title: LeafBlade_90DAT_12:00_2010

description: Gene expression of leaf blade at daytime 90 days after transplanting in 2010

source_name: Leaf blade, 90 days after transplanting, 12:00, 2010

value: 90 days after transplanting


title: LNCaP siRNA-H Replicate 1

status: Public on Jul 20 2013

type: RNA

city: Ann Arbor

first: Matthew

last: Iyer

state: MI

address: 5316 CCGC 0940 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

country: USA

institute: University of Michigan

description:
Biological replicate 1 of 2 (siRNA H)
07012011_251485068573_S01_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Control Features were omitted. The LogRatio and PValueLogRatio columns from each feature file were then merged into a single processed data matrix

molecule: total RNA

organism: Homo sapiens

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Cells were grown in RPMI 1640 (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNA was isolated using Trizol and an RNeasy Kit (Invitrogen) with DNase I digestion according to the manufacturer’s instructions.

treatment_protocol: Cells were plated in 100mM plates at a desired concentration and transfected with 20uM experimental siRNA oligos or non-targeting controls twice, at 12 hours and 36 hours post-plating.  Knockdowns were performed with Oligofectamine and Optimem.  Knockdown efficiency was determined by qPCR.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cells

tag: transfected with

value: 20uM SChLAP1-siRNA oligos at 12 hr and 36 hr post-plating

source_name: LNCaP_non-targeting siRNA

value: 20uM non-targeting control-siRNA oligos at 12 hr and 36 hr post-plating


title: 22Rv1 siRNA-J Replicate 3

description:
Biological replicate 2 of 2 (siRNA J)
07092011_251485068627_S01_GE2-v5_95_Feb07_1_4.txt

source_name: 22Rv1_non-targeting siRNA


title: LNCaP siRNA-H Replicate 3

description:
Biological replicate 1 of 2 (siRNA H)
07262011_251485068650_S01_GE2-v5_95_Feb07_1_2.txt


title: LeafBlade_83DAT_12:00_2010

city: Tsukuba

first: Yutaka

last: Sato

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression of leaf blade at daytime 83 days after transplanting in 2010

hyb_protocol: For hybridization, 1650 ng of cyanine 3-labeled cRNA is fragmented and hybridized on the slide of rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75 percentile normalization and log2 transformation with GenespringGX12(Agilent).

organism: Oryza sativa Japonica Group

source_name: Leaf blade, 83 days after transplanting, 12:00, 2010

label_protocol: 400 ng of total RNA was added with one-color spike-mix and labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent) in the presence of cyanine-3-CTP accoring to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN), and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: All plants were grown in paddy field in Tsukuba, Japan (~36o N latitude) during a normal rice growing season in 2010.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) according to the manufacturer's protocol, quantitied using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: cultivar

value: Nipponbare

tag: organ/tissue

value: Leaf Blade

tag: growth/development stage

value: 83 days after transplanting

tag: sampling time

value: Daytime 12:00


title: [reference]_[low exposed_female_rep2]

city: Wilrijk

first: An

last: Hagenaars

state: Antwerp

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

description:
Total RNA extraction: Trizol method
Fluorescently labeled cRNA: Quick Amp labeling kit Agilent
Hybridization: Agilent’s two-color microarray-based gene expression analysis protocol
Scanning: Genepix Personal 4100A confocal scanner

hyb_protocol: The hybridization was performed according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Two probe volumes (Cy3 vs. Cy5) corresponding with 300ng cRNA were mixed and applied onto every microarray. The microarray slides were incubated at 65°C for 17 hours in a hybridization chamber which was placed in a rotating (10rpm) Agilent hybridization oven. The slides were washed with Agilent wash buffers and acetonitrile and finally submersed in Agilent stabilization and drying solution to protect against ozone-induced degradation of the cyanine dyes.

scan_protocol: Microarrays were scanned at 532 and 635 nm using the Genepix Personal 4100A confocal scanner (Axon instruments, Union City, USA) at a resolution of 5µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing: Statistical analysis was performed in the open source statistical programming environment R, using the Bioconductor package limma (Linear Models for Microarray Data) (Smyth, 2005). Briefly, spots for which the mean foreground signal was lower than the mean local BG+2SD (BG: background signal, SD: standard deviation of the background) and spots with oversaturated signal intensities on all microarrays were filtered out before analysis. Intensity data were corrected using a normal-exponential convolution model (Ritchie et al., 2007) and normalized using the lowess method (Smyth and Speed, 2003). An empirical Bayes method was used to estimate contrasts of interest from the normalized and linear model-fitted data (Smyth, 2004). The different exposure concentrations of males and females were contrasted against their respective controls. Gene transcripts were considered significantly different if the log2 ratio of a contrast was ≤-0.75 or ≥+0.75 and the p-value was <0.05.

organism: Danio rerio

source_name: reference

label_protocol: Fluorescently labelled cRNA was constructed using the Quick Amp labelling kit (Agilent Technologies, Diegem, Belgium) according to Agilent’s two-color microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com). Briefly, total RNA was reverse transcribed into first and second strand cDNA. Using T7 RNA polymerase, the second strand cDNA was converted in cRNA while either Cy3-CTP or Cy5-CTP was incorporated. The labelled cRNA was purified using the Qiagen RNeasy mini spin column kit (Qiagen, Venlo, The Netherlands) and labelling efficiency was determined by spectrophotometry at 550nm (Cy3) and 650nm (Cy5) (NanoDrop, NanoDrop Technologies, Rockland, USA).

extract_protocol: The livers of the fish were homogenized in liquid nitrogen and total liver RNA was extracted applying the Trizol-RNA extraction procedure (Gibco BRL, Life Technologies, Merelbeke, Belgium). The extracted RNA was purified using Dnase I and RNase inhibitor (Fermentas, St. Leon-Rot, Germany) followed by a phenol/chloroform extraction. RNA integrity was checked by denaturing formaldehyde-agarose gel electrophoresis. RNA quality was measured using spectrophotometry (NanoDrop, NanoDrop Technologies, Rockland, DE, USA): absorbance at 260nm (RNA), 280nm (proteins) and 230nm (organic contaminants and solvents) was determined and all RNA samples had 260/280 and 260/230 ratios >1.8.

treatment_protocol: The liver of the fish was dissected on ice and the livers from 6 fish per biological replicate (males and females separately) were pooled and snap frozen in liquid nitrogen. All samples were stored at -80°C until further analysis.

tag: reference

value: equal amounts of pooled RNA from all samples of the experiment

source_name: low exposed_female_rep2

tag: gender

value: female

tag: tissue

value: liver

tag: exposure condition

value: exposed to 0.1mg/l PFOA


title: LeafBlade_62DAT_12:00_2010

description: Gene expression of leaf blade at daytime 62 days after transplanting in 2010

source_name: Leaf blade, 62 days after transplanting, 12:00, 2010

value: 62 days after transplanting


title: LeafBlade_69DAT_12:00_2010

description: Gene expression of leaf blade at daytime 69 days after transplanting in 2010

source_name: Leaf blade, 69 days after transplanting, 12:00, 2010

value: 69 days after transplanting


title: 22Rv1 siRNA-J Replicate 1

description:
Biological replicate 2 of 2 (siRNA J)
07012011_251485068572_S01_GE2-v5_95_Feb07_1_2.txt


title: LeafBlade_76DAT_12:00_2010

description: Gene expression of leaf blade at daytime 76 days after transplanting in 2010

source_name: Leaf blade, 76 days after transplanting, 12:00, 2010

value: 76 days after transplanting


title: 22Rv1 siRNA-J Replicate 2

description:
Biological replicate 2 of 2 (siRNA J)
07092011_251485068627_S01_GE2-v5_95_Feb07_1_3.txt


title: [high exposed_female_rep1]_[reference]

source_name: high exposed_female_rep1

value: exposed to 1mg/l PFOA


title: LeafBlade_48DAT_12:00_2010

description: Gene expression of leaf blade at daytime 48 days after transplanting in 2010

source_name: Leaf blade, 48 days after transplanting, 12:00, 2010

value: 48 days after transplanting


title: [control_female_rep2]_[low exposed_female_rep2]

value: control


title: [control_female_rep2]_[reference]


title: [Reference]_[high exposed_female_rep2]

source_name: Reference

source_name: high exposed_female_rep2


title: LeafBlade_41DAT_12:00_2010

description: Gene expression of leaf blade at daytime 41 days after transplanting in 2010

source_name: Leaf blade, 41 days after transplanting, 12:00, 2010

value: 41 days after transplanting


title: 22Rv1 siRNA-H Replicate 2

description:
Biological replicate 1 of 2 (siRNA H)
07092011_251485068627_S01_GE2-v5_95_Feb07_1_1.txt

value: prostate cancer cells

value: 20uM SChLAP1-siRNA oligos at 12 hr and 36 hr post-plating


title: [reference]_[control_female_rep1]


title: LeafBlade_20DAT_12:00_2010

description: Gene expression of leaf blade at daytime 20 days after transplanting in 2010

