title: 14189494_Srrb-_120m_Cy5_M_120m_Cy3_MDS.mev.refIsIA.out

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA)

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early stationary phase(120 min)

tag: strain

tag: growth phase

value: Staphylococcus aureus subsp.aureus strain Newman srrb knockout


title: UNC990229A

status: Public on Dec 31 2011

type: RNA

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

country: USA

institute: University of North Carolina at Chapel Hill

description: Agilent Custom array of UNC990229A

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

molecule: total RNA

organism: Homo sapiens

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

extract_protocol: Qiagen RNeasy Mini Kit.

tag: tissue

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: positive

tag: age at diagnosis (year)

tag: menopause status

value: Post

tag: histopathology

value: Invasive

tag: breast cancer subtype (pam50)

value: unknown

tag: er status

tag: hormone treated

value: yes

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: Gcn4Leu3 30min_3AT_3

city: singapore

first: Xiaowei

last: XUE

address: 60 Biopolis Street, #02-01, Genome

department: systems biology 1

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

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

label: biotin

organism: Saccharomyces cerevisiae

source_name: BY4741 GCN4LEU3 double deletion

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

growth_protocol: Yeast strain was precultured in SC medium at 28ºC overnight and transferred into fresh SC medium to dilute to 1.4 liter (6  time points) or 1.6 liter (8 time points).

extract_protocol: Extraction of total RNA was performed as manufacture's instractions

treatment_protocol: 200ml cells were collected and harvested when cells grew in SC medium to reach OD600nm=0.5 as time point 0. 3-aminotriazol was added to a final concentration of 100mM to induce amino acid starvation. 200ml cells were taken and pelleted at each time point after 3AT treatment.

tag: genotype

value: GCN4LEU3 double deletion

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: Gcn4Leu3 10min_3AT_2


title: UNC980006A

description: Agilent Custom array of UNC980006A

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

tag: sample type

tag: composition

tag: tissue

tag: patient id

value: negative

value: no


title: Gcn4Leu3 20min_3AT_1


title: Gcn4Leu3 10min_3AT_3


title: 9QSA_aerobic_stationary_newman_cy5_yhcR_cy3_14192480_MDS.mev.refIsIB.out

city: Rockville

first: Chun-Hua

last: Wan

state: MD

address: 9704 Medical Center Dr

department: Pathogen Functional Genomics Resources Center (PFGRC)

institute: The J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min. The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were heated to 95 C degree prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.  Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Newman yhcR knockout(query) total RNA extracted at midlog phase under aerobic growth condition

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to stationary phase under aerobic conditions.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manusfacturer.

tag: strain

value: Newman yhcR knockout

tag: phase

value: stationary

tag: growth condition

value: aerobic

source_name: Newman (reference) total RNA extracted at midlog phase under aerobic growth condition

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to stationary under aerobic conditions.

value: Newman


title: 9QSA_anaerobic_stationary_newman_cy3_yhcR_cy5_14194569_MDS.mev.refIsIA.out

source_name: Newman (reference) total RNA extracted at stationary phase under anaerobic growth condition

value: anaerobic

source_name: Newman yhcR knockout(query) total RNA extracted at stationary phase under anaerobic growth condition


title: UNC950185A

description: Agilent Custom array of UNC950185A

tag: active or "inactive"

tag: age at diagnosis (year)

tag: menopause status

value: Pre

tag: histopathology

tag: breast cancer subtype (pam50)

tag: er status

tag: hormone treated


title: UNC960606A

description: Agilent Custom array of UNC960606A

value: reference

tag: her2 status

tag: tumor grade

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: UNC960040A

description: Agilent Custom array of UNC960040A

tag: sample type

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: tissue


title: 9QSA_anaerobic_midlog_newman_cy3_yhcR_cy5_14194567_MDS.mev.refIsIA.out

source_name: Newman (reference) total RNA extracted at midlog phase under anaerobic growth condition

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to midlog phase under aerobic conditions.

tag: strain

tag: phase

value: midlog

source_name: Newman yhcR knockout(query) total RNA extracted at midlog phase under anaerobic growth condition


title: UNC950117A

description: Agilent Custom array of UNC950117A

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: positive


title: UNC950138A

description: Agilent Custom array of UNC950138A

tag: age at diagnosis (year)

tag: menopause status

value: Invasive


title: UNC950094A

description: Agilent Custom array of UNC950094A

tag: histopathology

tag: breast cancer subtype (pam50)

value: unknown


title: Gcn4Leu3 20min_3AT_2

tag: genotype

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: Gcn4Leu3 0min_3AT_2

value: baseline


title: 9QSA_aerobic_stationary_newman_cy3_yhcR_cy5_14192481_MDS.mev.refIsIA.out

source_name: Newman (reference) total RNA extracted at stationary phase under aerobic growth condition

tag: growth condition

source_name: Newman yhcR knockout(query) total RNA extracted at stationary phase under aerobic growth condition


title: 9QSA_aerobic_midlog_newman_cy5_yhcR_cy3_14192475_MDS.mev.refIsIB.out

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to midlog under aerobic conditions.


title: Gcn4Leu3 0min_3AT_3

value: GCN4LEU3 double deletion


title: 14189490_Srrb-_90m_Cy5_M_90m_Cy3_MDS.mev.refIsIA.out

first: Fatma

last: Onmus-Leone

address: 9704 Medical Center Dr.

institute: JCVI

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus subsp.aureus strain Newman (reference)

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to late log(90 min).

value: Staphylococcus aureus subsp. aureus strain Newman

tag: growth phase

value: late log

source_name: Staphylococcus aureus subsp.aureus strain Newman srrb knockout

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early log late log(90 min).


title: Gcn4Leu3 0min_3AT_1


title: Gcn4Leu3 10min_3AT_1


title: Gat1Gcn4 30min_3AT_3

source_name: BY4741 GAT1GCN4 double deletion

value: GAT1GCN4 double deletion


title: Gat1Gcn4 45min_3AT_2


title: Gat1Gcn4 60min_3AT_2


title: Gat1Gcn4 45min_3AT_3


title: Gat1Gcn4 60min_3AT_3


title: 9QSA_aerobic_midlog_newman_cy3_yhcR_cy5_14192476_MDS.mev.refIsIA.out

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to mid log phase under aerobic conditions.

