title: CXMDJ 1 hour after initial respiration 3

status: Public on Oct 31 2012

type: RNA

city: Matsumoto

first: Akinori

last: Nakamura

state: Nagano

address: Asahi 3-1-1

department: Department of Neurology and Rheumatology

country: Japan

institute: Shinshu University School of Medicine

description: Gen expression 1 hour after initial respiration in nCXMDJ diaphragm

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 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Canine Gene Expression Microarray V2 (G2514F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and  1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 10-100%(XDR)).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_95_Feb07 and Grid: 021193_D_F_20080808) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Canis lupus familiaris

source_name: CXMDJ, Diaphragm, 1 hour after initital respiration

label_protocol: Total RNA (100 ng) from each sample was used to synthesize double-stranded cDNA (One-Cycle cDNA Synthesis Kit, Affymetrix). The double-stranded cDNA samples were subsequently reverse transcribed, amplified, biotin-labeled according to the Affymetrix standard protocol.

extract_protocol: Total RNA was isolated from the skeletal muscle using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington DE) before cDNA synthesis.

tag: tissue

value: diaphragm

tag: gender

value: male

tag: age

tag: disease state

value: Canine muscular dystrophy

tag: time

value: 1 hour after initial respiration

tag: breed

value: beagle


title: Normal Beagle dogs 1hour after initial respiration 3

description: Gen expression 1 hour after initial respiration in normal Beagle dog diaphragm

source_name: Normal Beagle dog, Diaphragm, 1 hour after initial respirtaion

value: normal


title: CXMDJ 1 hour after initial respiration 1


title: CXMDJ before initial respiration 4

description: Gen expression before initial respiration in nCXMDJ diaphragm

source_name: CXMDJ, Diaphragm, before intial respiration

value: before initial respiration


title: CXMDJ 1 hour after initial respiration 2


title: Normal Beagle dogs before initial respiration 3

description: Gen expression before initial respiration in normal Beagle dog diaphragm

source_name: Norml Beagle dog, Diaphragm, before initial respiration


title: Normal Beagle dogs 1hour after initial respiration 1

value: female


title: Normal Beagle dogs 1hour after initial respiration 2


title: CXMDJ 1 hour after initial respiration 4


title: CXMDJ before initial respiration 3


title: Normal Beagle dogs before initial respiration 2


title: CXMDJ before initial respiration 2


title: Normal Beagle dogs before initial respiration 1


title: CXMDJ before initial respiration 1


title: Normal Beagle dogs before initial respiration 4


title: Sample 909-0357, Aorta

city: Boston

first: Lan

last: Hu

address: 450 Brookline Ave

country: USA

institute: Dan-Farber Cancer Institute

hyb_protocol: Hybridization protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

scan_protocol: Scan protocol with GeneChip® Scanner 3000 7G, according to Affymetrix® GeneChip® Expression Analysis Technical Manual

data_processing: CEL files were imported using R Bioconductor. Raw gene expression data were normalized using gcRMA 31 which accounts for GC content in gene sequence while adjusting the relative gene expression levels to allow comparison of between samples.

label: biotin

organism: Homo sapiens

source_name: Aorta

label_protocol: Labeling protocol according to Affymetrix® GeneChip® Expression Analysis Technical Manual

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's instructions

treatment_protocol: The mammary and aortic tissues were harvested at time of CABG. The surgeon dissected the two most distal aspects of LIMA and RIMA segments and obtained a ≥1cm sample for the tissue bank.

value: Aorta

value: Male


title: Sample 908-0305, RIMA

source_name: RIMA

value: Right Internal Mammary Artery (RIMA)


title: Sample 909-0357, RIMA


title: Sample 908-0302, RIMA


title: Sample 908-0305, LIMA

source_name: LIMA

value: Left Internal Mammary Artery (LIMA)


title: Sample 909-0357, LIMA


title: Sample 908-0280, LIMA


title: Sample 908-0280, RIMA


title: Sample 908-0280, Aorta


title: Sample 908-0224, Aorta


title: Sample 908-0302, Aorta


title: Sample 908-0305, Aorta


title: Sample 908-0244, Aorta


title: Sample 908-0219, LIMA


title: Sample 908-0219, RIMA


title: Sample 908-0193, RIMA

value: Female


title: Sample 908-0173, LIMA


title: Sample 908-0184, LIMA


title: Sample 908-0169, Aorta


title: Sample 908-0184, Aorta


title: Sample 908-0186, Aorta


title: Sample 908-0169, RIMA


title: Sample 908-0173, Aorta


title: Sample 908-0186, RIMA


title: Sample 908-0148, Aorta


title: Sample 908-0116, LIMA


title: Sample 908-0116, RIMA


title: Sample 908-0122, Aorta


title: Sample 908-0148, RIMA


title: Sample 908-0075, RIMA


title: Sample 908-0124, RIMA


title: Sample 908-0124, Aorta


title: Sample 908-0097, Aorta


title: Sample 911-0788, LIMA


title: Sample 908-0050, LIMA


title: Sample 908-0116, Aorta


title: Sample 908-0075, LIMA


title: Sample 908-0050, RIMA


title: Sample 908-0122, LIMA


title: Sample 908-0075, Aorta


title: Sample 908-0050, Aorta


title: Sample 908-0069, Aorta


title: Sample 908-0193, Aorta


title: Sample 911-0788, RIMA


title: Sample 911-0782, LIMA


title: Sample 911-0782, RIMA


title: Sample 911-0788, Aorta


title: Sample 911-0782, Aorta


title: Sample 910-0743, Aorta


title: Sample 910-0675, LIMA


title: Sample 910-0675, RIMA


title: Sample 908-0163, Aorta


title: Sample 910-0743, RIMA


title: Sample 910-0691, Aorta


title: Sample 910-0675, Aorta


title: Sample 910-0665, Aorta


title: Sample 910-0665, LIMA


title: Sample 910-0619, LIMA


title: Sample 910-0566, Aorta


title: Sample 909-0508, RIMA


title: Sample 910-0691, LIMA


title: Sample 910-0619, RIMA


title: Sample 910-0665, RIMA


title: Sample 910-0650, RIMA


title: Sample 910-0619, Aorta


title: Sample 910-0566, RIMA


title: Sample 909-0361, LIMA


title: Sample 910-0650, LIMA


title: Sample 909-0361, Aorta


title: Sample 909-0361, RIMA


title: Sample 909-0508, Aorta


title: Sample 910-0566, LIMA


title: Sample 909-0508, LIMA


title: Rice_K+-deficient_5 d_rep3

city: Beijing

first: Wei-Hua

last: Wu

state: Beijing

address: No.2 Yuanmingyuan West Road

department: College of Biological Sciences

country: China

institute: China Agricultural University

description: Rice cultivar Nipponbare (Oryza sativa L. ssp. japonica) plants were cultured hydroponically in growth chamber whose relative humidity was kept at 50%-70%. The light/dark period was 12 h/12 h, and temperatures were 30℃ during daytime and 25℃ at night, respectively. The composition of nutrient solution contains 1.427 mM NH4NO3, 0.323 mM NaH2PO4·2H2O, 0.512 mM K2SO4, 0.998 mM CaCl2, 1.643 mM MgSO4·7H2O, 9.474 µm MnCl2·4H2O, 0.075 µm (NH4)6Mo7O24·4H2O, 18.882 µm H3BO3, 0.152 µm ZnSO4·7H2O, 0.155 µm CuSO4·5H2O, 0.031 mM FeSO4·7H2O, 0.031 mM Na2EDTA·2H2O, pH=5.5 (Yoshida et al., 1976). The nutrient solution was replaced every other day. After growing in normal nutrient solution for two weeks, half of the rice seedlings were then transferred into -K nutrient solution (K2SO4 was removed) as K+-deficient treatment (LK). The other rice seedlings were still cultured in normal nutrient solution (+K) as control (CK). After that, the roots of both control and treated seedlings were collected at indicated times for the further assays.

hyb_protocol: Fragmented cRNA (15 g) was added into 300 L of hybridization solution, 200 L of this mixture was used for hybridization on Affymetrix rice genome arrays for 16 h at 45℃.

scan_protocol: The standard wash and double-stain protocols were applied using Affymetrix GeneChip Fluidics Station 450. The arrays were scanned on Affymetrix GeneChip scanner 3000.

data_processing:
First, the scanned arrays were analyzed using Affymetrix GCOS 1.0 (MAS 5.0) software to generate raw data, which were saved as CEL files. Then, DNA-Chip Analyzer (dChip) 2007 software (Parmigiani et al., 2003; www.dchip.org) was used to normalize all the eighteen array sets.
A gene was considered to be expressed when it had detection call ‘‘P’’ in all three replicates, and the detection P-value must be less than 0.05.

organism: Oryza sativa Japonica Group

source_name: roots of rice seedlings, K+-deficient treatment, 5 d, rep3

label_protocol: The purified RNA was used to generate first strand cDNA in a reverse transcription reaction (One-Cycle Target Labeling and Control Reagents, Affymetrix), 42℃ for 2 h and 16℃ for 1 h. The double-stranded cDNAs were used to generate cRNA via in vitro transcriptional reaction. The cRNA was labeled with biotin, and 20 g of labeled cRNA was fragmented. The size distribution of cRNAs and fragmented cRNAs was assessed using an Eppendorf Biophotometer and electrophoresis.

extract_protocol: The total RNA of rice roots was extracted using Trizol reagent (Invitrogen, Carlsbad, CA). Quality characterization of RNA samples were determined and confirmed by using NanoDrop 2000 fluorospectrometer and formaldehyde denaturing gel electrophoresis. Then, the total RNA was purified using the RNeasy Mini Kit (Qiagen).

treatment_protocol: The composition of nutrient solution contains 1.427 mM NH4NO3, 0.323 mM NaH2PO4•2H2O, 0.512 mM K2SO4, 0.998 mM CaCl2, 1.643 mM MgSO4•7H2O, 9.474 µm MnCl2•4H2O, 0.075 µm (NH4)6Mo7O24•4H2O, 18.882 µm H3BO3, 0.152 µm ZnSO4•7H2O, 0.155 µm CuSO4•5H2O, 0.031 mM FeSO4•7H2O, 0.031 mM Na2EDTA•2H2O, pH=5.5 (Yoshida et al., 1976). The nutrient solution was replaced every other day. After growing in normal nutrient solution for two weeks, half of the rice seedlings were then transferred into -K nutrient solution (K2SO4 was removed) as K+-deficient treatment (LK). The other rice seedlings were still cultured in normal nutrient solution (+K) as control (CK).

value: roots of rice seedlings

value: two-week-old

tag: treatment

value: K+-deficient

tag: time point


title: Rice_K+-deficient_5 d_rep2

source_name: roots of rice seedlings, K+-deficient treatment, 5 d, rep2

growth_protocol: Rice cultivar Nipponbare (Oryza sativa L. ssp. japonica) plants were cultured hydroponically in growth chamber whose relative humidity was kept at 50%-70%. The light/dark period was 12 h/12 h, and temperatures were 30℃ during daytime and 25℃ at night, respectively.


title: Rice_K+-replete_5 d_rep1

source_name: roots of rice seedlings, K+-replete treatment, 5 d, rep1

value: K+-replete


title: Rice_K+-replete_5 d_rep3

source_name: roots of rice seedlings, K+-replete treatment, 5 d, rep3


title: Rice_K+-deficient_3 d_rep1

source_name: roots of rice seedlings, K+-deficient treatment, 3 d, rep1


title: Rice_K+-deficient_3 d_rep3

source_name: roots of rice seedlings, K+-deficient treatment, 3 d, rep3


title: Rice_K+-deficient_5 d_rep1

source_name: roots of rice seedlings, K+-deficient treatment, 5 d, rep1


title: Rice_K+-replete_5 d_rep2

source_name: roots of rice seedlings, K+-replete treatment, 5 d, rep2


title: Rice_K+-replete_3 d_rep2

source_name: roots of rice seedlings, K+-replete treatment, 3 d, rep2


title: Rice_K+-deficient_6 h_rep1

source_name: roots of rice seedlings, K+-deficient treatment, 6 h, rep1


title: Rice_K+-deficient_6 h_rep3

source_name: roots of rice seedlings, K+-deficient treatment, 6 h, rep3


title: Rice_K+-deficient_3 d_rep2

source_name: roots of rice seedlings, K+-deficient treatment, 3 d, rep2


title: Rice_K+-replete_6 h_rep1

source_name: roots of rice seedlings, K+-replete treatment, 6 h, rep1


title: Rice_K+-replete_3 d_rep3

source_name: roots of rice seedlings, K+-replete treatment, 3 d, rep3


title: Cln1/5 dko 4

city: Helsinki

first: Tea

last: Blom

address: P.O.Box 104

department: Public Health Genomics

country: Finland

institute: National Institute for Health and Welfare

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Chipster

organism: Mus musculus

source_name: mouse cortex

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

extract_protocol: Total RNA was isolated with Qiagen Lipit Tissue kit according to manufacturer's protocol. RNA concentration was measured with NanoDrop, and quality control was performed with Agilent Bioanalyzer.