source_name: Leaf blade, 20 days after transplanting, 12:00, 2010

value: Nipponbare

value: 20 days after transplanting


title: LeafBlade_13DAT_12:00_2010

description: Gene expression of leaf blade at daytime 13 days after transplanting in 2010

source_name: Leaf blade, 13 days after transplanting, 12:00, 2010

value: Leaf Blade

value: 13 days after transplanting


title: LeafBlade_34DAT_12:00_2010

description: Gene expression of leaf blade at daytime 34 days after transplanting in 2010

source_name: Leaf blade, 34 days after transplanting, 12:00, 2010

value: 34 days after transplanting

value: Daytime 12:00


title: LeafBlade_55DAT_12:00_2010

description: Gene expression of leaf blade at daytime 55 days after transplanting in 2010

source_name: Leaf blade, 55 days after transplanting, 12:00, 2010

value: 55 days after transplanting


title: p4 3

status: Public on Jul 19 2013

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

hyb_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit and Agilent 60-mer oligo microarray processing protocol; Agilent, Palo Alto, CA

scan_protocol: Agilent laser-based detection system (Agilent, Palo Alto, CA)

data_processing:
Raw expression data were imported into JMP® Genomics v3.2 (SAS, Cary, NC).  Raw intensity data for each microarray were normalized using a ratio design (Cy5/Cy3)
data first filtered by signal intensity

organism: Pimephales promelas

source_name: ovulated eggs

extract_protocol: Total RNA for microarray analysis was extracted from FHM ovary using RNA STAT-60 reagent (TEL-TEST Inc., Friendswood, TX, USA)

treatment_protocol: The ovaries were exposed to media containing 500 ng/L progesterone (Sigma) or a control consisting of 0.05% of the carrier solvent (95% ethanol). Exposures were run in duplicate at 25 °C for 4 hours.

value: ovulated eggs

tag: treatment

value: progesterone

source_name: mixed ovulated eggs

value: mixed reference


title: 22Rv1 siRNA-H Replicate 3

description:
Biological replicate 1 of 2 (siRNA H)
07092011_251485068627_S01_GE2-v5_95_Feb07_1_2.txt

source_name: 22Rv1_non-targeting siRNA

value: 20uM non-targeting control-siRNA oligos at 12 hr and 36 hr post-plating


title: control 3

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit and Agilent 60-mer oligo microarray processing protocol; Agilent, Palo Alto, CA

value: solvent


title: p4 2


title: [high exposed_female_rep2]_[control_female_rep2]

value: female

value: liver

value: exposed to 1mg/l PFOA


title: p4 1


title: control 2


title: [high exposed_male_rep2]_[high exposed_female_rep2]

source_name: high exposed_male_rep2

value: male


title: 22Rv1 siRNA-H Replicate 1

description:
Biological replicate 1 of 2 (siRNA H)
07012011_251485068572_S01_GE2-v5_95_Feb07_1_1.txt

value: prostate cancer cells

value: 20uM SChLAP1-siRNA oligos at 12 hr and 36 hr post-plating


title: Retina_PTC_7days_rep2

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Con vs PTC 2_252665512820_1_4

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

organism: Mus musculus

source_name: retina, 7 days

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: We intravitreally injected PBS or titanium dioxide nanoparticles (PTC and 10 times PTC) into the right eyes of 8-week-old male C57BL/6 mice. One week later, the mice were sacrificed and the eyes were enucleated.

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

treatment_protocol: Retinal tissues were prepared from the enucleated eyes. Four retinal tissues were pooled into 1 test tube.

tag: strain

value: retina

tag: developmental stage

value: adult

value: control

tag: age

value: PTC


title: Retina_10PTC_7days_rep2

description: Con vs 10PTC-2_252665512821_1_3


title: Retina_10PTC_7days_rep1

description: Con vs 10PTC-1_252665512821_1_2


title: [control_male_rep1]_[high_exposed_male_rep1]


title: [high exposed_female_rep1]_[control_female_rep1]


title: LeafBlade_27DAT_12:00_2010

description: Gene expression of leaf blade at daytime 27 days after transplanting in 2010

source_name: Leaf blade, 27 days after transplanting, 12:00, 2010

value: Nipponbare

value: Leaf Blade

value: 27 days after transplanting

value: Daytime 12:00


title: p4 4

value: ovulated eggs

value: progesterone

value: mixed reference


title: Retina_PTC_7days_rep1

description: Con vs PTC 1_252665512820_1_3


title: Retina_10PTC_7days_rep3

description: Con vs 10PTC-3_252665512821_1_4


title: Retina_PTC_7days_rep3

description: Con vs PTC 3_252665512821_1_1


title: control 1

value: solvent


title: adjacent tissue normal glands TYC0062N

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: frozen tissue extracted by Trizol

hyb_protocol: Total RNA was reverse transcripted to cDNA, reverse transcripted to labelled aRNA, purified, fragmented, and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The arrays were then washed using Affymetrix fluidics stations, and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data were normalized using the RMA method .

label: Biotin

source_name: adjacent normal tissue

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted and purified by standard Trizol method and followed with qualification check by Agilent 2100.

value: adjacent tissue normal gastric glands


title: tumor tissue cardia of gastric TYC0059T

description: frozen tissue extracted by Trizol

source_name: tumor tissue

value: tumor tissue cardia of stomach


title: [reference]_[control_male_rep1]

source_name: reference

value: equal amounts of pooled RNA from all samples of the experiment

value: male

value: liver


title: tumor tissue cardia of gastric TYC0057T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0060T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0061T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0061N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0058N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0053T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0053N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0056T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0059N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0057N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0060N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0058T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0062T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0054N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0051N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0055T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0055N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0049T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0052N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0052T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0056N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0050N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0049N

description: frozen tissue extracted by Trizol


title: [low exposed_female_rep2]_[high exposed_female_rep1]

source_name: low exposed_female_rep2

value: female

value: exposed to 0.1mg/l PFOA

source_name: high exposed_female_rep1

value: exposed to 1mg/l PFOA


title: tumor tissue cardia of gastric TYC0050T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0051T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0054T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0048T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0045T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0046T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0046N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0043N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0042N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0043T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0045N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0047T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0041T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0047N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0041N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0044N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0042T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0040T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0044T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0040N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0039T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0048N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0038N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0037N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0036T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0037T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0039N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0034T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0034N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0038T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0035T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0036N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0033T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0032N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0028N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0033N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0030N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0031N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0032T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0035N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0030T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0026N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0029N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0029T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0025T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0027N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0028T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0031T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0027T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0024T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0025N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0023N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0022N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0020T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0023T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0021T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0022T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0024N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0021N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0018T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0020N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0019N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0018N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0019T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0026T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0017N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0016N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0013T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0012T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0015T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0016T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0014N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0010T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0010N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0014T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0013N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0015N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0017T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0012N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0009N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0011T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0005T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0011N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0009T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0008N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0006T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0007N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0003N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0008T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0007T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0002T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0004T

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0001T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0070T

description: frozen tissue extracted by Trizol

value: tumor tissue non-cardia of stomach


title: adjacent tissue normal glands TYC0002N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0072T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0004N

description: frozen tissue extracted by Trizol


title: tumor tissue cardia of gastric TYC0003T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0071N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0005N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0069N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0070N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0068T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0072N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0069T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0001N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0068N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0067T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0071T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0067N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYC0006N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0065T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0062T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0065N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0062N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0064N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0066N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0066T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0061N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0057T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0063T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0060T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0064T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0059T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0063N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0056N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0058T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0057N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0058N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0061T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0054N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0056T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0060N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0055N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0059N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0055T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0052T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0052N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0051N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0049T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0051T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0049N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0054T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0048N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0050T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0053N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0048T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0046N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0044T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0047N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0045T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0047T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0045N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0043T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0041N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0041T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0044N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0039N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0042T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0037T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0050N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0040T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0037N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0035N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0043N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0034T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0040N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0039T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0046T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0036N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0038T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0038N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0042N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0034N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0031N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0035T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0031T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0033N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0036T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0028N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0028T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0030T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0027N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0032N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0026T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0033T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0030N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0029T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0027T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0032T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0025T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0025N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0023N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0026N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0024N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0053T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0029N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0022T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0022N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0024T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0020N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0021T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0023T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0018N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0019T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0021N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0019N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0018T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0017N

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0016N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0020T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0017T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0016T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0015N

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4121

type: genomic

first: Vijay

last: Nagarajan

state: Maryland

address: 10 Center Drive, 10/10N248

department: National Eye Institute

institute: National Institutes Of Health

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
Quality analysis was performed by importing the CEL files into Genotyping Console (GTC 4.0) according to the “Quality Control Assessment 123 in Genotyping Console”
primary data description: #SNP List=KMD_2_33S_99
primary data description: #GenomeWideSNP_6.na31.annot.db
primary data description: #%genome-version-ucsc=hg19
primary data description: #%genome-version-ncbi=GRCh37

molecule: genomic DNA

source_name: B cells isolated from peripheral blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: B cells were isolated from peripheral blood during flow sorting using anti-CD19 antibody (BD Biosciences)

extract_protocol: DNA targets from patients and healthy controls were prepared and hybridized to Affymetrix Genome-Wide Human SNP array 6.0 chips following the manufacturer’s recommendations.