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to midlog phase under aerobicconditions.

value: Newman yhcR knockout


title: Gat1Gcn4 60min_3AT_1


title: HTCC1062 Light to Dark-1

city: Madison

first: Michael

middle: S

last: Schwalbach

state: WI

address: 1550 Linden Dr

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin-Madison

hyb_protocol: 5 μg of biotinylated aRNA for each samples was fractionated and then hybridized (45°C) overnight to custom ‘Candidatus Pelagibacter ubique’ Affymetrix GeneChip arrays that contained probes for HTCC1002, HTCC1062 and HTCC7211 (Pubiquea520471f) using Affymetrix GeneChip Fluidics Station 450, and Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: Bacteria, SAR11 strain HTCC1062

label_protocol: RNA was labeled via the inclusion of biotinylated-nucleotides (perkin-elmer) during the in vitro transcription (IVT) reaction.

growth_protocol: Cultures were grown in autoclaved, filtered seawater amended with pyruvate (80 µM), oxaloacetate (40 µM), taurine (40 µM), betaine (1 µM), glycine (50 µM), methionine (50 µM), iron source (1 µM) and vitamins (Rappe et al. 2002).

extract_protocol: RNA was extracted using RNeasy Mini kits (Qiagen) and amplified and biotin-labeled using the MessageAmp-II Bacteria RNA amplification kit (Ambion) per the manufacturer’s instructions; 10-15 ng of template RNA was used per reaction.

treatment_protocol: Cells were pelleted, treated with Bacteria Protect reagent (Qiagen) then frozen at -80C prior to extraction

value: SAR11 HTCC1062

value: stationary phase

value: six hours after transfer to darkness


title: 14189485_Srrb-_240m_Cy5_M_240m_Cy3_MDS.mev.refIsIA.out

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanne

growth_protocol: Cells were grown in TSA media overnight. Overnight cultures were diluted to an OD600 of 0.1. Cells were grown to late stationary phase (240 min).

value: late stationary phase

source_name: Staphylococcus aureus subsp.aureus strain Newman srrb knockout(query)

value: stationary phase.


title: HTCC1062 Light to Dark-3


title: HTCC1062 Light to Dark-2


title: Male TFA+MSG diet heart, biological rep1

city: Riyadh

first: Kate

last: Collison

address: Department Biological & Medical Research

country: Saudi Arabia

institute: King Faisal Specialist Hospital & Research Centre

description: Gene expression data from 32-week Male TFA+MSG diet heart.

hyb_protocol: Following fragmentation, 5.5 ug of ssDNA was hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Scanner and GeneChip Operating Software version 1.4 to produce .CEL files

data_processing: Microarray analysis was performed using the Partek genomic suite software version 6.3 (Partek, MO, USA).  We imported the interrogating probes using the file MoGene-1_0-st-v1.na30.1.mm9.probeset.csv.zip downloaded from http://www.affymetrix.com/support/technical/byproduct.affx?product=mogene-1_0-st-v1  for the annotation purpose. Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm, no log, a pre-background adjustment for probe sequence was also applied.

organism: Mus musculus

source_name: 32-week male mouse cardiac tissue

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Technical Manual, 2009, Affymetrix).

growth_protocol: Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating.

extract_protocol: Total RNA was prepared from snap-frozen cardiac tissue using QIAGEN RNeasy® Kit Fibrous Tissue according to manufacturers' instructions. The integrity of the RNA was measured using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies).

treatment_protocol: The four dietary regimens used in this study were: [1] Standard Chow (Control diet) with ad lib drinking water. [2] Standard Chow, with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (MSG diet). [3] Trans fat diet of 20% (w/w) Partially Hydrogenated Vegetable Shortening containing 8.68% w/w Trans fatty acids(TFA diet).  [4] Trans fat Diet #5C4M together with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (TFA+MSG diet). Following mating, the 4 groups of dams were maintained on their respective diets throughout the gestation and nursing period. Male and female offspring used in the following experiments were weighed, weaned onto the same diets and maintained on their respective dietary regimens until they reached 32 weeks of age.

tag: diet

value: TFA+MSG diet

tag: biological replicate

tag: gender

value: Male

tag: age

value: heart


title: HTCC1062 log phase dark biorep3

source_name: Bacteria, SAR11 strain HTCC1062, exponential phase

growth_protocol: Cells cultivated in autoclaved, filtered seawater amended with 1uM methionine, 1uM serine, 10uM NH4, 1uM PO4, 10nM FeCl3, 50uM glucose and 50uM pyruvate.

extract_protocol: NA was extracted using RNeasy Mini kits (Qiagen) and amplified and biotin-labeled using the MessageAmp-II Bacteria RNA amplification kit (Ambion) per the manufacturer’s instructions; 10-15 ng of template RNA was used per reaction.

tag: strain

value: exponential phase

value: 24 hour dark


title: HTCC1062 log phase dark biorep1


title: Female TFA+MSG diet heart, biological rep1

description: Gene expression data from 32-week Female TFA+MSG diet heart.

source_name: 32-week female mouse cardiac tissue

value: Female

tag: tissue


title: Gat1Gcn4 30min_3AT_2


title: Male TFA+MSG diet heart, biological rep2


title: HTCC1062 log phase dark biorep2


title: Gat1Gcn4 20min_3AT_3


title: Gat1Gcn4 20min_3AT_2


title: HTCC1062 log phase light biorep3

value: 24 hr light

tag: light intensity

value: 250 µmol photons m-2 s-1


title: Female TFA diet heart, biological rep2

description: Gene expression data from 32-week Female TFA diet heart.

value: TFA diet


title: Male TFA diet heart, biological rep2

description: Gene expression data from 32-week Male TFA diet heart.


title: Female TFA diet heart, biological rep1


title: Female TFA+MSG diet heart, biological rep2


title: Male TFA diet heart, biological rep1


title: HTCC1062 log phase light biorep2


title: Female MSG diet heart, biological rep2

description: Gene expression data from 32-week Female MSG diet heart.

value: MSG diet


title: Female MSG diet heart, biological rep1


title: Gat1Gcn4 30min_3AT_1

value: GAT1GCN4 double deletion


title: HTCC1062 sta phase light biorep2

source_name: Bacteria, SAR11 strain HTCC1062, stationary phase

value: 12:12 hr light/dark cycle


title: HTCC1062 sta phase light biorep3

value: SAR11 HTCC1062


title: Gat1Gcn4 20min_3AT_1


title: Gat1Gcn4 10min_3AT_3


title: Gat1Gcn4 10min_3AT_2


title: Male MSG diet heart, biological rep2

description: Gene expression data from 32-week Male MSG diet heart.


title: Gat1Gcn4 0min_3AT_3

value: baseline


title: HTCC1062 sta phase dark biorep1

value: stationary phase

value: no light


title: Gat1Gcn4 10min_3AT_1


title: HTCC1062 log phase light biorep1


title: HTCC1062 sta phase dark biorep2


title: HTCC1062 sta phase dark biorep3


title: HTCC1062 sta phase light biorep1


title: Male MSG diet heart, biological rep1


title: Rem Mac 3

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: F4/80hi cell from NZB/W kidney (3-4 weeks after entering complete remission with a single dose of cyclophosphamide + 6 doses of CTLA4Ig + anti-CD154)

hyb_protocol: Refer to the Affymetrix gene expression manual

scan_protocol: GeneChip Scanner 3000 7G

data_processing: The data were analyzed using GenePattern pipeline: RMA method and Mouse Entrez Gene custom CDF annotation version 10 were used for the normalization.

source_name: Macrophages from kidneys after remission

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

extract_protocol: Total RNA was isolated using picopure RNA isolation kit (Arcturus Molecular Device Corporation, Sunnyvale, CA).

