle: Ezra

last: Hoffman

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

description: All protocols performed by an Agilent-certified service provider

hyb_protocol: Agilent's Gene Expression Hybridization Kit followed by Agilent's Gene Expression Wash Buffer Kit

scan_protocol: Agilent’s Microarray Scanner with SureScan technology

data_processing: Agilent Feature Extraction Software, data were analyzed using the Rosetta Luminator gene expression data analysis system. Value = log10(intensity2/intensity1).

source_name: Mock siRNA (negative control)

label_protocol: mRNA converted to Cyanine 3-labeled cRNA using Agilent's Quick Amp Labeling Kit

extract_protocol: Qiagen RNeasy mini kit with on-column DNAse digestion

tag: cell line

value: MCF7 cells

value: transfected with a mock siRNA (Negative Control)

tag: replicate

source_name: CLOCK KO

label_protocol: mRNA converted to Cyanine 5-labeled cRNA using Agilent's Quick Amp Labeling Kit

value: transfected with an siRNA targeting CLOCK


title: CLOCK KO Rep 1


title: Female mice kidney sample No.4 (diseased)


title: Female mice kidney sample No.10-3 (diseased)


title: Female mice kidney sample No.5 (diseased)


title: Male mice kidney sample No.30-4 (diseased)

description: Gene expression data from diseased male mice kidney

source_name: Balb/c male mice kidney

tag: Male


title: Male mice kidney sample No.30-3 (diseased)


title: Male mice kidney sample No.9 (diseased)


title: Female mice kidney sample No.10-1 (healthy)

description: Gene expression data from healthy female mice kidney

tag: Healthy mice kidney


title: Female mice kidney sample No.No5 (healthy)


title: Female mice kidney sample No.1 (healthy)


title: Male mice kidney sample No.11 (diseased)


title: Male mice kidney sample No.7 (diseased)


title: Female mice kidney sample No.3 (diseased)


title: Non brain-dead ventilated control 3

city: Mannheim

first: Benito

last: Yard

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University hospital Mannheim

description: Gene expression data from intestinal cells from transgenic rats.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.1, from SAS. Gene expression profiling was performed using arrays of rat genome 230 2.0 -type from Affymetrix. A Custom CDF Version 11 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

organism: Rattus norvegicus

source_name: small intestine of BD animals, 6 hours anaesthetised ventilated rats

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA was isolated from the tissue using Trizol®-Reagent (Invitrogen, Carlsbad, CA).

value: small intestine


title: Brain-dead control 4

source_name: small intestine of BD animals, 6 hours after brain death


title: Female mice kidney sample No.30-6 (healthy)


title: Male mice kidney sample No.30-1 (healthy)

description: Gene expression data from healthy male mice kidney


title: Female mice kidney sample No.10-2 (healthy)


title: Male mice kidney sample No.30-2 (healthy)


title: Non brain-dead ventilated control 1


title: Male mice kidney sample No.12 (healthy)


title: Brain-dead control 6


title: Non brain-dead ventilated control 4


title: Male mice kidney sample No.30-5 (healthy)


title: Male mice kidney sample No.13 (healthy)


title: Brain-dead with vagal stimulation 4


title: Brain-dead control 3


title: Brain-dead with vagal stimulation 2


title: Brain-dead control 1


title: Brain-dead with vagal stimulation 3


title: STR-Wildtype-Valproate-rep4

status: Public on Nov 24 2009

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: Labeled cRNA samples (750 ng) were then hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina, Inc., San Diego, CA) in accordance with Illumina’s standard protocols for hybridization, staining, and data acquisition.

scan_protocol: BeadChips were imaged using the Illumina BeadArray Reader (Infinium I FastScan scanner protocol), a two-channel 0.8 μm resolution confocal laser scanner. The Illumina BeadScan software (version 3, 2006) was used for the identification of bead positions and the extraction of raw-data.

data_processing: Raw data (TIFF files) were loaded into the beadarray package (v1.10.0) of the BioConductor open-source library in the R statistical environment (v2.8.1). Following BASH analysis using default settings to mask spatial artefacts data was pre-processed using the Edwards background correction method and normalized using variance-stabilizing normalization as implemented in the vsn package (v3.8.0).

source_name: striatum, wildtype mouse, chronic treatment with valproate

label_protocol: Biotinylated and amplified cRNA was generated using Illumina® TotalPrep RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX).

growth_protocol: Animals were bred and housed at the SLRI/MSH animal facility. Standard protocols were followed.

extract_protocol: Standard laboratory procedures for the handling of RNA were followed. All equipment was decontaminated of RNase with RNase Erase® solution followed by 90% ethanol and DEPC-treated water.  Tissue was homogenized and lysed using Trizol® Reagent (Invitrogen Life Technologies Corporation, Carlsbad, CA). Chloroform was used to separate the aqueous and organic phases. The aqueous phase was washed with 70% ethanol at 0°C. Total RNA was purified from this solution using the Absolutely RNA Miniprep® kit (Stratagene, La Jolla, CA) according to the manufacturer’s instructions. Yield and quality of total RNA obtained was estimated by optical density measurements. An A260/280 value between 1.7 and 2.1 was considered relatively free of protein and suitable for further analysis. RNA samples were concentrated to approximately 0.08-0.1 µg/µL using Microcron YM-10 centrifugal filter devices (Millipore Corporation, Bedford, MA). Aliquots of 10 µL were taken and sent for microarray analysis.

treatment_protocol: Valproate (200 mg/kg, i.p) were given chronically (twice a day 9-10 am and 5-6 pm; for 15 days). Mice were tested in PPI on the next day after the last injection. Separated cohort of mice, treated in the same manner, have been used for molegular-genetic analysis. Brains were removed on the next day after the last injection of valproate.