tag: strain

tag: genotype

value: Cln1/5 dko

value: 1 month

tag: Sex

value: cortex


title: Rice_K+-replete_3 d_rep1

source_name: roots of rice seedlings, K+-replete treatment, 3 d, rep1


title: Rice_K+-deficient_6 h_rep2

source_name: roots of rice seedlings, K+-deficient treatment, 6 h, rep2


title: Cln1/5 dko 3


title: wild-type 2

value: wt


title: Cln1/5 dko 2


title: Cln1/5 dko 1


title: wild-type 1


title: Cln1/5 dko 6


title: Rice_K+-replete_6 h_rep3

source_name: roots of rice seedlings, K+-replete treatment, 6 h, rep3


title: wild-type 4


title: wild-type 5


title: Cln1/5 dko 5


title: Rice_K+-replete_6 h_rep2

source_name: roots of rice seedlings, K+-replete treatment, 6 h, rep2


title: wild-type 3


title: TGFbeta treated

city: Nishihara

first: Hideyuki

last: Yamamoto

state: Okinawa

address: 207 Uehara

department: Faculty of medicine

institute: University of the Ryukyus

description: A549 cells

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v1.r2.pgf
meta-probeset file: HuEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: A549 cells treated with transforming growth factor beta 1

label_protocol: Total RNA was reverse transcribed to cDNA by WT Expression Kit (Ambion, TX). Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: A549 cells were grown on 60-mm Petri dishes in a culture medimum consisting DMEM and 0.45% glucose and 10% FCS.

extract_protocol: Total RNA was extracted using an Rneasy Mini Kit (Qiagen, MD) .

treatment_protocol: A548 cells were treated with 2 micro g/ml flagellin or 10 ng/ml transforming growth factor beta 1 for 24 hours in DMEM containing 0.1% FCS.

tag: cell line

tag: cell type

value: alveolar epithelial


title: wild-type 6


title: human bronchial epithelial cells from asthmatic donor 7

city: Chapel Hill

first: Melanie

middle: J.

last: Jardim

state: NC

address: 104 Mason Farm Road

department: NHEERL

institute: U.S. EPA

description: miRNA expression data

hyb_protocol: Hybridization was perfomed according to manufacturers protocol.

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

data_processing: The data were analyzed with miRNA QC tool provided by Affymetrix.

source_name: Primary bronchial epithelial cells

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

growth_protocol: HBECS were plated on transwells and grown at air-liquid interface

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

treatment_protocol: (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

value: Primary bronchial epithelial cells

value: ashtma


title: Flagellin treated

description: A549 cells

source_name: A549 cells treated with flagellin


title: human bronchial epithelial cells from healthy donor 6

description: miRNA expression data

value: healthy


title: Control

description: A549 cells

source_name: A549 cells treated without flagellin or transforming growth factor beta 1 (Control)


title: human bronchial epithelial cells from asthmatic donor 3

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 4

description: miRNA expression data


title: human bronchial epithelial cells from asthmatic donor 5

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 3

description: miRNA expression data


title: human bronchial epithelial cells from asthmatic donor 1

description: miRNA expression data


title: human bronchial epithelial cells from asthmatic donor 6

description: miRNA expression data


title: human bronchial epithelial cells from asthmatic donor 4

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 1

description: miRNA expression data


title: human bronchial epithelial cells from asthmatic donor 2

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 7

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 2

description: miRNA expression data


title: human bronchial epithelial cells from healthy donor 5

description: miRNA expression data


title: Indirect +PMN 3

city: Aurora

first: Eric

middle: L

last: Campbell

state: CO

address: 12700 East 19th Ave

institute: University of Colorado - Anschutz Medical Campus

description: Gene expression 2hrs after incubation with cell-free supernatants from cells after neutrophil transmigration

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (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 dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (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 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using combined rank consistency filtering with LOWESS intensity normalization in Agilent Feature Extraction software. Data was subsequently analyzed by GeneSpring (Agilent).

source_name: T84, 2hrs post-conditioned media, from migration with PMN, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.

growth_protocol: T84 intestinal epithelia were cultured in DMEM/F12 with 10% FCS at 37oC with 5% CO2. Experimental cells were seeded and grown to confluence (TER>1,000 Ohms.cm2) on the underside of 3cm2 3um-pore Transwell permeable supports (Corning).

extract_protocol: RNA was prepared using TRIzol reagent (Invitrogen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: On day of experiment monolayers were transferred to Hanks Buffered Saline, with 1uM fMLP on the apical surface (bottom chamber), to establish chemotactic gradient. Neutrophils were freshly isolated from healthy volunteer venous blood and used for either direct or indirect migration.

value: intestinal epithelial

tag: migration model

value: Indirect

tag: neutrophils

value: yes


title: Indirect +PMN 1

source_name: T84, 2hrs post-conditioned media, from migration with PMN, replicate 1


title: Indirect -PMN 1

description: Gene expression 2hrs after incubation with cell-free supernatants from cells incubated without neutrophils

source_name: T84, 2hrs post-conditioned media, from migration with no PMN, replicate 1

value: no


title: Indirect -PMN 3

source_name: T84, 2hrs post-conditioned media, from migration with no PMN, replicate 3


title: Direct +PMN 3

description: Gene expression 2hrs after neutrophil transmigration

source_name: T84, 2hrs post-migration, with PMN, replicate 3

value: Direct


title: Direct -PMN 1

description: Gene expression 2hrs after incubation with no neutrophils

source_name: T84, 2hrs post-migration, no PMN, replicate 1


title: Direct -PMN 3

source_name: T84, 2hrs post-migration, no PMN, replicate 3


title: Indirect +PMN 2

source_name: T84, 2hrs post-conditioned media, from migration with PMN, replicate 2


title: Indirect -PMN 2

source_name: T84, 2hrs post-conditioned media, from migration with no PMN, replicate 2


title: Direct -PMN 2

source_name: T84, 2hrs post-migration, no PMN, replicate 2


title: Direct +PMN 2

source_name: T84, 2hrs post-migration, with PMN, replicate 2


title: ESC UNDIFF LINE WA14 PASSAGE 39

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
ESC UNDIFF LINE WA14 PASSAGE 39
Raw data file: SAMPLE 230.txt

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ESC UNDIFF LINE WA14 PASSAGE 39 (SAMPLE 230)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells.  Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.  Embryoid bodies were cultured in fibroblast medium (FBS; EB_mesend) or in hESC medium without bFGF (EB_ecto) in 60mm Corning Low Attachment dishes for a total of 8 days. Media were changed by sedimentation every 2 days. An important point to note is that the same lot number of FBS was used for all studies.

extract_protocol: RNA was extracted using a modification of the basic Trizol (Invitrogen) protocol. Briefly, 1ml of Trizol was added to sedimented colonies or EBs and triturated to dissociate the cells. At this point the lysates were stored at -80oC until all samples for that cell line were collected. Upon thaw, lysates were incubated at room temperature for 10 mins, mixed with 200ul chloroform and centrifuged in a Phase-Lock Gel (Heavy) Eppendorf tube (Qiagen). RNA was precipitated from the aqueous phase by the addition of 250ul of isopropanol and 250ul of a high salt buffer (0.8 M sodium citrate and 1.2 M NaCl) followed by centrifugation. The RNA pellet was washed twice with 75% ethanol, dried and resuspended in nuclease-free water. RNA was DNase treated for 20 mins and the DNAse removed using Ambion’s DNA-Free kit. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: ESC

tag: condition

value: UNDIFF

tag: line

tag: passage

value: MALE

tag: processing control

value: SAMPLE 144


title: Direct +PMN 1

source_name: T84, 2hrs post-migration, with PMN, replicate 1


title: ESC KSR LINE WA13 PASSAGE 80

description:
ESC KSR LINE WA13 PASSAGE 80
Raw data file: SAMPLE 223.txt

source_name: ESC KSR LINE WA13 PASSAGE 80 (SAMPLE 223)

value: KSR

tag: gender


title: ESC UNDIFF LINE WA09 PASSAGE 45

description:
ESC UNDIFF LINE WA09 PASSAGE 45
Raw data file: SAMPLE 218.txt

source_name: ESC UNDIFF LINE WA09 PASSAGE 45 (SAMPLE 218)

value: FEMALE

value: SAMPLE 143


title: ESC KSR LINE WA14 PASSAGE 35

description:
ESC KSR LINE WA14 PASSAGE 35
Raw data file: SAMPLE 226.txt

source_name: ESC KSR LINE WA14 PASSAGE 35 (SAMPLE 226)


title: ESC UNDIFF LINE WA14 PASSAGE 35

description:
ESC UNDIFF LINE WA14 PASSAGE 35
Raw data file: SAMPLE 227.txt

source_name: ESC UNDIFF LINE WA14 PASSAGE 35 (SAMPLE 227)


title: ESC FBS LINE WA13 PASSAGE 80

description:
ESC FBS LINE WA13 PASSAGE 80
Raw data file: SAMPLE 222.txt

source_name: ESC FBS LINE WA13 PASSAGE 80 (SAMPLE 222)

value: FBS


title: ESC UNDIFF LINE WA09 PASSAGE 41

description:
ESC UNDIFF LINE WA09 PASSAGE 41
Raw data file: SAMPLE 215.txt

source_name: ESC UNDIFF LINE WA09 PASSAGE 41 (SAMPLE 215)


title: ESC KSR LINE WA09 PASSAGE 45

description:
ESC KSR LINE WA09 PASSAGE 45
Raw data file: SAMPLE 217.txt

source_name: ESC KSR LINE WA09 PASSAGE 45 (SAMPLE 217)


title: ESC FBS LINE WA13 PASSAGE 76

description:
ESC FBS LINE WA13 PASSAGE 76
Raw data file: SAMPLE 219.txt

source_name: ESC FBS LINE WA13 PASSAGE 76 (SAMPLE 219)


title: ESC FBS LINE WA14 PASSAGE 35

description:
ESC FBS LINE WA14 PASSAGE 35
Raw data file: SAMPLE 225.txt

source_name: ESC FBS LINE WA14 PASSAGE 35 (SAMPLE 225)


title: ESC FBS LINE WA14 PASSAGE 39

description:
ESC FBS LINE WA14 PASSAGE 39
Raw data file: SAMPLE 228.txt

source_name: ESC FBS LINE WA14 PASSAGE 39 (SAMPLE 228)


title: ESC FBS LINE WA09 PASSAGE 41

description:
ESC FBS LINE WA09 PASSAGE 41
Raw data file: SAMPLE 213.txt

source_name: ESC FBS LINE WA09 PASSAGE 41 (SAMPLE 213)


title: ESC KSR LINE WA13 PASSAGE 76

description:
ESC KSR LINE WA13 PASSAGE 76
Raw data file: SAMPLE 220.txt

source_name: ESC KSR LINE WA13 PASSAGE 76 (SAMPLE 220)


title: ESC FBS LINE WA09 PASSAGE 45

description:
ESC FBS LINE WA09 PASSAGE 45
Raw data file: SAMPLE 216.txt

source_name: ESC FBS LINE WA09 PASSAGE 45 (SAMPLE 216)


title: ESC UNDIFF LINE WA13 PASSAGE 80

description:
ESC UNDIFF LINE WA13 PASSAGE 80
Raw data file: SAMPLE 224.txt

source_name: ESC UNDIFF LINE WA13 PASSAGE 80 (SAMPLE 224)


title: ESC KSR LINE WA14 PASSAGE 39

description:
ESC KSR LINE WA14 PASSAGE 39
Raw data file: SAMPLE 229.txt

source_name: ESC KSR LINE WA14 PASSAGE 39 (SAMPLE 229)


title: ESC KSR LINE WA09 PASSAGE 41

description:
ESC KSR LINE WA09 PASSAGE 41
Raw data file: SAMPLE 214.txt

source_name: ESC KSR LINE WA09 PASSAGE 41 (SAMPLE 214)


title: ESC KSR LINE WA07 PASSAGE 47

description:
ESC KSR LINE WA07 PASSAGE 47
Raw data file: SAMPLE 211.txt

source_name: ESC KSR LINE WA07 PASSAGE 47 (SAMPLE 211)