tag: cell type

value: NZB/W

value: kidney

tag: sample time


title: Rem Mac 1

value: 3-4 weeks after entering complete remission with a single dose of cyclophosphamide + 6 doses of CTLA4Ig + anti-CD154


title: Female control diet heart, biological rep2

description: Gene expression data from 32-week Female control diet heart.

value: control diet

value: heart


title: Sick Mac 5

description: F4/80hi cell from NZB/W kidney (2-6 weeks after proteinuria onset, but before the development of terminal renal failure)

source_name: Macrophages from nephritic, lupus nephritis kidneys


title: Female control diet heart, biological rep1


title: Sick Mac 6

value: 2-6 weeks after proteinuria onset, but before the development of terminal renal failure


title: Rem Mac 4


title: Gat1 120min_3AT_3

source_name: BY4741 GAT1 deletion

value: GAT1 deletion


title: Gat1 120min_3AT_2


title: Rem Mac 2


title: Sick Mac 4


title: Male control diet heart, biological rep2

description: Gene expression data from 32-week Male control diet heart.

value: Male


title: Gat1Gcn4 0min_3AT_1


title: Sick Mac 3


title: blood_cancer1_family413_rep1

city: Tampere

first: Henna

last: Mattila

address: Biokatu 8

department: Institute of Medical Technology

country: Finland

institute: University of Tampere

description: miRNA expression in lymphoblastoid cells

hyb_protocol: Labeled and purified RNA was dried down in speedvac (1h +45C). RNA was resuspended in 18 ul of H2O. 4.5ul of 10x Blocking agent and 22.5 ul 2x Hybrdization buffer was added. The hybridization assembly was mounted and the arrays were hybridized for 20h at +55C.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.5.1. (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Outliers were excluded.

data_processing: For data analysis, low quality samples and non-expressed miRNAs were first removed. Inside every family the directional distance of healthy individuals from patients was calculated. The distance used here was based on Kendal’s tau (distance = (1-tau)/2) and the distance between clusters was computed using Ward’s method. By decomposing Kendal’s tau into each miRNA’s contribution the distance induced by every miRNA can be quantified separately. The direction of this distance inside every family is marked positive if the average rank miRNA expression for patients is higher than for healthy individuals and negative if the average rank miRNA expression for healthy individuals is higher than for patients. The overall directional distance for every miRNA is obtained by summing up these directional distances over all families. Then the permutation p-value was computed by permuting healthy individuals and patients randomly inside every family, computing the overall directional distance, repeating this many times and the final permutation p-value is the proportion of these permuted distances higher or lower than the original distance. The analysis was not performed on probe level, but on miRNA level with the help of ranks and gTotalGeneSignal.

source_name: blood

label_protocol: 100 ng of total RNA was used as a starting material, and miRNAs were labeled with Cy3 using the Agilent miRNA Labeling Kit according to the instructions of the manufacturer.

growth_protocol: The lymphoblastoid cell lines were derived by Epstein-Barr virus transformation of peripheral mononuclear leukocytes from patients and their healthy brothers. Lymphoblastoid cell lines were grown in RPMI-1640 medium (Lonza, Walkersville, MD, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA) and antibiotics.

extract_protocol: Total RNA was extracted from cells with Trizol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA yields were quantified using an ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: The samples were not treated.

value: male

tag: cancer status

value: Prostate cancer patient

tag: diagnosis age

tag: gleason score

value: lymphoblastoid cell line

tag: individual


title: Sick Mac 2


title: Sick Mac 7


title: blood_healthy1_family413_rep1

value: Healthy


title: blood_healthy1_family408_rep1


title: Sick Mac 1


title: Gat1 120min_3AT_1

tag: genotype

tag: collection time after 3at treatment

tag: genetic background


title: Young Mac 4

description: F4/80hi cell from NZB/W kidney (8-16 wks old mice)

source_name: Macrophages from prenephritic kidneys

value: 8-16 wks old mice


title: Gat1 90min_3AT_3

tag: treatment


title: Gat1 90min_3AT_2


title: Young Mac 3


title: Young Mac 2


title: blood_healthy2_family402_rep1


title: Young Mac 5


title: blood_healthy1_family402_rep1


title: Young Mac 1


title: Gat1 90min_3AT_1


title: blood_cancer2_family402_rep1


title: Gat1 60min_3AT_3


title: blood_cancer1_family408_rep1


title: Young Mac 6


title: blood_healthy2_family362_rep1


title: MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#3

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs cytoplasmic RNA extracted from doxorubicin treated MCF7 cells,  biological replicate 3 of 3

hyb_protocol: Please see manufacturer's web site at http://www.agilent.com/

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies, Santa Clara, CA) at 5 micron resolution with the manufacturer’s software (Agilent ScanControl 8.1.3).

data_processing: Agilent Feature Extraction Software version 10.7.7.1 (standard protocol GE2_107_Sep09) was used for data extraction, background correction and Lowess normalization

source_name: MCF7 cells, doxorubicin treated, 4h, HuR RIP-Chip

growth_protocol: MCF7 cells were cultured in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2mM glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin at 37 °C in a humidified atmosphere of 5% CO2.

extract_protocol: HuR was coimmunoprecipitated with mRNA, mRNA was isolated using TriZol reagentm(Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.

treatment_protocol: MCF7 cells were seeded on adherent plates and starved for 24h and treated with 10 uM of doxorubicin for 4 hours

tag: cell line

value: MCF7 cells

tag: agent

value: doxorubicin

tag: sample type

value: HuR RIP-Chip

tag: antibody

value: Mouse anti-HuR

tag: vendor

value: SantaCruz Biotechnology

tag: lot/catalog#

source_name: MCF7 cells, doxorubicin treated, 4h, cytoplasmic RNA

extract_protocol: total RNA was isolated from cell cytoplasm using TriZol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.

value: cytoplasmic RNA


title: Male control diet heart, biological rep1

tag: diet

tag: biological replicate

tag: gender

tag: age

tag: tissue


title: Gat1 60min_3AT_2


title: Gat1 60min_3AT_1


title: MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#1

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs cytoplasmic RNA extracted from doxorubicin treated MCF7 cells,  biological replicate 1 of 3

label_protocol: Please see manufacturer's web site at http://www.agilent.com/


title: MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#4

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs IgG RIP-Chip from doxorubicin treated MCF7 cells,  biological replicate 4 of 4

source_name: MCF7 cells, doxorubicin treated, 4h, IgG RIP-Chip

extract_protocol: IgG was coimmunoprecipitated with mRNA, mRNA was isolated using TriZol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up.