tag: strain

value: wildtype

tag: sex

value: 10-12 weeks

value: striatum

tag: drug

value: Valproate


title: STR-Disc1Mutant-Valproate-rep4

source_name: striatum, L100P mutant mouse, chronic treatment with valproate

value: mutation Disc1 ENU L100P/L100P

tag: tissue


title: STR-Disc1Mutant-Vehicle-rep4

source_name: striatum, L100P mutant mouse, chronic treatment with vehicle

value: female

value: Saline


title: Brain-dead with vagal stimulation 1


title: STR-Disc1Mutant-Valproate-rep5


title: STR-Wildtype-Valproate-rep5


title: STR-Disc1Mutant-Valproate-rep3


title: STR-Disc1Mutant-Valproate-rep2


title: STR-Disc1Mutant-Vehicle-rep1


title: STR-Disc1Mutant-Vehicle-rep3


title: STR-Wildtype-Valproate-rep1


title: STR-Disc1Mutant-Valproate-rep1


title: STR-Wildtype-Valproate-rep3


title: STR-Wildtype-Vehicle-rep3

source_name: striatum, wildtype mouse, chronic treatment with vehicle


title: STR-Wildtype-Vehicle-rep1


title: STR-Wildtype-Vehicle-rep2


title: HIP-Disc1Mutant-Valproate-rep1

source_name: hippocampus, L100P mutant mouse, chronic treatment with valproate

value: hippocampus


title: HIP-Disc1Mutant-Valproate-rep3


title: HIP-Disc1Mutant-Valproate-rep2


title: HIP-Disc1Mutant-Valproate-rep4


title: HIP-Disc1Mutant-Vehicle-rep4

source_name: hippocampus, L100P mutant mouse, chronic treatment with vehicle


title: STR-Wildtype-Valproate-rep2


title: STR-Disc1Mutant-Vehicle-rep2


title: HIP-Disc1Mutant-Vehicle-rep1


title: HIP-Wildtype-Valproate-rep5

source_name: hippocampus, wildtype mouse, chronic treatment with valproate


title: HIP-Disc1Mutant-Vehicle-rep5


title: HIP-Wildtype-Valproate-rep2


title: HIP-Wildtype-Vehicle-rep5

source_name: hippocampus, wildtype mouse, chronic treatment with vehicle


title: HIP-Disc1Mutant-Vehicle-rep3


title: HIP-Wildtype-Valproate-rep4


title: HIP-Wildtype-Vehicle-rep2


title: HIP-Wildtype-Vehicle-rep4


title: HIP-Wildtype-Valproate-rep3


title: HIP-Wildtype-Vehicle-rep1


title: HIP-Wildtype-Valproate-rep1


title: FC-Disc1Mutant-Valproate-rep5

source_name: frontal cortex, L100P mutant mouse, chronic treatment with valproate

value: frontal cortex


title: HIP-Disc1Mutant-Vehicle-rep2

value: male


title: FC-Disc1Mutant-Valproate-rep3


title: FC-Disc1Mutant-Valproate-rep4


title: HIP-Wildtype-Vehicle-rep3


title: FC-Disc1Mutant-Vehicle-rep4

source_name: frontal cortex, L100P mutant mouse, chronic treatment with vehicle


title: FC-Disc1Mutant-Vehicle-rep1


title: FC-Disc1Mutant-Valproate-rep1


title: FC-Disc1Mutant-Valproate-rep2


title: FC-Wildtype-Vehicle-rep2

source_name: frontal cortex, wildtype mouse, chronic treatment with vehicle


title: FC-Disc1Mutant-Vehicle-rep3


title: FC-Wildtype-Valproate-rep4

source_name: frontal cortex, wildtype mouse, chronic treatment with valproate


title: FC-Wildtype-Vehicle-rep1


title: FC-Wildtype-Valproate-rep1


title: FC-Wildtype-Valproate-rep5


title: FC-Wildtype-Valproate-rep3


title: FC-Wildtype-Valproate-rep2


title: BS-Disc1Mutant-Valproate-rep3

source_name: brain stem, L100P mutant mouse, chronic treatment with valproate

value: brain stem


title: BS-Disc1Mutant-Vehicle-rep2

source_name: brain stem, L100P mutant mouse, chronic treatment with vehicle


title: BS-Disc1Mutant-Vehicle-rep3


title: BS-Disc1Mutant-Valproate-rep1


title: BS-Wildtype-Valproate-rep6

source_name: brain stem, wildtype mouse, chronic treatment with valproate


title: BS-Disc1Mutant-Valproate-rep2


title: FC-Disc1Mutant-Vehicle-rep2


title: FC-Wildtype-Vehicle-rep3


title: BS-Disc1Mutant-Vehicle-rep4


title: BS-Disc1Mutant-Vehicle-rep1


title: pdr-1 mutant vs. N2, replicate 2

status: Public on Nov 01 2009

type: other

first: Suvi

middle: Tuulia

last: Asikainen

state: Huddinge

address: Karolinska University Hospital

department: CLINTEC

institute: Karolinska Institutet

description: VC1024 (pdr-1; gk448), loss of function mutation in parkin pdr-1 gene

hyb_protocol: NCode miRNA Labeling System was used as manufacturer's instructions (Invitrogen) for labeling and hybridization. The work flow of protocol: poly(A) tailing reaction of all small RNAs, ligation of capture sequence provided by kit, purification (in this step labelled samples were pooled) and hybridization of tagged miRNA to microarray by incubation over night, wash, hybridization with Alexa Fluor 3 and 5 capture reagents, wash, drying.

scan_protocol: Arrays were scanned using ScanArray 5000 (GSI Lumonics) and ScanArray Express (Perkin Elmer)-software generating two color signal intensity images.

data_processing: TIGR Spotfinder-software (Saeed et al., 2003) was used to filter unreliable spots based on Otsu's method-algorithm (Liao et al., 2001) and to convert "good" (flag A,B or C) spots in microarray images to numerical form. Raw signal values were analyzed using mean centering to normalize signal values between channels. Signals from Alexa Fluor® Dye Control-probes were excluded from normalization process due their over-saturation leaving only probe intensities from C.elegans miRNAs to use in normalization. Signal intensity ratios were calculated for each signal pair yielding fold change values for each miRNAs from strain of investigation.