tag: diagnosis

value: Systemic Capillary Leak Syndrome (Clarkson disease)


title: tumor tissue non-cardia of gastric TYB0014T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0014N

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4127


title: tumor tissue non-cardia of gastric TYB0015T

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4125


title: SCLS_Patient_4117


title: Reference_4129

source_name: Affymetrix reference


title: adjacent tissue normal glands TYB0013N

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4120


title: SCLS_Patient_4128


title: SCLS_Patient_4119


title: adjacent tissue normal glands TYB0012N

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4118


title: tumor tissue non-cardia of gastric TYB0012T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0013T

description: frozen tissue extracted by Trizol


title: SCLS_Patient_4114


title: SCLS_Patient_4115


title: Relative_4112

value: healthy


title: SCLS_Patient_4123


title: tumor tissue non-cardia of gastric TYB0010T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0011T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0011N

description: frozen tissue extracted by Trizol


title: Healthy_Donor_4107


title: inducedHepSC_Cholang_diff_rep2

city: Shanghai

first: Pu

last: You

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Gene expression Cholangiocyte differentiation derived from iHepSC6

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: iHepSC Cholangiocyte differentiation, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: iHepSCs which were converted form fibroblasts by transduction of Hnf1β and Foxa3 were sustained in hepatic stem cell medium (DMEM/F12 medium supplemented with 10% FBS, 1% penicillin/streptomycin, 0.1 mmol/L 2-mercaptoethanol, 10 ng/mL HGF, 10 ng/mL EGF,1×ITS, 10-7 mol/L dexamethasone, 10 ng/mL nicotinamide, and 50 mg/mL gentamicin). iHepSCs-derived cholangiocytes were induced from iHepSCs cultured in 3D collagen type 1 systerm. MEFs and LEPCs were cultured in DMEM supplemented with 10%FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNAs  were  prepared from  MEFs, iHepSCs, LEPCs  and  iHepSC-derived cholangiocytes using an RNeasy MiniKit (Qiagen) following the manufacturer's recommendations.

treatment_protocol: iHepSCs, MEFs and LEPCs were collected after trypsinized with 0.05% Trypsin/EDTA. iHepSCs-derived cholangiocytes were recovered from collagen I gel digested with Collagenase IV.

value: induced differention cells


title: Healthy_Donor_4108


title: SCLS_Patient_4116


title: Relative_4111


title: inducedHepSC_Cholang_diff_rep1

description: Gene expression Cholangiocyte differentiation derived from iHepSC2

source_name: iHepSC Cholangiocyte differentiation, replicate 1


title: Healthy_Donor_4106


title: Healthy_Donor_4110


title: MEF_rep1

description: Gene expression MEF1

source_name: MEF, replicate 1

value: embryonic fibroblast


title: LiverEpiProgCells_rep1

description: Gene expression LEPCs

source_name: liver epithelial progenitor cells, replicate 1

value: adult liver progenitor cells


title: Healthy_Donor_4109


title: MEF_rep2

description: Gene expression MEF2

source_name: MEF, replicate 2


title: adjacent tissue normal glands TYB0006N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0008T

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0009T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0007N

description: frozen tissue extracted by Trizol


title: inducedHepSC_rep3

description: Gene expression iHepSC clone 4

source_name: induced Hepatic Stem Cells, replicate 3

value: embryonic fibroblast induced cells


title: adjacent tissue normal glands TYB0008N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0006T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0009N

description: frozen tissue extracted by Trizol


title: inducedHepSC_rep4

description: GeGene expression iHepSC clone 6

source_name: induced Hepatic Stem Cells, replicate 4


title: tumor tissue non-cardia of gastric TYB0007T

description: frozen tissue extracted by Trizol


title: adjacent tissue normal glands TYB0005N

description: frozen tissue extracted by Trizol


title: inducedHepSC_rep2

description: Gene expression iHepSC clone 3

source_name: induced Hepatic Stem Cells, replicate 2


title: Healthy_Donor_4104


title: tumor tissue non-cardia of gastric TYB0005T

description: frozen tissue extracted by Trizol


title: Healthy_Donor_4100


title: Healthy_Donor_4101


title: dental follicle cells differentiation 2

city: Regensburg

first: Oliver

last: Felthaus

address: Franz-Josef-Strauss-Allee 11

department: Department of Cranio- and Maxillofacial Surgery

country: Germany

institute: University Hospital Regensburg

description: Gene expression of dental follicle cells

hyb_protocol: Hybridization to Affymetrix oligonucleotide microarray Human Gene 1.1 ST array was carried out overnight with 1biotin-labeled cRNA in a hybridization oven 640.

scan_protocol: GeneTitan scanner (Affymetrix)

data_processing:
Affymetrix GeneChip Operating Software (GCOS) 1.4 and the Expression Console 1.1. Software. For the creation of the summarized log-signal the robust multi-chip analysis (RMA) algorithm was used.
For the creation of the summarized log-signal the robust multi-chip analysis (RAM) algorithm was used

label: biotin

source_name: dental follicle cells in StemPro osteogenic differentiation  medium

label_protocol: Double-stranded cDNA was prepared from 5 μg of total cellular RNA (cDNA synthesis kit, Affymetrix Santa Clara, CA, USA), in vitro transcribed using an IVT labeling kit, and the cRNA product purified using a GeneChip Sample Cleanup Module (Affymetrix). All procedures according to the Affymetrix protocol.

growth_protocol: Cell were grown in DMEM medium (PAA, Pasching, Austria) and 10 % serum at 37°C in 5% CO2.

extract_protocol: Total RNAs were extracted using the kit NucleoSpin® RNA II kit (Macherey Nagel, Düren, Germany) and quality-controlled using the RNA 6000 Nano LabChip (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: After subconfluence cells at passage 6 were grown 7 days in the STEMPRO® Osteogenesis Differentiation Kit (Invitrogen).

value: dental progenitor/stem cells


title: dental follicle cells differentiation 1


title: dental follicle cells control 2

source_name: dental follicle cells in standard  medium


title: tumor tissue non-cardia of gastric TYB0004T

description: frozen tissue extracted by Trizol


title: Healthy_Donor_4103


title: adjacent tissue normal glands TYB0004N

description: frozen tissue extracted by Trizol

source_name: adjacent normal tissue


title: tumor tissue non-cardia of gastric TYB0003T

description: frozen tissue extracted by Trizol

source_name: tumor tissue


title: Healthy_Donor_4105


title: adjacent tissue normal glands TYB0003N

description: frozen tissue extracted by Trizol


title: tumor tissue non-cardia of gastric TYB0002T

description: frozen tissue extracted by Trizol


title: ETV2-indeuced vascular endothelial cells 3

city: Tokyo

first: Rimpei

last: Morita

address: 35 Shinanomachi, Shinjyuku-ku

institute: Keio University School of Medicine

hyb_protocol: 300 ng of Cy3-labelled cRNA was fragmented 1x Agilent fragmentation buffer and hybridized to Agilent SurePrint G3 Human GE Microarray ( x 60K) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (v.10.7.3.1) (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Culture cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using an RNeasy Plus Micro Kit with a genomic DNA Eliminator (QIAGEN) according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Culture cells


title: Human adult skin fibroblast 2

source_name: Skin

value: Skin


title: U2OS 3

city: Woolloongabba

first: Liliana

middle: Beatriz

last: Endo-Munoz

state: Queensland

address: TRI, 37 Kent St

department: Diamantina Institute

country: Australia

institute: University of Queensland

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol on an Illumina Human HT-12_V3_0_R1_11283641_A BeadChip

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised using quantile normalisation with lumi R package

source_name: osteosarcoma cell line

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

growth_protocol: DMEM/10%FCS/PSG, 5% CO2 for 24 h until 80% confluent

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: Untreated

tag: metastatic

value: no


title: ETV2-indeuced vascular endothelial cells 2


title: U2OS 1

description: replicate 1

tag: cell line


title: Healthy_Donor_4097

source_name: B cells isolated from peripheral blood


title: HOS 3

description: replicate 3

value: HOS


title: U2OS 2

description: replicate 2


title: Healthy_Donor_4096

value: unknown


title: Human adult skin fibroblast 3


title: HOS 1

description: replicate 1


title: Human adult skin fibroblast 1


title: adjacent tissue normal glands TYB0002N

description: frozen tissue extracted by Trizol

value: adjacent tissue normal gastric glands


title: KRIB 3

description: replicate 3

value: KRIB

value: yes


title: Healthy_Donor_4102

value: male


title: inducedHepSC_rep1

description: Gene expression iHepSC clone 2

source_name: induced Hepatic Stem Cells, replicate 1


title: KHOS 3

description: replicate 3

value: KHOS


title: tumor tissue non-cardia of gastric TYB0001T

description: frozen tissue extracted by Trizol

value: tumor tissue non-cardia of stomach


title: KHOS 1

description: replicate 1


title: KRIB 1

description: replicate 1


title: human unbilical vein endothelial cell 1

source_name: Umbilical cord

value: Umbilical cord

value: female


title: DIA_VIII_2 [II]

status: Public on Jul 18 2013

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with preprocessCore in R.

