title: EC20_AS_Q2_pool_9-9

source_name: Lung


title: EC20_AS_Q2_pool_9-4

status: Public on May 25 2008

type: RNA

city: Santa Clara

first: Thomas

middle: R

last: Gingeras

state: CA

address: 3380 Central Expressway

country: USA

institute: Affymetrix, Inc.

description: 5' and 3' RACE reactions were performed using using the BD SMARTTM RACE cDNA amplification kit (BD Clontech Cat. No.634914) following the manufacturer's instructions. RACE oligonucleotides were designed with primer3(http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi) with the following parameters: 23 <= primer size <= 27, optimal size = 25, 68oC <= primer Tm <= 72oC, optimal Tm = 70oC,50% = primer GC percentage = 70%.

hyb_protocol: The labeled products were used directly for hybridization to Affymetrix Chromosome 21/22 2.0R Array for 18 h at 450C in a 3 M tetramethyl ammonium chloride/1x MES-based solution containing 100ug/mL Herring Sperm DNA, 0.02% Triton and 30pM of biotinylated control oligo B2 (Affymetrix). All reagents were from Invitrogen, except where noted otherwise.

scan_protocol: Standard Affymetrix protocols

data_processing: The maps of probe intensities versus the genomic positions were generated using Tiling array Software(TAS; http://www.affymetrix.com/support/developer/downloads/TilingArrayTools/index.affx).The graphs were generated without smoothing and median scaling. Each value on the graph represents intensity of the perfect match (PM) probe minus the intensity of the cognate mismatch (MM) probe. The coordinates of the probe always represent the "left" genomic coordinate of a 25-mer.All data is in the coordinates of the hs.NCBIv35 version of the human genome. To minimize the number of falsely positive probes arising from cross-hybridization on the tiling array, we discard all positive probes having more than one perfect hit without gap in the whole genome. RACEfrags were built using a 99.7% percentile in the probe intensity value as a threshold. Two probes are included in the same RACEfrag if they are less than 25 nucleotides away (maxgap), and the minimum length of a RACEfrag (minrun) is 25 nucleotides.

label: Affymetrix DNA labeling reagent (#900542).

molecule: polyA RNA

organism: Homo sapiens

source_name: Spleen

label_protocol: The pooled amplicons were then fragmented to ~ 50-100 nucleotides using DNAse I (Epicenter) at concentration of 0.00625U/ug of DNA for 8 minutes at 37oC followed by boiling for 10 min and cooling on ice. The fragmented amplicons were labeled in the following conditions: 1X terminal transferase(TdT) reaction buffer (Roche); 2.5mM CoCl2, DNA labeling reagent (DLR; Affymetrix; 1.125nmol per 1ug of fragmented DNA) and 200 units of recombinant TdT (Roche) for 3 hours at 37oC

extract_protocol: The products of RACE PCR reactions were pooled and purified by ethanol precipitation.

tag: The sample characteristics which is specific to each pool is detailed in http://genome.imim.es/datasets/racearrays2007


title: EC20_AS_Q2_pool_9-5

source_name: Liver


title: PI_20_AS_Q1_pool_1_37

data_processing: The maps of probe intensities versus the genomic positions were generated using Tiling array Software(TAS; http://www.affymetrix.com/support/developer/downloads/TilingArrayTools/index.affx).The graphs were generated without smoothing and median scaling. Each value on the graph represents intensity of the perfect match (PM) probe minus the intensity of the cognate mismatch (MM) probe. The coordinates of the probe always represent the ”left” genomic coordinate of a 25-mer.All data is in the coordinates of the hs.NCBIv35 version of the human genome. To minimize the number of falsely positive probes arising from cross-hybridization on the tiling array, we discard all positive probes having more than one perfect hit without gap in the whole genome. RACEfrags were built using a 99.7% percentile in the probe intensity value as a threshold. Two probes are included in the same RACEfrag if they are less than 25 nucleotides away (maxgap), and the minimum length of a RACEfrag (minrun) is 25 nucleotides.

source_name: Tonsil


title: PI_20_AS_Q1_pool_1_35

source_name: Spinal Cord


title: PI_20_AS_Q1_pool_1_34

source_name: Lymph Node


title: EC20_AS_Q2_pool_9-3

source_name: Heart


title: EC20_AS_Q2_pool_9-6

source_name: Colon


title: PI_20_AS_Q1_pool_1_33

source_name: Epididymus


title: EC20_AS_Q2_pool_9-7

source_name: Small Intestine


title: PI_20_AS_Q1_pool_1_31

source_name: Brain Hippocampus


title: PI_20_AS_Q1_pool_1_36

source_name: Tongue


title: EC20_AS_Q2_pool_9-1

source_name: Brain


title: PI_20_AS_Q1_pool_1_30

source_name: Brain Frontal lob


title: EC20_AS_Q2_pool_9-2

source_name: Kidney


title: EC20_AS_Q2_pool_8-12

source_name: Placenta


title: EC20_AS_Q2_pool_8-11

source_name: Testis


title: PI_20_AS_Q1_pool_1_29

source_name: Bladder


title: EC20_AS_Q2_pool_8-10

source_name: Stomach


title: EC20_AS_Q2_pool_8-9

source_name: Lung


title: PI_20_AS_Q1_pool_1_32

source_name: Brain Hypothalamus


title: PI_20_AS_Q1_pool_1_28

source_name: Uterus


title: PI_20_AS_Q1_pool_1_27

source_name: Pituitary Gland


title: PI_20_AS_Q1_pool_1_26

source_name: Brain Cerebelum


title: PI_20_AS_Q1_pool_1_25

source_name: Adrenal Gland


title: EC20_AS_Q2_pool_8-6

source_name: Colon


title: EC20_AS_Q2_pool_8-4

source_name: Spleen


title: EC20_AS_Q2_pool_8-7

source_name: Small Intestine


title: EC20_AS_Q2_pool_8-2


title: EC20_AS_Q2_pool_8-5

source_name: Liver


title: PI_20_AS_Q1_pool_1_21

source_name: Prostate


title: PI_20_AS_Q1_pool_1_22

source_name: Thyroid


title: PI_20_AS_Q1_pool_1_24

source_name: Salivary Gland


title: PI_20_AS_Q1_pool_1_23

source_name: Ovary


title: EC20_AS_Q2_pool_8-3

source_name: Heart


title: EC20_AS_Q2_pool_8-8

source_name: Muscle


title: EC20_AS_Q2_pool_8-1

source_name: Brain


title: PI_20_AS_Q1_pool_1_20

source_name: Mammary Gland


title: PI_20_AS_Q1_pool_1_19

source_name: Pancreas


title: EC20_AS_Q2_pool_7-12

source_name: Placenta


title: PI_20_AS_Q1_pool_1_18

source_name: Thymus


title: EC20_AS_Q2_pool_7-11

source_name: Testis


title: EC20_AS_Q2_pool_7-9

source_name: Lung


title: PI_20_AS_Q1_pool_1_16

source_name: Fetal Kidney


title: EC20_AS_Q2_pool_7-10

source_name: Stomach


title: EC20_AS_Q2_pool_7-8


title: PI_20_AS_Q1_pool_1_17

source_name: Fetal Spleen


title: fibrosis F4 - patient 6 -hyb 1

status: Public on May 24 2008

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

country: France

institute: Faculty of Medicine and Pharmacy

description: advanced fibrosis

hyb_protocol: Hybridization of the [α 33P]-labeled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

molecule: total RNA

source_name: liver fibrosis - Metavir score : F4, advanced fibrosis

label_protocol: Within each RNA preparation prepared as above the target poly(N) mRNAs were labeled as follows : 200ng amplified RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg random oligonucleotides were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labeled cDNAs were immediately used for hybridization.

extract_protocol: RNA extraction from tissues was done with MiniRNA isolation I kit (Zymo Research) then was amplified with MessageAmp™ II aRNA Amplification Kit (Ambion).