label: Alexa Fluor 3 dye

molecule: other

organism: Caenorhabditis elegans

source_name: N2 strain C.elegans (wild type)

growth_protocol: worms were grown in 20 degrees Celsius, fed OP50 E.coli, synchronized, larval 4 stage was used in experiment

extract_protocol: total small RNA (<200nt) was isolated using mirVana™ miRNA Isolation Kit

value: N2, wild type

label: Alexa Fluor 5 dye

source_name: pdr-1 mutant C.elegans


title: pdr-1 mutant vs. N2, replicate 1

label_protocol: NCode miRNA Labeling System was used as manufacturer's instructions (Invitrogen)


title: pdr-1 mutant vs. N2, replicate 3


title: BS-Wildtype-Valproate-rep1


title: cat-1 mutant C.elegans vs. N2 wild type replicate 3

description: strain CB1111 (cat-1; e1111), loss of function mutation in catecholamine transporter gene cat-1

source_name: cat-1 mutant C.elegans


title: pdr-1 mutant vs. N2, replicate 4


title: BS-Wildtype-Valproate-rep4


title: BS-Wildtype-Vehicle-rep2

source_name: brain stem, wildtype mouse, chronic treatment with vehicle


title: BS-Wildtype-Vehicle-rep3


title: BS-Wildtype-Vehicle-rep1


title: BS-Wildtype-Valproate-rep3


title: BS-Wildtype-Valproate-rep2


title: BS-Wildtype-Valproate-rep5


title: cat-1 mutant C.elegans vs. N2 wild type replicate 2


title: cat-1 mutant C.elegans vs. N2 wild type replicate 1


title: alpha-synuclein transgenic strain vs N2, replicate 4

description: Human alpha-synuclein A53T transgenic C. elegans strain, constructed by M. Lakso et al. (2003), J neurochemistry.

source_name: alpha-synuclein transgenic C.elegans


title: cat-1 mutant C.elegans vs. N2 wild type replicate 4


title: alpha-synuclein transgenic strain vs N2, replicate 1

value: Human alpha-synuclein A53T transgenic C. elegans


title: miR 0h 1st rep

city: Norwich

first: Daniel

last: MacLean

address: Colney Lane

department: Bioinformatics

country: United Kingdom

institute: The Sainsbury Laboratory

description: Gene expression on leaves of 35S:miR393 inoculated with water (control)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Arabidopsis Genome ATH1 microarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000

data_processing: background corrected using RMA, quantile normalized, values summarised by median-polish

source_name: 5weeks old arabidopsis leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in short day environment (8hrs light/16 hrs dark) for 5 weeks at 20C.

extract_protocol: Trizol extraction according to the manufacturer instruction. The total RNA was then DNAse treated using the Qiagen DNAse. Purification was performed using the RNAeasy columns following the manufacturer instruction

treatment_protocol: Leaves were inoculated with PstDc3000 at 10^6cfu/ml or with water. Tissues were harvested at 24hrs post inoculation

value: Leaf


title: AFB1 PSTDC3000 24h 2nd rep

description: Gene expression on leaves inoculated with PstDc3000 (10^6cfu/ml). Plant 35S:AFB1, time point 24hrs


title: AFB1 0h rep 1

description: Gene expression on leaves of 35S:AFB1 inoculated with water (control)


title: AFB1 0h rep 2


title: miR PSTDC3000 24h 2nd rep

description: Gene expression on leaves inoculated with PstDc3000 (10^6cfu/ml). Plant 35S:miR393, time point 24hrs


title: miR 0h 2nd rep


title: miR PSTDC3000 24h 1st rep


title: AFB1 PSTDC3000 24h 3rd rep


title: miR 0h 3rd rep


title: Col 0h 2nd rep

description: Gene expression on leaves of Col-0 inoculated with water (control)


title: Col PSTDC3000 24h 3rd rep

description: Gene expression on leaves inoculated with PstDc3000 (10^6cfu/ml). Plant Col-0, time point 24hrs


title: miR PSTDC3000 24h 3rd rep


title: alpha-synuclein transgenic strain vs N2, replicate 3


title: Col 0h 3rd rep


title: AFB1 0h rep 3


title: Col PSTDC3000 24h 2nd rep


title: AFB1 PSTDC3000 24h 1st rep


title: Col PSTDC3000 24h 1st rep


title: miR393 flg22 2h 3rd rep

description: Genes expression on leaf tissue in 35S:miR393 plant after flg22 (100nM) treatment

value: Leaf tissue


title: AFB1 flg22 2h 2nd rep

description: Genes expression on leaf tissue in 35S:AFB1 plant after flg22 (100nM) treatment


title: Wild type Atum 1h 3rd rep

description: Genes expression on leaf tissue after treatment with inactive flg22 (100nM) from Agrobacterium tumefasciens


title: Wild type NAA/flg 1h 2nd rep

description: Genes expression on leaf tissue after auxin (NAA, 10µM) and flg22 (100nM) treatment


title: Wild type NAA/flg 2h 3rd rep


title: Wild type NAA 1h 2nd rep

description: Genes expression on leaf tissue after auxin (NAA, 10µM) treatment


title: miR393 0h 2nd rep

description: Genes expression on leaf tissue on 35S:miR393 plant


title: AFB1 0h 3rd rep

description: Genes expression on leaf tissue in 35S:AFB1 plant


title: miR393 flg22 2h 1st rep


title: Col 0h 1st rep


title: Wild type NAA 2h 1st rep


title: Wild type 0h 2nd rep

description: Genes expression on leaf tissue


title: HuCNJE-SP4

status: Public on Oct 30 2009

city: New York

first: J. Mario

last: Wolosin

address: One Gustave levy Pl

department: Ophthalmology

institute: Mount Siani School of Medicine

description: Human conjunctiva (CNJ) from donor cadaver- Sample #4. Caucasian. Dead from heart infarct at age 55.

hyb_protocol: Appropriately fragmented biotin-labeled cRNA was hybridized to HG-U133 plus 2.0 GeneChips® (Affymetrix) oligonucleotide microarray following the manufacture protocol.

scan_protocol: Hybridized microarrays were stained with a streptavidin-phycoerythrin reagent and fluorescence images were captured using a G2500A (Agilent, Santa Clara CA) laser scanner.