source_name: Striatum of 6-10 week old C57BL/6J mice

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

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

tag: timepoint

tag: drug

value: Diazepam


title: BUS_IV_1 [II]

value: Buspirone


title: SAL_IV_5 [II]

value: Saline


title: TRA_II_3 [II]

value: Tranylcypromine


title: HYD_VIII_3 [II]

value: Hydroxizine


title: KHOS 2

description: replicate 2


title: KRIB 2

description: replicate 2


title: MIA_I_1 [II]

value: Mianserin


title: TWE_VIII_3 [II]

value: Tween 80


title: ETV2-indeuced vascular endothelial cells 1

value: Culture cells


title: dental follicle cells control 1

tag: cell type

value: dental progenitor/stem cells


title: HYD_II_1 [II]


title: human unbilical vein endothelial cell 2


title: Healthy_Donor_4098

value: healthy


title: adjacent tissue normal glands TYB0001N

description: frozen tissue extracted by Trizol

value: adjacent tissue normal gastric glands


title: DIA_I_3 [II]


title: NAI_VIII_2 [II]

value: Naive


title: SAL_IV_1 [II]


title: HAL_II_2 [II]

value: Haloperidol


title: TWE_I_3 [II]


title: RIS_VIII_3 [II]

value: Risperidone


title: adjacent tissue normal glands TYB0010N

description: frozen tissue extracted by Trizol


title: HOS 2

description: replicate 2

value: HOS

value: no


title: NAI_I_2 [II]


title: TRA_IV_2 [II]


title: KLO_II_3 [II]

value: Clozapine


title: control RKO cells, technical rep3

city: Guangzhou

first: Ying

last: Lin

state: Guangdong

address: 107 West Yanjiang Road

department: Gastroenterology and Hepatology

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen Univeristy

description:
CTRL-3
Gene expression data from control vector-transfected RKO human colon cancer cells.

hyb_protocol: Following fragmentation, the aRNA were hybridized with the GeneChip® Human Genome U133 Plus 2.0 Array for 16hr. After hybridization, washing and staining steps were performed with the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned with the Affymetrix 3000 7G Plus scanner.

data_processing: CEL files were obtained by the AGCC software, and the CHP files were generated with the MAS5.0 method by Affymetrix Expression Console. After that, the data were imported into the Agilent GeneSpring GX software for further analysis.

source_name: RKO cells stably transfected with control vector

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol (GeneChip® 3' IVT Express Kit user manual, 2010, Affymetrix).

growth_protocol: Cells were growing in Eagle's Minimal Essential Medium with 10% fetal bovine serum in a humidified atmosphere with 5% CO2 at 37°C.

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

treatment_protocol: After lipofectamine-mediated transfection of the TAGLN-carrying plasmid or the vector-only control plasmid, stable transfectants were selected and cultured in medium containing 25 μg/ml blasticidin followed by RNA extraction and hybridization on Affymetrix microarrays.

value: RKO

value: colon cancer cell line

tag: stable transfection

value: vector control


title: TAGLN-overexpressing RKO cells, technical rep2

description:
TAGLN-2
Gene expression data from TAGLN-overexpressing RKO human colon cancer cells.

source_name: RKO cells stably expressing TAGLN

value: TAGLN


title: control RKO cells, technical rep2

description:
CTRL-2
Gene expression data from control vector-transfected RKO human colon cancer cells.


title: TRA_I_3 [II]

value: Tranylcypromine


title: HAL_IV_1 [II]


title: control RKO cells, technical rep1

description:
CTRL-1
Gene expression data from control vector-transfected RKO human colon cancer cells.


title: NAI_IV_2 [II]


title: KLO_VIII_3 [II]


title: SAL_II_1 [II]

value: Saline


title: TRA_II_2 [II]


title: TAGLN-overexpressing RKO cells, technical rep3

description:
TAGLN-3
Gene expression data from TAGLN-overexpressing RKO human colon cancer cells.


title: RIS_IV_3 [II]


title: TWE_VIII_2 [II]

value: Tween 80


title: Healthy_Donor_4099

value: male


title: KLO_I_3 [II]


title: NAI_VIII_1 [II]


title: TAGLN-overexpressing RKO cells, technical rep1

description:
TAGLN-1
Gene expression data from TAGLN-overexpressing RKO human colon cancer cells.


title: SKOV3_Luc shRNA

city: Taipei

first: kuo-tai

last: hua

address: No.2, Xu-Zhou Road

country: Taiwan

institute: National Taiwan University

description: Gene expression data from SKOV3 cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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: SKOV3 cells with Luc shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

value: ovarian cancer

tag: genotype/variation

value: expressing luciferase shRNA


title: SKOV3_G9a shRNA2

description: Gene expression data from SKOV3 cells with G9a depletion

source_name: SKOV3 cells with G9a shRNA

value: expressing G9a shRNA


title: TWE_IV_3 [II]


title: HAL_II_1 [II]


title: HAL_I_2 [II]


title: PBMC_NORREF_29

city: Leiden

first: Yolande

middle: F. M.

last: Ramos

address: Einthovenweg 20

department: Molecular Epidemiology

country: Netherlands

institute: Leiden University Medical Center

description:
4802668036_I
PBMC_Control_mRNA

hyb_protocol: Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit

scan_protocol: Slides were scanned with the Illumina Beadscanner 500GX

data_processing: Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization or background substraction and with imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst)

label_protocol: To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.

extract_protocol: RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).

value: Female

tag: age (yrs)

value: blood

value: PBMC

tag: disease state

value: control


title: PBMC_NORREF_31

description:
4802668036_B
PBMC_Control_mRNA

tag: gender


title: PBMC_NORREF_33

description:
4802668036_D
PBMC_Control_mRNA

tag: tissue


title: PBMC_NORREF_32

description:
4778071027_L
PBMC_Control_mRNA

value: Male


title: PBMC_NORREF_28

description:
4802668036_G
PBMC_Control_mRNA


title: BUS_II_1 [II]

value: Buspirone


title: PBMC_NORREF_27

description:
4802668036_E
PBMC_Control_mRNA


title: SKOV3_G9a shRNA1


title: HYD_I_1 [II]

value: Hydroxizine


title: PBMC_NORREF_30

description:
4802668036_K
PBMC_Control_mRNA


title: PBMC_NORREF_26

description:
4802668036_C
PBMC_Control_mRNA


title: SAL_II_5 [II]


title: PBMC_NORREF_22

description:
4778071052_L
PBMC_Control_mRNA


title: SAL_VIII_4 [II]


title: PBMC_NORREF_21

description:
4802668004_F
PBMC_Control_mRNA


title: DIA_II_2 [II]

value: Diazepam


title: HYD_IV_3 [II]


title: PBMC_NORREF_25

description:
4802668036_A
PBMC_Control_mRNA


title: DIA_IV_2 [II]


title: PBMC_NORREF_23

description:
4778071055_J
PBMC_Control_mRNA


title: PBMC_NORREF_20

description:
4778071026_L
PBMC_Control_mRNA


title: BUS_IV_3 [II]


title: PBMC_NORREF_24

description:
4802668034_L
PBMC_Control_mRNA


title: SAL_I_5 [II]


title: PBMC_NORREF_18

description:
4802668034_H
PBMC_Control_mRNA


title: BUS_II_3 [II]


title: PBMC_NORREF_19

description:
4802668034_J
PBMC_Control_mRNA


title: PBMC_NORREF_13

description:
4778071028_J
PBMC_Control_mRNA


title: PBMC_NORREF_16

description:
4802668016_L
PBMC_Control_mRNA


title: HYD_I_3 [II]


title: PBMC_NORREF_14

description:
4778071028_L
PBMC_Control_mRNA


title: PBMC_NORREF_15

description:
4778071055_L
PBMC_Control_mRNA


title: BUS_I_1 [II]


title: HYD_VIII_2 [II]


title: PBMC_NORREF_8

description:
4802668054_L
PBMC_Control_mRNA


title: PBMC_NORREF_11

description:
4778071052_J
PBMC_Control_mRNA


title: DIA_VIII_1 [II]


title: PBMC_NORREF_17

description:
4802668034_F
PBMC_Control_mRNA


title: SAL_IV_4 [II]


title: TRA_VIII_2 [II]


title: PBMC_NORREF_9

description:
4802668034_K
PBMC_Control_mRNA


title: HAL_VIII_1 [II]

value: Haloperidol


title: KLO_IV_3 [II]

value: Clozapine


title: TWE_II_3 [II]


title: PBMC_NORREF_7

description:
4802668052_L
PBMC_Control_mRNA


title: DIA_I_2 [II]