title: ESC KSR LINE WA07 PASSAGE 43

description:
ESC KSR LINE WA07 PASSAGE 43
Raw data file: SAMPLE 208.txt

source_name: ESC KSR LINE WA07 PASSAGE 43 (SAMPLE 208)


title: ESC FBS LINE WA07 PASSAGE 47

description:
ESC FBS LINE WA07 PASSAGE 47
Raw data file: SAMPLE 210.txt

source_name: ESC FBS LINE WA07 PASSAGE 47 (SAMPLE 210)


title: ESC UNDIFF LINE WA13 PASSAGE 76

description:
ESC UNDIFF LINE WA13 PASSAGE 76
Raw data file: SAMPLE 221.txt

source_name: ESC UNDIFF LINE WA13 PASSAGE 76 (SAMPLE 221)


title: ESC FBS LINE WA01 PASSAGE 56

description:
ESC FBS LINE WA01 PASSAGE 56
Raw data file: SAMPLE 204.txt

source_name: ESC FBS LINE WA01 PASSAGE 56 (SAMPLE 204)

value: SAMPLE 142


title: ESC UNDIFF LINE WA07 PASSAGE 43

description:
ESC UNDIFF LINE WA07 PASSAGE 43
Raw data file: SAMPLE 209.txt

source_name: ESC UNDIFF LINE WA07 PASSAGE 43 (SAMPLE 209)


title: ESC UNDIFF LINE WA01 PASSAGE 52

description:
ESC UNDIFF LINE WA01 PASSAGE 52
Raw data file: SAMPLE 203.txt

source_name: ESC UNDIFF LINE WA01 PASSAGE 52 (SAMPLE 203)


title: ESC KSR LINE WA01 PASSAGE 56

description:
ESC KSR LINE WA01 PASSAGE 56
Raw data file: SAMPLE 205.txt

source_name: ESC KSR LINE WA01 PASSAGE 56 (SAMPLE 205)


title: ESC FBS LINE WA07 PASSAGE 43

description:
ESC FBS LINE WA07 PASSAGE 43
Raw data file: SAMPLE 207.txt

source_name: ESC FBS LINE WA07 PASSAGE 43 (SAMPLE 207)


title: ESC UNDIFF LINE UC06 PASSAGE 59

description:
ESC UNDIFF LINE UC06 PASSAGE 59
Raw data file: SAMPLE 200.txt

source_name: ESC UNDIFF LINE UC06 PASSAGE 59 (SAMPLE 200)

value: SAMPLE 140


title: ESC UNDIFF LINE WA07 PASSAGE 47

description:
ESC UNDIFF LINE WA07 PASSAGE 47
Raw data file: SAMPLE 212.txt

source_name: ESC UNDIFF LINE WA07 PASSAGE 47 (SAMPLE 212)


title: ESC UNDIFF LINE WA01 PASSAGE 56

description:
ESC UNDIFF LINE WA01 PASSAGE 56
Raw data file: SAMPLE 206.txt

source_name: ESC UNDIFF LINE WA01 PASSAGE 56 (SAMPLE 206)


title: ESC FBS LINE WA01 PASSAGE 52

description:
ESC FBS LINE WA01 PASSAGE 52
Raw data file: SAMPLE 201.txt

source_name: ESC FBS LINE WA01 PASSAGE 52 (SAMPLE 201)


title: ESC UNDIFF LINE UC06 PASSAGE 55

description:
ESC UNDIFF LINE UC06 PASSAGE 55
Raw data file: SAMPLE 197.txt

source_name: ESC UNDIFF LINE UC06 PASSAGE 55 (SAMPLE 197)


title: ESC FBS LINE UC06 PASSAGE 59

description:
ESC FBS LINE UC06 PASSAGE 59
Raw data file: SAMPLE 198.txt

source_name: ESC FBS LINE UC06 PASSAGE 59 (SAMPLE 198)


title: ESC KSR LINE WA01 PASSAGE 52

description:
ESC KSR LINE WA01 PASSAGE 52
Raw data file: SAMPLE 202.txt

source_name: ESC KSR LINE WA01 PASSAGE 52 (SAMPLE 202)


title: ESC KSR LINE UC06 PASSAGE 59

description:
ESC KSR LINE UC06 PASSAGE 59
Raw data file: SAMPLE 199.txt

source_name: ESC KSR LINE UC06 PASSAGE 59 (SAMPLE 199)


title: ESC KSR LINE UC06 PASSAGE 114

description:
ESC KSR LINE UC06 PASSAGE 114
Raw data file: SAMPLE 193.txt

source_name: ESC KSR LINE UC06 PASSAGE 114 (SAMPLE 193)

value: SAMPLE 141


title: ESC FBS LINE UC06 PASSAGE 55

description:
ESC FBS LINE UC06 PASSAGE 55
Raw data file: SAMPLE 195.txt

source_name: ESC FBS LINE UC06 PASSAGE 55 (SAMPLE 195)


title: ESC UNDIFF LINE UC06 PASSAGE 114

description:
ESC UNDIFF LINE UC06 PASSAGE 114
Raw data file: SAMPLE 194.txt

source_name: ESC UNDIFF LINE UC06 PASSAGE 114 (SAMPLE 194)

value: SAMPLE 139


title: ESC KSR LINE UC06 PASSAGE 55

description:
ESC KSR LINE UC06 PASSAGE 55
Raw data file: SAMPLE 196.txt

source_name: ESC KSR LINE UC06 PASSAGE 55 (SAMPLE 196)


title: ESC KSR LINE UC06 PASSAGE 110

description:
ESC KSR LINE UC06 PASSAGE 110
Raw data file: SAMPLE 190.txt

source_name: ESC KSR LINE UC06 PASSAGE 110 (SAMPLE 190)


title: ESC UNDIFF LINE UC06 PASSAGE 110

description:
ESC UNDIFF LINE UC06 PASSAGE 110
Raw data file: SAMPLE 191.txt

source_name: ESC UNDIFF LINE UC06 PASSAGE 110 (SAMPLE 191)


title: ESC FBS LINE UC06 PASSAGE 110

description:
ESC FBS LINE UC06 PASSAGE 110
Raw data file: SAMPLE 189.txt

source_name: ESC FBS LINE UC06 PASSAGE 110 (SAMPLE 189)


title: ESC UNDIFF LINE TE06 PASSAGE 64

description:
ESC UNDIFF LINE TE06 PASSAGE 64
Raw data file: SAMPLE 182.txt

source_name: ESC UNDIFF LINE TE06 PASSAGE 64 (SAMPLE 182)

value: SAMPLE 135


title: ESC FBS LINE TE06 PASSAGE 64

description:
ESC FBS LINE TE06 PASSAGE 64
Raw data file: SAMPLE 180.txt

source_name: ESC FBS LINE TE06 PASSAGE 64 (SAMPLE 180)


title: ESC FBS LINE UC06 PASSAGE 114

description:
ESC FBS LINE UC06 PASSAGE 114
Raw data file: SAMPLE 192.txt

source_name: ESC FBS LINE UC06 PASSAGE 114 (SAMPLE 192)


title: ESC UNDIFF LINE TE06 PASSAGE 60

description:
ESC UNDIFF LINE TE06 PASSAGE 60
Raw data file: SAMPLE 179.txt

source_name: ESC UNDIFF LINE TE06 PASSAGE 60 (SAMPLE 179)


title: ESC KSR LINE TE06 PASSAGE 64

description:
ESC KSR LINE TE06 PASSAGE 64
Raw data file: SAMPLE 181.txt

source_name: ESC KSR LINE TE06 PASSAGE 64 (SAMPLE 181)


title: ESC UNDIFF LINE TE04 PASSAGE 36

description:
ESC UNDIFF LINE TE04 PASSAGE 36
Raw data file: SAMPLE 176.txt

source_name: ESC UNDIFF LINE TE04 PASSAGE 36 (SAMPLE 176)

value: SAMPLE 134


title: ESC KSR LINE TE06 PASSAGE 60

description:
ESC KSR LINE TE06 PASSAGE 60
Raw data file: SAMPLE 178.txt

source_name: ESC KSR LINE TE06 PASSAGE 60 (SAMPLE 178)


title: ESC UNDIFF LINE TE04 PASSAGE 32

description:
ESC UNDIFF LINE TE04 PASSAGE 32
Raw data file: SAMPLE 173.txt

source_name: ESC UNDIFF LINE TE04 PASSAGE 32 (SAMPLE 173)


title: ESC FBS LINE TE06 PASSAGE 60

description:
ESC FBS LINE TE06 PASSAGE 60
Raw data file: SAMPLE 177.txt

source_name: ESC FBS LINE TE06 PASSAGE 60 (SAMPLE 177)


title: ESC KSR LINE TE04 PASSAGE 36

description:
ESC KSR LINE TE04 PASSAGE 36
Raw data file: SAMPLE 175.txt

source_name: ESC KSR LINE TE04 PASSAGE 36 (SAMPLE 175)


title: ESC KSR LINE TE04 PASSAGE 32

description:
ESC KSR LINE TE04 PASSAGE 32
Raw data file: SAMPLE 172.txt

source_name: ESC KSR LINE TE04 PASSAGE 32 (SAMPLE 172)


title: ESC FBS LINE TE04 PASSAGE 36

description:
ESC FBS LINE TE04 PASSAGE 36
Raw data file: SAMPLE 174.txt

source_name: ESC FBS LINE TE04 PASSAGE 36 (SAMPLE 174)


title: ESC UNDIFF LINE TE03 PASSAGE 70

description:
ESC UNDIFF LINE TE03 PASSAGE 70
Raw data file: SAMPLE 170.txt

source_name: ESC UNDIFF LINE TE03 PASSAGE 70 (SAMPLE 170)

value: SAMPLE 133


title: ESC KSR LINE SA02 PASSAGE 39

description:
ESC KSR LINE SA02 PASSAGE 39
Raw data file: SAMPLE 163.txt

source_name: ESC KSR LINE SA02 PASSAGE 39 (SAMPLE 163)

value: SAMPLE 132


title: ESC FBS LINE TE03 PASSAGE 66

description:
ESC FBS LINE TE03 PASSAGE 66
Raw data file: SAMPLE 165.txt

source_name: ESC FBS LINE TE03 PASSAGE 66 (SAMPLE 165)


title: ESC KSR LINE TE03 PASSAGE 66

description:
ESC KSR LINE TE03 PASSAGE 66
Raw data file: SAMPLE 166.txt

source_name: ESC KSR LINE TE03 PASSAGE 66 (SAMPLE 166)


title: ESC UNDIFF LINE TE03 PASSAGE 66

description:
ESC UNDIFF LINE TE03 PASSAGE 66
Raw data file: SAMPLE 167.txt

source_name: ESC UNDIFF LINE TE03 PASSAGE 66 (SAMPLE 167)


title: ESC UNDIFF LINE SA02 PASSAGE 39

description:
ESC UNDIFF LINE SA02 PASSAGE 39
Raw data file: SAMPLE 164.txt

source_name: ESC UNDIFF LINE SA02 PASSAGE 39 (SAMPLE 164)


title: ESC KSR LINE TE03 PASSAGE 70

description:
ESC KSR LINE TE03 PASSAGE 70
Raw data file: SAMPLE 169.txt

source_name: ESC KSR LINE TE03 PASSAGE 70 (SAMPLE 169)


title: ESC FBS LINE TE04 PASSAGE 32

description:
ESC FBS LINE TE04 PASSAGE 32
Raw data file: SAMPLE 171.txt

source_name: ESC FBS LINE TE04 PASSAGE 32 (SAMPLE 171)


title: ESC UNDIFF LINE SA01 PASSAGE 28

description:
ESC UNDIFF LINE SA01 PASSAGE 28
Raw data file: SAMPLE 155.txt

source_name: ESC UNDIFF LINE SA01 PASSAGE 28 (SAMPLE 155)

value: SAMPLE 131


title: UniRef Processing Control_SAMPLE 152

description:
UniRef Processing Control
Raw data file: SAMPLE 152.txt

source_name: UniRef Processing Control (SAMPLE 152)

value: UniRef


title: UniRef Processing Control_SAMPLE 150

description:
UniRef Processing Control
Raw data file: SAMPLE 150.txt

source_name: UniRef Processing Control (SAMPLE 150)


title: ESC FBS LINE SA02 PASSAGE 35

description:
ESC FBS LINE SA02 PASSAGE 35
Raw data file: SAMPLE 159.txt

source_name: ESC FBS LINE SA02 PASSAGE 35 (SAMPLE 159)