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values from the SP cells.

label_protocol: RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).

growth_protocol:
Sieved single cells were centrifuged at  200 g, the  cell pellet was resuspended in SHEM medium  (D/F12 complemented with, 5 % FBS, 10ng/ml cholera toxin, 10 ng/ml epidermal growth factor (EGF),    plated in 75 cm2 flasks at  a density of 80,000-100,000 cells/cm2 and cultured overnight (14-16 hr) at 37 ºC in a 5% CO2 incubator.
After overnight culture the medium was refreshed with pre-warmed solution to remove floating cells (60- 70  % of total plated) and complemented with 5 μg/ml Hoechst 33342 for 1.5 hr. The treated cells were then released by trypsinization (2 min-37º C), spun down and resuspended in ice-cold phenol red-free D/F12 complemented with 5% serum and 1 μg/ml propidium iodide.

extract_protocol: Cell sorting was performed in an INFLUX (Cytopeia, Seattle, WA) flow cytometer.  The source tube was maintained at 4 ºC at all times. Light scattering gates that has been previously determined to exclude non epithelial cells from the sorting populations were applied and the cohort of non side population cells from the Hoechst blue/red emission plot was collected in 750 μl of Tri-Reagent LS (Molecular Research Center, Cincinnati, OH) solutions that was continuously stirred by means of mini-magnets and a custom-designed stirrer Tri-Reagent LS solutions containing the collected SP and nSP cells volumes were  adjusted to 1.0 ml by the addition of H2O and 0.5 μl polycryl  RNA carrier (MRC). RNA was isolated according to the manufacturer instructions.

treatment_protocol: Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored.  The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board.   The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase  (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix  (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding.  Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS),  suspensions were sequentially sieved through 100 and 40 μm filters.

tag: Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr B


title: HuCNJE-nSP4

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values from the nSP cells sorted along with the SP cells in the fourth (#4) experiment.

source_name: Non side population (Hoechst 33342-stained cells; nSP)

tag: Non  side population (Hoechst 33342-stained;nSP) from freshly isolated epithelial cells cultured for 12 hr.


title: Wilt type flg22 2h 2nd rep

description: Genes expression on leaf tissue after flg22 (100nM) treatment


title: HuCNJE-SP3

description: Human conjunctiva (CNJ) from donor cadaver. Sample #3. Caucasian. Dead from lung cancer at age 64.

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the SP cells.

tag: Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr.


title: alpha-synuclein transgenic strain vs N2, replicate 2

description: Human alpha-synuclein A53T transgenic C. elegans strain, constructed by M. Lakso et al. (2003), J neurochemistry.


title: Wild type NAA 1h 3rd rep


title: AFB1 0h 1st rep


title: HuCNJE-SP2

description: Human conjunctiva (CNJ) from donor cadaver- Sample #2. Caucasian. Dead from heart infarct at age 58

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values. for SP cells.

label_protocol: RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplicfication the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetr

treatment_protocol: Whole human conjunctivae from an unidentifiable cadaver donor was obtained from the National Disease Research Interchange (NDRI, Philadelphia, PA) within 48 hours of collection. No donor details apart from age, and cause of death were released and stored.  The use of human tissue in the study was in accordance with the provisions of the Declaration of Helsinki and sanctioned by the Institutional Review Board.   The conjunctiva was quartered and incubated for 16-20 hr at 4°C in a culture flask containing 5 mg/ml Dispase  (Roche, Nutley, NJ) dissolved in -(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid-buffered (hb), penicillin-streptomycin-complemented Dulbecco’s modified Eagle’s medium and Ham-F12 1:1 mix  (D/F-12) under slow (20-30 cycles/min) side-to-side tilting motion . At the end of this incubation the epithelial sheet is essentially separated from the underlying stroma and can be floated into the bathing solution with gentle mechanical prodding.  Epithelial sheets were transferred to 50 ml conical tube containing 15 ml trypsin solution and incubated for 20-25 min at 37º C under 40 cycles/ min orbital agitation. After trypsin neutralization with hbDF/12-20 % fetal bovine serum (FBS),  suspensions were sequentially sieved through 100 and 40 μm filters

tag: Side population (Hoechst 33342-transporting cells; SP) from freshly isolated epithelial cells cultured for 12 hr


title: HuCNJE-nSP3

description: Human conjunctiva (CNJ) from donor cadaver- Sample #3. Caucasian. Dead from lung cancer at age 64.

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the nSP cells sorted along with SP cells in the third (#3) experiment.

tag: Non  side population (Hoechst 33342-stained cells; nSP) from freshly isolated epithelial cells cultured for 12 hr


title: Wild type Atum 1h 2nd rep


title: HuCNJE-nSP2

description: Human conjunctiva (CNJ) from donor cadaver- Sample #2. Caucasian. Dead from heart infarct at age 58.

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for nSP cells sorted along with the SP cells.

tag: Non  Side population (Hoechst 33342-stained cells; nSP) from freshly isolated epithelial cells cultured for 12 hr.


title: HuCNJE-nSP1

description: Human conjunctiva (CNJ) from donor cadaver- Sample #1. Caucasian dead at 62 from a brain embolism.

data_processing: Expression data was extracted from the fluorescent images using Affymetrix Microarray Suite, version 5.0 (MAS 5.0). The  MAS 5.0 signal intensity (SI) values, the P/A/M detection ‘calls’ representing the chances that the SI value is a true (P, for present), a false (A for absent) or a marginal (M) positive for all 4 pairs of SP/nSP microarrays and the MAS5.0 p-values for these detection calls, were collected in a single Excel (Microsoft, Redmont, WA) file containing 8x3 = 24 columns.  The average signal intensity value per transcripts in each sample (SnAv) and the all sample average (Av-SnAv = 299.97/transcript) were calculated. Each SI value was then  multiplied by the corresponding 299.97/SnAv quotient to generate normalized experiments in which each the  average SI value/transcript is 299.97. The submitted data includes these normalized SI values and the MAS 5.0 P/A/M calls and p-values for the nSP cells sorted along with the SP cells.

label_protocol: RNAs was adjusted by either addition of water or evaporative concentration to a 3 ng/ul and 10 ul were converted into cDNA using SuperScript Choice reverse transcriptase ( Gibco BRL, Bethesda, MD). After two rounds of RNA amplification the final cDNA was synthetized was transcribed in vitro transcription to generate biotin labeled cRNA using the ENZO BioArray™ HighYield™ Kit (Affymetrix).