title: PBMC_NORREF_12

description:
4802668034_D
PBMC_Control_mRNA


title: NAI_II_2 [II]

value: Naive


title: PBMC_NORREF_6

description:
4802668053_L
PBMC_Control_mRNA


title: TRA_IV_1 [II]

value: Tranylcypromine


title: PBMC_NORREF_3

description:
4802668034_E
PBMC_Control_mRNA


title: PBMC_NORREF_4

description:
4802668034_G
PBMC_Control_mRNA


title: KLO_I_2 [II]


title: TWE_I_2 [II]

value: Tween 80


title: PBMC_GARP_106

description:
4778071052_H
PBMC_OA_mRNA

value: case


title: KLO_II_2 [II]


title: MIA_II_1 [II]

value: Mianserin


title: MIA_VIII_3 [II]


title: PBMC_NORREF_1

description:
4802668034_A
PBMC_Control_mRNA


title: RIS_IV_2 [II]

value: Risperidone


title: SAL_I_1 [II]

value: Saline


title: RIS_VIII_2 [II]


title: BUP_IV_3 [II]

value: Bupropion


title: TRA_II_1 [II]


title: PBMC_NORREF_2

description:
4802668034_C
PBMC_Control_mRNA

value: Female

value: blood


title: RIS_II_3 [II]


title: NAI_I_1 [II]


title: BUP_II_3 [II]


title: PBMC_NORREF_10

description:
4802668034_B
PBMC_Control_mRNA

value: PBMC

value: control


title: PBMC_GARP_105

description:
4778071028_H
PBMC_OA_mRNA


title: KLO_VIII_2 [II]


title: TWE_IV_2 [II]


title: TRA_I_2 [II]


title: HAL_I_1 [II]


title: NAI_IV_1 [II]


title: SAL_VIII_1 [II]


title: PBMC_GARP_100

description:
4802668053_D
PBMC_OA_mRNA


title: PBMC_GARP_101

description:
4802668053_F
PBMC_OA_mRNA


title: TWE_VIII_1 [II]


title: BUS_VIII_3 [II]

value: Buspirone


title: MIA_IV_3 [II]


title: PBMC_GARP_99

description:
4778071027_H
PBMC_OA_mRNA


title: RIS_II_2 [II]


title: TRA_I_1 [II]


title: MIA_II_3 [II]


title: PBMC_GARP_98

description:
4778071027_F
PBMC_OA_mRNA


title: RIS_I_2 [II]


title: TRA_VIII_1 [II]


title: KLO_VIII_1 [II]


title: BUP_VIII_2 [II]


title: BUP_I_3 [II]


title: PBMC_GARP_97

description:
4778071027_K
PBMC_OA_mRNA


title: PBMC_GARP_102

description:
4802668053_H
PBMC_OA_mRNA


title: PBMC_GARP_95

description:
4778071028_G
PBMC_OA_mRNA


title: SAL_VIII_3 [II]


title: TWE_II_2 [II]


title: RIS_I_3 [II]


title: KLO_IV_1 [II]


title: PBMC_GARP_103

description:
4802668053_J
PBMC_OA_mRNA


title: NAI_II_1 [II]


title: PBMC_GARP_96

description:
4778071027_I
PBMC_OA_mRNA


title: BUS_VIII_1 [II]


title: DIA_II_3 [II]


title: PBMC_GARP_94

description:
4778071028_E
PBMC_OA_mRNA


title: KLO_IV_2 [II]


title: BUP_VIII_3 [II]


title: SAL_I_6 [II]


title: SAL_VIII_5 [II]


title: SAL_I_4 [II]


title: HYD_II_2 [II]

value: Hydroxizine


title: PBMC_GARP_88

description:
4802668054_I
PBMC_OA_mRNA


title: BUS_IV_2 [II]


title: HYD_IV_1 [II]


title: PBMC_GARP_93

description:
4778071027_G
PBMC_OA_mRNA


title: BUS_I_2 [II]


title: PBMC_GARP_89

description:
4802668054_K
PBMC_OA_mRNA

value: Male


title: DIA_VIII_3 [II]

value: Diazepam


title: PBMC_GARP_87

description:
4778071052_D
PBMC_OA_mRNA


title: PBMC_GARP_91

description:
4802668052_J
PBMC_OA_mRNA


title: DIA_II_1 [II]


title: HYD_VIII_1 [II]


title: HYD_II_3 [II]


title: PBMC_NORREF_5

description:
4802668034_I
PBMC_Control_mRNA


title: SAL_IV_6 [II]


title: PBMC_GARP_86

description:
4778071052_B
PBMC_OA_mRNA


title: PBMC_GARP_90

description:
4802668052_H
PBMC_OA_mRNA


title: DIA_IV_3 [II]


title: HYD_I_2 [II]


title: BUS_II_2 [II]


title: PBMC_GARP_92

description:
4778071027_E
PBMC_OA_mRNA


title: PBMC_GARP_104

description:
4778071028_F
PBMC_OA_mRNA


title: DIA_I_1 [II]


title: SAL_II_4 [II]


title: PBMC_GARP_85

description:
4778071027_C
PBMC_OA_mRNA


title: BUS_VIII_2 [II]


title: PBMC_GARP_84

description:
4778071027_A
PBMC_OA_mRNA


title: PBMC_GARP_83

description:
4778071026_H
PBMC_OA_mRNA


title: SAL_II_6 [II]


title: TWE_IV_1 [II]


title: SAL_VIII_6 [II]


title: HYD_IV_2 [II]


title: RIS_VIII_1 [II]


title: KLO_II_1 [II]

value: Clozapine


title: BUS_I_3 [II]


title: RIS_IV_1 [II]


title: PBMC_GARP_81

description:
4802668054_J
PBMC_OA_mRNA


title: PBMC_GARP_78

description:
4778071028_D
PBMC_OA_mRNA


title: BUP_IV_2 [II]


title: SAL_II_3 [II]


title: KLO_I_1 [II]


title: DIA_IV_1 [II]


title: SAL_IV_3 [II]


title: PBMC_GARP_79

description:
4802668054_B
PBMC_OA_mRNA


title: PBMC_GARP_82

description:
4778071026_F
PBMC_OA_mRNA


title: MIA_VIII_2 [II]


title: HAL_IV_2 [II]

value: Haloperidol


title: BUP_II_2 [II]


title: RIS_II_1 [II]


title: SAL_I_3 [II]


title: PBMC_GARP_76

description:
4802668018_J
PBMC_OA_mRNA


title: PBMC_GARP_80

description:
4802668054_D
PBMC_OA_mRNA


title: PBMC_GARP_77

description:
4802668018_L
PBMC_OA_mRNA


title: PBMC_GARP_75

description:
4802668036_H
PBMC_OA_mRNA


title: TWE_II_1 [II]


title: MIA_I_3 [II]


title: MIA_IV_2 [II]


title: BUP_I_2 [II]


title: PBMC_GARP_72

description:
4778071052_E
PBMC_OA_mRNA


title: TWE_I_1 [II]


title: PBMC_GARP_73

description:
4778071052_G
PBMC_OA_mRNA


title: RIS_I_1 [II]


title: PBMC_GARP_74

description:
4778071052_K
PBMC_OA_mRNA


title: BUP_VIII_1 [II]


title: SAL_IV_2 [II]


title: HAL_VIII_3 [II]


title: NAI_I_3 [II]

value: Naive


title: HAL_IV_3 [II]


title: MIA_II_2 [II]


title: PBMC_GARP_69

description:
4802668036_F
PBMC_OA_mRNA


title: NAI_VIII_3 [II]


title: PBMC_GARP_70

description:
4778071052_A
PBMC_OA_mRNA


title: PBMC_GARP_68

description:
4802668052_F
PBMC_OA_mRNA


title: SAL_VIII_2 [II]


title: HAL_II_3 [II]


title: MIA_I_2 [II]


title: TRA_IV_3 [II]

value: Tranylcypromine


title: SAL_II_2 [II]


title: BUP_II_1 [II]


title: PBMC_GARP_66

description:
4778071028_B
PBMC_OA_mRNA

value: case


title: PBMC_GARP_71

description:
4778071052_C
PBMC_OA_mRNA


title: MIA_VIII_1 [II]

value: Mianserin


title: PBMC_GARP_64

description:
4802668004_K
PBMC_OA_mRNA


title: TRA_VIII_3 [II]


title: BUP_I_1 [II]


title: HAL_VIII_2 [II]


title: PBMC_GARP_62

description:
4802668004_G
PBMC_OA_mRNA


title: NAI_IV_3 [II]


title: PBMC_GARP_63

description:
4802668004_I
PBMC_OA_mRNA


title: HAL_I_3 [II]


title: PBMC_GARP_67

description:
4802668004_D
PBMC_OA_mRNA


title: PBMC_GARP_65

description:
4802668004_B
PBMC_OA_mRNA


title: PBMC_GARP_59

description:
4802668004_E
PBMC_OA_mRNA


title: SAL_I_2 [II]


title: NAI_II_3 [II]