tag: Age

value: 58 years old

tag: Sex

value: female

tag: HCV-infected


title: PI_20_AS_Q1_pool_1_13

source_name: Skin


title: fibrosis F4 - patient 5 -hyb 3

description: advanced fibrosis

value: 20 years old

value: male


title: EC20_AS_Q2_pool_7-5

source_name: Liver


title: PI_20_AS_Q1_pool_1_14

source_name: Fetal Brain


title: fibrosis F4 - patient 5 -hyb 2

description: advanced fibrosis


title: EC20_AS_Q2_pool_7-6

source_name: Colon


title: fibrosis F4 - patient 4 -hyb 3

description: advanced fibrosis

value: 55 years old


title: EC20_AS_Q2_pool_7-7

source_name: Small Intestine


title: fibrosis F4 - patient 4 -hyb 2

description: advanced fibrosis


title: fibrosis F4 - patient 4 -hyb 1

description: advanced fibrosis


title: PI_20_AS_Q1_pool_1_12


title: fibrosis F4 - patient 3 -hyb 3

description: advanced fibrosis

value: 57 years old


title: fibrosis F4 - patient 5 -hyb 1

description: advanced fibrosis


title: fibrosis F4 - patient 3 -hyb 2

description: advanced fibrosis


title: fibrosis F4 - patient 2 -hyb 3

description: advanced fibrosis

value: 69 years old


title: fibrosis F4 - patient 2 -hyb 2

description: advanced fibrosis


title: EC20_AS_Q2_pool_7-4

source_name: Spleen


title: fibrosis F4 - patient 2 -hyb 1

description: advanced fibrosis


title: fibrosis F4 - patient 1 -hyb 3

description: advanced fibrosis

value: 68 years old


title: PI_20_AS_Q1_pool_1_8

source_name: Muscle


title: PI_20_AS_Q1_pool_1_11


title: fibrosis F4 - patient 1 -hyb 1

description: advanced fibrosis


title: fibrosis F1 - patient 8 -hyb 3

description: mild fibrosis

source_name: liver fibrosis - Metavir score : F1, mild fibrosis

value: 39 years old


title: fibrosis F4 - patient 1 -hyb 2

description: advanced fibrosis


title: EC20_AS_Q2_pool_7-3

source_name: Heart


title: fibrosis F1 - patient 8 -hyb 1

description: mild fibrosis


title: EC20_AS_Q2_pool_6-12

source_name: Placenta


title: fibrosis F1 - patient 7 -hyb 3

description: mild fibrosis

value: 37 years old


title: PI_20_AS_Q1_pool_1_9


title: fibrosis F1 - patient 7 -hyb 1

description: mild fibrosis


title: fibrosis F1 - patient 7 -hyb 2

description: mild fibrosis


title: fibrosis F1 - patient 6 -hyb 3

description: mild fibrosis

value: 65 years old


title: fibrosis F1 - patient 6 -hyb 1

description: mild fibrosis


title: fibrosis F1 - patient 6 -hyb 2

description: mild fibrosis


title: fibrosis F1 - patient 5 -hyb 3

description: mild fibrosis

value: 54 years old


title: PI_20_AS_Q1_pool_1_7


title: fibrosis F1 - patient 8 -hyb 2

description: mild fibrosis


title: fibrosis F1 - patient 5 -hyb 2

description: mild fibrosis


title: fibrosis F4 - patient 3 -hyb 1

description: advanced fibrosis


title: fibrosis F1 - patient 4 -hyb 2

description: mild fibrosis

value: 41 years old


title: fibrosis F1 - patient 4 -hyb 3

description: mild fibrosis


title: EC20_AS_Q2_pool_7-1

source_name: Brain


title: fibrosis F1 - patient 5 -hyb 1

description: mild fibrosis


title: fibrosis F1 - patient 3 -hyb 2

description: mild fibrosis

value: 50 years old


title: fibrosis F1 - patient 3 -hyb 3

description: mild fibrosis


title: fibrosis F1 - patient 2 -hyb 3

description: mild fibrosis

value: 61 years old


title: fibrosis F1 - patient 4 -hyb 1

description: mild fibrosis


title: fibrosis F1 - patient 3 -hyb 1

description: mild fibrosis


title: PI_20_AS_Q1_pool_1_15

source_name: Fetal Liver


title: fibrosis F1 - patient 1 -hyb 3

description: mild fibrosis

value: 34 years old


title: fibrosis F1 - patient 1 -hyb 1

description: mild fibrosis


title: fibrosis F1 - patient 2 -hyb 2

description: mild fibrosis


title: PI_20_AS_Q1_pool_1_10


title: fibrosis F1 - patient 1 -hyb 2

description: mild fibrosis


title: fibrosis F4 - patient 8 -hyb 2

description: advanced fibrosis


title: fibrosis F4 - patient 8 -hyb 3

description: advanced fibrosis


title: PI_20_AS_Q1_pool_1_6


title: fibrosis F1 - patient 2 -hyb 1

description: mild fibrosis


title: fibrosis F4 - patient 7 -hyb 2

description: advanced fibrosis

value: 63 years old


title: fibrosis F4 - patient 6 -hyb 2

description: advanced fibrosis

value: 58 years old


title: PI_20_AS_Q1_pool_1_3


title: EC20_AS_Q2_pool_6-9

source_name: Lung


title: fibrosis F4 - patient 6 -hyb 3

description: advanced fibrosis

value: female


title: fibrosis F4 - patient 7 -hyb 3

description: advanced fibrosis


title: EC20_AS_Q2_pool_6-7


title: EC20_AS_Q2_pool_6-11

source_name: Testis


title: blood_Healthy_GECM-061_79

city: Athens

first: George

middle: Panayiotis

last: Stathopoulos

state: Attiki

address: Souidias 55

department: Oncology Department

country: Greece

institute: Errikos Dunant hospital

description: blood_Healthy_GECM-061_ 79

hyb_protocol: 10 µg of digoxigenin-labeled cRNA samples were fragmented and hybridized for 16h to Human Genome Survey Microarrays V2.0 (Applied Biosystems) at a temperature of 55°C.  After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.

scan_protocol: chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene-specific 60-mer probes detecting more than 27000 different genes.The software platform R (Version 2.4.0) and the Bioconductor packages ABarray (25) and Limma (26) as well as the software Spotfire Decision Site for Functional Genomics 9.0 were used for biostatistical data analysis and visualization.