tag: Non side population (Hoechst 33342-stained;nSP) from freshly isolated epithelial cells cultured for 12 hr.


title: HuCNJE-SP1

source_name: Side population (Hoechst 33342-transporting cells; SP)


title: whole body 1

status: Public on Oct 15 2009

city: Boston

middle: Joseph

last: OConnell

state: MA

address: 77 Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Gene expression data E16.5 TMJ

hyb_protocol: Following fragmentation, cRNA was hybridized on [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix Protocol

data_processing: Data was analyzed using Limma on Bioconductor for R

source_name: E16.5 Mouse

growth_protocol: SAC pregnant females at noon 16.5 days after detection of the copulation plug

extract_protocol: Molecular Devices Pico-Pure Isolation Kit

treatment_protocol: Laser capture microdissection of fresh frozen tissue

value: whole body

tag: developmental stage

value: embryo

tag: age


title: fossa 1

description: Gene expression data E16.5 TMJ

value: TMJ fossa


title: fossa 2

description: Gene expression data E16.5 TMJ


title: condyle 1

description: Gene expression data E16.5 TMJ

value: TMJ condyle


title: whole body 3

description: Gene expression data E16.5 TMJ


title: condyle 3

description: Gene expression data E16.5 TMJ


title: fossa 3

description: Gene expression data E16.5 TMJ


title: whole body 2

description: Gene expression data E16.5 TMJ


title: TA_Habituated_Rep1

city: Sherbrooke

first: Nathalie

last: Beaudoin

state: Quebec

address: 2500, Blvd Universite

department: Faculte des Sciences

institute: Universite de Sherbrooke

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Fluidics protocol EukGE_WS2v5_450

scan_protocol: GeneChip scanner

data_processing: Robust Multichip Average (RMA) via FlexArray software package (http://genomequebec.mcgill.ca/FlexArray).

organism: Populus trichocarpa x Populus deltoides

source_name: 40mL suspension cells, habituated to 1.3µM TA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Hybrid poplar cell suspensions (Populus trichocarpa x Populus deltoides H11-11) maintained in the dark in Murashige and Skoog (MS) medium (pH 5.7) supplemented with B5 vitamins were subcultured weekly in a 1:4 dilution or biweekly for TA-habituated cell suspensions.

extract_protocol: Cells were vacuum-filtered. Then 500 mg were ground in liquid N2 and mixed vigorously with hot extraction buffer consisting in one part of RNA buffer (100 mM Tris pH 8, 10 mM EDTA, 100 mM LiCl, 1% SDS) and one part of equilibrated phenol heated at 80°C. Samples were extracted with chloroform/isoamyl alcohol (24:1) and RNA was precipitated from the supernatant with 4 M LiCl. Pellets were resuspended in DEPC-treated water and extracted with phenol/chloroform/isoamyl alcohol (25:24:1). RNA was precipitated from the aqueous phase with 3 M sodium acetate and ethanol. RNA pellets were dissolved in DEPC-treated water.

treatment_protocol: Habituation of poplar cell suspensions to 1.3 μM TA was performed by adding increasing levels of TA at each subculture over a period of 12 months, beginning with 0.1 μM thaxtomin A. From 2 to 4 subcultures were performed between each step-up in TA concentration. Poplar cells used as control received the same volume of methanol as that added to TA-habituated cells. From a concentration of 0.4 μM TA, TA-habituated cells were subcultured every two weeks due to the reduced growth rate. After 12 months, half of the cells adapted to 1.3 μM of thaxtomin A were transferred to culture medium without TA. These cells are referred to as TA(-)hab cells. These cell suspensions were subcultured every two weeks in the absence of TA for an additional period of at least 18 months (more than 40 subcultures) before performing analyses. TA was diluted in methanol.

tag: genotype

value: Fifth day after sub-culture


title: TA_Habituated_Rep3

value: Populus trichocarpa x Populus deltoides H11-11


title: condyle 2

description: Gene expression data E16.5 TMJ


title: Non-habituated_Rep1

source_name: 40mL suspension cells, without any treatment


title: Non-habituated_Rep3


title: TA_Habituated_Rep2


title: Non-habituated_Rep2


title: E.coliO157_0%sodiumbenzoate_60min_rep1

status: Public on Oct 05 2009

city: Griffin

first: Faith

last: Critzer

state: GA

address: 1109 Experiment St

department: Center for Food Safety/Food Science & Technology

institute: The University of Georgia

description: Affymetrix Prokaryotic Sample and Array Processing Procedures were followed for this microarray experiment using Affymetrix E. coli Genome 2.0 Array

hyb_protocol: Standard Affymetrix Prokaryotic Sample and Array Processing Procedures

data_processing: Affymetrix Microarray Suite/GCOS

organism: Escherichia coli O157:H7 str. EDL933

source_name: 0% sodiumbenzoate_60min

label_protocol: 3ug cDNA used to produce biotin labeled cDNA- per Affymetrix Prokaryotic Sample and Array Processing Procedures

growth_protocol: Cells were incubated at 37C prior to extraction

extract_protocol:
The RNeasy Mini Purification Kit (Qiagen; Valencia, CA) was used to extract total RNA from E. coli O157:H7 cultures.  RNAlater Stabilization Reagent (1.2 ml) (Qiagen; Valencia, CA) was combined with 0.6 ml E. coli O157:H7.  After 10 min at room temperature, the mixture was centrifuged at 8000 x g for 10 min under refrigeration.  The supernatant was decanted and the bacterial pellet was stored at -70°C until further processed (2-10 h).
One hundred µl tris-EDTA buffer (10 mM Tris-Cl, 1 mM EDTA, ph 8.0; Promega; Madison, WI) containing lysozyme (3 mg/ml; Sigma-Aldrich; St. Louis, MO) was added to each cell pellet.  The pellet was thoroughly mixed and incubated at room temperature for 10 min.  Buffer RLT (350 µl) was combined with the tris-EDTA/lysozyme cell suspension to further lyse cells.  The total volume was combined with 250 µl of 200 proof ethanol (Aaper Alcohol; Shelbyville, KY) to solubilize the cell lysate, and the entire sample was transferred to the RNeasy Mini Spin Column in a collection tube and centrifuged at 8000 x g for 15 sec at room temperature.  The silica-based membrane efficiently binds up to 100 µg of RNA longer than 200 bases.  The collection tube and eluate were discarded, and the spin column was placed in a new collection tube.  Buffer RW1 (700 µl) was applied to the column, centrifuged, and flow-through was discarded as described previously.  Twice, 500 µl of buffer RPE was applied to the spin column allowing 5 min prior to centrifugation at 8000 x g for 15 sec.  The spin column was placed in a 1.5 ml collection tube that was used for long-term storage.  In order to elute RNA from the spin column, 30 µl RNase-free water was applied directly to the membrane and centrifuged at 8000 x g for 15 sec.  The RNA eluate was stored at -80°C until evaluated for quantity, quality, and purity.