title: PBMC_GARP_60

description:
4778071026_J
PBMC_OA_mRNA


title: FLU_VIII_3 [I]

value: Fluoxetine


title: IMI_IV_1 [I]

value: Imipramine


title: FLU_IV_3 [I]


title: PBMC_GARP_58

description:
4802668004_C
PBMC_OA_mRNA


title: TIA_II_1 [I]

value: Tianeptine


title: NAI_I_1 [I]


title: PBMC_GARP_61

description:
4778071055_H
PBMC_OA_mRNA

value: Female


title: MIA_IV_1 [II]


title: IMI_II_1 [I]


title: SAL_VIII_3 [I]

value: Saline


title: TIA_I_1 [I]


title: SAL_IV_3 [I]


title: FLU_I_3 [I]


title: PBMC_GARP_56

description:
4802668054_H
PBMC_OA_mRNA

value: blood

value: PBMC


title: SAL_II_3 [I]


title: IMI_I_1 [I]


title: PBMC_GARP_57

description:
4802668053_B
PBMC_OA_mRNA


title: FLU_II_3 [I]


title: NAI_VIII_3 [I]


title: NAI_IV_3 [I]


title: IMI_VIII_3 [I]


title: PBMC_GARP_52

description:
4802668016_H
PBMC_OA_mRNA


title: SAL_I_3 [I]


title: PBMC_GARP_55

description:
4802668054_F
PBMC_OA_mRNA


title: PBMC_GARP_54

description:
4802668004_A
PBMC_OA_mRNA


title: TIA_VIII_3 [I]


title: IMI_IV_3 [I]


title: TIA_II_3 [I]


title: FLU_VIII_2 [I]


title: PBMC_GARP_49

description:
4778071026_B
PBMC_OA_mRNA


title: PBMC_GARP_51

description:
4778071026_D
PBMC_OA_mRNA


title: PBMC_GARP_48

description:
4778071026_K
PBMC_OA_mRNA


title: PBMC_GARP_50

description:
4802668016_F
PBMC_OA_mRNA


title: PBMC_GARP_53

description:
4802668016_J
PBMC_OA_mRNA


title: FLU_IV_2 [I]


title: TIA_IV_3 [I]


title: NAI_II_3 [I]


title: NAI_I_3 [I]


title: SAL_VIII_2 [I]


title: BUP_IV_1 [II]

value: Bupropion


title: IMI_II_3 [I]


title: IMI_I_3 [I]


title: TIA_I_3 [I]


title: FLU_II_2 [I]


title: PBMC_GARP_45

description:
4802668053_E
PBMC_OA_mRNA


title: TIA_VIII_2 [I]


title: NAI_IV_2 [I]


title: NAI_VIII_2 [I]


title: PBMC_GARP_43

description:
4802668016_B
PBMC_OA_mRNA


title: FLU_I_2 [I]


title: SAL_IV_2 [I]


title: IMI_VIII_2 [I]


title: SAL_II_2 [I]


title: PBMC_GARP_47

description:
4778071026_I
PBMC_OA_mRNA


title: PBMC_GARP_44

description:
4802668016_D
PBMC_OA_mRNA


title: PBMC_GARP_46

description:
4802668053_G
PBMC_OA_mRNA


title: TIA_IV_2 [I]


title: FLU_VIII_1 [I]


title: NAI_II_2 [I]


title: PBMC_GARP_40

description:
4802668016_I
PBMC_OA_mRNA


title: PBMC_GARP_42

description:
4778071027_D
PBMC_OA_mRNA


title: SAL_I_2 [I]


title: NAI_I_2 [I]


title: FLU_IV_1 [I]


title: TIA_II_2 [I]


title: PBMC_GARP_39

description:
4802668018_H
PBMC_OA_mRNA


title: PBMC_GARP_41

description:
4802668016_K
PBMC_OA_mRNA


title: SAL_VIII_1 [I]


title: IMI_II_2 [I]


title: IMI_IV_2 [I]


title: TIA_I_2 [I]


title: SAL_II_1 [I]


title: PBMC_GARP_37

description:
4802668018_D
PBMC_OA_mRNA


title: PBMC_GARP_38

description:
4802668018_F
PBMC_OA_mRNA


title: PBMC_GARP_36

description:
4802668018_B
PBMC_OA_mRNA


title: FLU_I_1 [I]


title: TIA_IV_1 [I]


title: SAL_I_1 [I]


title: PBMC_GARP_31

description:
4802668016_G
PBMC_OA_mRNA


title: TIA_VIII_1 [I]


title: IMI_VIII_1 [I]


title: PBMC_GARP_34

description:
4802668018_E
PBMC_OA_mRNA


title: SAL_IV_1 [I]


title: PBMC_GARP_33

description:
4778071027_B
PBMC_OA_mRNA


title: Med1fl/fl + Ad-LacZ (3 days)

city: Chicago

first: Navin

last: Viswakarma

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Control - 3 days

hyb_protocol: Standard Illumina hybridization protocol

data_processing: No normalization is done

source_name: Mouse Liver

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit as per manufacturer instructions in the kit. RNA quality control (RIN) was performed with Agilent Bioanalyzer.

treatment_protocol: 5.5 weeks old Med1 floxed mice were injected intravenously with Ad-Med1 (test) and Ad-LacZ (control) and killed at day 3 and day 5 post injection.

tag: strain background

value: Med1 floxed mice (Med1fl/fl)

value: 5.5 wks

tag: injected with

value: Ad-LacZ (adenovirus expression beta-galactosidase gene)

tag: time point

value: 3 days after injection

value: liver


title: Med1fl/fl + Ad-LacZ (5 days)

description: Control - 5 days

value: 5 days after injection


title: Colon_Control_pool

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.16.0).

source_name: colon, after 2 weeks of control diet (40en% fat), pooled RNA of n=8 mice

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Eight week-old male C57Bl/6 mice (Harlan, Horst, the Netherlands) were housed individually in a light-and-temperature controlled facility (lights on 6:30 to 18:30, 21°C) and acclimated for 1 week. Mice were fed standard laboratory chow and had free access to water.

extract_protocol: RNA was isolated from colonic scarpings using TRIzol reagent, followed by purification of total RNA using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). Equal amounts of RNA from n=8 mice per group were pooled and analysed by microarray.

treatment_protocol: At nine weeks of age mice were fed control and heme-supplemented (0.5 umol/g) diets for 2 weeks. Mice had free access to feed and water. After 2 weeks of diet intervention all mice were sacrificed and colons were taken out and mesenteric fat was removed. Next colons were cut open longitudinally, washed in PBS and scraped.

tag: strain

value: male

value: 11 weeks

value: colon

tag: treatment

value: high fat (without heme)

tag: treatment duration

value: 14 days


title: PBMC_GARP_28

description:
4802668016_A
PBMC_OA_mRNA

value: case


title: Colon_Heme_pool

source_name: colon, after 2 weeks of heme diet (40en% fat plus  0.5 umol/g), pooled RNA of n=8 mice

tag: age

value: high fat with heme (0.5 umol/g)


title: PBMC_GARP_27

description:
4802668052_K
PBMC_OA_mRNA

value: Female


title: PBMC_GARP_30

description:
4802668016_E
PBMC_OA_mRNA

value: blood


title: MCF7 cyclin D1 siRNA Estradiol Rep1

first: Mathew

middle: Casimiro

last: Casimiro

state: United States

address: 233 South 10th St, Rm 1035

department: 233 South 10th St, Rm 1035

institute: Thomas Jefferson University

hyb_protocol: 2.5ug of ST cDNA were hybridized for 18h at 45 degrees on theAffymetrix Gene ChIP Human gene 1.0 ST Array

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip¬Æ Scanner 3000 with Command Console Software

data_processing: Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the ‚Äúcore‚Äù probesets and exported

label_protocol: Biotinylated cDNA were prepared according to standard NuGEN protocol from 50ug total RNA.

growth_protocol: MCF7 cells grown in phenol red free DMEM supplemented with 5% charcoal stripped media

extract_protocol: Trizol extraction of RNA was performed as per manufacturer's instructions and purified using Qiagen RNAeasy Mini kit

treatment_protocol: MCF7 cells were transfected with control or cyclin D1 siRNA. Cells were maintained for 48hrs to allow for efficient knock-down. Estradiol or vehicle treated cells were maintained for a further 24 hrs and then processed.