data_processing: Normalization compensates for varying global signal intensities of the microarrays and adjusts them to a uniform level, thus making the individual microarrays comparable for downstream analysis.  Quantile normalization was applied to the data set .  The quantile normalized, log2 transformed data were averaged within the subgroups A, B, C, D, E and N. The quantile normalized, log2 transformed data were also averaged within the category “double cancer” (group AB), and within the category “single cancer” (group CDE). The extent and direction of differential expression between the groups are presented in a fold change value on the log scale (see “statistical significance” below). The similarity of global gene expression profiles of the different patient blood samples was assessed by correlation analysis. For this purpose, MA plots were generated from the quantile normalized data. To analyze the comparisons of interest, design matrices were created which assign the samples to the subgroups A through N and to the categories AB, CDE and N. A linear model was then fitted for every gene and contrast matrices were generated to extract the statistical parameters for the different comparisons. All possible comparisons among the participating groups in this study were determined.  The contrasts were extracted after fitting the linear model and were tested for statistical significance using an ANOVA-like test (moderated F-Test, empirical Bayes method).   To correct for multiple testing, the FDR-based method was applied. The p-value adjusted for multiple testing is usually several orders of magnitude higher than the unadjusted p-value.   To allow for the identification of the “significant” comparison(s), a decision matrix was created. This matrix includes all comparisons within the contrast matrix and is filled with the values 0, 1 and -1. The value 1 indicates that the respective comparison achieves statistical significance in the sense of up-regulation, and the value -1 indicates significant down-regulation. The value 0 specifies a non-significant result of the test. The quintile normalized, log transformed signal values were used as the basis for hierarchical clustering, and the clustering method “complete linkage” was applied within the software Spotfire Decision Site for Functional Genomics 9.0.  The identification of differentially regulated processes and pathways for all of the genes obtained as well as the enrichment of biological classes and pathways in comparison to the whole genome was carried out. (http://www.pantherdb.org).   As a matter of principle, the percentage distributions shown in the pie charts  (results not shown) do not indicate if a certain biological process, molecular function or pathway is in fact overrepresented, or if they just reflect the average percentage of the respective class in the human genome. To elucidate this question, the induced gene IDs were compared to all gene IDs represented on the Human AB1700 Microarray V2.0; (http://www.pantherdb.org/ > Tools > Gene Express Data Analysis > Compare gene lists) and whether a specific class was overrepresented when compared to the distribution of all genes on the microarray, was calculated. A p-value is given for the significance of this enrichment, based on the binomial test. From our experience, p-values approximately 10-6, can be regarded as a sign of manifest enrichment in the context of a Panther analysis for biological processes and molecular functions. For Panther Pathway enrichment analysis, we found that the threshold can be slightly increased to p-values approximately10-6.  Classification analysis  Classification analysis was performed using the support vector machine (SVM) paradigm. We performed SVM on the highest quality subset of the probes measured in the Human Genome Survey Microarray V2.0. This subset was determined as those probes that had a Signal/noise (S/N) ratio of more than or equal to 3 and a flag value of 8192 or more, for all samples tested. This quality filter was passed by a total of 4121 probes. The quantile-normalized expression levels of these probes were then standardized using the function scale within R 2.5.1., resulting in a set of 4121 variables of which all had a mean of 0 and a standard deviation of 1, thus giving each probe an equal chance to enter as a factor into a classifier.  To build the classifiers for the various combinations of outcomes compared, the following procedure was chosen:  1) Application of an ANOVA analysis on the standardized quantile normalized probe expression levels and sorting the probes by p-values from the analysis.  2) From the subset of the 300 probes with the lowest p-values, choice of a further subset by means of a reversible direction Monte-Carlo adding, sampling and reduction method developed especially for this study.  3) The quality of classifiers was judged by the cross-validation error, which was aimed to be minimized. The number of cross-validations for each step was set to half the effective sample size, i.e. the number of samples with class designations being part of the combination of outcome investigated. At this point it should be noted that the accuracy of prediction in the total set of data was 100% in all cases (i.e. the training error was 0 in all cases).  The relative importance of a probe was calculated as follows: first, the cross-validation error for the total classifier was recorded, then in turn, each of the probes was left out of the classifier. For each of these reduced classifiers, the cross-validation error, which was expected and indeed found to be increased in every case, was recorded. The cross-validation errors of the reduced classifiers were then normalized such that the probe with the largest increase in cross-validation error was assigned a relative importance of 1.00 with all the other probes having increasingly lower importance slowly approaching 0 for the least important variables. This normalization was done by dividing each of the probe-specific increases in error by the maximum increase in error. These normalized values are designated as relative importances.   Out of a total of 65 classifiers that were built, the seven most important denominated by the diagnostic categories used in their building are:  AB vs CDE, AB vs N, CDE vs N, AB vs CDE vs N, AB vs C, AB vs D, AB vs E.

label: Digoxigenin

source_name: blood, healthy

label_protocol: 750 ng total RNA were introduced into an RT-IVT reaction: the RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in-vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides (Roche Diagnostics).

extract_protocol: RNA was obtained by peripheral blood from patients and healthy individuals by using the PAXgene Blood RNA system (Qiagen) according to the manufacturer’s instructions. In order to avoid epithelial cell contamination of our samples the first 5 ml of blood in each case after vein puncture, were discarded.   RNA concentration and purity was determined on the NanoDrop ND-1000 spectral photometer (peqlab), whereas RNA integrity was determined by capillary electrophoresis of total RNA samples, using the 2100 Bioanalyzer (Agilent Technologies).

value: Female

tag: 49 years old


title: blood_single primary malignacy_GECM-061_62

description: blood_single primary malignacy_GECM-061_ 62

source_name: blood, one primary malignancy

tag: 60 years old ovarian cancer


title: PI_20_AS_Q1_pool_1_5


title: blood_Healthy_GECM-061_77

description: blood_Healthy_GECM-061_ 77

tag: 60 years old


title: blood_single primary malignacy_GECM-061_63

description: blood_single primary malignacy_GECM-061_ 63

tag: 54 years old

tag: ovarian cancer


title: blood_single primary malignacy_GECM-061_61

description: add

tag: 61 years old


title: blood_Healthy_GECM-061_73

description: blood_Healthy_GECM-061_ 73

tag: 57 years old


title: blood_Healthy_GECM-061_70

description: blood_Healthy_GECM-061_ 70

value: Male

tag: 73 years old


title: blood_Healthy_GECM-061_71

description: blood_Healthy_GECM-061_ 71

tag: 70 years old


title: blood_Healthy_GECM-061_75

description: blood_Healthy_GECM-061_ 75

tag: 48 years old


title: blood_Healthy_GECM-061_76

description: blood_Healthy_GECM-061_ 76

tag: 66 years old


title: blood_single primary malignacy_GECM-061_60

description: blood_single primary malignacy_GECM-061_ 60

tag: 41 years old

tag: breast cancer


title: blood_Healthy_GECM-061_74

description: blood_Healthy_GECM-061_ 74


title: blood_Healthy_GECM-061_78

description: blood_Healthy_GECM-061_ 78

tag: 72 years old


title: EC20_AS_Q2_pool_7-2

source_name: Kidney

tag: The sample characteristics which is specific to each pool is detailed in http://genome.imim.es/datasets/racearrays2007


title: PI_20_AS_Q1_pool_1_4


title: blood_single primary malignacy_GECM-061_57

description: blood_single primary malignacy_GECM-061_ 57

tag: Sex

tag: 61 years old colon cancer


title: EC20_AS_Q2_pool_6-10

source_name: Stomach


title: blood_two primary malignacies_GECM-061_56

description: blood_two primary malignacies_GECM-061_ 56

source_name: blood, two primary malignancies

tag: 65 years old

tag: breast cancer and lymphoma


title: blood_two primary malignacies_GECM-061_59

description: blood_two primary malignacies_GECM-061_ 59

tag: colon and ovarian cancer


title: PI_20_AS_Q1_pool_1_1


title: PI_20_AS_Q1_pool_1_2


title: blood_single primary malignacy_GECM-061_53

description: blood_single primary malignacy_GECM-061_ 53

tag: 58 years old


title: blood_two primary malignacies_GECM-061_58

description: blood_two primary malignacies_GECM-061_ 58

tag: breast cancer and lemphoma


title: fibrosis F4 - patient 7 -hyb 1

description: advanced fibrosis

source_name: liver fibrosis - Metavir score : F4, advanced fibrosis

tag: Age

tag: HCV-infected


title: EC20_AS_Q2_pool_6-8


title: blood_single primary malignacy_GECM-061_52

description: blood_single primary malignacy_GECM-061_ 52

tag: 67 years old

tag: ovarian cancer


title: blood_single primary malignacy_GECM-061_50

description: blood_single primary malignacy_GECM-061_ 50

tag: 50 years old


title: blood_single primary malignacy_GECM-061_36

description: blood_single primary malignacy_GECM-061_ 36

tag: 37 years old


title: blood_single primary malignacy_GECM-061_42

description: blood_single primary malignacy_GECM-061_ 42

tag: 41 years old


title: blood_single primary malignacy_GECM-061_38

description: blood_single primary malignacy_GECM-061_ 38

tag: breast cancer


title: blood_single primary malignacy_GECM-061_44

description: blood_single primary malignacy_GECM-061_ 44

tag: 49 years old


title: blood_single primary malignacy_GECM-061_55

description: blood_single primary malignacy_GECM-061_ 55

tag: 55 years old


title: blood_single primary malignacy_GECM-061_51

description: blood_single primary malignacy_GECM-061_ 51

tag: Sex

tag: 48 years old


title: blood_single primary malignacy_GECM-061_34

description: blood_single primary malignacy_GECM-061_ 34

tag: 70 years old

tag: colon cancer


title: blood_single primary malignacy_GECM-061_47

description: blood_single primary malignacy_GECM-061_ 47

tag: 66 years old


title: blood_single primary malignacy_GECM-061_41

description: blood_single primary malignacy_GECM-061_ 41


title: blood_single primary malignacy_GECM-061_49

description: blood_single primary malignacy_GECM-061_ 49

tag: 59 years old


title: blood_single primary malignacy_GECM-061_45

description: blood_single primary malignacy_GECM-061_ 45

tag: 45 years old


title: blood_single primary malignacy_GECM-061_35

description: blood_single primary malignacy_GECM-061_ 35

tag: 61 years old


title: blood_single primary malignacy_GECM-061_30

description: blood_single primary malignacy_GECM-061_ 30


title: blood_single primary malignacy_GECM-061_32

description: blood_single primary malignacy_GECM-061_ 32

tag: 23 years old


title: blood_single primary malignacy_GECM-061_39

description: blood_single primary malignacy_GECM-061_ 39

tag: 53 years old


title: fibrosis F4 - patient 8 -hyb 1

description: advanced fibrosis

tag: Age

value: male

tag: HCV-infected


title: blood_single primary malignacy_GECM-061_40

description: blood_single primary malignacy_GECM-061_ 40

tag: 65 years old


title: blood_two primary malignacies_GECM-061_22

description: blood_two primary malignacies_GECM-061_ 22

tag: colon and prostate cancer.