value: IgG RIP-Chip

value: Normal mouse IgG


title: Gat1 45min_3AT_3


title: MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#2

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs cytoplasmic RNA extracted from doxorubicin treated MCF7 cells,  biological replicate 2 of 3


title: MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#2

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs IgG RIP-Chip from doxorubicin treated MCF7 cells,  biological replicate 2 of 4


title: Gat1 45min_3AT_1


title: blood_healthy1_family362_rep1

tag: cancer status

tag: cell type


title: MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#4

description: Cytoplasmic RNA extracted from doxorubicin treated MCF7 cells vs cytoplasmic RNA from untreated MCF7 cells,  biological replicate 4 of 4

source_name: MCF7 cells, untreated, cytoplasmic RNA

treatment_protocol: MCF7 cells were seeded on adherent plates and starved for 24h

value: untreated


title: MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#1

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs IgG RIP-Chip from doxorubicin treated MCF7 cells,  biological replicate 1 of 4


title: Gat1 30min_3AT_3

tag: genotype


title: blood_cancer1_family362_rep1

tag: diagnosis age

tag: gleason score

tag: individual


title: Gat1 45min_3AT_2

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#2

description: Cytoplasmic RNA extracted from doxorubicin treated MCF7 cells vs cytoplasmic RNA from untreated MCF7 cells,  biological replicate 2 of 4

tag: cell line

tag: agent

tag: sample type


title: blood_healthy1_family292_rep1


title: blood_cancer2_family362_rep1


title: blood_cancer1_family292_rep1


title: blood_cancer1_family248_rep1


title: MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#3

description: Cytoplasmic RNA extracted from doxorubicin treated MCF7 cells vs cytoplasmic RNA from untreated MCF7 cells,  biological replicate 3 of 4


title: Gat1 30min_3AT_2


title: blood_healthy1_family248_rep1


title: CLL SO_only_48h_rep7

city: Modena

first: Rossana

last: Maffei

state: Modena

address: Via del Pozzo 71

department: Dept of Hematology and Oncology

institute: University of Modena and Reggio Emilia

description: Gene expression of CLL cells collected from peripheral blood and then cultured in medium alone for 48 hours

hyb_protocol: Cy3-labeled cRNAs (1.65 ug) were fragmented to an average size of 50-100 nt by incubation at 60°C for 30 min using in situ Hybridization kit-plus (Agilent). Samples were hybridized for 17 hours at 65°C on 4x44K Whole Human Genome Microarray (Agilent).

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

data_processing: Fluorescence data were analyzed with Feature Extraction Software v.10.5 (Agilent Technologies) an QC Chart tool v.1.3 to obtain background subtracted, spatially detrended Processed Signal intensities and quality control analyses.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CLL only 48hr

label_protocol: High quality RNAs were amplified and Cy3-labeled using Low Input Quick Amp Labeling kit (Agilent Technologies, Palo alto, CA, USA). Agilent RNA One-Color Spike-In was added in each sample to provide positive controls for monitoring the microarray workflow from sample amplification and labelling to microarray processing. It contains 10 in vitro synthesized, polyadenylated transcripts derived from the Adenovirus E1A transcriptome that are premixed at various ratios. All cRNA products were purified using RNeasy columns (QIAGEN). Dye incorporation and cRNA yield were checked with InfiniteM200 (Tecan).Samples had to contain at least 6 pmole of cyanine dye/ug of cRNA to be considered suitable for subsequent hybridization.

growth_protocol: Purified CD19+ CLL cells were suspended at a final concentration of 1 x 106/ml in AIM-V medium (Invitrogen, Carlsbad, CA, USA) with 10% fetal bovine serum and then plated in 24-well plates (CLL only). For co-culture experiments, HUVEC cells were incubated until reaching 70% confluent and CLL cells were then seeded onto HUVEC layer at a final concentration of 1 x 106/ml in AIM V supplemented with 10% FBS (CLL HC). At the indicated time points, CLL cells were collected by removal of the supernatant leaving HUVEC cells intact and then being assayed for cell viability and gene expression profiling.

extract_protocol: total RNAs were extracted from purified CD19+ cells using RNeasy Midi kit Plus (QIAGEN, Valencia, CA, USA) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion. RNAs were quantified using InfiniteM200 (Tecan).

tag: tissue origin

value: peripheral blood

value: Chronic lymphocytic leukemic B cells (CLL)


title: Gat1 20min_3AT_2

value: GAT1 deletion


title: CLL FG_only_48h_rep8


title: CLL STRG_only_48h_rep9


title: Gat1 30min_3AT_1


title: CLL MV_only_48h_rep6


title: blood_cancer1_family 402_rep1

value: male

value: cancer1_family 402


title: CLL COM_only_48h_rep1


title: CLL DM_only_48h_rep4


title: blood_cancer1_family_236_rep1

value: Prostate cancer patient

value: lymphoblastoid cell line


title: MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#1

description: Cytoplasmic RNA extracted from doxorubicin treated MCF7 cells vs cytoplasmic RNA from untreated MCF7 cells,  biological replicate 1 of 4


title: CLL SG_only_48h_rep5


title: Gat1 20min_3AT_1


title: CLL GA_only_48h_rep2


title: CLL PL_only_48h_rep3


title: CLL STRG_co-culture_48h_rep9

description: Gene expression of CLL cells collected from peripheral blood and then cultured on endothelial cell layer for 48 hours

source_name: CLL co-cultured 48h on HUVEC layer  48hr


title: CLL FG_co-culture_48h_rep8


title: MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#3

description: HuR RIP-Chip from doxorubicin treated MCF7 cells vs IgG RIP-Chip from doxorubicin treated MCF7 cells,  biological replicate 3 of 4

tag: antibody

tag: vendor

tag: lot/catalog#


title: blood_healthy1_family236_rep1

tag: gender

value: Healthy


title: Gat1 10min_3AT_2


title: Gat1 0min_3AT_3

value: baseline


title: blood_cancer1_family232_rep1

tag: cancer status


title: CLL SO_co-culture_48h_rep7

tag: cell type


title: Gat1 10min_3AT_1

tag: genotype


title: blood_healthy1_family232_rep1


title: blood_cancer2_family232_rep1

tag: diagnosis age


title: blood_healthy2_family232_rep1


title: CLL MV_co-culture_48h_rep6


title: Gat1 0min_3AT_2


title: blood_healthy1_family43_rep1


title: CLL GA_co-culture_48h_rep2


title: CLL COM_co-culture_48h_rep1


title: CLL SG_co-culture_48h_rep5


title: Gat1 10min_3AT_3


title: CLL SO_baseline_0h_rep7

description: Gene expression of CLL cells collected from peripheral blood

source_name: CLL baseline untreated 0h


title: CLL STRG_baseline_0h_rep9


title: CLL DM_co-culture_48h_rep4


title: blood_cancer1_family43_rep1

tag: gleason score


title: Leu3 120min_3AT_3

source_name: BY4741 LEU3 deletion

value: LEU3 deletion


title: blood_healthy1_family15_rep1

tag: individual


title: CLL FG_baseline_0h_rep8


title: CLL PL_co-culture_48h_rep3


title: Gat1 0min_3AT_1

tag: collection time after 3at treatment


title: CLL SG_baseline_0h_rep4


title: CLL MV_baseline_0h_rep5


title: CLL COM_baseline_0h_rep6


title: CLL DM_baseline_0h_rep3


title: CLL PL_baseline_0h_rep2


title: Day19 a VSN

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

description: mouse ES cells (D3, ATCC CRL 1934) transfected with the alpha-MHC-Pac-IRES-EGFP vector

hyb_protocol: Sample was hybridized to a GeneChip® miRNA Array (Affymetrix, Santa Claraq, CA, USA) at 48°C and 60 rpm for 16 hours then washed and stained on Fluidics Station 450 (Fluidics script FS450_0003).