value: ESC


title: ESC UNDIFF LINE SA02 PASSAGE 35

description:
ESC UNDIFF LINE SA02 PASSAGE 35
Raw data file: SAMPLE 161.txt

source_name: ESC UNDIFF LINE SA02 PASSAGE 35 (SAMPLE 161)

value: UNDIFF


title: ESC FBS LINE SA02 PASSAGE 39

description:
ESC FBS LINE SA02 PASSAGE 39
Raw data file: SAMPLE 162.txt

source_name: ESC FBS LINE SA02 PASSAGE 39 (SAMPLE 162)


title: ESC KSR LINE SA02 PASSAGE 35

description:
ESC KSR LINE SA02 PASSAGE 35
Raw data file: SAMPLE 160.txt

source_name: ESC KSR LINE SA02 PASSAGE 35 (SAMPLE 160)


title: ESC UNDIFF LINE SA01 PASSAGE 32

description:
ESC UNDIFF LINE SA01 PASSAGE 32
Raw data file: SAMPLE 158.txt

source_name: ESC UNDIFF LINE SA01 PASSAGE 32 (SAMPLE 158)

value: MALE


title: ESC FBS LINE TE03 PASSAGE 70

description:
ESC FBS LINE TE03 PASSAGE 70
Raw data file: SAMPLE 168.txt

source_name: ESC FBS LINE TE03 PASSAGE 70 (SAMPLE 168)


title: ESC FBS LINE SA01 PASSAGE 32

description:
ESC FBS LINE SA01 PASSAGE 32
Raw data file: SAMPLE 156.txt

source_name: ESC FBS LINE SA01 PASSAGE 32 (SAMPLE 156)


title: ESC FBS LINE SA01 PASSAGE 28

description:
ESC FBS LINE SA01 PASSAGE 28
Raw data file: SAMPLE 153.txt

source_name: ESC FBS LINE SA01 PASSAGE 28 (SAMPLE 153)


title: UniRef Processing Control_SAMPLE 149

description:
UniRef Processing Control
Raw data file: SAMPLE 149.txt

source_name: UniRef Processing Control (SAMPLE 149)


title: ESC KSR LINE SA01 PASSAGE 28

description:
ESC KSR LINE SA01 PASSAGE 28
Raw data file: SAMPLE 154.txt

source_name: ESC KSR LINE SA01 PASSAGE 28 (SAMPLE 154)

value: KSR


title: UniRef Processing Control_SAMPLE 151

description:
UniRef Processing Control
Raw data file: SAMPLE 151.txt

source_name: UniRef Processing Control (SAMPLE 151)


title: ESC KSR LINE SA01 PASSAGE 32

description:
ESC KSR LINE SA01 PASSAGE 32
Raw data file: SAMPLE 157.txt

source_name: ESC KSR LINE SA01 PASSAGE 32 (SAMPLE 157)


title: UniRef Processing Control_SAMPLE 148

description:
UniRef Processing Control
Raw data file: SAMPLE 148.txt

source_name: UniRef Processing Control (SAMPLE 148)


title: UniRef Processing Control_SAMPLE 147

description:
UniRef Processing Control
Raw data file: SAMPLE 147.txt

source_name: UniRef Processing Control (SAMPLE 147)


title: UniRef Processing Control_SAMPLE 145

description:
UniRef Processing Control
Raw data file: SAMPLE 145.txt

source_name: UniRef Processing Control (SAMPLE 145)


title: UniRef Processing Control_SAMPLE 143

description:
UniRef Processing Control
Raw data file: SAMPLE 143.txt

source_name: UniRef Processing Control (SAMPLE 143)


title: UniRef Processing Control_SAMPLE 146

description:
UniRef Processing Control
Raw data file: SAMPLE 146.txt

source_name: UniRef Processing Control (SAMPLE 146)


title: UniRef Processing Control_SAMPLE 144

description:
UniRef Processing Control
Raw data file: SAMPLE 144.txt

source_name: UniRef Processing Control (SAMPLE 144)


title: UniRef Processing Control_SAMPLE 142

description:
UniRef Processing Control
Raw data file: SAMPLE 142.txt

source_name: UniRef Processing Control (SAMPLE 142)


title: UniRef Processing Control_SAMPLE 139

description:
UniRef Processing Control
Raw data file: SAMPLE 139.txt

source_name: UniRef Processing Control (SAMPLE 139)


title: UniRef Processing Control_SAMPLE 137

description:
UniRef Processing Control
Raw data file: SAMPLE 137.txt

source_name: UniRef Processing Control (SAMPLE 137)


title: UniRef Processing Control_SAMPLE 141

description:
UniRef Processing Control
Raw data file: SAMPLE 141.txt

source_name: UniRef Processing Control (SAMPLE 141)


title: UniRef Processing Control_SAMPLE 136

description:
UniRef Processing Control
Raw data file: SAMPLE 136.txt

source_name: UniRef Processing Control (SAMPLE 136)


title: UniRef Processing Control_SAMPLE 131

description:
UniRef Processing Control
Raw data file: SAMPLE 131.txt

source_name: UniRef Processing Control (SAMPLE 131)


title: UniRef Processing Control_SAMPLE 138

description:
UniRef Processing Control
Raw data file: SAMPLE 138.txt

source_name: UniRef Processing Control (SAMPLE 138)


title: UniRef Processing Control_SAMPLE 140

description:
UniRef Processing Control
Raw data file: SAMPLE 140.txt

source_name: UniRef Processing Control (SAMPLE 140)


title: UniRef Processing Control_SAMPLE 135

description:
UniRef Processing Control
Raw data file: SAMPLE 135.txt

source_name: UniRef Processing Control (SAMPLE 135)


title: UniRef Processing Control_SAMPLE 134

description:
UniRef Processing Control
Raw data file: SAMPLE 134.txt

source_name: UniRef Processing Control (SAMPLE 134)


title: UniRef Processing Control_SAMPLE 132

description:
UniRef Processing Control
Raw data file: SAMPLE 132.txt

source_name: UniRef Processing Control (SAMPLE 132)


title: UniRef Processing Control_SAMPLE 130

description:
UniRef Processing Control
Raw data file: SAMPLE 130.txt

source_name: UniRef Processing Control (SAMPLE 130)


title: UniRef Processing Control_SAMPLE 127

description:
UniRef Processing Control
Raw data file: SAMPLE 127.txt

source_name: UniRef Processing Control (SAMPLE 127)


title: UniRef Processing Control_SAMPLE 124

description:
UniRef Processing Control
Raw data file: SAMPLE 124.txt

source_name: UniRef Processing Control (SAMPLE 124)


title: UniRef Processing Control_SAMPLE 125

description:
UniRef Processing Control
Raw data file: SAMPLE 125.txt

source_name: UniRef Processing Control (SAMPLE 125)


title: UniRef Processing Control_SAMPLE 123

description:
UniRef Processing Control
Raw data file: SAMPLE 123.txt

source_name: UniRef Processing Control (SAMPLE 123)


title: UniRef Processing Control_SAMPLE 126

description:
UniRef Processing Control
Raw data file: SAMPLE 126.txt

source_name: UniRef Processing Control (SAMPLE 126)


title: UniRef Processing Control_SAMPLE 133

description:
UniRef Processing Control
Raw data file: SAMPLE 133.txt

source_name: UniRef Processing Control (SAMPLE 133)


title: UniRef Processing Control_SAMPLE 122

description:
UniRef Processing Control
Raw data file: SAMPLE 122.txt

source_name: UniRef Processing Control (SAMPLE 122)


title: UniRef Processing Control_SAMPLE 121

description:
UniRef Processing Control
Raw data file: SAMPLE 121.txt

source_name: UniRef Processing Control (SAMPLE 121)


title: DM PT biological rep 2

city: Porto

first: Sílvia

last: Coimbra

address: Rua do Campo Alegre

department: Biology

country: Portugal

institute: University of Porto

description: Arabidopsis PT DM2

hyb_protocol: 15 µg of fragmented aRNA was used in a 300 µl hybridization cocktail containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45 °C. Standard post hybridization wash and double-stain protocols (FS450_0004; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix Expression Console software to obtain Absent/Present calls and to assure that all quality parameters were in the recommended range. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Cheng Li Lab, Harvard). The 6 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model. Replicate data (triplicates) for the conditions were weighted gene-wise by using inverse squared standard error as weights. Genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.3. The lower confidence bound criterion means that we can be 90% confident that the fold change is a value between the lower confidence bound and a variable upper confidence bound.

organism: Arabidopsis thaliana

source_name: double mutant_pollen tube

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Arabidopsis ATH1 Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Pollen was collected from newly opened flowers and germinated for 8h in the dark in growth medium (5 mM KCl, 5 mM CaCl2, 1 mM MgSO4, 0.01 % H3BO3, 10 % Sucrose, pH 7.4)

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit from Qiagen.

tag: ecotype

value: Nossen

tag: genotype/variation

value: agp6 agp11 double null mutant (Ds transposon tagged)

value: after 8h of in vitro germination

tag: tissue

value: pollen tube


title: DM PT biological rep 3

description: Arabidopsis PT DM3

tag: time point


title: WT PT biological rep 2

description: Arabidopsis PT WT2

source_name: wild type_pollen tube

value: wild type


title: iPSC UNDIFF LINE i7 PASSAGE 21

description:
iPSC UNDIFF LINE i7 PASSAGE 21
Raw data file: SAMPLE 120.txt

source_name: iPSC UNDIFF LINE i7 PASSAGE 21 (SAMPLE 120)

value: iPSC

value: FEMALE

value: SAMPLE 152


title: WT PT biological rep 3

description: Arabidopsis PT WT3


title: iPSC KSR LINE i7 PASSAGE 21

description:
iPSC KSR LINE i7 PASSAGE 21
Raw data file: SAMPLE 119.txt

source_name: iPSC KSR LINE i7 PASSAGE 21 (SAMPLE 119)


title: DM PT biological rep 1

description: Arabidopsis PT DM1


title: iPSC KSR LINE i5 PASSAGE 21

description:
iPSC KSR LINE i5 PASSAGE 21
Raw data file: SAMPLE 113.txt

source_name: iPSC KSR LINE i5 PASSAGE 21 (SAMPLE 113)

value: SAMPLE 151


title: iPSC KSR LINE i7 PASSAGE 17

description:
iPSC KSR LINE i7 PASSAGE 17
Raw data file: SAMPLE 116.txt

source_name: iPSC KSR LINE i7 PASSAGE 17 (SAMPLE 116)


title: iPSC FBS LINE i7 PASSAGE 21

description:
iPSC FBS LINE i7 PASSAGE 21
Raw data file: SAMPLE 118.txt

source_name: iPSC FBS LINE i7 PASSAGE 21 (SAMPLE 118)

value: FBS


title: iPSC UNDIFF LINE i5 PASSAGE 21

description:
iPSC UNDIFF LINE i5 PASSAGE 21
Raw data file: SAMPLE 114.txt

source_name: iPSC UNDIFF LINE i5 PASSAGE 21 (SAMPLE 114)


title: iPSC FBS LINE i5 PASSAGE 21

description:
iPSC FBS LINE i5 PASSAGE 21
Raw data file: SAMPLE 112.txt

source_name: iPSC FBS LINE i5 PASSAGE 21 (SAMPLE 112)


title: iPSC UNDIFF LINE i7 PASSAGE 17

description:
iPSC UNDIFF LINE i7 PASSAGE 17
Raw data file: SAMPLE 117.txt

source_name: iPSC UNDIFF LINE i7 PASSAGE 17 (SAMPLE 117)


title: iPSC UNDIFF LINE i5 PASSAGE 17

description:
iPSC UNDIFF LINE i5 PASSAGE 17
Raw data file: SAMPLE 111.txt

source_name: iPSC UNDIFF LINE i5 PASSAGE 17 (SAMPLE 111)


title: UniRef Processing Control_SAMPLE 128

description:
UniRef Processing Control
Raw data file: SAMPLE 128.txt

source_name: UniRef Processing Control (SAMPLE 128)


title: 20°C+Cu/24°C+Cu [30_slide13_SubB_20-40-CY3vs24-40-Cy5.gpr.txt]

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal / processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: Digestive gland tissue, individual samples exposed to 20°C + 40 µg/L of copper during 4 days

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

value: female

source_name: Digestive gland tissue, individual samples exposed to 24°C + 40 µg/L of copper during 4 days


title: UniRef Processing Control_SAMPLE 129

description:
UniRef Processing Control
Raw data file: SAMPLE 129.txt

source_name: UniRef Processing Control (SAMPLE 129)


title: 24°C/24°C+Cu [36_slide11-SubB_CTR24-CY5vs24-40-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 24°C during 4 days.