value: Cyclin D1 siRNA Estradiol

tag: cell line


title: NAI_IV_1 [I]

tag: timepoint

value: Naive


title: NAI_II_1 [I]

tag: drug


title: FLU_II_1 [I]

value: Fluoxetine


title: MCF7 cyclin D1 siRNA Vehicle Rep2

value: Cyclin D1 siRNA Vehicle


title: PBMC_GARP_35

description:
4802668018_G
PBMC_OA_mRNA

value: PBMC


title: PBMC_GARP_32

description:
4778071027_J
PBMC_OA_mRNA


title: NAI_VIII_1 [I]


title: Med1fl/fl + Ad-Med1 (5 days)

description: Test - 5 days

value: Med1 floxed mice (Med1fl/fl)

value: 5.5 wks

value: Ad-His-Med1 (adenovirus expressing Med1 gene)


title: PBMC_GARP_29

description:
4802668016_C
PBMC_OA_mRNA


title: MCF7 control siRNA Estradiol Rep2

value: Control siRNA Estradiol


title: MCF7 cyclin D1 siRNA Estradiol Rep2


title: Med1fl/fl + Ad-Med1 (3 days)

description: Test - 3 days

value: 3 days after injection

value: liver


title: PBMC_GARP_26

description:
4802668052_I
PBMC_OA_mRNA


title: IMI_I_2 [I]

value: Imipramine


title: MCF7 cyclin D1 siRNA Vehicle Rep1


title: MCF7 control siRNA Vehicle Rep2

value: Control siRNA Vehicle


title: MCF7 control siRNA Estradiol Rep1


title: Panc-1GLI1ER_10nM beta-estradiol (E2)_3hrs

city: Aichi

first: Shingo

last: Inaguma

address: Nagakute

department: Department of Pathology and Promoting Center for Clinical Research

institute: Aichi Medical University School of Medicine

description: Panc-1GLI1ER E2 treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20060725) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Panc-1GLI1ER, 10nM beta-estradiol (E2), 3hrs.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in DMEM containing 10% of activated-charcoal treated FBS.

extract_protocol: QIAGEN RNeasy mini kit was used.

treatment_protocol: 10 nM of beta-estradiol (E2) was added to the medium.

value: Panc-1GLI1ER (derived from pancreatic cancer cell line Panc-1)

tag: agent

tag: time

value: 3 hrs


title: PBMC_GARP_25

description:
4802668052_C
PBMC_OA_mRNA

value: Female

value: case


title: Panc-1ER_10nM beta-estradiol (E2)_3hrs

description: Panc-1ER E2 treatment

source_name: Panc-1ER, 10nM beta-estradiol (E2), 3hrs

value: Panc-1ER (derived from pancreatic cancer cell line Panc-1)


title: PBMC_GARP_24

description:
4802668052_A
PBMC_OA_mRNA

value: blood


title: Panc-1GLI1ER_0hrs (control)

description: Panc-1GLI1ER control

source_name: Panc-1GLI1ER, 0hrs

value: control

value: 0 hrs


title: PBMC_GARP_17

description:
4778071055_I
PBMC_OA_mRNA

value: PBMC


title: PBMC_GARP_23

description:
4778071028_K
PBMC_OA_mRNA


title: PBMC_GARP_18

description:
4778071055_D
PBMC_OA_mRNA


title: ARF1 siRNA knockdown MDA-MB-231 sample 2

city: New York

first: Yongzhong

last: Zhao

state: New York

address: 1470 Madison Avenue btw. 101st and 102nd Streets

department: Genetics

institute: Mount Sinai Medical Center

description:
siRNA_2
MDA231 with ARF1 knockdown sample 2

scan_protocol: Standard Illumina scanning protocol using the Beadarray reader.

data_processing: Beadstudio v.2.3.47 was used for processing the raw data and the Average method was used for normalization. Averaged data were filtered for probes with detection pvalue < 0.01 in at least one sample.

label_protocol: Illumina® TotalPrep RNA Amplification kit (Ambion®) was used to convert 500 ng of RNA to cDNA which was then transcribed in vitro to generate biotin-labeled RNA.

growth_protocol: MDA231 cells were obtained from ATCC (Manassas, Virginia) and were cultured in RPMI1640 and DMEM media, respectively, supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol: Total RNA was isolated using Purelink™ RNA isolation kit (Invitrogen®) as per the manufacturer's recommended protocol. RNA quantity and quality was assessed on a Bioanalyzer™ 2100 instrument (Agilent®). The RNA preparations had 260 nm/280 nm absorbance ratios in the 1.9-2.0 range, 260 nm/230 nm absorbance ratios >1.8, and RNA integrity numbers >7

treatment_protocol: Arf1 SMART Pool siRNA was purchased from Dharmacon (catalog #M-011580-01-0005). On the day prior to transfection, cells were plated at a density of 1x105 cells/well in a 6-well plate. Cells were transfected with 100nM siRNA (final concentration) using Oligofectamine according to the manufacturer’s instructions.

value: MDA-MB-231 breast cancer cell line

tag: genotype/variation

value: ARF1 siRNA


title: PBMC_GARP_21

description:
4802668018_C
PBMC_OA_mRNA

tag: age (yrs)


title: PBMC_GARP_16

description:
4802668054_G
PBMC_OA_mRNA

tag: disease state


title: PBMC_GARP_20

description:
4802668018_A
PBMC_OA_mRNA

tag: gender


title: PBMC_GARP_15

description:
4802668054_E
PBMC_OA_mRNA

tag: tissue


title: ARF1 siRNA knockdown MDA-MB-231 sample 5

description:
siRNA_5
MDA231 with ARF1 knockdown sample 5


title: ARF1 siRNA knockdown MDA-MB-231 sample 8

description:
siRNA_8
MDA231 with ARF1 knockdown sample 8


title: ARF1 siRNA knockdown MDA-MB-231 sample 3

description:
siRNA_3
MDA231 with ARF1 knockdown sample 3


title: ARF1 siRNA knockdown MDA-MB-231 sample 4

description:
siRNA_4
MDA231 with ARF1 knockdown sample 4


title: Panc-1ER_0hrs (control)

description: Panc-1ER control

source_name: Panc-1ER, 0hrs


title: ARF1 siRNA knockdown MDA-MB-231 sample 9

description:
siRNA_9
MDA231 with ARF1 knockdown sample 9


title: siRNA scramble_control  MDA-MB-231 sample 1

description:
scramble_1
siRNA scramble_control  MDA231 sample 1

source_name: 231/NS (nonsilence)

value: scramble


title: MCF7 control siRNA Vehicle Rep1


title: ARF1 siRNA knockdown MDA-MB-231 sample 1

description:
siRNA_1
MDA231 with ARF1 knockdown sample 1


title: PBMC_GARP_19

description:
4778071055_F
PBMC_OA_mRNA


title: siRNA scramble_control  MDA-MB-231 sample 3

description:
scramble_3
siRNA scramble_control  MDA231 sample 3

source_name: 231/NS (nonsilence)_3


title: PBMC_GARP_14

description:
4802668054_C
PBMC_OA_mRNA


title: PBMC_GARP_22

description:
4778071028_I
PBMC_OA_mRNA


title: PBMC_GARP_13

description:
4802668054_A
PBMC_OA_mRNA


title: ARF1 siRNA knockdown MDA-MB-231 sample 6

description:
siRNA_6
MDA231 with ARF1 knockdown sample 6


title: siRNA scramble_control  MDA-MB-231 sample 2

description:
scramble_2
siRNA scramble_control  MDA231 sample 2

source_name: 231/NS (nonsilence)_2


title: EE2-250 [US10173810_252799910054_S01_GE1_107_Sep09_2_3]

first: Christopher

last: Martyniuk

address: CEHT Mowry Road

institute: UF

hyb_protocol: Agilent one color protocol; Microarrays were washed the following day according to the supplemental Agilent protocol “Preventing Ozone-Related Problems”.  Slides were washed in GE Wash Buffer 1 at room temperature for 1 min, followed by GE Wash Buffer 2 at 37ºC for 1 min, acetonitrile wash at room temperature for 1 min, and Stabilizing and Drying Solution wash at room temperature for 30 s.

scan_protocol: Microarrays were kept in the dark until scanned at 5 μm at both 10 and 100 PMT (Agilent G2505 B Microarray Scanner).  Agilent Feature Extraction Software (v10.7) formed a composite of the two scans and calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is Quantile Normalization.

organism: Fundulus heteroclitus

source_name: liver

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Microarray analysis was performed with five biological replicates (5 control, 5 EE2 50 ng/L and 5 EE2 250 ng/L treatment).  Adult female livers were used for the microarray analysis.