scan_protocol: Microarray was finally scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing:
Data was normalized with VSN (Bioconductor, vsn package).
Normalization and probe set summarization was carried out on the mouse-specific probe sets only.

source_name: cardiomyocyte-specific differentiated murine ES cell

label_protocol: Total RNA containing low molecular weight RNA was labelled using the flashtag RNA labeling kit (Genisphere, Hatfield, PA, USA) according to the manufacturer’s instructions.

growth_protocol: aPIG 44 cells were cultured on mouse embroynic fibroblasts in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with nonessential amino acids (0.1 mM), L-glutamine (2 mM), beta-mercaptoethanol (0.1 mM), LIF (ESGR) (500 U/ml), neomycin (6 µg/mL), and batch-tested fetal calf serum (FCS) (15% v/v) (all Invitrogen, Karlsruhe, Germany).

extract_protocol: Total RNAs were extracted by using PeqGold RNApure (Peqlab Biotechnology, Erlangen, Germany) according to the manufacturer's instructions.

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 14 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.

value: ES-D3 murine pluripotent cells

tag: atcc catalog#

tag: time

value: day 19


title: Day19 b VSN

tag: cell line


title: Day26 a VSN

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 21 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.

value: day 26


title: Day26 b VSN


title: CLL GA_baseline_0h_rep1


title: blood_cancer1_family1_rep1

description: miRNA expression in lymphoblastoid cells


title: blood_cancer1_family15_rep1


title: Leu3 120min_3AT_1

growth_protocol: Yeast strain was precultured in SC medium at 28ºC overnight and transferred into fresh SC medium to dilute to 1.4 liter (6  time points) or 1.6 liter (8 time points).

tag: genetic background

tag: treatment


title: Leu3 90min_3AT_3


title: Day12 b

scan_protocol: Mircroarray was finally scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing:
Data was normalized with RMA (Bioconductor, affy package).
Normalization and probe set summarization was carried out on the mouse-specific probe sets only.

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and -mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.

value: day 12


title: Day19 a

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 7 days before extracting RNA.


title: Day26 b

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 21 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 6h before extracting RNA.


title: Day19 b

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 14 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish and cultured for 6h before extracting RNA.


title: Day26 a


title: Leu3 120min_3AT_2


title: Day0 b VSN

source_name: undifferentiated murine embryonic stem cell

treatment_protocol: ES cells were trypsinized at d-2, seeded onto a gelatin-coated 6cm TC dish (Becton Dickinson, Heidelberg, Germany), and cultured for 48h in DMEM 15% FCS.  The timing of this last passage was in parallel with the ES cell passage used to initiate differentiation.

value: day 0


title: Day12 a VSN

treatment_protocol: ES cells were trypsinized (d0) and cultured in suspension to form embryoid bodies (EBs). Briefly, ES cells were transferred into Iscove's modified Dulbecco's Medium (IMDM) with 20% batch-tested FCS, nonessential amino acids (0.1 mM) and beta-mercaptoethanol (0.1 mM) (Invitrogen, Karlsruhe, Germany) in a 10 cm bacterial Petri dish and cultured on a shaker for 48 h. At d2, EBs were transferred into spinner flasks (Integra Cell Spin, IBS, Fernwald, Germany) and cultured for additional 7 days at 37°C, 5% CO2, and 95% humidity. Medium was exchanged at d5, d7, and d9; and at day 9 Puromyicn was added to select for cardiomyocytes. At d12, remaining cardiobodies were trypsinized to obtain a single cell suspension of cardiomyocytes (Cor.At cardiomyocytes). Cor.At cells were seeded onto a Fibronectin coated 10cm dish as described above, and cultured for 6h before extracting RNA.


title: Day0 a VSN


title: Day12 b VSN


title: Leu3 90min_3AT_2


title: Leu3 60min_3AT_2


title: Leu3 90min_3AT_1


title: blood_healthy1_family1_rep1


title: blood_healthy2_family1_rep1


title: Leu3 60min_3AT_1


title: Leu3 60min_3AT_3


title: 14249024 - ein3eil1 - Fe 3 vs ein3eil1 + Fe 3

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Response of ein3eil1 mutants to Fe deficiency

hyb_protocol: ein3eil1 + Fe 3 Cy5 / ein3eil1 - Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: ein3eil1 + Fe 3

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

growth_protocol: whole plant - Media : Hoagland  hygrometry : sterile plate  Temperature : 21°C  Light : 16h light

extract_protocol: ein3eil1 + Fe 3:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:with Fe - environmental treatment - fe deficiency,fe:quantity 50uM time 6day . Seedlings were germinated and grown in the presence of 50 µM Fe or absence of Fe (0 µM) on Hoagland medium agar plates until the age of 6 days. Whole seedlings were harvested for transcriptome analysis, in a total of three biological replicates.

tag: ecotype

value: columbia

tag: genotype/variation

value: mutant (ein3 eil1 ko)

tag: age

tag: dev.stage (boyes et al. plant cell 2001)

value: Fe

source_name: ein3eil1 - Fe 3

extract_protocol: ein3eil1 - Fe 3:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:without Fe - environmental treatment - fe deficiency,fe:quantity 0uM time 6day . Seedlings were germinated and grown in the presence of 50 µM Fe or absence of Fe (0 µM) on Hoagland medium agar plates until the age of 6 days. Whole seedlings were harvested for transcriptome analysis, in a total of three biological replicates.

value: no Fe


title: Day12 a


title: Day0 b


title: 14249118 - ein3eil1 - Fe 2 vs ein3eil1 + Fe 2

hyb_protocol: ein3eil1 + Fe 2 Cy5 / ein3eil1 - Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ein3eil1 + Fe 2

extract_protocol: ein3eil1 + Fe 2:5ug. (Qiagen_RNeasy.pdf)

source_name: ein3eil1 - Fe 2

extract_protocol: ein3eil1 - Fe 2:5ug. (Qiagen_RNeasy.pdf)


title: Day0 a


title: Leu3 45min_3AT_3


title: 14249114 - ein3eil1 + Fe 2 vs ein3eil1 - Fe 2

hyb_protocol: ein3eil1 - Fe 2 Cy5 / ein3eil1 + Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14249023 - ein3eil1 + Fe 3 vs ein3eil1 - Fe 3

hyb_protocol: ein3eil1 - Fe 3 Cy5 / ein3eil1 + Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14249020 - WT - Fe 3 vs WT + Fe 3