title: 24°C/24°C+Cu [34_slide2-subA_CTR24-CY3vs24-40-CY5.gpr.txt]


title: 24°C/24°C+Cu [33_slide2_SubB_CTR24-CY5vs24-40-CY3.gpr.txt]


title: 20°C+Cu/24°C+Cu [31_slide14_SubA_20-40-CY5vs24-40-CY3.gpr.txt]


title: iPSC KSR LINE i5 PASSAGE 17

description:
iPSC KSR LINE i5 PASSAGE 17
Raw data file: SAMPLE 110.txt

source_name: iPSC KSR LINE i5 PASSAGE 17 (SAMPLE 110)


title: 24°C/24°C+Cu [35_slide11-SubA-CTR24-CY3vs24-40-CY5.gpr.txt]


title: 20°C+Cu/24°C+Cu [32_slide14_SubB_20-40-CY5vs24-40-CY3.gpr.txt]


title: iPSC FBS LINE i7 PASSAGE 17

description:
iPSC FBS LINE i7 PASSAGE 17
Raw data file: SAMPLE 115.txt

source_name: iPSC FBS LINE i7 PASSAGE 17 (SAMPLE 115)


title: WT PT biological rep 1

description: Arabidopsis PT WT1

source_name: wild type_pollen tube


title: 20°C+Cu/24°C+Cu [29_slide13_SubA_20-40-CY3vs24-40-Cy5.gpr.txt]


title: 20°C/20°C+Cu [28_slide5_subB_CTR20-Cy5vs20-40-Cy3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 20°C  during 4 days


title: Disc Cells in 3D_TNF-a (222)

city: Charlotte

first: Helen

last: Gruber

address: 1542 Graden Terrace

department: Orthopaedic Surgery

institute: Carolinas HealthCare System

hyb_protocol: Fragmented cRNA was hybridized to the  X3P chip in the Affymetrix hybridiztion buffer for 16 hrs at 45oC. X3P chips were washed and labeled in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned once via the Affymetrix 3000G scanner.

data_processing: The data were analyzed with the GCOS Affymetrix GeneChip Operating System (version 1.2) and Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling as normalization were used. Further normalization was acheived using GC-RMA (robust multiarray average) via GeneSifter analysis software (Viz Labs LLC, Seattle , WA; http://www.genesifter.net).

source_name: Disc Tissue

label_protocol: Biotin-labeled cRNA were prepard according to the Affymetrix protocol for IVT labeling.

growth_protocol: Human annulus disc cells (100,000) were seeded into each piece (~0.5 cm3) of a collagen construct (Gelfoam; Pharmacia & Upjohn Co., Kalamazoo, MI). They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 10e3 PM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.

extract_protocol: Each piece of Gelfoam was homongenized and RNA isolated using TRIzol reagent

treatment_protocol: They were fed 3 times per week for 9 days with minimal essential medium with 20% fetal bovine serum (MEM20) +/- 103 pM TNF-a. Cells were allowed to grow an additional 5 days without changing the media.

value: Disc Tissue

tag: tissue grade

value: II

value: annulus cells

tag: agent

value: TNF-a


title: iPSC FBS LINE i5 PASSAGE 17

description:
iPSC FBS LINE i5 PASSAGE 17
Raw data file: SAMPLE 109.txt

source_name: iPSC FBS LINE i5 PASSAGE 17 (SAMPLE 109)

value: MALE


title: Disc Cells in 3D_TNF-a (126)

value: III


title: Disc Cells in 3D_Control (222)

value: control


title: iPSC UNDIFF LINE i4 PASSAGE 14

description:
iPSC UNDIFF LINE i4 PASSAGE 14
Raw data file: SAMPLE 108.txt

source_name: iPSC UNDIFF LINE i4 PASSAGE 14 (SAMPLE 108)

value: UNDIFF

value: SAMPLE 150


title: Disc Cells in 3D_Control (126)


title: 20°C/20°C+Cu [25_Slide1_SubB_CTR20-CY5vs20-40-CY3.gpr.txt]


title: 20°C/20°C+Cu [26_slide1_subA_CTR20-CY3vs20-40-Cy5.gpr.txt]


title: 20°C/24°C [24_slide8_subB_CTR20-CY5vsCTR24-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 24°C  during 4 days


title: Disc Cells in 3D_TNF-a (95)

value: IV


title: 20°C/24°C [23_slide8_subA_CTR20-CY5vsCTR24-Cy3.gpr.txt]


title: Disc Cells in 3D_TNF-a (154)


title: Disc Cells in 3D_Control (154)


title: iPSC KSR LINE i4 PASSAGE 14

description:
iPSC KSR LINE i4 PASSAGE 14
Raw data file: SAMPLE 107.txt

source_name: iPSC KSR LINE i4 PASSAGE 14 (SAMPLE 107)

value: KSR


title: 20°C/24°C [22_slide7_subB_CTR20-CY3vsCTR24-CY5.gpr.txt]


title: Disc Cells in 3D_Control (95)


title: 16°C+Cu/24°C+Cu [18_slide17_subB_16-40-CY5vs24-40-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 16°C + 40 µg/L of copper during 4 days


title: 20°C/24°C [21_slide7_subA_CTR20-CY3vsCTR24-CY5.gpr.txt]


title: 16°C+Cu/24°C+Cu [19_slide18_subB_16-40-CY3vs24-40-CY5.gpr.txt]


title: iPSC FBS LINE i4 PASSAGE 14

description:
iPSC FBS LINE i4 PASSAGE 14
Raw data file: SAMPLE 106.txt

source_name: iPSC FBS LINE i4 PASSAGE 14 (SAMPLE 106)

value: iPSC


title: 16°C+Cu/20°C+Cu [16_slide20_subA_16-40-CY3vs20-40-CY5.gpr.txt]


title: 16°C+Cu/24°C+Cu [17_slide16_subA_16-40-CY5vs24-40-CY3.gpr.txt]


title: 16°C+Cu/24°C+Cu [20_slide20_subB_16-40-CY3vs24-40-CY5.gpr.txt]


title: 16°C+Cu/20°C+Cu [15_slide18_subA_16-40-CY3vs20-40-CY5.gpr.txt]


title: iPSC UNDIFF LINE i4 PASSAGE 10

description:
iPSC UNDIFF LINE i4 PASSAGE 10
Raw data file: SAMPLE 105.txt

source_name: iPSC UNDIFF LINE i4 PASSAGE 10 (SAMPLE 105)


title: 16°C+Cu/20°C+Cu [14_slide17_subA_16-40-CY5vs20-40-CY3.gpr.txt]


title: iPSC FBS LINE i4 PASSAGE 10

description:
iPSC FBS LINE i4 PASSAGE 10
Raw data file: SAMPLE 103.txt

source_name: iPSC FBS LINE i4 PASSAGE 10 (SAMPLE 103)


title: iPSC UNDIFF LINE i2 PASSAGE 23

description:
iPSC UNDIFF LINE i2 PASSAGE 23
Raw data file: SAMPLE 102.txt

source_name: iPSC UNDIFF LINE i2 PASSAGE 23 (SAMPLE 102)

value: SAMPLE 149


title: 16°C+Cu/20°C+Cu [13_slide16_subB_16-40-CY5vs20-40-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 20°C + 40 µg/L of copper during 4 days


title: 16°C/16°C+Cu [12_slide 15_SubA_CTR16-CY5vs16-40-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 16°C considered as absolute control


title: iPSC KSR LINE i4 PASSAGE 10

description:
iPSC KSR LINE i4 PASSAGE 10
Raw data file: SAMPLE 104.txt

source_name: iPSC KSR LINE i4 PASSAGE 10 (SAMPLE 104)


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample C, replicate 2

city: Chieti

first: Mirko

last: Pesce

address: Via Vestini

country: Italy

institute: University G. D'Annunzio

hyb_protocol: Microarrays were dehydrated in ethanol for 2 minutes at room temperature, and dried using compressed air. Microarrays were rehydrated by soaking in prehybridization solution (5x SSPE pH 7, 0.1% SDS, 1% BSA) for 2 hours at 42°C, then were washed in deionized water twice for 1 minute each, and dried by briefly spinning in a centrifuge. Labeled aRNA was denatured at 95°C for 5 minutes, and applied to microarray slide. Microarrays and labeled aRNA were then covered with cover slips (Knittel Glass), placed in Hyb chamber (Gene Machine) and hybridized for 14-16 hours at 42°C. Microarray slides were washed in 2x SSPE, 0.1% SDS at 42°C for 5 minutes, then in 0.1x SSPE, 0.1% SDS once for 2 minutes at room temperature. Slides were then washed three times for 1 minute each at room temperature in 0.1x SSPE, immediately dried by briefly spinning in a centrifuge, and stored in a dark box.

scan_protocol: After hybridization, Cy3-Cy5 fluorescent signals were captured by a Confocal Laser Scanner "ScanArray Express" (Packard BioScience) and analysed using the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer).

data_processing: The values of the median signal intensity from each spot were subtracted by the local median background intensity. For each slide after local background subtraction, a LOWESS algorithm was used for raw data normalization to evaluate the signal-to-noise ratio of test sample vs. reference signal with the software "ScanArray Express - MicroArray Analysis System" version 3.0 (Perkin Elmer).

source_name: HaCaT cells, non-exposed control

label_protocol: Five to twenty microgram of amplified aRNA was fluorescently labelled with Cy3 (Amersham, Pharmacia Biotech, Buckinghamshire, UK).

extract_protocol: RNA was isolated from HaCaT cells using SV Total RNA Isolation System (Promega, Madison, WI, USA). RNA quality was determined by both evaluation of the integrity of rRNA bands using agarose electrophoresis, and absorbtion readings at 260 and 280 nm, and a 260:280 ratio of 1.7 was considered acceptable for analysis. Extracted RNA was linearly amplified using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA).

value: HaCaT

value: keratinocyte cells

tag: stimulus

value: sham

source_name: HaCaT cells exposed to ELF-EMF for 1 hour

label_protocol: Five to twenty microgram of amplified aRNA was fluorescently labelled with Cy5 (Amersham, Pharmacia Biotech, Buckinghamshire, UK).

value: exposed to ELF-EMF 1mT 50Hz for 1 hour


title: 16°C/16°C+Cu [11_slide14_SubA_CTR16-CY5vs16-40-CY3.gpr.txt]

value: female


title: iPSC KSR LINE i2 PASSAGE 19

description:
iPSC KSR LINE i2 PASSAGE 19
Raw data file: SAMPLE 99.txt

source_name: iPSC KSR LINE i2 PASSAGE 19 (SAMPLE 99)


title: iPSC FBS LINE i2 PASSAGE 23

description:
iPSC FBS LINE i2 PASSAGE 23
Raw data file: SAMPLE 101.txt

source_name: iPSC FBS LINE i2 PASSAGE 23 (SAMPLE 101)

value: FBS


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample C, dye swap

tag: cell line


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample C, replicate 1

tag: cell type


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample B, dye swap


title: iPSC UNDIFF LINE i2 PASSAGE 19

description:
iPSC UNDIFF LINE i2 PASSAGE 19
Raw data file: SAMPLE 100.txt

source_name: iPSC UNDIFF LINE i2 PASSAGE 19 (SAMPLE 100)


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample B, replicate 2


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample B, replicate 1


title: iPSC FBS LINE i2 PASSAGE 19

description:
iPSC FBS LINE i2 PASSAGE 19
Raw data file: SAMPLE 98.txt

source_name: iPSC FBS LINE i2 PASSAGE 19 (SAMPLE 98)


title: 16°C/16°C+Cu [10_slide13last_SubB_CTR16-CY3vs16-40-CY5.gpr.txt]


title: 16°C/16°C+Cu [09_slide13last_SubA_CTR16-CY3vs16-40-CY5.gpr.txt]


title: 16°C/24°C [08_slide6_subB_CTR16-CY5vsCTR24-CY3.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 24°C during 4 days.


title: 16°C/20°C [04_slide4_subB_CTR16-CY3vsCTR20-CY5.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 20°C during 4 days.


title: 16°C/24°C [07_slide6_subA_CTR16-CY5vsCTR24-CY3.gpr.txt]


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample A, replicate 2


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample A, replicate 1


title: 16°C/24°C [06_slide5_subB_CTR16-CY3vsCTR24-CY5.gpr.txt]


title: ESC UNDIFF LINE UC06 PASSAGE 114

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: BeadStudio software v3.2, non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: undifferentiated human embryonic stem cell line

label_protocol: Cy5 and Cy3

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human pluripotent stem cells were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. Pluripotent stem cells were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer’s instructions.