title: blood_single primary malignacy_GECM-061_29

description: blood_single primary malignacy_GECM-061_ 29

tag: 62 years old


title: blood_single primary malignacy_GECM-061_23

description: blood_single primary malignacy_GECM-061_ 23

tag: 75 years old


title: blood_single primary malignacy_GECM-061_28

description: blood_single primary malignacy_GECM-061_ 28

tag: 72 years old


title: blood_two primary malignacies_GECM-061_12

description: blood_two primary malignacies_GECM-061_ 12

tag: Sex

tag: carcinoid tumor and breast cancer


title: blood_two primary malignacies_GECM-061_21

description: blood_two primary malignacies_GECM-061_ 21

tag: 64 years old

tag: colon and prostate cancer


title: blood_single primary malignacy_GECM-061_27

description: blood_single primary malignacy_GECM-061_ 27

tag: 58 years old

tag: colon cancer


title: blood_two primary malignacies_GECM-061_18

description: blood_two primary malignacies_GECM-061_ 18

tag: 67 years old


title: blood_single primary malignacy_GECM-061_26

description: blood_single primary malignacy_GECM-061_ 26

tag: 55 years old


title: blood_two primary malignacies_GECM-061_5

description: blood_two primary malignacies_GECM-061_ 5

tag: 45 years old

tag: breast and colon cancer


title: blood_two primary malignacies_GECM-061_20

description: blood_two primary malignacies_GECM-061_ 20

tag: 63 years old

tag: lung and colon cancer


title: blood_two primary malignacies_GECM-061_2

description: blood_two primary malignacies_GECM-061_ 2

tag: 43 years old

tag: colon and ovarian cancer


title: blood_two primary malignacies_GECM-061_16

description: blood_two primary malignacies_GECM-061_ 16

tag: 54 years old

tag: ovary and urinary bladder cancer


title: blood_single primary malignacy_GECM-061_24

description: blood_single primary malignacy_GECM-061_ 24


title: blood_two primary malignacies_GECM-061_15

description: blood_two primary malignacies_GECM-061_ 15

tag: 50 years old

tag: breast an gastric cancer


title: blood_two primary malignacies_GECM-061_19

description: blood_two primary malignacies_GECM-061_ 19

tag: Sex

tag: colon and gastric cancer


title: blood_two primary malignacies_GECM-061_11

description: blood_two primary malignacies_GECM-061_ 11

tag: 71 years old


title: blood_two primary malignacies_GECM-061_13

description: blood_two primary malignacies_GECM-061_ 13

tag: breast and ovarian cancer


title: blood_two primary malignacies_GECM-061_6

description: blood_two primary malignacies_GECM-061_ 6

tag: 82 years old


title: blood_two primary malignacies_GECM-061_17

description: blood_two primary malignacies_GECM-061_ 17

tag: 73 years old

tag: colon and prostate cancer


title: blood_two primary malignacies_GECM-061_10

description: blood_two primary malignacies_GECM-061_ 10

tag: 56 years old

tag: breast cancer and intestinal stromal cell


title: blood_two primary malignacies_GECM-061_8

description: blood_two primary malignacies_GECM-061_ 8

tag: 78 years old

tag: breast and colon cancer


title: blood_two primary malignacies_GECM-061_1

description: blood_two primary malignacies_GECM-061_ 1

tag: 66 years old


title: blood_two primary malignacies_GECM-061_9

description: blood_two primary malignacies_GECM-061_ 9

tag: 69 years old

tag: colon and breast cancer


title: blood_two primary malignacies_GECM-061_4

description: blood_two primary malignacies_GECM-061_ 4

tag: 60 years old


title: blood_two primary malignacies_GECM-061_3

description: blood_two primary malignacies_GECM-061_ 3

tag: 46 years old

tag: ovarian and colon cancer


title: Male Untreated/Female Untreated comparison/Replicate #2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The RNA expression profile for a single male liver pool and a single female liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in untreated rat liver gene expression.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: LOWESS normalized expression ratios, Rosetta Resolver pipeline

label: Alexa 647

organism: Rattus norvegicus

source_name: Frozen adult female rat liver tissue prepared using Trizol

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction

tag: Strain

value: Fischer 344

tag: Treatment

value: untreated

tag: Sex

tag: Tissue

value: liver

tag: Age

value: 12 weeks

label: Alexa 555

source_name: Frozen adult male rat liver tissue prepared using Trizol


title: Male Hypox + single GH/Male Hypox comparison/Replicate #2

description: The RNA expression profile for a single liver pool of male Hypox rats treated with a single GH injection and a single male Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight differences in Hypox + single GH injection vs. Hypox rat liver gene expression.

value: Hypophysectomy (‘Hypox’)

value: Hypophysectomy (‘Hypox’) + single GH injection


title: Male Untreated/Female Untreated comparison/Replicate #1


title: Male Hypox + single GH/Male Hypox comparison/Replicate #1

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash.


title: Minimal vs tuber 2 - dye swap

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: Biological tuber replicate 2, technical replicate with dye swap

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed with Agilent Gene Expression Wash Buffers 1 and 2.

scan_protocol: Scanned on an Axon 4200 AL scanner (Axon Instruments) Images were quantified using GenePix Pro 6.0

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Scale was normalized with MAD, separate normalization for stem and tuber samples. R software was used with limma package.

organism: Pectobacterium atrosepticum

source_name: Bacterial cells

label_protocol: 10 µg of total RNA and 2,5 µg random hexamers were incubated in 70°C for 10 min, then reversed transcribed at 37°C for 4 h in the presence of 400 U reverse transcriptase (Promega); 7.5 mM DTT; 1.25 mM dATP/dTTP/dGTP; 0.5 mM dCTP and 2.5 mM Cy3 or Cy5 (GE healthcare).

growth_protocol: Exponential phase, incubation 24h, 15 °C, 150 rpm

extract_protocol: Total RNA extracted using Summers method (Summers, W.C. (1970). A simple method for extraction of RNA of E.coli utilizing DEPC. Anal Biochem 33, 459-463.)

treatment_protocol: Incubation in minimal medium supplemented with tuber extract

tag: strain SCRI1043

treatment_protocol: Incubation in minimal medium


title: Minimal vs tuber 2

description: Biological tuber replicate 2


title: AVGSignalH11_53

status: Public on May 23 2008

city: Baltimore

first: Carlo

last: Colantuoni

state: MD

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

description: Postmortem human brain RNA from BA10 (orbitofrontal cortex)

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
All the data processing was performed using the R statistical language (http://www.r-project.org). Following local background correction upon scanning, microarray data were transformed into the log base 2 scale. Log2 intensities for all genes were converted to log2 ratios relative to the grand mean for each gene across all arrays. These log2 ratios were then normalized to the local mean log2 ratio across expression level within each array using the loess function in R (Colantuoni 2002, PMID: 12424128). The local variance correction described in this reference was not necessary for the Illumina array data presented here. Instead, a global standard deviation calculated across log2 ratios within each array was used to generate the final gene expression Zscores used in this analysis.
As described in associated Platform GPL6893, there exist multiple probes for individual genes on the Illumina array. The gene expression measures reported in the Sample data tables are those reported in PMID: 18470533. These expression measures reflect within gene mean-centered and Z-transformed data averaged from all probes within a specific set of 31 genes, and are adjusted for PMI, brain pH, and RIN using multiple linear regression.

label: biotin-16-UTP (Roche Cat. #1388908)

source_name: Human Brain (BA10)

label_protocol: Standard Illumina protocol

growth_protocol: All human brain specimens were obtained from the DC and Northern VA Medical Examiner's Offices.

extract_protocol: TRIZOL

tag: RNA integrity number (RIN)

tag: age

tag: Gender

tag: Ethnicity

value: African–American

tag: Postmortem interval (h)

tag: Brain pH


title: AVGSignalH10_46

treatment_protocol: All human brain specimens were obtained from the DC and Northern VA Medical Examiner's Offices.