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

source_name: WT + Fe 3

extract_protocol: WT + Fe 3:5ug. (Qiagen_RNeasy.pdf)

value: wildtype

source_name: WT - Fe 3

extract_protocol: WT - Fe 3:5ug. (Qiagen_RNeasy.pdf)


title: Leu3 45min_3AT_1

extract_protocol: Extraction of total RNA was performed as manufacture's instractions


title: Leu3 30min_3AT_3


title: Leu3 30min_3AT_2


title: Leu3 30min_3AT_1


title: PNC-H-2

city: La Jolla

first: Dan

last: Zhou

state: CA

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Embryonic Primary Neurons

hyb_protocol: Hybridizations were carried out by using the Illumina gene expression system according to the manufacturer's instructions.

scan_protocol: Illumina scanner

data_processing: Normalized average intensity of the bead type/target in the group using Cubic spline normalization with BeadStudio.

label: Biotin

source_name: Embryonic primary neuronal culture under hypoxic condition

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit following the manufacturer's instructions. Input amount: 100ng of total RNA.

extract_protocol: Total RNA was extracted from frozen tissues of using RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: tissue

value: brain

tag: strain

value: embryonic primary neurons

tag: embryo age

tag: culture time

value: 8 days

tag: Sex

value: embryos, and used 1-2 litters per experiments, so most likely a mix of lames and females


title: Leu3 20min_3AT_3

tag: genotype


title: Leu3 45min_3AT_2


title: 14249002 - WT - Fe 2 vs WT + Fe 2

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

source_name: WT + Fe 2

extract_protocol: WT + Fe 2:5ug. (Qiagen_RNeasy.pdf)

source_name: WT - Fe 2

extract_protocol: WT - Fe 2:5ug. (Qiagen_RNeasy.pdf)


title: 14249119 - WT + Fe 3 vs WT - Fe 3

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


title: 14248999 - ein3eil1 + Fe 1 vs ein3eil1 - Fe 1

hyb_protocol: ein3eil1 - Fe 1 Cy5 / ein3eil1 + Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ein3eil1 - Fe 1

extract_protocol: ein3eil1 - Fe 1:5ug. (Qiagen_RNeasy.pdf)

source_name: ein3eil1 + Fe 1

extract_protocol: ein3eil1 + Fe 1:5ug. (Qiagen_RNeasy.pdf)


title: PNC-H-1

description: Embryonic Primary Neurons

tag: cell type


title: PNC-H-3

description: Embryonic Primary Neurons


title: NSC-H-3

description: Neural stem cell (NSC) line C17.2

source_name: Neural stem cell cultured under hypoxic condition

value: C57BL/6J x CD1

value: neural stem cell (NSC) line C17.2

value: not known if originated from male or female

tag: tag

value: Immortalized with c-myc, has the LacZ as a marker/tracer

value: culture by the time of RNA extraction is 3-4 days (50% confluence)


title: 14249000 - ein3eil1 - Fe 1 vs ein3eil1 + Fe 1

hyb_protocol: ein3eil1 + Fe 1 Cy5 / ein3eil1 - Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NSC-H-1

description: Neural stem cell (NSC) line C17.2


title: NSC-H-2

description: Neural stem cell (NSC) line C17.2


title: MMC-H-3

description: NSC cell line C17.2 with mitomycin-induced differentiation

source_name: Mitomycin-treated neural stem cell cultured under hypoxic condition

tag: tissue of origin

value: The culture by the time of RNA extraction is 8 days

value: cannot tell if originated from male or female


title: Leu3 20min_3AT_2

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

value: LEU3 deletion

tag: collection time after 3at treatment


title: 14249001 - WT + Fe 2 vs WT - Fe 2

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

value: columbia


title: Leu3 20min_3AT_1


title: 14248998 - WT - Fe 1 vs WT + Fe 1

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

source_name: WT + Fe 1

extract_protocol: WT + Fe 1:5ug. (Qiagen_RNeasy.pdf)

source_name: WT - Fe 1

extract_protocol: WT - Fe 1:5ug. (Qiagen_RNeasy.pdf)


title: MMC-H-2

tag: cell line


title: 2x' Ez f/wt

city: San Francisco

first: Alisha

last: Holloway

address: 1650 Owens Street

institute: Gladstone Institutes

description: wild type

hyb_protocol: Affymetrix mouse Gene ST 1.0 arrays were hybridized according to manufacturer recommendations.

scan_protocol: Affymetrix mouse Gene ST 1.0 arrays were scanned according to manufacturer recommendations.

data_processing: Raw intensities from CEL files were analyzed using Affymetrix Power Tools (APT, version 1.10.1) to generate RMA (robust multi-array average) expression intensities on a log2 scale for each probe set.

source_name: adult hearts

label_protocol: Standard Affymetrix methods for biotin labeling were used.

growth_protocol: Dissected adult hearts.

extract_protocol: Total RNA was isolated using TRIzol reagent following the manufacturer's instructions.

treatment_protocol: The right ventricle and the interventricular septum of five wild type (Ezh2f/f) and four Ezh2-deficient (Ezh2f/f;Mef2cAHF::Cre) mice were isolated in cold PBS and homogenized in Trizol reagent (Invitrogen).

value: mixed background of C57BL/6

value: heart

tag: developmental stage

value: adult


title: Leu3 10min_3AT_2

source_name: BY4741 LEU3 deletion

treatment_protocol: 200ml cells were collected and harvested when cells grew in SC medium to reach OD600nm=0.5 as time point 0. 3-aminotriazol was added to a final concentration of 100mM to induce amino acid starvation. 200ml cells were taken and pelleted at each time point after 3AT treatment.

tag: genetic background

tag: treatment


title: Leu3 10min_3AT_3


title: 4x' Ez f/fMef2c-cre


title: MMC-H-1


title: Leu3 10min_3AT_1


title: 3x Ez f/wt

description: wild type


title: Leu3 0min_3AT_3

value: baseline


title: e2 Ez f/f Mef2c-cre


title: e1 Ez f/fMef2c-cre


title: e4 Ez f/wt

description: wild type


title: 8x  Ez f/fMef2c-cre


title: Leu3 0min_3AT_2


title: 14163085 - WT - Fe 2 vs ein3eil1 - Fe 2

hyb_protocol: ein3eil1 - Fe 2 Cy5 / WT - Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: genotype/variation

value: mutant (ein3 eil1 ko)

value: no Fe

value: wildtype


title: e5 Ez f/wt

description: wild type


title: 14163086 - ein3eil1 - Fe 2 vs WT - Fe 2

hyb_protocol: WT - Fe 2 Cy5 / ein3eil1 - Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: age

tag: dev.stage (boyes et al. plant cell 2001)


title: 14163087 - WT + Fe 3 vs ein3eil1 + Fe 3

hyb_protocol: ein3eil1 + Fe 3 Cy5 / WT + Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ein3eil1 + Fe 3

value: Fe


title: Leu3 0min_3AT_1


title: 14248996 - WT + Fe 1 vs WT - Fe 1

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


title: 14163088 - ein3eil1 + Fe 3 vs WT + Fe 3

hyb_protocol: WT + Fe 3 Cy5 / ein3eil1 + Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14163084 - ein3eil1 + Fe 2 vs WT + Fe 2