value: embryonic stem cell

value: Undifferenciated


title: 16°C/20°C [03_slide4_subA_CTR16-CY3vsCTR20-CY5.gpr.txt]


title: iPSC UNDIFF LINE i12 PASSAGE 14

description:
iPSC UNDIFF LINE i12 PASSAGE 14
Raw data file: SAMPLE 91.txt

source_name: iPSC UNDIFF LINE i12 PASSAGE 14 (SAMPLE 91)

value: FEMALE

value: SAMPLE 147


title: 16°C/20°C [01_slide3_subA_CTR16-CY5vsCTR20-CY3.gpr.txt]


title: 16°C/20°C [02_slide3_subB_CTR16-CY5vsCTR20-CY3.gpr.txt]


title: iPSC UNDIFF LINE i5 PASSAGE 21

source_name: undifferentiated induced pluripotent stem cell line

value: induced pluripotent stem cells

value: male


title: iPSC UNDIFF LINE i7 PASSAGE 21


title: iPSC UNDIFF LINE i12 PASSAGE 14


title: 16°C/24°C [05_slide4_subB_CTR16-CY3vsCTR20-CY5.gpr.txt]


title: ESC UNDIFF LINE TE03 PASSAGE 70


title: iPSC FBS LINE i12 PASSAGE 14

description:
iPSC FBS LINE i12 PASSAGE 14
Raw data file: SAMPLE 89.txt

source_name: iPSC FBS LINE i12 PASSAGE 14 (SAMPLE 89)


title: iPSC KSR LINE i12 PASSAGE 10

description:
iPSC KSR LINE i12 PASSAGE 10
Raw data file: SAMPLE 87.txt

source_name: iPSC KSR LINE i12 PASSAGE 10 (SAMPLE 87)


title: iPSC UNDIFF LINE i4 PASSAGE 14


title: ESC UNDIFF LINE TE04 PASSAGE 32


title: iPSC FBS LINE i12 PASSAGE 10

description:
iPSC FBS LINE i12 PASSAGE 10
Raw data file: SAMPLE 86.txt

source_name: iPSC FBS LINE i12 PASSAGE 10 (SAMPLE 86)


title: iPSC KSR LINE i12 PASSAGE 14

description:
iPSC KSR LINE i12 PASSAGE 14
Raw data file: SAMPLE 90.txt

source_name: iPSC KSR LINE i12 PASSAGE 14 (SAMPLE 90)


title: ESC UNDIFF LINE WA07 PASSAGE 43


title: iPSC UNDIFF LINE i1 PASSAGE 12


title: HaCaT exposed to ELF-EMF 1mT 50Hz for 1 h vs. non-exposed cells, sample A, dye swap


title: iPSC KSR LINE i11 PASSAGE 25

description:
iPSC KSR LINE i11 PASSAGE 25
Raw data file: SAMPLE 84.txt

source_name: iPSC KSR LINE i11 PASSAGE 25 (SAMPLE 84)

value: MALE

value: SAMPLE 146


title: iPSC UNDIFF LINE i12 PASSAGE 10

description:
iPSC UNDIFF LINE i12 PASSAGE 10
Raw data file: SAMPLE 88.txt

source_name: iPSC UNDIFF LINE i12 PASSAGE 10 (SAMPLE 88)

value: UNDIFF


title: iPSC UNDIFF LINE i11 PASSAGE 25

description:
iPSC UNDIFF LINE i11 PASSAGE 25
Raw data file: SAMPLE 85.txt

source_name: iPSC UNDIFF LINE i11 PASSAGE 25 (SAMPLE 85)

value: iPSC


title: ESC UNDIFF LINE WA14 PASSAGE 39


title: iPSC FBS LINE i11 PASSAGE 25

description:
iPSC FBS LINE i11 PASSAGE 25
Raw data file: SAMPLE 83.txt

source_name: iPSC FBS LINE i11 PASSAGE 25 (SAMPLE 83)


title: ESC UNDIFF LINE WA09 PASSAGE 45


title: ESC UNDIFF LINE WA01 PASSAGE 56


title: iPSC UNDIFF LINE i1 PASSAGE 16

description:
iPSC UNDIFF LINE i1 PASSAGE 16
Raw data file: SAMPLE 80.txt

source_name: iPSC UNDIFF LINE i1 PASSAGE 16 (SAMPLE 80)

value: SAMPLE 145


title: iPSC KSR LINE i1 PASSAGE 16

description:
iPSC KSR LINE i1 PASSAGE 16
Raw data file: SAMPLE 79.txt

source_name: iPSC KSR LINE i1 PASSAGE 16 (SAMPLE 79)

value: KSR


title: ESC UNDIFF LINE TE06 PASSAGE 60


title: iPSC FBS LINE i1 PASSAGE 16

description:
iPSC FBS LINE i1 PASSAGE 16
Raw data file: SAMPLE 78.txt

source_name: iPSC FBS LINE i1 PASSAGE 16 (SAMPLE 78)


title: ESC UNDIFF LINE WA13 PASSAGE 76


title: ESC UNDIFF LINE SA01 PASSAGE 32


title: iPSC KSR LINE i11 PASSAGE 21

description:
iPSC KSR LINE i11 PASSAGE 21
Raw data file: SAMPLE 81.txt

source_name: iPSC KSR LINE i11 PASSAGE 21 (SAMPLE 81)


title: iPSC UNDIFF LINE i1 PASSAGE 12

description:
iPSC UNDIFF LINE i1 PASSAGE 12
Raw data file: SAMPLE 77.txt

source_name: iPSC UNDIFF LINE i1 PASSAGE 12 (SAMPLE 77)


title: iPSC UNDIFF LINE i11 PASSAGE 21

description:
iPSC UNDIFF LINE i11 PASSAGE 21
Raw data file: SAMPLE 82.txt

source_name: iPSC UNDIFF LINE i11 PASSAGE 21 (SAMPLE 82)


title: ESC UNDIFF LINE UC06 PASSAGE 49

source_name: undifferentiated human embryonic stem cell line


title: ESC UNDIFF LINE ES06 PASSAGE 62


title: ESC UNDIFF LINE ES03 PASSAGE 88


title: ESC UNDIFF LINE ES02 PASSAGE 49


title: 20°C/20°C+Cu [27_slide5_subA_CTR20CY3vs20-40-Cy5.gpr.txt]

source_name: Digestive gland tissue, individual samples exposed to 20°C  during 4 days

source_name: Digestive gland tissue, individual samples exposed to 20°C + 40 µg/L of copper during 4 days


title: ESC UNDIFF LINE ES05 PASSAGE 59


title: Somatic Tissue Trachea

description:
Somatic Tissue Trachea
Raw data file: SAMPLE 73.txt

source_name: Somatic Tissue Trachea (SAMPLE 73)

value: Somatic Tissue

value: SAMPLE 137


title: Somatic Tissue Colon

description:
Somatic Tissue Colon
Raw data file: SAMPLE 74.txt

source_name: Somatic Tissue Colon (SAMPLE 74)

value: SAMPLE 134


title: ESC UNDIFF LINE ES01 PASSAGE 71

value: female


title: iPSC KSR LINE i1 PASSAGE 12

description:
iPSC KSR LINE i1 PASSAGE 12
Raw data file: SAMPLE 76.txt

source_name: iPSC KSR LINE i1 PASSAGE 12 (SAMPLE 76)


title: iPSC FBS LINE i1 PASSAGE 12

description:
iPSC FBS LINE i1 PASSAGE 12
Raw data file: SAMPLE 75.txt

source_name: iPSC FBS LINE i1 PASSAGE 12 (SAMPLE 75)

value: FBS


title: Somatic Tissue Thyroid

description:
Somatic Tissue Thyroid
Raw data file: SAMPLE 72.txt

source_name: Somatic Tissue Thyroid (SAMPLE 72)

value: SAMPLE 136


title: ESC UNDIFF LINE BG03 PASSAGE 54

value: embryonic stem cell

value: Undifferenciated


title: Somatic Tissue Thymus

description:
Somatic Tissue Thymus
Raw data file: SAMPLE 71.txt

source_name: Somatic Tissue Thymus (SAMPLE 71)

value: SAMPLE 139


title: ESC UNDIFF LINE BG02 PASSAGE 54


title: Somatic Tissue Testes

description:
Somatic Tissue Testes
Raw data file: SAMPLE 70.txt

source_name: Somatic Tissue Testes (SAMPLE 70)


title: Somatic Tissue Spleen

description:
Somatic Tissue Spleen
Raw data file: SAMPLE 69.txt

source_name: Somatic Tissue Spleen (SAMPLE 69)

value: SAMPLE 125


title: ESC UNDIFF LINE BG01 PASSAGE 67

value: male


title: Somatic Tissue Skeletal Muscle

description:
Somatic Tissue Skeletal Muscle
Raw data file: SAMPLE 67.txt

source_name: Somatic Tissue Skeletal Muscle (SAMPLE 67)

value: MALE

value: SAMPLE 135


title: 12066-6

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Gene expression data from BALB/c Mouse involuted normal mammary gland 30 days post weaning
hei1_12066_6-7.CEL

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse Genome 430 2.0 GeneChip, washed and stained following the manufacturer’s recommendation.

scan_protocol: Microarrays were scanned with the GeneChip Scanner 3000 7G.

data_processing: An alternative probe set mapping published by the AffyProbeMiner project (remapped gene consistent cdf-file, using validated complete coding sequences in GenBank, version 1.8.0) was used to calculate probe set signals. RMA background correction and quantile normalization were used.

label: Biotin

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

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen) followed by DNA digestion (TURBO DNA-free; Ambion) according to the manufacturer’s instructions. Total RNA from tumor samples and normal mammary gland was cleaned up using RNeasy mini kit according to the manufacturer’s instructions (Qiagen).

tag: strain

value: BALB/c

value: involuted normal mammary gland

tag: time

value: 30 days post weaning


title: 12132-6

description:
Gene expression data from BALB/c Mouse involuted normal mammary gland 30 days post weaning
hei1_12132_6-7.CEL


title: Somatic Tissue Small Intestine

description:
Somatic Tissue Small Intestine
Raw data file: SAMPLE 68.txt

source_name: Somatic Tissue Small Intestine (SAMPLE 68)

tag: class

value: SAMPLE 147


title: Somatic Tissue Prostate

description:
Somatic Tissue Prostate
Raw data file: SAMPLE 66.txt

source_name: Somatic Tissue Prostate (SAMPLE 66)

value: Somatic Tissue

tag: condition

value: SAMPLE 152


title: HeLa treated with Cas-II-gly, biological rep1

city: Mexico City

first: Karol

last: Baca Lopez

address: Periferico sur

country: Mexico

institute: National Institute of Genomic Medicine

description:
Gene expression data from HeLa cells treated with Cas-II-gly.
Cas_II-gly-1

hyb_protocol: Hybridization to Affymetrix U133plus2 GeneChips, staining and washing were carried out as described (Affymetrix, Santa Clara).

scan_protocol: Scanning procedure was carried out as described by Affymetrix, Santa Clara.

data_processing: Data pre-processing was performed by using the affy library in BioConductor running under [R].

source_name: HeLa cells treated with Cas-II-gly

label_protocol: Biotinylated cRNA were prepared according to Affymetrix, Santa Clara CA Inc. protocol from 400 ng total RNA.

growth_protocol: HeLa cells were mantained at room temperature in 5% CO2 under sterile conditions in  DMEM, Sigma),  supplemented with 10% fetal bovine serum (Sigma).

extract_protocol: Total RNA isolated using AllPrep DNA-RNA Mini Kit 50.

treatment_protocol: Cells were treated with Cas II-gly in 6-well microplates by 6h. In order to diminish biological variability, pools of 3 wells were made and combined into a single sample before proceeding to chip hybridization.