treatment_protocol: EE2 waterborne exposure at 50 and 250 ng/L for 14 days

value: 250 ng/L EE2

value: adult

value: female


title: C [US10173810_252799910054_S01_GE1_107_Sep09_2_2]


title: EE2-50 [US10173810_252799910054_S01_GE1_107_Sep09_2_4]

value: 50 ng/L EE2


title: C [US10173810_252799910054_S01_GE1_107_Sep09_1_4]


title: EE2-50 [US10173810_252799910054_S01_GE1_107_Sep09_1_3]


title: PBMC_GARP_12

description:
4802668036_L
PBMC_OA_mRNA


title: PBMC_GARP_10

description:
4802668053_C
PBMC_OA_mRNA


title: PBMC_GARP_11

description:
4802668036_J
PBMC_OA_mRNA


title: PBMC_GARP_8

description:
4778071026_G
PBMC_OA_mRNA


title: PBMC_GARP_9

description:
4802668053_A
PBMC_OA_mRNA


title: EE2-250 [US10173810_252799910053_S01_GE1_107_Sep09_1_3]


title: EE2-250 [US10173810_252799910053_S01_GE1_107_Sep09_1_4]


title: EE2-250 [US10173810_252799910054_S01_GE1_107_Sep09_1_2]


title: EE2-50 [US10173810_252799910053_S01_GE1_107_Sep09_2_2]


title: C [US10173810_252799910053_S01_GE1_107_Sep09_2_3]


title: EE2-250 [US10173810_252799910053_S01_GE1_107_Sep09_2_1]


title: C [US10173810_252799910054_S01_GE1_107_Sep09_1_1]


title: EE2-50 [US10173810_252799910054_S01_GE1_107_Sep09_2_1]


title: PBMC_GARP_4

description:
4778071026_A
PBMC_OA_mRNA


title: C [US10173810_252799910053_S01_GE1_107_Sep09_1_2]


title: EE2-50 [US10173810_252799910053_S01_GE1_107_Sep09_1_1]


title: PBMC_GARP_7

description:
4778071026_E
PBMC_OA_mRNA


title: PBMC_GARP_5

description:
4778071026_C
PBMC_OA_mRNA


title: PBMC_GARP_6

description:
4778071028_C
PBMC_OA_mRNA


title: PBMC_GARP_2

description:
4778071055_A
PBMC_OA_mRNA


title: islet_pancreatectomy_3days

city: Yokohama

first: Jun

last: Shirakawa

state: Kanagawa

address: 3-9, Fuku-ura, Kanazawa-ku

institute: Yokohama City university

description: Four replicates: 1_3, 1_4, 2_3, 2_4

hyb_protocol: Cy3-labelled cRNA was fragmented by using Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays (G4858A) in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.
The microarray intensities ([sham](raw) and [Px](raw)) were processed by the percentile shift method (75th percentile) using the GeneSpring GX12.5 (Agilent Technologies) to normalize the range of expression intensities

source_name: isolated pancreatic islets, 3days, pancreatectomy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using the Rneasy total RNA extraction kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Islets were isolated from 8-week old C57BL/6J mice 3 days after 60% pancreatectomy or sham operation.

value: pancreatectomy

value: pancreatic islets


title: PBMC_GARP_3

description:
4778071055_C
PBMC_OA_mRNA


title: PBMC_GARP_1

description:
4778071028_A
PBMC_OA_mRNA


title: MinusTet.PlusE2.6h rep2

status: Public on Jul 17 2013

city: Cambridge

first: Mauro

middle: Antonio

last: Alves Castro

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description:
replicate 2
K2

data_processing: Raw image files were processed and analysed using the Beadarray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available

source_name: MCF-7 cell line treated with estrogen (minus tetracycline)

label_protocol: Standard Illumina label protocol

growth_protocol: MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2. The FGFR2b tetracycline-inducible over-expression MCF7 line was established by double-transfection of FspI-linearised F2b-pcDNA4/TO and pcDNA6/TR in a 1:5 ratio by DNA weight. Single cell clones were expanded under selection using 500μg/mL Zeocin and 3μg/mL blasticidin. Tetracycline induction of FGFR2b expression was confirmed by Western blot

extract_protocol: RNA was extracted using the miRNeasy spin column kit (Qiagen) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949)

treatment_protocol: Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen). FGFR2b over-expression was induced by tetracycline (final concentration of 1mg/mL)

tag: group

value: MinusTet

tag: treatment duration (hs)


title: MinusTet.PlusE2.6h rep3

description:
replicate 3
K3


title: islet_sham_3days

description: Four replicates: 1_1, 1_2, 2_1, 1_2

source_name: isolated pancreatic islets, 3days, sham

value: sham


title: MinusTet.PlusE2.3h rep4

description:
replicate 4
E4


title: MinusTet.PlusE2.12h rep2

description:
replicate 2
Q2


title: MinusTet.PlusE2.6h rep5

description:
replicate 5
K5


title: MinusTet.VEH.24h rep3

description:
replicate 3
U3

source_name: MCF-7 cell line treated with vehicle  (minus tetracycline)


title: MinusTet.VEH.24h rep2

description:
replicate 2
U2


title: MinusTet.VEH.12h rep2

description:
replicate 2
O2


title: MinusTet.VEH.12h rep5

description:
replicate 5
O5


title: MinusTet.PlusE2.12h rep4

description:
replicate 4
Q4


title: MinusTet.VEH.24h rep4

description:
replicate 4
U4


title: MinusTet.PlusE2.24h rep1

description:
replicate 1
W1


title: MinusTet.PlusE2.6h rep4

description:
replicate 4
K4


title: MinusTet.PlusE2.3h rep3

description:
replicate 3
E3


title: MinusTet.VEH.24h rep5

description:
replicate 5
U5


title: MinusTet.PlusE2.3h rep2

description:
replicate 2
E2


title: MinusTet.VEH.12h rep3

description:
replicate 3
O3


title: MinusTet.PlusE2.12h rep1

description:
replicate 1
Q1


title: MinusTet.VEH.24h rep1

description:
replicate 1
U1


title: MinusTet.VEH.6h rep3

description:
replicate 3
I4


title: MinusTet.PlusE2.12h rep3

description:
replicate 3
Q3


title: MinusTet.PlusE2.6h rep1

description:
replicate 1
K1


title: MinusTet.PlusE2.3h rep5

description:
replicate 5
E5


title: MinusTet.VEH.6h rep4

description:
replicate 4
I5


title: ARF1 siRNA knockdown MDA-MB-231 sample 7

description:
siRNA_7
MDA231 with ARF1 knockdown sample 7


title: MinusTet.VEH.12h rep1

description:
replicate 1
O1


title: MinusTet.VEH.12h rep4

description:
replicate 4
O4


title: MinusTet.PlusE2.12h rep5

description:
replicate 5
Q5


title: MinusTet.VEH.6h rep2

description:
replicate 2
I3


title: MinusTet.VEH.0h rep2

description:
replicate 2
A2


title: MinusTet.VEH.3h rep1

description:
replicate 1
C1


title: MinusTet.VEH.3h rep3

description:
replicate 3
C3


title: MA_R6

description:
replicate 6
t24.E2.FGF10 rep6

source_name: MCF-7 cell line treated with estrogen and FGF10

growth_protocol: MCF7 human breast cancer cells were cultured in DMEM supplemented with 10% HI-FCS and antibiotics. Cell synchronisation via estrogen deprivation was carried out for at least 3 days in phenol red-free DMEM (Invitrogen) supplemented with 5% charcoal dextran-treated HI-FBS (Hyclone) and 1% penicillin-streptomycin. All cells were grown at 37oC in 5% CO2

treatment_protocol: Estrogen deprived cells were stimulated with 1nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen); 100ng/mL PD173074 (Sigma-Aldrich). iF2 was activated with 100nM AP20187 (Takara Biosciences)


title: MinusTet.VEH.3h rep2

description:
replicate 2
C2


title: MinusTet.VEH.0h rep1

description:
replicate 1
A1


title: MinusTet.VEH.0h rep3

description:
replicate 3
A3


title: MA_W2

description:
replicate 2
t6.E2.FGF10 rep2


title: MA_P5

description:
replicate 5
t24.E2.AP20187.PD rep5

source_name: MCF-7 cell line treated with estrogen, AP20187 and PD173074


title: MA_R3

description:
replicate 3
t24.E2.FGF10 rep3


title: MinusTet.VEH.6h rep1

description:
replicate 1
I1


title: MinusTet.VEH.3h rep5

description:
replicate 5
C5


title: MA_R5

description:
replicate 5
t24.E2.FGF10 rep5


title: MA_R4

description:
replicate 4
t24.E2.FGF10 rep4


title: MA_W6

description:
replicate 5
t6.E2.FGF10 rep5


title: MA_W4

description:
replicate 4
t6.E2.FGF10 rep4


title: MA_R1

description:
replicate 1
t24.E2.FGF10 rep1


title: MA_W1

description:
replicate 1
t6.E2.FGF10 rep1


title: MA_R2

description:
replicate 2
t24.E2.FGF10 rep2


title: MA_W3

description:
replicate 3
t6.E2.FGF10 rep3


title: MA_P6

description:
replicate 6
t24.E2.AP20187.PD rep6


title: MinusTet.VEH.0h rep4

description:
replicate 4
A4


title: MA_P2

description:
replicate 2
t24.E2.AP20187.PD rep2


title: MinusTet.VEH.3h rep4

description:
replicate 4
C4


title: MinusTet.VEH.0h rep5

description:
replicate 5
A5


title: MA_P4

description:
replicate 4
t24.E2.AP20187.PD rep4


title: MA_P3

description:
replicate 3
t24.E2.AP20187.PD rep3


title: MA_P1

description:
replicate 1
t24.E2.AP20187.PD rep1


title: MA_U6

description:
replicate 6
t6.E2.AP20187.PD rep6


title: MA_U4

description:
replicate 4
t6.E2.AP20187.PD rep4


title: MA_U3

description:
replicate 3
t6.E2.AP20187.PD rep3