hyb_protocol: WT + Fe 2 Cy5 / ein3eil1 + Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 3x'  Ez f/wt

description: wild type

tag: strain

tag: tissue


title: Gcn4 120min_3AT_2

source_name: BY4741 GCN4 deletion

value: GCN4 deletion


title: Gcn4 120min_3AT_3


title: 14163083 - WT + Fe 2 vs ein3eil1 + Fe 2

hyb_protocol: ein3eil1 + Fe 2 Cy5 / WT + Fe 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ein3eil1 + Fe 2


title: 14163082 - ein3eil1 - Fe 1 vs WT - Fe 1

hyb_protocol: WT - Fe 1 Cy5 / ein3eil1 - Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Gcn4 120min_3AT_1


title: 14163080 - ein3eil1 + Fe 1 vs WT + Fe 1

hyb_protocol: WT + Fe 1 Cy5 / ein3eil1 + Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14163081 - WT - Fe 1 vs ein3eil1 - Fe 1

hyb_protocol: ein3eil1 - Fe 1 Cy5 / WT - Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Gcn4 90min_3AT_2


title: 14163079 - WT + Fe 1 vs ein3eil1 + Fe 1

hyb_protocol: ein3eil1 + Fe 1 Cy5 / WT + Fe 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Gcn4 90min_3AT_1


title: Gcn4 60min_3AT_3


title: Gcn4 90min_3AT_3


title: Gcn4 60min_3AT_1


title: 14163076 - WT - Fe 3 vs ein3eil1 - Fe 3

hyb_protocol: ein3eil1 - Fe 3 Cy5 / WT - Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ein3eil1 - Fe 3


title: Gcn4 45min_3AT_3


title: ZF4 LPS 12hr post-treatment Replicate 1

city: Taipei

first: gen

middle: hwa

last: lin

state: Nankang

address: 128,section2,academia road

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Biological replicate 1 of 2.LPS_12hr post-treatment

hyb_protocol: We used the  Ncode™ Rapid labeling system and following the procedure to hybridize the labeled miRNA to  triplicate NCode™ multi-species miRNA micoarray kit V2 (Invitrogen). After hybridization, slides were washed sequential.

scan_protocol: The arrays were scanned on an Axon GenePix 4000B scanner.(Molecular Devices, Sunnyvale, USA).

data_processing: The median spot intensity was determined using an Axon GenePix Pro5.1  Software.

label: Alexa 5

organism: Danio rerio

source_name: ZF4_LPS_12hr post-treatment

label_protocol: About 500 ng of the enriched miRNA was labeled with the Ncode™ Rapid labeling system and hybridized to triplicate NCode™ multi-species miRNA micoarray kit V2 (Invitrogen). Briefly, the miRNA fraction from IPNV infected or LPS treated cell was labeled with Alexa 5 dye (red) and the control cell miRNA fraction was labeled with Alexa 3 (green). A second slide we done the dyeswap. A total of six data points for each miRNA can be obtained.

growth_protocol: Zebrafish ZF4 cell line derived from 24-hpf zebrafish embryos was purchased from the American Type Culture Collection (CRL-2050) and cultured in RPMI 1640 medium supplemented with 10% (v/v) fetal bovine serum and penicillin-streptomycin. The isolated virus, E1-S, a member of the Ab strain of IPNV, was isolated from Japanese eels in Taiwan.

extract_protocol: Approximately 105 ZF4 cells/ml were seeded in a 100-mm Petri dish (Nunc, Denmark) and cultivated for more than 24 h. These cells were infected with IPNV at an MOI of 5 and incubated for 0, 3, 6, 12 or 24 h. At the end of the incubation period, the culture medium was aspirated, and the cells were washed with PBS and lysed in 1.0 ml TRIzol reagent (Invitrogen). Total RNA was further purified using On-Column RNase-free DNase digestion (QIAGEN, Germany) to remove possible genomic DNA contamination. Small RNA was further isolated using the PureLink miRNA isolation kit (Invitrogen) according to the manufacturer’s instructions. The RIN value of the RNA samples before being applied to the microarray was measured using an Agilent 2100 Bioanalyzer (USA) and was 10.0. RNA concentrations were determined with a NanoDrop instrument (NanoDrop Technologies).

treatment_protocol: The E1S virus was propagated in ZF4 cell monolayer at a 5 multiplicity of infection (MOI) per cell. Infected cultures were incubated at 18°C and collected sample. Approximately 105 ZF4 cells/ml were seeded in a 60-mm Petri dish (Nunc) and cultured for 24 h. For groups treated with lipopolysaccharide (Sigma Aldrich, USA) to induce TNFα expression, confluent cells were cultured in 60-mm-diameter plastic tissue culture plates that had been treated with 1 μg/ml lipopolysaccharide for 6 h in 10% FBS RPMI 1640 (Invitrogen).

value: LPS

tag: time

label: Alexa 3

source_name: Zebrafish ZF4 cell line

tag: sample type

value: control


title: ZF4 LPS 24hr post-treatment Replicate 1

description: Biological replicate 1 of 2. LPS_24hr post-treatment

source_name: ZF4_LPS_24hr post-treatment


title: Gcn4 45min_3AT_2

hyb_protocol: Afer fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Yeast Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. The protocol used for infividual module array stain is EuKGE_WS2v4_450.

tag: genotype


title: Gcn4 45min_3AT_1


title: ZF4 LPS 6hr post-treatment Replicate 2

description: Biological replicate 2 of 2. LPS_6hr post-treatment,dye swap

source_name: ZF4_LPS_6hr post-treatment


title: HMVEC_PEDF/VEGF treated cells vs. HMVEC_control (untreated cells)

city: Chicago

first: Dauren

last: Biyashev

address: 300 E.Superior St.

institute: Northwestern University

description: S03-PEDF/VEGF (Cy3) was compared to S04-Control (Cy5).

hyb_protocol: Performed by LC Sciences.

scan_protocol: Performed by LC Sciences.

data_processing: All expression profiling and further analyses, including statistical analysis, were performed by LC Sciences. The signal values were derived by background subtraction and normalization, and then p values were calculated.

source_name: HMVEC treated with PEDF/VEGF

label_protocol: Performed by LC Sciences.

growth_protocol: Human microvascular endothelial cells (HMVECs, Lonza) were cultured in endothelial cell growth medium (EGM1), 5% fetal bovine serum (FBS) and the EGM bullet kit (Lonza).