value: cervical cancer (HeLa) cells

value: Cas II-gly


title: 12133-6

description:
Gene expression data from BALB/c Mouse involuted normal mammary gland 30 days post weaning
hei1_12133_6-7.CEL


title: HeLa treated with Cas-II-gly, biological rep3

description:
Gene expression data from HeLa cells treated with Cas-II-gly.
Cas_II-gly-3


title: HeLa treated with Cas-II-gly, biological rep2

description:
Gene expression data from HeLa cells treated with Cas-II-gly.
Cas_II-gly-2


title: HeLa control, biological rep3

description:
Gene expression data from untreated Hela cells.
Cas_Control-3

source_name: Untreated HeLa cells

value: control


title: 12198-6

description:
Gene expression data from WAP-T1 Mouse involuted normal mammary gland 30 days post weaning
hei1_12198_6-7.CEL

tag: transgenic line


title: Somatic Tissue Placenta

description:
Somatic Tissue Placenta
Raw data file: SAMPLE 65.txt

source_name: Somatic Tissue Placenta (SAMPLE 65)

tag: line

tag: passage

value: SAMPLE 133


title: HeLa control, biological rep2

description:
Gene expression data from untreated Hela cells.
Cas_Control-2


title: Somatic Tissue Ovary

description:
Somatic Tissue Ovary
Raw data file: SAMPLE 64.txt

source_name: Somatic Tissue Ovary (SAMPLE 64)

tag: gender

tag: processing control


title: 12200-6

description:
Gene expression data from WAP-T1 Mouse involuted normal mammary gland 30 days post weaning
hei1_12200_6-7.CEL


title: 12614-6/7

description:
Reference
Gene expression data from involuted normal mammary gland of BALB/c mouse strain 50 days post weaning

data_processing: An alternative probe set mapping is published by the AffyProbeMiner project [remapped gene consistent cdf-file, using validated complete coding sequences in GenBank, version 1.0.0; AffyProbeMiner cdf (mouse4302geneccds) version 1.8.0]. Note: The R/Bioconductor version of the CDF file was used to calculate probe set signals. RMA background correction and quantile normalization were used.

source_name: BALB/c Mouse involuted normal mammary gland 50 days post weaning

value: normal mammary gland

tag: tumour grade

value: Reference Tissue


title: Somatic Tissue Kidney

description:
Somatic Tissue Kidney
Raw data file: SAMPLE 61.txt

source_name: Somatic Tissue Kidney (SAMPLE 61)

value: SAMPLE 142


title: ESC UNDIFF LINE ES03 PASSAGE 88

description:
ESC UNDIFF LINE ES03 PASSAGE 88
SAMPLE_17

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the BeadArray Reader (Illumina).

data_processing: The scanned data files were processed by BeadStudio (Illumina). BeadStudio was also used to calculate the Log R ratio and B allele frequency using a cluster file (Human1M-Duov3_B.egt) supplied by Illumina.

label: Alexa555 and Alexa647

source_name: ESC UNDIFF LINE ES03 PASSAGE 88

label_protocol: As per manufacturer (Illumina)

value: ESC

value: UNDIFF

value: FEMALE


title: 12615-6/7

tag: tissue


title: 12613-6/7


title: HeLa control, biological rep1

description:
Gene expression data from untreated Hela cells.
Cas_Control-1


title: ESC UNDIFF LINE ES02 PASSAGE 49

description:
ESC UNDIFF LINE ES02 PASSAGE 49
SAMPLE_16

source_name: ESC UNDIFF LINE ES02 PASSAGE 49


title: 11155-7

description:
G12-T1
Gene expression data from mammary carcinoma developed in WAP-SV40 T1 mouse line

source_name: WAP-T1 Mouse Mammary Carcinoma, Grade 2

tag: tumor

value: WAP-T1 Mouse Mammary Carcinoma

value: Balb/c

value: Grade 2


title: Somatic Tissue Esophagus

description:
Somatic Tissue Esophagus
Raw data file: SAMPLE 59.txt

source_name: Somatic Tissue Esophagus (SAMPLE 59)

value: MALE

value: SAMPLE 143


title: Somatic Tissue Heart

description:
Somatic Tissue Heart
Raw data file: SAMPLE 60.txt

source_name: Somatic Tissue Heart (SAMPLE 60)

value: Somatic Tissue

value: SAMPLE 128


title: Somatic Tissue Brain

description:
Somatic Tissue Brain
Raw data file: SAMPLE 57.txt

source_name: Somatic Tissue Brain (SAMPLE 57)

value: SAMPLE 127


title: Somatic Tissue Cervix

description:
Somatic Tissue Cervix
Raw data file: SAMPLE 58.txt

source_name: Somatic Tissue Cervix (SAMPLE 58)

value: SAMPLE 132


title: 12199-6

description:
Gene expression data from WAP-T1 Mouse involuted normal mammary gland 30 days post weaning
hei1_12199_6-7.CEL

value: BALB/c

value: involuted normal mammary gland

value: 30 days post weaning


title: Somatic Tissue Lung

description:
Somatic Tissue Lung
Raw data file: SAMPLE 63.txt

source_name: Somatic Tissue Lung (SAMPLE 63)

value: SAMPLE 122


title: ESC UNDIFF LINE WA13 PASSAGE 76

description:
ESC UNDIFF LINE WA13 PASSAGE 76
SAMPLE_14

source_name: ESC UNDIFF LINE WA13 PASSAGE 76


title: ESC UNDIFF LINE SA01 PASSAGE 32

description:
ESC UNDIFF LINE SA01 PASSAGE 32
SAMPLE_12

source_name: ESC UNDIFF LINE SA01 PASSAGE 32


title: 11191-2

description:
G34-T1
Gene expression data from mammary carcinoma developed in WAP-SV40 T1 mouse line

source_name: WAP-T1 Mouse Mammary Carcinoma, Grade 3

value: Grade 3


title: Somatic Tissue Liver

description:
Somatic Tissue Liver
Raw data file: SAMPLE 62.txt

source_name: Somatic Tissue Liver (SAMPLE 62)

value: SAMPLE 141


title: ESC UNDIFF LINE SA02 PASSAGE 39

description:
ESC UNDIFF LINE SA02 PASSAGE 39
SAMPLE_13

source_name: ESC UNDIFF LINE SA02 PASSAGE 39

value: ESC

value: UNDIFF


title: ESC UNDIFF LINE WA07 PASSAGE 43

description:
ESC UNDIFF LINE WA07 PASSAGE 43
SAMPLE_8

source_name: ESC UNDIFF LINE WA07 PASSAGE 43

value: FEMALE


title: 11089-1

value: WAP-T1 Mouse Mammary Carcinoma

value: Balb/c


title: 11043-4

source_name: WAP-T1 Mouse Mammary Carcinoma, Grade 4

value: Grade 4


title: ESC UNDIFF LINE WA14 PASSAGE 39

description:
ESC UNDIFF LINE WA14 PASSAGE 39
SAMPLE_15

source_name: ESC UNDIFF LINE WA14 PASSAGE 39

value: MALE


title: 10911-7

value: Grade 2


title: ESC FBS LINE ES06 PASSAGE 62

description:
ESC FBS LINE ES06 PASSAGE 62
Raw data file: SAMPLE 52.txt

source_name: ESC FBS LINE ES06 PASSAGE 62 (SAMPLE 52)

value: FBS

value: SAMPLE 130


title: 11155-4


title: ESC KSR LINE ES06 PASSAGE 62

description:
ESC KSR LINE ES06 PASSAGE 62
Raw data file: SAMPLE 53.txt

source_name: ESC KSR LINE ES06 PASSAGE 62 (SAMPLE 53)

value: KSR


title: Somatic Tissue Adipose

description:
Somatic Tissue Adipose
Raw data file: SAMPLE 55.txt

source_name: Somatic Tissue Adipose (SAMPLE 55)

value: Somatic Tissue

value: SAMPLE 126


title: 11096-3

description:
G12-T1
Gene expression data from mammary carcinoma developed in WAP-SV40 T1 mouse line

source_name: WAP-T1 Mouse Mammary Carcinoma, Grade 1

value: Grade 1


title: 10864-6


title: ESC UNDIFF LINE ES06 PASSAGE 58

description:
ESC UNDIFF LINE ES06 PASSAGE 58
Raw data file: SAMPLE 51.txt

source_name: ESC UNDIFF LINE ES06 PASSAGE 58 (SAMPLE 51)


title: 10760-8


title: ESC UNDIFF LINE ES06 PASSAGE 62

description:
ESC UNDIFF LINE ES06 PASSAGE 62
Raw data file: SAMPLE 54.txt

source_name: ESC UNDIFF LINE ES06 PASSAGE 62 (SAMPLE 54)


title: ESC FBS LINE ES06 PASSAGE 58

description:
ESC FBS LINE ES06 PASSAGE 58
Raw data file: SAMPLE 49.txt

source_name: ESC FBS LINE ES06 PASSAGE 58 (SAMPLE 49)


title: ESC UNDIFF LINE BG02 PASSAGE 54

description:
ESC UNDIFF LINE BG02 PASSAGE 54
SAMPLE_7

source_name: ESC UNDIFF LINE BG02 PASSAGE 54


title: Somatic Tissue Bladder

description:
Somatic Tissue Bladder
Raw data file: SAMPLE 56.txt

source_name: Somatic Tissue Bladder (SAMPLE 56)

value: SAMPLE 124


title: ESC UNDIFF LINE ES05 PASSAGE 59

description:
ESC UNDIFF LINE ES05 PASSAGE 59
SAMPLE_10

source_name: ESC UNDIFF LINE ES05 PASSAGE 59


title: 12192-2

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810200_S01_CGH-v4_95_Feb07_1_2.txt.

hyb_protocol: Hybridization on the arrays was performed according to the manufacturers protocols (Agilent Olgonucleotide Array-Based CGH for Genomic DNA Analysis, version 5.0, June 2007).

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: The obtained log2-ratios (sample vs. reference sample) were Loess normalized on R statistical platform (package limma, version 2.12.10). Based on the original annotation provided by Agilent, the annotation provided in the GPL11288 platform and the NCBI/37 (mm9) mouse assembly information an updated platform annotation was created: GPL14006. Probes lacking a clearly defined genomic allocation were regarded as low identity probes and skipped in our further analysis.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 4

label_protocol: Extracted genomic DNA was labeled with Cy3 and Cy5 according to the manufacturers protocols (Agilent Olgonucleotide Array-Based CGH for Genomic DNA Analysis, version 5.0, June 2007).

extract_protocol: Genomic DNA from tumor samples and liver was isolated using Puregene Genomic DNA Purification Kit according to the manufacturer’s instruction (Gentra)

value: WAP-NP8 Mouse Mammary Carcinoma

tag: tumor grade

source_name: [reference] WAP-NP8 Mouse liver

tag: reference

value: WAP-NP8 Mouse liver reference


title: ESC UNDIFF LINE ES05 PASSAGE 59

description:
ESC UNDIFF LINE ES05 PASSAGE 59
Raw data file: SAMPLE 48.txt

source_name: ESC UNDIFF LINE ES05 PASSAGE 59 (SAMPLE 48)

value: ESC

value: SAMPLE 129


title: ESC KSR LINE ES06 PASSAGE 58

description:
ESC KSR LINE ES06 PASSAGE 58
Raw data file: SAMPLE 50.txt

source_name: ESC KSR LINE ES06 PASSAGE 58 (SAMPLE 50)

value: FEMALE


title: ESC UNDIFF LINE TE04 PASSAGE 32

description:
ESC UNDIFF LINE TE04 PASSAGE 32
SAMPLE_2

source_name: ESC UNDIFF LINE TE04 PASSAGE 32

value: UNDIFF


title: ESC KSR LINE ES05 PASSAGE 55

description:
ESC KSR LINE ES05 PASSAGE 55
Raw data file: SAMPLE 44.txt

source_name: ESC KSR LINE ES05 PASSAGE 55 (SAMPLE 44)


title: ESC UNDIFF LINE ES04 PASSAGE 76

description:
ESC UNDIFF LINE ES04 PASSAGE 76
Raw data file: SAMPLE 42.txt

source_name: ESC UNDIFF LINE ES04 PASSAGE 76 (SAMPLE 42)

value: SAMPLE 128


title: 12212-2

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810199_S01_CGH-v4_95_Feb07_1_3.txt.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 3

value: Balb/c

value: Grade 3


title: 11885-5

description:
G12-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 2

value: Grade 2


title: ESC UNDIFF LINE ES01 PASSAGE 71

description:
ESC UNDIFF LINE ES01 PASSAGE 71
SAMPLE_1

source_name: ESC UNDIFF LINE ES01 PASSAGE 71


title: 11885-2


title: 11304-3

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810199_S01_CGH-v4_95_Feb07_1_4.txt.


title: ESC UNDIFF LINE UC06 PASSAGE 49

description:
ESC UNDIFF LINE UC06 PASSAGE 49
SAMPLE_3

source_name: ESC UNDIFF LINE UC06 PASSAGE 49


title: 11093-8

description:
G34-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 4

value: Grade 4


title: ESC FBS LINE ES05 PASSAGE 55

description:
ESC FBS LINE ES05 PASSAGE 55
Raw data file: SAMPLE 43.txt

source_name: ESC FBS LINE ES05 PASSAGE 55 (SAMPLE 43)

value: FBS

value: MALE


title: ESC FBS LINE ES04 PASSAGE 76

description:
ESC FBS LINE ES04 PASSAGE 76
Raw data file: SAMPLE 40.txt

source_name: ESC FBS LINE ES04 PASSAGE 76 (SAMPLE 40)


title: 11093-8

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810200_S01_CGH-v4_95_Feb07_1_3.txt.