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0% sodium benozate for 60 minutes

tag: growth phase

value: stationary


title: E.coliO157_0.5% (w/v)sodiumbenzoate_30min_rep1

scan_protocol: Standard Affymetrix Prokaryotic Sample and Array Processing Procedures

source_name: 0.5% (w/v) sodiumbenzoate_30min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0.5% sodium benozate for 30 minutes


title: E.coliO157_0.5% (w/v)sodiumbenzoate_60min_rep2

source_name: 0.5% (w/v) sodiumbenzoate_60min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0.5% sodium benozate for 60 minutes


title: E.coliO157_0%sodiumbenzoate_30min_rep2

source_name: 0% sodiumbenzoate_30min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0% sodium benozate for 30 minutes


title: E.coliO157_0%sodiumbenzoate_60min_rep2


title: E.coliO157_0%sodiumbenzoate_30min_rep1


title: E.coliO157_0%sodiumbenzoate_15min_rep2

source_name: 0% sodiumbenzoate_15min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0% sodium benozate for 15 minutes


title: E.coliO157_0.5% (w/v)sodiumbenzoate_30min_rep2


title: E.coliO157_0%sodiumbenzoate_5min_rep1

source_name: 0% sodiumbenzoate_5min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0% sodium benozate for 5 minutes


title: E.coliO157_0.5% (w/v) sodiumbenzoate_5min_rep2

source_name: 0.5% (w/v) sodiumbenzoate_5min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0.5% sodium benozate for 5 minutes


title: E.coliO157_0%sodiumbenzoate_15min_rep1


title: E.coliO157_0.5% (w/v)sodiumbenzoate_15min_rep2

source_name: 0.5% (w/v) sodiumbenzoate_15min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0.5% sodium benozate for 15 minutes


title: E.coliO157_0.5% (w/v)sodiumbenzoate_15min_rep1


title: E.coliO157_0.5% (w/v)sodiumbenzoate_60min_rep1


title: E.coliO157_0.5% (w/v)sodiumbenzoate_5min_rep1


title: E.coliO157_0.5% (w/v)sodiumbenzoate_0min_rep1

source_name: 0.5% (w/v) sodiumbenzoate_0min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with 0.5% (w/v) sodium benozate


title: E.coliO157_0%sodiumbenzoate_0min_rep1

source_name: 0% sodiumbenzoate_0min

treatment_protocol: Stationary phase growth (24hr) ~8 log CFU/ml was centrifuged at 8000xg 4C and resuspended in Luria-Bertaini broth with no sodium benozate


title: E.coliO157_0%sodiumbenzoate_5min_rep2


title: H51 untreated hESCs, biological rep2

status: Public on Oct 02 2009

city: Jerusalem

first: Reba

last: Condiotti

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah Medical Center

description: Gene expression data from hESCs differentiating without NIC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: hESCs differentiating without NIC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Differentiation of hESCs in suspension in the presence of 10% FCS for 4 weeks.

treatment_protocol: Differentiation was in the presence or absence of nicotinamide (NIC) for 4 weeks.

tag: cell type

value: human ES cells

tag: treatment

value: Differentiating for 4 weeks in suspension without NIC


title: H50 untreated hESCs, biological rep1


title: E.coliO157_0%sodiumbenzoate_0min_rep2


title: H53 NIC-treated hESCs, biological rep1

description: Gene expression data from hESCs differentiating with NIC

source_name: hESCs differentiating with NIC

value: Differentiating for 4 weeks in suspension with NIC


title: H52 untreated hESCs, biological rep3


title: H54 NIC-treated hESCs, biological rep2


title: H55 NIC-treated hESCs, biological rep3

description:
Gene expression data from hESCs differentiating with NIC
CEL file H55 U133A2.CEL is missing


title: B-ALL, No molecular abnormalities 5 (microRNA)

status: Public on Oct 01 2009

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: Gene expression data from patient with newly diagnosed ALL  (percentage of leukemic cells at least 80%)

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies)

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: Data were analyzed with R. Signal values from each array were background subtracted (array background value was set as quantified by the service provider), quantile-normalized between the 7 intra-array replicates and the signal value for each miRNA summarized as the average of repeating spots. Processed miRNA intensity values were normalized between-array by quantile normalization.

source_name: Bone Marrow

label_protocol: Lc Sciences proprietary labeling method which utilizes an affinity tag for signal amplification after miRNA hybridization to the chip

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

tag: gender

value: Male

value: Bone Marrow

tag: phenotype

value: B


title: B-ALL, No molecular abnormalities 6 (microRNA)

value: B common


title: Populus_ARK2 overexpression lines_rep3

city: davis

first: Andrew

last: Groover

state: CA

address: 1731 research park drive

department: Institute of Forest Genetics

institute: USDA FOREST SERVICE

description: total RNA extracted from two month old transgenics populus stem tissue