title: Minimal vs tuber 1 - dye swap

description: Biological tuber replicate 1, technical replicate with dye swap


title: Col-0 grown at 22ºC (Cy3) vs. NRG1 grown at 22ºC (cy5)

city: Shanghai

first: Li

last: Qun

state: Shanghai

address: 300 Fenglin Road

department: National Key Laboratory of Plant Molecular Genetics

country: China

institute: Institute of plant physiology & ecology, SIBS, CAS

description: The small RNAs (< 300 nt) were purified, labeled and hybridized by LC Sciences (Houston, TX, USA).

hyb_protocol: Hybridization was performed overnight on a µParafloTM microfluidic chip.

scan_protocol: Array images were obtained using an Axon GenePix 4000B laser scanner and digitized using the Array-Pro image software (Media Cybernetics).

data_processing: Total Data on all six chips were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Col-0 grown at 22ºC, biological replicate 1

label_protocol: Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3ºC-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

tag: 4-week-old whole plants

source_name: Arabidopsis thaliana NRG1 grown at 22ºC, biological replicate 1


title: Minimal vs stem 1

description: Biological stem replicate 1

treatment_protocol: Incubation in minimal medium supplemented with stem extract


title: AVGSignalH09_19

value: Caucasian


title: Minimal vs stem 2

description: Biological stem replicate 2


title: Minimal vs tuber 1

description: Biological tuber replicate 1


title: Col-0 grown at 22ºC (Cy3) vs. NRG1 grown at 30ºC (cy5)

source_name: Arabidopsis thaliana Col-0 grown at 22ºC, biological replicate 3

source_name: Arabidopsis thaliana NRG1 grown at 30ºC, biological replicate 1


title: AVGSignalH08_64


title: Male Hypox/Male Untreated comparison/Replicate #2

description: The RNA expression profile for a single male Hypox liver pool and a single male untreated liver pool is given as a normalized ratio. The purpose of this comparison is to highlight differences in Hypox vs. untreated male rat liver gene expression.


title: NRG1 grown at 22ºC (Cy3) vs. Col-0 grown at 30ºC (cy5)

source_name: Arabidopsis thaliana NRG1 grown at 22ºC, biological replicate 2

source_name: Arabidopsis thaliana Col-0 grown at 30ºC, biological replicate 2


title: genomic V4-L1-F8

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description:
After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.
Filters were stripped by pouring 3X150 ml boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane. The first time, the stripping buffer was immediately changed while after the second and third washes the filters were left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter or re-scanned with the Phosphorimager.

hyb_protocol: Hybridization Solution was: 5XSSC, 5XDenhart’s, 0.5% SDS and 100 µg herring sperm DNA/ml. The hybridization protocol used was as follows. Filters were inserted in 12.5X2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 3X10exp6 dpm/mL of radioactive sample and hybridized for 44h. Washing conditions were: 1h at 65ºC for 20 min in 2XSSC, 0.1% SDS, and twice at 65ºC for 30 min in 0.2XSSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager.

data_processing: Raw image quantization background subtracted

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: W303-1a strain

label_protocol:
Yeast genomic DNA was labeled following a random priming procedure. 800 ng genomic DNA in 45 µl distilled water was denatured for 5 minutes by boiling, added to a microcentrifuge tube of Ready-To-Go DNA labeling beads (Amersham Biosciences) and mixed with 50 µCi [α–33P] dCTP (2500 Ci/mmol).
The mixture was incubated at 37ºC for 1–2 h. In order to eliminate non-incorporated components, Probe Quant G–50 columns (Amersham Biosciences) were used.

extract_protocol:
Genomic DNA was isolated from yeast cells by phenol extraction with glass beads, essentially as described by
Hoffman CS, Winston F (1987) A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for
transformation of Escherichia coli. Gene 57:267–272

tag: V4-L1-F8 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.


title: genomic V4-L1-F10

tag: V4-L1-F10 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.


title: Male Hypox/Male Untreated comparison/Replicate #1


title: Male Hypox + two GH/Male Hypox comparison/Replicate #1

description: The RNA expression profile for a single liver pool of male Hypox rats treated with two GH injections and a single male Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight differences in Hypox + 2 GH injections vs. Hypox rat liver gene expression.

value: Hypophysectomy (‘Hypox’) + two GH injections


title: genomic V4-L1-F9

tag: V4-L1-F9 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.


title: Col-0 grown at 30ºC (Cy3) vs. NRG1 grown at 30ºC (cy5)

source_name: Arabidopsis thaliana Col-0 grown at 30ºC, biological replicate 3

source_name: Arabidopsis thaliana NRG1 grown at 30ºC, biological replicate 3


title: NRG1 grown at 30ºC (Cy3) vs. NRG1 grown at 22ºC (cy5)

source_name: Arabidopsis thaliana NRG1 grown at 30ºC, biological replicate 2

source_name: Arabidopsis thaliana NRG1 grown at 22ºC, biological replicate 3


title: genomic V4-L1-F7

tag: V4-L1-F7 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.


title: Male Hypox/Female Hypox comparison/Replicate #1

description: The RNA expression profile for a single male Hypox liver pool and a single female Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox rat liver gene expression.

tag: Strain


title: Col-0 grown at 30ºC (Cy3) vs. Col-0 grown at 22ºC (cy5)

source_name: Arabidopsis thaliana Col-0 grown at 30ºC, biological replicate 1

source_name: Arabidopsis thaliana Col-0 grown at 22ºC, biological replicate 2


title: Terbutyl stress TR t71 replicate 2

data_processing: Raw image quantization background subtracted.

source_name: W303-1a strain replicate 2 growing in exponential phase

label_protocol:
In vivo labeling by run-on (GRO) using 33P-UTP.
Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were washed in cold water and the cell pellet was resuspended in 900 µl of sterile cold water (final volume 950 µl). Then, the cell suspension was transferred to a fresh micro centrifuge tube, 50 µl of 10% sarkosyl were added and cells were incubated for 20 minutes on ice. After the permeabilization step, cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 120 µl of 2.5x transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µl of AGC mix (10 mM each of CTP, ATP and GTP), 6 µl of DTT (0.1 M) and 13 µl of [α-33P]UTP (3000 Ci/mmol, 10 μCi/µL). Cells were maintained on ice at all times. The final volume was adjusted to 300 µl with distilled water and the mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

extract_protocol:
Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells.
Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics.
Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t71: 71 minutes after adding t-butyl.

tag: In vivo labeled total RNA from W303-1a yeast strain.

value: 71 minutes after adding terbutyl.

tag: Hybridization on macrochip F5.


title: AVGSignalH07_64


title: Female Hypox/Female Untreated comparison/Replicate #1

description: The RNA expression profile for a single female Hypox liver pool and a single female untreated liver pool is given as a normalized ratio. The purpose of this comparison is to highlight differences in Hypox vs. untreated female rat liver gene expression.

source_name: frozen adult female rat liver tissue prepared using Trizol

tag: Treatment

tag: Sex

tag: Tissue


title: Male Hypox/Female Hypox comparison/Replicate #2

source_name: Frozen adult female rat liver tissue prepared using Trizol

tag: Age

source_name: Frozen adult male rat liver tissue prepared using Trizol


title: Female Hypox/Female Untreated comparison/Replicate #2


title: AVGSignalH06_38

source_name: Human Brain (BA10)

tag: RNA integrity number (RIN)

tag: age


title: Male Hypox + two GH/Male Hypox comparison/Replicate #2

description: The RNA expression profile for a single liver pool of male Hypox rats treated with two GH injections and a single male Hypox liver pool is given as a normalized ratio. The purpose of this comparison is to highlight differences in Hypox +2 GH injections vs. Hypox rat liver gene expression.

value: Hypophysectomy (‘Hypox’)  + two GH injections


title: genomic V4-L1-F6

tag: V4-L1-F6 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP


title: AVGSignalH05_44

tag: Gender

tag: Ethnicity

tag: Postmortem interval (h)


title: AVGSignalH03_49

tag: Brain pH


title: AVGSignalH01_34


title: genomic V4-L1-F5

tag: V4-L1-F5 filter hybridization with labeled yeast genomic (W303-1a) DNA. DNA labeling by random priming procedure and 33P-dCTP.