title: 12192-8

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810199_S01_CGH-v4_95_Feb07_1_2.txt.


title: ESC KSR LINE ES04 PASSAGE 76

description:
ESC KSR LINE ES04 PASSAGE 76
Raw data file: SAMPLE 41.txt

source_name: ESC KSR LINE ES04 PASSAGE 76 (SAMPLE 41)

value: KSR


title: ESC KSR LINE ES05 PASSAGE 59

description:
ESC KSR LINE ES05 PASSAGE 59
Raw data file: SAMPLE 47.txt

source_name: ESC KSR LINE ES05 PASSAGE 59 (SAMPLE 47)


title: 11084-6

description:
G12-T1
Gene expression data from mammary carcinoma developed in WAP-SV40 T1 mouse line

source_name: WAP-T1 Mouse Mammary Carcinoma, Grade 1

value: WAP-T1 Mouse Mammary Carcinoma


title: 10870-6

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810200_S01_CGH-v4_95_Feb07_1_1.txt.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 4


title: ESC UNDIFF LINE ES04 PASSAGE 72

description:
ESC UNDIFF LINE ES04 PASSAGE 72
Raw data file: SAMPLE 39.txt

source_name: ESC UNDIFF LINE ES04 PASSAGE 72 (SAMPLE 39)


title: ESC UNDIFF LINE WA09 PASSAGE 45

description:
ESC UNDIFF LINE WA09 PASSAGE 45
SAMPLE_9

source_name: ESC UNDIFF LINE WA09 PASSAGE 45


title: ESC UNDIFF LINE BG01 PASSAGE 67

description:
ESC UNDIFF LINE BG01 PASSAGE 67
SAMPLE_6

source_name: ESC UNDIFF LINE BG01 PASSAGE 67


title: ESC UNDIFF LINE WA01 PASSAGE 56

description:
ESC UNDIFF LINE WA01 PASSAGE 56
SAMPLE_4

source_name: ESC UNDIFF LINE WA01 PASSAGE 56


title: ESC UNDIFF LINE BG03 PASSAGE 54

description:
ESC UNDIFF LINE BG03 PASSAGE 54
SAMPLE_5

source_name: ESC UNDIFF LINE BG03 PASSAGE 54


title: 10811-2

description:
G12-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line


title: 10667-2


title: 12159-6

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 1

value: Grade 1


title: 12271-5


title: ESC UNDIFF LINE ES05 PASSAGE 55

description:
ESC UNDIFF LINE ES05 PASSAGE 55
Raw data file: SAMPLE 45.txt

source_name: ESC UNDIFF LINE ES05 PASSAGE 55 (SAMPLE 45)


title: Leaf_Head excision_50days_rep1

city: Castelar

first: Paula

last: Fernandez

state: Buenos Aires

address: N. Repetto y Los Reseros S/N

country: Argentina

institute: INTA Castelar

description: Gene expression after 50 days in Head excision leaf

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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 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.

organism: Helianthus annuus

source_name: Head excision leaf, 50d, rep1

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.

growth_protocol: Field experiments were carried out at INTA Balcarce Experimental Station (37°45’S,  8°18’W) during the 2004/2005 crop season. Sunﬂower hybrid VDH 481 (Advanta Seeds) was sown at a 7.2  plants/m2 density and seeds emerged 11 days later. Diseases, weeds, and insects were adequately controlled. Soil fertility assured maximum yields under adequate water conditions. Rainfall was complemented with irrigation when necessary to avoid water deﬁcit, except for the case of water deﬁcit treatment.

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen using the Trizol® method (Invitrogen, Argentina). The genomic DNA was eliminated after treatment with Dnase I for 20 min at RT using DNAse I® (Invitrogen, Argentina).  RNA concentration was measured using a Nanodrop ND-100 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware USA). Purity and integrity of total RNA was determined by 260/280 nm ratio and the integrity was checked by electrophoresis in 1% agarose gel and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Water Deficit: a mild water deficit was achieved by covering the soil with a 200 mm plastic mesh to avoid rainfall penetration into the soil. The mesh was installed 10 days before flowering, and reduced about 40% the volumetric humidity of the soil. Controlled irrigation allowed keeping the deficit level from treatment application up to the sample harvest day.  Flower excision: the flower of several plants was cut with a fine scalpel 4 days before flowering, in order to suppress the reproductive sink.  Control: Untreated plants were kept as controls.

value: Leaf

tag: age

tag: stress

value: Head excision


title: 10667-2

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810197_S01_CGH-v4_95_Feb07_1_4.txt.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 2

value: WAP-NP8 Mouse Mammary Carcinoma

source_name: [reference] WAP-NP8 Mouse liver

value: WAP-NP8 Mouse liver reference


title: ESC KSR LINE ES04 PASSAGE 72

description:
ESC KSR LINE ES04 PASSAGE 72
Raw data file: SAMPLE 38.txt

source_name: ESC KSR LINE ES04 PASSAGE 72 (SAMPLE 38)

value: ESC


title: 12109-1

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810199_S01_CGH-v4_95_Feb07_1_1.txt.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 3


title: 11885-2

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810198_S01_CGH-v4_95_Feb07_1_2.txt.


title: 10811-2

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810198_S01_CGH-v4_95_Feb07_1_1.txt.


title: 12108-5

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810198_S01_CGH-v4_95_Feb07_1_4.txt.


title: ESC UNDIFF LINE ES03 PASSAGE 84

description:
ESC UNDIFF LINE ES03 PASSAGE 84
Raw data file: SAMPLE 33.txt

source_name: ESC UNDIFF LINE ES03 PASSAGE 84 (SAMPLE 33)

value: FEMALE

value: SAMPLE 127


title: Leaf_Control_50days_rep1

description: Gene expression after 50 days in control leaf

source_name: Control leaf, 50d, rep1

value: Control


title: ESC FBS LINE ES03 PASSAGE 88

description:
ESC FBS LINE ES03 PASSAGE 88
Raw data file: SAMPLE 34.txt

source_name: ESC FBS LINE ES03 PASSAGE 88 (SAMPLE 34)


title: ESC KSR LINE ES03 PASSAGE 88

description:
ESC KSR LINE ES03 PASSAGE 88
Raw data file: SAMPLE 35.txt

source_name: ESC KSR LINE ES03 PASSAGE 88 (SAMPLE 35)


title: ESC UNDIFF LINE ES06 PASSAGE 62

description:
ESC UNDIFF LINE ES06 PASSAGE 62
SAMPLE_11

source_name: ESC UNDIFF LINE ES06 PASSAGE 62

value: UNDIFF

tag: cell line


title: Leaf_Water deﬁcit_45days_rep2

description: Gene expression after 45 days in Water deﬁcit leaf

source_name: Water deﬁcit leaf, 45d, rep2

value: Water deﬁcit


title: 12159-6

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810197_S01_CGH-v4_95_Feb07_1_3.txt.

source_name: [test] WAP-NP8 Mouse Mammary Carcinoma, Grade 1

tag: strain

value: Balb/c


title: ESC KSR LINE ES03 PASSAGE 84

description:
ESC KSR LINE ES03 PASSAGE 84
Raw data file: SAMPLE 32.txt

source_name: ESC KSR LINE ES03 PASSAGE 84 (SAMPLE 32)


title: ESC FBS LINE ES03 PASSAGE 84

description:
ESC FBS LINE ES03 PASSAGE 84
Raw data file: SAMPLE 31.txt

source_name: ESC FBS LINE ES03 PASSAGE 84 (SAMPLE 31)


title: 12271-5

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810197_S01_CGH-v4_95_Feb07_1_2.txt.


title: ESC UNDIFF LINE ES03 PASSAGE 88

description:
ESC UNDIFF LINE ES03 PASSAGE 88
Raw data file: SAMPLE 36.txt

source_name: ESC UNDIFF LINE ES03 PASSAGE 88 (SAMPLE 36)


title: ESC FBS LINE ES04 PASSAGE 72

description:
ESC FBS LINE ES04 PASSAGE 72
Raw data file: SAMPLE 37.txt

source_name: ESC FBS LINE ES04 PASSAGE 72 (SAMPLE 37)

value: SAMPLE 128


title: Leaf_Control_50days_rep3

source_name: Control leaf, 50d, rep3


title: 12030-4

description:
G12-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 1


title: Leaf_Control_45days_rep2

description: Gene expression after 45 days in control leaf

source_name: Control leaf, 45d, rep2


title: 10870-6

description:
G34-NP8
Gene expression data from mammary carcinoma developed in WAP-SV40 NP8 mouse line

source_name: WAP-NP8 Mouse Mammary Carcinoma, Grade 4

value: Grade 4


title: ESC FBS LINE ES05 PASSAGE 59

description:
ESC FBS LINE ES05 PASSAGE 59
Raw data file: SAMPLE 46.txt

source_name: ESC FBS LINE ES05 PASSAGE 59 (SAMPLE 46)

value: FBS

value: MALE

value: SAMPLE 129


title: Retinoblastoma serum -Replicate2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction Software 10.0 (Agilent) using default parameters

source_name: Whole blood serum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions

extract_protocol: RNA was prepared using the mirVana RNA Isolation kit(Ambion) following the manufacturer's recommendations

treatment_protocol: Freshly isolated whole blood serum from normal healthy individual and Retinoblastoma patients were obtained then perserved at -80 ºC

tag: cell type

value: Retinoblastoma


title: ESC UNDIFF LINE ES02 PASSAGE 49

description:
ESC UNDIFF LINE ES02 PASSAGE 49
Raw data file: SAMPLE 30.txt

source_name: ESC UNDIFF LINE ES02 PASSAGE 49 (SAMPLE 30)

tag: class

value: SAMPLE 126


title: Non-Retinoblastoma serum -Replicate3

value: Non-Retinoblastoma


title: ESC KSR LINE ES02 PASSAGE 49

description:
ESC KSR LINE ES02 PASSAGE 49
Raw data file: SAMPLE 29.txt

source_name: ESC KSR LINE ES02 PASSAGE 49 (SAMPLE 29)

tag: condition

value: KSR


title: Retinoblastoma serum -Replicate1


title: 12030-4

description:
aCGH data from mammary carcinoma developed in WAP NP8 mouse line.
Raw data file: US22502513_251502810197_S01_CGH-v4_95_Feb07_1_1.txt.

value: WAP-NP8 Mouse Mammary Carcinoma

value: Grade 1

source_name: [reference] WAP-NP8 Mouse liver

value: WAP-NP8 Mouse liver reference


title: Leaf_Water deﬁcit_45days_rep1

source_name: Water deﬁcit leaf, 45d, rep1

value: Leaf


title: 4TO7 compliant basal set1

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Road, Rm 2404

institute: Case Western Reserve University

hyb_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

data_processing:
The Thermo Scientific Dharmacon Synthetic microRNA Reference Probe Set is an equimolar mixture of 5'-Thermo Scientific DyLight 547-labeled, single-stranded synthetic miRNAs targeting all mature human, mouse, and rat miRNA sequences in the Sanger miRBase sequence database.  This  internal reference provides reproducible data normalization and controls for variations due to up-stream processes (array manufacture, washing and    hybridization processes, pipeting variation, etc.).
Data processing was performed with total 36 samples, yet data for 24 samples are presented. Relative intensity data for 36 samples was subjected to statistical quality filtering, keeping miRNA probes with P-value <=0.05 in at least 18 of the 36 experiments.  This resulted in 338 miRNA probes passing statistical quality fliters.  The remaining data was inter-array scaled and transformed to log2 prior to performing one-way ANOVA analyses for each cell line.
Post hoc analysis was undertaken to identify miRs whose expression was significantly (P<0.01) upregulated following administration of TGF-beta.

growth_protocol: 67NR, 4TO7, and 4T1 cells were propagated for 6 days in 3D organotypic cultures

extract_protocol: Total RNA was prepared using the Qiagen Rneasy Plus Mini Kit and following the supplementary protocol for purification of miRNA (Qiagen).

treatment_protocol: Cells were treated with TGF-beta or a TGF-beta-type-I-receptor inhibitor

value: systemically invasive breast carcioma cells

tag: treated with

tag: microenvironment

value: compliant

tag: molecule subtype

value: microRNA


title: 4TO7 rigid basal set2

scan_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

value: rigid


title: 67NR rigid TGFb set1

label_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

value: nonmetastatic breast carcioma cells

value: TGFb


title: 67NR compliant basal set2


title: 4T1 rigid basal set1

value: highly metastatic breast carcioma cells


title: Retinoblastoma serum -Replicate3