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen).

treatment_protocol: The cells were treated with either VEGF (1ng/ml) or PEDF(10nM)/VEGF(1ng/ml) or left untreated (control), and incubated for 16 hrs at 5%CO2, 37C.

value: HMVEC

tag: cell type

value: human microvascular endothelial cells

value: pigment epithelial-derived factor (PEDF) and vascular endothelial growth factor (VEGF)

source_name: HMVEC control


title: ZF4 LPS 12hr post-treatment Replicate 2

description: Biological replicate 2 of 2. LPS_12hr post-treatment,dye swap


title: ZF4 LPS 24hr post-treatment Replicate 2

description: Biological replicate 2 of 2. LPS_24hr post-treatment,dye swap


title: 14119470 - ein3eil1 - Fe 3 vs WT - Fe 3

hyb_protocol: WT - Fe 3 Cy5 / ein3eil1 - Fe 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: WT - Fe 3


title: ZF4 IPNV 24hr postinfection Replicate 1

description: Biological replicate 1 of 2.IPNV_24hr postinfection

source_name: ZF4_IPNV_24hr postinfection

tag: infection

value: Infectious pancreatic necrosis virus


title: ZF4 IPNV 24hr postinfection Replicate 2

description: Biological replicate 2 of 2.IPNV_24hr postinfection,dye swap


title: ZF4 LPS 6hr post-treatment Replicate 1

description: Biological replicate 1 of 2. LPS_6hr post-treatment


title: Gcn4 30min_3AT_3

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.


title: Gcn4 20min_3AT_3


title: Gcn4 30min_3AT_1


title: HMVEC_control (untreated cells) vs. HMVEC_VEGF treated cells

description: S01-Control (Cy3) was compared to S02-VEGF (Cy5).

source_name: HMVEC treated with VEGF

value: vascular endothelial growth factor (VEGF)


title: Gcn4 30min_3AT_2


title: Gcn4 20min_3AT_2


title: ZF4 IPNV 12hr postinfection Replicate 1

description: Biological replicate 1 of 2. IPNV_12hr postinfection

source_name: ZF4_IPNV_12hr postinfection


title: ZF4 IPNV 6hr postinfection Replicate 2

description: Biological replicate 2 of 2. IPNV_6hr postinfection,dye swap

source_name: ZF4_IPNV_6hr postinfection


title: Gcn4 10min_3AT_3


title: cardiac differentiation d11, rep1

city: Baltimore

first: Hideki

last: Uosaki

address: 720 Rutland Ave, Ross 954

department: Division of Cardiology

institute: Johns Hopkins University

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Human Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpringGXv11 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 2.

source_name: cells at day 11 of differentiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA.

growth_protocol: Cells were differentiated in RPMI+B27 medium.

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

treatment_protocol: Cells were treated with Activin A (day 0-1), BMP4+bFGF (day 1-5), and Dkk1 (day 5-7).

value: hiPSC derivatives

tag: differentiation time

value: day 11


title: medulloblastoma_02

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

hyb_protocol: The resultant labeled cDNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner GCS3000 7G plus.

data_processing: The data were analyzed with Bioconductor in R statistical software.

source_name: fresh frozen tissue

label_protocol: amplified and labeled according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript Sense Target Labeling protocol

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy Mini kit (Hilden, Germany).

value: medulloblastoma

tag: Sex

value: F

tag: age(month)

tag: histology

value: Classic

tag: seeding(metastasis)

value: N

tag: death

value: alive


title: cardiac differentiation d9, rep2

source_name: cells at day 9 of differentiation

tag: cell line

value: day 9


title: Gcn4 10min_3AT_2

first: Xiaowei

last: XUE

address: 60 Biopolis Street, #02-01, Genome

institute: Genome Institute of Singapore

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

source_name: BY4741 GCN4 deletion

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

tag: collection time after 3at treatment

tag: genetic background

tag: treatment


title: cardiac differentiation d7, rep1

source_name: cells at day 7 of differentiation

value: day 7


title: Gcn4 10min_3AT_1

value: GCN4 deletion


title: cardiac differentiation d7, rep2


title: cardiac differentiation d2, rep2

source_name: cells at day 2 of differentiation

value: day 2


title: cardiac differentiation d11, rep2


title: cardiac differentiation d9, rep1


title: ZF4 IPNV 12hr postinfection Replicate 2

description: Biological replicate 2 of 2. IPNV_12hr postinfection,dye swap

value: control


title: cardiac differentiation d2, rep1


title: cardiac differentiation d5, rep2

source_name: cells at day 5 of differentiation

value: day 5


title: cardiac differentiation d5, rep1


title: cardiac differentiation d0, rep1

source_name: cells at day 0 of differentiation

value: day 0


title: Gcn4 0min_3AT_2

value: baseline


title: Gcn4 20min_3AT_1


title: Gcn4 0min_3AT_1


title: Whole Tissue_SD 4h Light_bhlh93_rep1

city: Austin

first: Enamul

last: Huq

state: TX

address: 24th St. and Whitis BIO labs ,

department: MCDB

institute: University of Texas at Austin

description:
394517_A8_22Feb10_532.pair
394517_A8_22Feb10_532_RMA.calls

hyb_protocol: Microarray hybridization experiment was performed according to user manual of Roche Nimbelgen Arabidopsis thaliana 12x135K Array (090717 Athal TAIR9 exp HX12; Cat No. 05543746001). 4 micrograms of labeled product were resuspended in sample tracking control, applied to the arrays, and hybridized overnight in a Maui 4-position hybridization chamber, according to Roche Nimblegen protcol version 2.3. The arrays were then washed and dried according to the same protocol.

scan_protocol: Arrays were scanned and analyzed according to Roche Nimblegen protcol version 2.3. Briefly, the arrays were scanned on an Axon 4000B scanner set at 5 micron resolution with 100% laser power and PMT gain between 500 and 600. The resulting TIF images were post-processed using Nimblescan version 2.3 to identify probe locations and each array was visually inspected for proper grid alignment.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: Whole tissue, 10d old in SD

label_protocol: Double stranded cDNA was created using the Invitrogen double stranded-cDNA synthesis kit(Cat #11917010) according to Roche Nimblegen instructions (Roche protocol version 2.3) using an oligo-dT primer. Double-stranded cDNA was then labeled using Cy3-labeled nonamers (TriLink, San Diego, CA) and Klenow (large fragment, NEB cat #M0210M) also according to the Roche protocol version 2.3).

growth_protocol: Seeds were surface sterilized and plated on Murashige and Skoog growth medium (GM) containing 0.9% agar without Suc (GM - Suc) as described (Shen et al., 2005). After 4 d of stratification at 4oC, seeds were exposed to SD.

extract_protocol: For microarray, total RNA was isolated from 10d-old bhlh93-1 mutant and wild-type Col-0 seedlings grown under SD using the RNeasy plant mini kit (Qiagen). Five µg RNA from 10d old SD grown seedling of Wt and bhlh93-1 mutants was reverse transcribed using the RT-PCR kit from Invitrogen.

treatment_protocol: Samples were harvested in dark and after 4h light treatment in SD growth conditions.

tag: cultivar

value: bhlh93-1 mutant

value: 4 hr


title: ZF4 IPNV 6hr postinfection Replicate 1

description: Biological replicate 1 of 2.IPNV_6hr postinfection

value: Infectious pancreatic necrosis virus

source_name: Zebrafish ZF4 cell line


title: Gcn4 0min_3AT_3

city: singapore


title: BY4741 120min_3AT_3

source_name: BY4741 wild-type

value: WT


title: cardiac differentiation d0, rep2

value: hiPSC derivatives