title: Terbutyl stress mRNA t16 replicate 3

source_name: W303-1a strain replicate 3 growing in exponential phase

label_protocol: About 30-40 µg of total RNA were reverse transcribed into cDNA by adding 200 us of RT polymerase SuperScript II and random hexamers (Invitrogen), 1 µL RNaseOUT (Invitrogen), 6 µL 5X First Strand Buffer (Invitrogen), 1.5 µL dNTP mix (16 mM dATP, dTTP, dGTP, and 100 µM dCTP) and 5 µL [α-33P]dCTP (3000 Ci/mmol, 10 µCi/microL) in a final reaction volume of 30 µL. The labeling reaction was incubated for 1 h at 43ºC. 1 µL of EDTA 0.5 M was added to stop the reaction. The labeled cDNAs were purified by a S300-HR MicroSpin column (Amersham BioSciences).

extract_protocol:
Total RNA from yeast cells was prepared as described by
Sherman et al. [1986], but using a multiple-sample automated
device (Fast-Prep, BIO101) to break the cells.
Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics.
Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t16: 16 minutes after adding t-butyl.

tag: Total RNA from W303-1a yeast strain.

value: 16 minutes after adding terbutyl.

tag: Hybridization on macrochip F9.


title: AVGSignalG12_56

value: Hispanic


title: Terbutyl stress mRNA t71 replicate 3

tag: Hybridization on macrochip F6.


title: AVGSignalG11_34


title: Terbutyl stress mRNA t41 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t41: 41 minutes after adding t-butyl.

value: 41 minutes after adding terbutyl.


title: AVGSignalG10_56


title: AVGSignalG06_39

value: female


title: Terbutyl stress mRNA t26 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t26: 26 minutes after adding t-butyl.

value: 26 minutes after adding terbutyl.

tag: Hybridization on macrochip F10.


title: AVGSignalG05_37

value: male


title: AVGSignalG08_51


title: AVGSignalG07_29


title: AVGSignalG04_31


title: Terbutyl stress mRNA t7 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t7: 7 minute after adding t-butyl.

value: 7 minutes after adding terbutyl.

tag: Hybridization on macrochip F8.


title: Terbutyl stress mRNA t26 replicate 2


title: Terbutyl stress mRNA t71 replicate 2

tag: Hybridization on macrochip F5.


title: Terbutyl stress mRNA t0 replicate 3

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t0: before adding t-butyl.

value: before adding terbutyl.

tag: Hybridization on macrochip F7.


title: AVGSignalG02_43


title: Terbutyl stress mRNA t41 replicate 2


title: AVGSignalH04_28


title: AVGSignalG01_28


title: AVGSignalF09_24


title: AVGSignalF11_49


title: AVGSignalF10_53


title: AVGSignalF08_29


title: AVGSignalF06_20


title: Terbutyl stress mRNA t7 replicate 2

treatment_protocol:
Oxidative stress conditions were created by addition of t-butyl hydroperoxide (t-BOOH) at 0.1 mM. Experiments were initiated on exponential cultures that had been grown in such conditions for at least ten generations, at concentrations of 1.5-2 x 10exp7 cells/ml.
t7: 7 minutes after adding t-butyl.


title: Terbutyl stress mRNA t0 replicate 2


title: Terbutyl stress mRNA t0 replicate 1

source_name: W303-1a strain replicate 1 growing in exponential phase


title: Terbutyl stress mRNA t16 replicate 2


title: AVGSignalF07_26


title: Terbutyl stress mRNA t26 replicate 1


title: Terbutyl stress mRNA t41 replicate 1

tag: Hibridization on macrochip F9.


title: AVGSignalF03_38


title: AVGSignalF02_53


title: AVGSignalF05_55


title: Terbutyl stress mRNA t71 replicate 1


title: Terbutyl stress mRNA t7 replicate 1


title: Terbutyl stress mRNA t16 replicate 1


title: AVGSignalF01_21


title: AVGSignalE10_58


title: AVGSignalE09_24


title: C6

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data C6

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: The raw data was filtered to exclude non-annotated transcripts. Data were normalized using VSN method. Differential gene expression analysis was performed using limma.

label: biotin

source_name: Squamous Cervical Carcinoma, positive for HLA class I expression

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


title: C5

description: Gene expression data C5

scan_protocol: Refer to the Illumina Gene Expression System Manual

tag: Squamous Cervical Carcinoma, positive for HLA class I expression


title: A10-2

description: Gene expression data A10-2

source_name: Squamous Cervical Carcinoma, negative for HLA class I expression

label_protocol: Refer to the Illumina Gene Expression System Manual


title: AVGSignalE08_24

tag: RNA integrity number (RIN)


title: C9-2

description: Gene expression data C9-2


title: C4

description: Gene expression data C4


title: C2

description: Gene expression data C2


title: C10

description: Gene expression data C10


title: AVGSignalE07_60

tag: age


title: C3

description: Gene expression data C3


title: C8-2

description: Gene expression data C8-2


title: C8-1

description: Gene expression data C8-1


title: AVGSignalE06_47


title: AVGSignalE11_62


title: AVGSignalE01_36


title: AVGSignalE04_49


title: AVGSignalE05_19


title: AVGSignalE02_27


title: AVGSignalD12_45


title: AVGSignalD10_29


title: B9

description: Gene expression data B9

source_name: Squamous Cervical Carcinoma, partially positive for HLA class I expression


title: AVGSignalD11_53


title: AVGSignalD05_48


title: B11

description: Gene expression data B11

tag: Squamous Cervical Carcinoma, partially positive for HLA class I expression


title: B10

description: Gene expression data B10


title: B6

description: Gene expression data B6


title: AVGSignalD04_64

tag: Gender


title: B7

description: Gene expression data B7


title: AVGSignalD08_18

tag: Ethnicity


title: C9-1

description: Gene expression data C9-1


title: AVGSignalD03_51

tag: Postmortem interval (h)


title: B8-2

description: Gene expression data B8-2


title: C7

description: Gene expression data C7


title: B8-1

description: Gene expression data B8-1


title: B4

description: Gene expression data B4


title: AVGSignalC12_58

value: Asian

tag: Brain pH


title: AVGSignalD01_67


title: AVGSignalC11_49


title: B3

description: Gene expression data B3


title: AVGSignalD07_36


title: AVGSignalD02_59


title: AVGSignalC06_48


title: AVGSignalC05_58


title: B5

description: Gene expression data B5


title: AVGSignalB10_26


title: AVGSignalC07_19


title: AVGSignalB03_56


title: AVGSignalB12_51


title: AVGSignalC02_57


title: B2

description: Gene expression data B2


title: AVGSignalB05_52


title: AVGSignalC10_63


title: A1-2

description: Gene expression data A1-2

tag: Squamous Cervical Carcinoma, negative for HLA class I expression


title: AVGSignalB08_43


title: AVGSignalA11_51


title: AVGSignalB01_24


title: AVGSignalB04_63


title: B1

description: Gene expression data B1


title: AVGSignalA09_52


title: AVGSignalB02_61


title: AVGSignalA03_20


title: AVGSignalA02_50


title: AVGSignalA06_52


title: A10-1

description: Gene expression data A10-1


title: A11

description: Gene expression data A11


title: A8

description: Gene expression data A8


title: AVGSignalA01_26


title: A9

description: Gene expression data A9


title: A7

description: Gene expression data A7


title: A6

description: Gene expression data A6


title: AVGSignalA05_58


title: A4

description: Gene expression data A4


title: A5

description: Gene expression data A5


title: A3

description: Gene expression data A3


title: A2

description: Gene expression data A2


title: Strain S27 Tachyzoite

status: Public on May 22 2008

type: mixed

city: Stanford

first: Jon

last: Boyle

address: 299 Campus Drive

department: Microbiology and Immunology

institute: Stanford University School of Medicine

description: PDS X CEP F1 Progeny clone S27

hyb_protocol: Labeled cDNA was applied to array slides, covered with a coverslip, and hybridized at 68 degrees for 16-20 h.  Slide were washed sequentially in 2X SSC, 1X SSC, and 0.5X SSC for 5 min each.