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Populus

source_name: ARK2 overexpression line5

label_protocol: Affymetrix one-cycle target kit (One-Cycle Target Labeling and Control Reagents, Affymetrix, P/N 900493)

extract_protocol: Qiagen RNeasy Plant Mini Kit Protocol

value: whole stem tissue without leaves

value: Two month old tissue culture

tag: transgenic

value: ark2 overexpression


title: E.coliO157_0.5% (w/v)sodiumbenzoate_0min_rep2


title: Populus_ARK2 overexpression lines_rep2

source_name: ARK2 overexpression transgenics lines2

tag: tissue

tag: transgenic plant


title: Populus_amiRNA lines_rep2

source_name: amiRNA lines replicate 2

value: ark2 artificial microRNA


title: Populus_amiRNA lines_rep3

source_name: amiRNA lines replicate 3


title: B-ALL, No molecular abnormalities 4 (microRNA)

value: pre B


title: B-ALL, No molecular abnormalities 3 (microRNA)

source_name: Peripheral Blood

value: Female

value: Peripheral Blood


title: Populus_wild type_rep4

description: total RNA extracted from two month old populus stem tissue

source_name: wild type replicate 4

value: no


title: B-ALL, No molecular abnormalities 1  (microRNA)


title: Populus_wild type_rep2

source_name: wild type replicate 2


title: Populus_ARK2 overexpression lines_rep1

source_name: ARK2 overexpression transgenics line1


title: Populus_amiRNA lines_rep1

source_name: amiRNA lines replicate 1


title: Populus_wild type_rep1

description: Total RNA extracted from two month old Populus stem tissue

label: Biotin labeling

source_name: wild type replicate 1


title: Populus_wild type_rep3

source_name: wild type replicate 3


title: B-ALL, No molecular abnormalities 2 (microRNA)

value: pro B


title: B-ALL, E2A/PBX1 3 (microRNA)


title: Universal Human Reference RNA_sample A_rep1 (A1)

city: Gaithersburg

first: Michael

middle: Ian

last: Brenner

state: MD

address: 217 Perry Parkway bld 5

institute: ExonHit Therapeutics

hyb_protocol: Standard hybridization methods of the labeled samples to the Affymetrix-formatted SpliceArrayTM were used following the manufacturer’s recommendations for the 49-format (Affymetrix - Expression analysis technical manual).  The arrays were stained and washed using the Affymetrix FS450-0001 fluidics protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G.  DAT and CEL images were visually inspected for anomalies and accurate grid placement.

data_processing: Data processing was performed using Partek® software (http://www.partek.com/). 12 .CEL files were imported into Partek® software.  All array data was pre-processed which included probe level RMA background correction, quantile normalization across all arrays, and Log2 transformation followed by median polish to summarize probes to obtain the overall score for each probe set.

source_name: Universal Human Reference RNA, # 740000 purchased from Stratagene (LaJolla, CA, USA)

label_protocol: Fragmentation and biotin-labeling of the amplified cDNA was performed using the FL-Ovation™ cDNA Biotin Module V2 (NuGen product #4200; Santa Clara, CA, USA) as per manufacturer’s instructions.

extract_protocol: Amplified cDNA was prepared using the WT-Ovation™ Pico RNA Amplification System (NuGen product #3300; Santa Clara, CA, USA) starting with 50 ng of each total RNA sample (A, B, C, D), as described by the manufacturer.  Briefly, the RNA is synthesized into double-stranded cDNA using a SPIA™ DNA/RNA primer.  The DNA portion of the primer binds poly (A) sequence or randomly across the transcript, and the RNA portion of the primer is incorporated into an unique DNA/RNA heteroduplex at one end of the cDNA.  RNase H degrades the RNA portion of the DNA/RNA heteroduplex allowing for additional SPIA™ primer to bind and initiate replication by DNA polymerase.  The process of SPIA™ DNA/RNA primer binding, DNA replication, strand displacement and RNA cleavage is repeated resulting in isothermal linear amplification of the cDNA.  On average, the cDNA yield from 50 ng of high quality total RNA ranges from 6 to 10 micrograms.

tag: maqc sample

value: A (Universal Human Reference RNA)


title: B-ALL, E2A/PBX1 1 (microRNA)


title: B-ALL, MLL/AF4 2 (microRNA)


title: B-ALL, MLL/AF4 3 (microRNA)


title: B-ALL, MLL/AF4 1 (microRNA)


title: Universal Human Reference RNA_sample A_rep2 (A2)


title: B-ALL, BCR/ABL 4 (microRNA)


title: Universal Human Reference RNA_sample A_rep3 (A3)


title: B-ALL, BCR/ABL 3 (microRNA)


title: 75% human universal reference+25% human brain RNA_sample C_rep1 (C1)

source_name: A mixture of sample A and B – 75% sample A + 25% sample B

value: C [75% sample A (Universal Human Reference RNA)+ 25% sample:B (Human Brain Total RNA)]


title: B-ALL, BCR/ABL 2 (microRNA)


title: 75% human universal reference+25% human brain RNA_sample C_rep3 (C3)


title: T-ALL, SIL/TAL 2 (microRNA)

value: T


title: B-ALL, BCR/ABL 1 (microRNA)


title: T-ALL, No molecular abnormalities 1 (microRNA)

value: pre T


title: Human Brain Total RNA_sample B_rep2 (B2)

source_name: Human Brain Total RNA, # AM7962 (sample B) purchased from Ambion (Austin, TX, USA)

value: B (Human Brain Total RNA)


title: B-ALL, E2A/PBX1 2 (microRNA)

value: Bone Marrow


title: T-ALL, No molecular abnormalities 2 (microRNA)

value: mature T


title: 25% human universal reference+75% human brain RNA_sample D_rep1 (D1)

source_name: A mixture of sample A and B – 25% sample A + 75% sample B

value: D [25% sample A (Universal Human Reference RNA)+ 75% sample:B (Human Brain Total RNA)]


title: Human Brain Total RNA_sample B_rep1 (B1)


title: T-ALL, SIL/TAL 1 (microRNA)

value: Male


title: 25% human universal reference+75% human brain RNA_sample D_rep3 (D3)


title: 75% human universal reference+25% human brain RNA_sample C_rep2 (C2)


title: Mouse_L2CreKlf4Loxp/Loxp_3mo_rep2

city: Philadelphia

first: Jonathan

middle: P.

last: Katz

state: PA

address: 913 BRBII/III, 421 Curie Blvd.