scan_protocol: Slides were scanned on a GenePix scanner

data_processing: log2 ratios were normalized to a mean of 0 for all slides

organism: Toxoplasma gondii

source_name: Tachyzoites

label_protocol: cDNA was synthesized from mRNA using oligo-dT priming and reverse transcription.  cDNA was then labeled with Cy5-dUTP using klenow (exo minus) and random primers

growth_protocol: Tachyzoites were grown in human foreskin fibroblasts in the presence of 10% serum in DMEM.  Cells were infected at an MOI of 10 tachyzoites per cell and growth was carried out for 24h

extract_protocol: Total RNA was extracted with Trizol using the manufacturers instruction.  mRNA was isolated from total RNA using the oligotex mRNA isolation kit (Qiagen)

tag: 24 h in vitro tachyzoite

molecule: other

organism: synthetic construct

source_name: empty pBluescript vector, in vitro transcribed

label_protocol: The polylinker region of the isolated plasmid was PCR-amplified using T3 and T7 primers. The PCR product was gel-purified using a Qiagen gel purification kit, and used as a template for in vitro transcription. The polylinker was transcribed in the presence of dUTP using the T7 RNA polymerase transcription kit (Maxiscript; Ambion).

growth_protocol: Vector was propagated in DH5alpha cells.

extract_protocol: Plasmid was isolated using Qiagen miniprep kit.

tag: common reference (in vitro transcribed RNA)


title: A1-1

description: Gene expression data A1-1


title: Strain S30 Tachyzoite

description: PDS X CEP F1 Progeny clone S30


title: Strain S25 Tachyzoite

description: PDS X CEP F1 Progeny clone S25


title: P28 Hdac3 null liver biological replicate

city: Nashville

first: Sarah

middle: K

last: Knutson

state: TN

address: 23rd and Pierce Ave

department: Biochemistry

institute: Vanderbilt University

description: Hybridization controls were used per Manufacturer’s instruction (see Hybridization procedures).

hyb_protocol: All hybridization reagents, hybridization controls, wash reagents, and chemiluminescent reagents were provided in the ABI CL Detection Kit, part#4342142, and the manufacturer’s protocol was followed. Briefly, the arrays were equilibrated to room temperature and then pre-hybridized with a 1ml volume for 60’ with agitation (100RPM) at 55C per manufacturer’s protocol. During the pre-hybridization, the DIG-labelled targets were fragmented and then stored on ice until the pre-hyb was completed. Once pre-hyb was completed the targets were mixed with the appropriate reagents, including Hybridization controls, and the 0.5ml target was added to the pre-hybridization through the port on the array chamber. The arrays were immediately returned to the 55C Hybridization oven and agitated exactly 16 hours at 100RPM. The arrays were then washed and incubated with Anti-Dig-APAntibody for 20 minutes. Following antibody washes, the arrays were incubated with Chemiluminescence Enhancing Solution, washed a final time and then stored in the last wash buffer at room temperature. Substrate for the chemiluminescence reaction was added to each array individually and then the array was immediately imaged on the 1700 Chemiluminescent Analyzer.

scan_protocol: Following addition of the chemiluminescence reaction substrate, each array was immediately imaged on the 1700 Chemiluminescent Analyzer. Each imaging was completed in approximately 15 minutes and the images were assessed for QC/QA and a primary analysis was completed by the AB1700 Expression Array System Software (v 1.1.1).

data_processing: As described in the VMSR ABI user manual, the .csv file contains the t-test results on all probes that passed a 'detectability' filter. If a probe is not detected (S/N < 3) in both subgroups, it is not included in the t test. If a probe is not detected in more than 50% of samples in a subgroup, it is not detected in that subgroup. Data was run through the R script ABarray for quantile normalization.  Log transformation was performed on quantile normalized data to generate the number in the VALUE column.

label: DIG

organism: Mus musculus

source_name: Liver, P28

label_protocol: All RNA Preps submitted to the VMSR were run on an Agilent 2100 Bioanalyzer to assess RNA integrity. Those samples meeting minimum requirements of RIN value of 7.0 and greater were used to generate targets for hybridization to ABI arrays. One (1) ug of Total RNA (30ng mRNA) was used to generate First Strand cDNA using the NanoAmp RT-IVT labeling kit according to manufacturer’s protocol (ABI, Cat#4365715). Following first strand synthesis, second strand synthesis was completed. The resulting cDNA was then purified using an ABI kit provided column and the entire reaction was used in an IVT reaction to generate DIG labeled cRNA. The cRNA was then purified using a kit provided column and assessed for quality on an Agilent Bioanalyzer. All reactions meeting ABI criteria in terms of quantity and size of target produced were fragmented and then hybridized to the appropriate array for 16 hours with agitation at 55C.

extract_protocol: Tissue was kept in RNAlater overnight at 4 degrees, and homogenized in lysis buffer containing TCEP. Protcol from PerfectPure RNA Fibrous Tissue Kit (Mat # 2900304), was followed exactly, including DNase step, and RNA eluted in 40-60 microliters of nuclease free water, and stored at -80 degrees.

tag: C57B/6 strain, Age

value: 28 days, Tissue:Liver, Pooled RNA from Hdac3-null livers of 5 mice


title: Strain CL15 Tachyzoite

description: PDS X CEP F1 Progeny clone CL15


title: P28 Hdac3 control liver technical replicate 1

value: 28 days, Tissue:Liver, Pooled RNA from 5 Hdac3 wild-type mice expressing Albumin-Cre


title: P28 Hdac3 control liver biological replicate

value: 28 days, Tissue:Liver, Pooled RNA from 5 Hdac3 wild-type or heterozygous mice expressing Albumin-Cre


title: P28 Hdac3 null liver technical replicate 1


title: Strain S26 Tachyzoite

description: PDS X CEP F1 Progeny clone S26


title: Strain S28 Tachyzoite

description: PDS X CEP F1 Progeny clone S28


title: P28 Hdac3 null liver technical replicate 2

value: 28 days, Tissue:Liver, Pooled RNA from Hdac3-null livers of 5 mice; same sample used for P28 Hdac3 null liver technical replicate 1 analysis, but run on a separate lot of microarray chips


title: Strain S21 Tachyzoite

description: PDS X CEP F1 Progeny clone S21


title: P28 Hdac3 control liver technical replicate 2

value: 28 days, Tissue:Liver, Pooled RNA from 5 Hdac3 wild-type mice expressing Albumin-Cre, exact same sample used for P28 Hdac3 control liver technical replicate 1, but run on a different lot of microarray chips


title: P17 Hdac3 null liver technical replicate 1

source_name: Liver, P17

value: 17 days, Tissue:Liver, Pooled RNA from Hdac3-null livers of 5 mice


title: P17 Hdac3 control liver technical replicate 2

value: 17 days, Tissue:Liver, Pooled RNA from 5 Hdac3 wild-type mice expressing Albumin-Cre.  Exact same sample as in P17 Hdac3 control liver technical replicate 1, but analyzed using a separate lot of microarray chips.


title: D.mel_Adapted_18th Generation_12-10

city: La Jolla

first: Dan

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

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

description:
Reference:
Zhou D, et al. Experimental selection for Drosophila survival in extremely low O2 environment. PLoS ONE. 2007 May 30;2:e490.

organism: Drosophila melanogaster

source_name: Adapted

tag: Strain

value: Drosophila melanogaster.

tag: Developmental Stage

value: adult.

tag: Tissue

value: Whole Organism.

source_name: Reference

value: Whole Organism of pooled parental lines.


title: Strain S29 Tachyzoite

description: PDS X CEP F1 Progeny clone S29


title: P17 Hdac3 control liver biological replicate

tag: C57B/6 strain

tag: Liver tissue from postnatal day 17 mice

tag: Pooled RNA sample from 5 Hdac3 wild-type or heterozygous mice, expressing Albumin-Cre


title: D.mel_Adapted_18th Generation_12-6

hyb_protocol: Zhou D, et al. Experimental selection for Drosophila survival in extremely low O2 environment. PLoS ONE. 2007 May 30;2:e490.


title: P17 Hdac3 control liver technical replicate 1

value: 17 days, Tissue:Liver, Pooled RNA from 5 Hdac3 wild-type mice expressing Albumin-Cre


title: P17 Hdac3 null liver technical replicate 2

value: 17 days, Tissue:Liver, Pooled RNA from Hdac3-null livers of 5 mice; exact same sample as in P17 Hdac3 null liver technical replicate 1, but run on a separate lot of microarray chips


title: Strain CL19 Tachyzoite

description: PDS X CEP F1 Progeny clone CL19


title: D.mel_Adapted_18th Generation_12-9

scan_protocol: Zhou D, et al. Experimental selection for Drosophila survival in extremely low O2 environment. PLoS ONE. 2007 May 30;2:e490.