department: Medicine/Gastroenterology

institute: University of Pennsylvania

description: no additional information

hyb_protocol: 15ug biotinylated cRNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to MOE430 2.0 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: An Affymetrix GCS3000 7G scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: rma was calculated with Partek Genomics Suite v6.4 from cel files, using default settings to exclude Afftymetrix-annotated control probesets, yielding values for 28853 non-control probesets.

source_name: Mouse, Klf4 deleted

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter.  Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript, and the resulting cRNA was fragmented and assessed by Bioanalyzer.

extract_protocol: Total RNA extraction was performed using Qiagen RNeasy mini kit according to the manufacturer's instructions.

tag: genotype/variation

value: Klf4 mutant

value: female

tag: strain

value: mixed genetic background

value: esophagus

value: epithelial

value: 3 months


title: Mouse_L2CreKlf4Loxp/Loxp_3mo_rep3

description: no additional information


title: Human Brain Total RNA_sample B_rep3 (B3)


title: Mouse_L2CreKlf4Loxp/Loxp_3mo_rep1

description: no additional information

value: male


title: Mouse_Klf4Loxp/Loxp_3mo_rep2

description: no additional information

source_name: Mouse, Control

value: control (lacking the Cre transgene)


title: Mouse_Klf4Loxp/Loxp_3mo_rep3

description: no additional information


title: Mouse_Klf4Loxp/Loxp_3mo_rep1

description: no additional information


title: DT40 expressing OsTIR1 (-IAA control)

city: Toyonaka

first: Masato

last: Kanemaki

state: Osaka

address: Machikaneyama 1-1,

department: Department of Biological Sciences,

country: Japan

institute: Osaka University

description: Gene expression after 6 hours

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: standard Agilent protocol

organism: Gallus gallus

source_name: DT40 cells expressing OsTIR1

label_protocol: standard Agilent protocol

growth_protocol: DT40 cells were grown in DMEM containing 10% FCS, 1% chicken serum and 10nM beta-ME at 38.5oC.

extract_protocol: Following the Qiagen RNeasy Midi Kit protocol.

treatment_protocol: 1/1000 vomume of 0.5M Indole-3-acetic acid (IAA) dissolved in EtOH was added to make final concentration at 500µM.  Cells were maintained at 38.5oC for 6 hours before harvest.

tag: cell line


title: SHEP21N_MYC_hypoxia

status: Public on Sep 30 2009

city: Genoa

first: Paolo

last: Fardin

address: Largo G. Gaslini 5

department: Molecular Biology

institute: Istiuto Giannina Gaslini

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, and 100 ug/mL streptomycin (Euroclone Ltd) at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2. Hypoxic conditions (1% O2) were achieved by culturing the cells in an anaerobic workstation incubator (BUG BOX, Jouan, ALC International S.r.l., Cologno Monzese, Milano, Italy) flushed with a gas mixture containing 1% O2, 5% CO2, and balanced N2 at 37°C in a humidified atmosphere. Oxygen tension in the medium was measured with a portable, trace oxygen analyzer (Oxi 315i/set, WTW; VWR International, Milano, Italy).

hyb_protocol: Fragmented cRNA was used for hybridization to Affymetrix HG-U133 plus 2.0 arrays according to the Affymetrix’s instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Expression values were quantified and array quality control was performed with the statistical algorithms implemented in Affymetrix Microarray Suite 5.0.

source_name: neuroblastoma cell line under hypoxic conditions

label_protocol: The RNA was reverse-transcribed into cDNA and biotin labeled according to the Affymetrix’s instructions.

extract_protocol: Total RNA was extracted from cell lines using Trizol (Invitrogen Life technologies, Irvine, CA) according to the manufacturer's instructions.

tag: mycn

value: with overexpression

tag: condition

value: hypoxia


title: DT40 expressing OsTIR1 (+500µMIAA)

description: Gene expression after 6 hours


title: LEC KSHV_Cluster, rep3

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

institute: UCL

description: Biological replicate 3 of 3.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hgu133plus2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix hgu133plus2 chips were scanned using the Affymetrix Scanner 3000 7G and the MAS 5.1 software as per the manufacturer's protocol http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf

data_processing: Data was preprocessed and normalised using the Bioconductor 'affy' package, specifically the robust multiarray algorithm ('RMA').

source_name: lymphatic endothelial cells, KSHV microRNA cluster

label_protocol: 1 ug of total RNA was used to generate cDNA using T7-linked oligo(dT)primer and the custom SuperScript dscDNA synthesis kit (Invitrogen). After second-strand syntheis, in vitro transcription was carried with biotinylated UTP and CTP using GeneChip® IVT Labeling Kit (http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf)

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from MVEC cells using a polyclonal antibody of podoplanin, a LEC-specific marker, and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C, in fibronectin-coated plates. KSHV microRNA Cluster-transfected LEC were grown under the same conditions. All cells were mycoplasma free.

extract_protocol: TRIzol solution (Invitrogen) extraction followed by RNeasy Mini kit (Qiagen) purification. Assessed RNA integrity and quantity using RNA 6000 Nano chips (Agilent).

treatment_protocol: Lymphatic endothelial cells (LECs) were plated in six well plates (10^5cells/well) and were transduced with lentiviruses encoding the KSHV microRNA cluster or empty vector (pSIN-MCS). Three days after infection, cultures were used for RNA extraction. Typically six wells of a 6-well plate were used per Affymetrix chip.

value: lymphatic endothelial cells

tag: vector

value: pSIN-MCS-KSCluster


title: SHEP21N_normoxia

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, 100 ug/mL streptomycin (Euroclone Ltd), and 50 ng/mL tetracycline (Sigma, St. Louis, MO)at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2.

source_name: neuroblastoma cell line under normoxic conditions

value: without overexpression

value: normoxia


title: SHEP21N_MYC_normoxia

description: The cell lines were cultured in RPMI 16140 (Euroclone Ltd., Celbio, Milan, Italy), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, Milan Italy), 2 mmol/L L-glutamine, 10 mM Hepes, 100 units/mL penicillin, and 100 ug/mL streptomycin (Euroclone Ltd) at 37° C in a humidified incubator containing 20% O2, 5% CO2, and 75% N2.