title: P17 Hdac3 null liver biological replicate


title: wild-type+0mg/kg PFOA, rep4

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

state: NC

department: Reproductive Toxicology

institute: U.S. EPA

description: Adult liver gene expression data from wild-type or PPARa-null mice exposed to either PFOA or Wy14,643

hyb_protocol: Hybridization of target cRNA, labeling controls, and hybridization controls was conducted at 55 C for 16 hrs in a dry shaking incubator using a vendor provided protocol and reagents (Chemiluminescence Detection Kit, Part #4342142, Applied Biosystems)

scan_protocol: Microarray images were obtained using an Applied Biosystems 1700 Chemiluminescent Microarray Analyzer and Expression Array System Software version 1.1.1.

data_processing: Data were quantile-normalized and log2 transformed using package ab1700 in Bioconductor

label: Digoxigenin-UTP

source_name: Male adult liver, 129SV background

label_protocol: Digoxigenin labeled cRNA was synthesized from 500 ng total RNA using a protocol and labeling kit obtained from the microarray manufacturer which included one round of T7 amplification (Nanoamp RT-IVT labeling kit, Part #4365715, Applied Biosystems).

extract_protocol: Collected tissue was immediately homogenized in TRI reagent and processed on the same day through alcohol precipitation according to the manufacturer's directions. RNA pellets were then washed in cold 80% ethanol and stored at -80 C until further use.  Following resuspension in nuclease-free water, the RNA was quantified and evaluated for purity (260nm/280nm ratio) using a NanoDrop ND-1000 spectrophotometer. 100 ug of each sample was then further purified using RNeasy spin columns according to the manufacturer's directions. Approximately 250 ng of each sample was evaluated for quality using an Agilent 2100 Bioanalyzer.  RNA samples were used only if they were found to have an RNA Integrity Number of at least 8.5.

treatment_protocol: Adult male mice were dosed by gavage for 7 consecutive days with either 0, 1, or 3 mg/kg  PFOA (ammonium salt) in deionized water; or,  0 or 50 mg/kg Wy14,643 in 0.5% methylcellulose.

tag: Samples were collected 24 hrs after the final compound dose.


title: D.mel_Adpated_18th Generation_12-5

label_protocol: Zhou D, et al. Experimental selection for Drosophila survival in extremely low O2 environment. PLoS ONE. 2007 May 30;2:e490.


title: D.mel_Adapted_18th Generation_12-2

extract_protocol: Zhou D, et al. Experimental selection for Drosophila survival in extremely low O2 environment. PLoS ONE. 2007 May 30;2:e490.


title: Strain CL16 Tachyzoite

description: PDS X CEP F1 Progeny clone CL16


title: PPARa-null+3mg/kg PFOA, rep4


title: wild-type+1mg/kg PFOA, rep4


title: Strain CL13 Tachyzoite

description: PDS X CEP F1 Progeny clone CL13


title: Strain CL12 Tachyzoite

description: PDS X CEP F1 Progeny clone CL12


title: Strain CL18 Tachyzoite

description: PDS X CEP F1 Progeny clone CL18


title: wild-type+3mg/kg PFOA, rep4


title: Strain CL11 Tachyzoite

description: PDS X CEP F1 Progeny clone CL11


title: D.mel_Adapted_18th Generation_12-1


title: PPARa-null+0mg/kg PFOA, rep3


title: D.mel_Control_18th Generation_12-9

source_name: Control


title: PPARa-null+0.5% methylcellulose, rep4


title: PPARa-null+0mg/kg PFOA, rep4


title: wild-type+0mg/kg PFOA, rep3


title: D. Melanogaster_control_18th generation_12-1

source_name: 18th generation Control

value: Drosophila melanogaster

value: adult

value: Whole Organism

value: Whole Organism of Parental Lines


title: Strain CL17 Tachyzoite

description: PDS X CEP F1 Progeny clone CL17


title: Strain S1T Tachyzoite

description: PDS X CEP F1 Progeny clone S1T


title: Strain S2T Tachyzoite

description: PDS X CEP F1 Progeny clone S2T


title: D.mel_Control_18th Generation_12-7


title: wild-type+50mg/kg Wy14,643, rep4


title: D.mel_Control_18th Generation_12-11


title: wild-type+50mg/kg Wy14,643, rep3


title: PPARa-null+50mg/kg Wy14,643, rep4


title: D.mel_Control_18th Generation_12-3


title: D.mel_Control_18th Generation_12-5


title: PPARa-null+50mg/kg Wy14,643, rep3


title: wild-type+1mg/kg PFOA, rep3


title: PPARa-null+0.5% methylcellulose, rep3


title: wild-type+3mg/kg PFOA, rep3


title: PPARa-null+0mg/kg PFOA, rep2


title: PPARa-null+1mg/kg PFOA, rep4


title: PPARa-null+3mg/kg PFOA, rep3


title: GFs+OHT rep 3

city: Oxford

first: Peter

last: Dudek

state: Oxfordshire

address: South Parks Road

country: United Kingdom

institute: University of Oxford

description: GF (IGF+EGF) + tamoxifen treated replicate 3

hyb_protocol: cDNA slides were placed into hybridization chambers (TeleChem International, SunnyVale, CA), and 10 ul of 3X SSC buffer was added to each groove in the chamber for humidifying. The mixed probes were heated for 1min at 95C, then spun in a microcentrifuge at max speed for 1min. The entire volume of the probe was pipetted onto the slide and covered with a cover slip. The chamber was then tightly sealed and immersed for 18 hours in a 64C bath. After this, the slides were removed from the chambers and washed for 2x5min in 2X SSC + 0.1% SDS buffer, followed by 2x1min in 0.2X SSC buffer, followed by 1min in 0.1X SSC buffer, followed by 5 min in 0.1X SSC + 0.1% TritonX-100. Slides were subsequently dried by centrifugation at 800 rf for 2min, and immediately scanned.

scan_protocol: Slides were scanned using an Agilent G2565B DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: LOWESS normalized, from log2 of processed Cy5/Cy3 using Genespring software.

source_name: MCF7.SH cells, GF+OHT treatment, 4 hours

label_protocol: 50 µg of RNA from each sample was used for each probe. mRNA was first amplified using the MessageAmp™ II aRNA amplification kit(Ambion). Labelled cDNA was subsequently prepared with the RT Superscript kit (Invitrogen), using 2 µg oligo-dT primers (Amersham Biosciences) and the following nucleotide concentrations: 0.5 mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.2 mM dCTP supplemented with 0.1 mM Cy5-dCTP (Amersham Biosciences) except for the control sample, which was supplemented with 0.1 mM Cy3-dCTP (Amersham Biosciences). After RT, RNA was hydrolyzed with 25mM EDTA and 1M NaOH for 10min at 65°C. The alkaline samples were then neutralized and buffered with 1M HCl and 1M Tris [pH 6.8]. The labelled probes were purified using a Qiagen MiniElute kit (Qiagen, Valencia, CA). To create the final probe mixture for hybridization, each Cy3-labelled treatment sample probe was mixed with an equimolar amount of the Cy5-labelled control sample probe and then concentrated to a volume of 19.4ul using a Microcon YM-30 kit (Millipore) and subsequently mixed with a SSC buffer containing 0.4% SDS to a final volume of 24ul.

growth_protocol: Cells were grown in phenol red-free Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (v/v) charcoal-treated fetal calf serum (FCS), 1 mM sodium pyruvate, 2 mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin.

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

treatment_protocol: Cells were treated for 4 hours with 50 μg/ml EGF and 50 μg/ml IGF-I  + 100 nM 4-hydroxytamoxifen (OHT). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.

tag: Cell line

source_name: Control replicate 3, total RNA from vehical treated MCF7.SH cells


title: Strain S22 Tachyzoite_2

description: PDS X CEP F1 Progeny clone S22 biological replicate 2


title: GFs+OHT rep 2

description: GF (IGF+EGF) + tamoxifen treated replicate 2

source_name: Control replicate 2, total RNA from vehical treated MCF7.SH cells


title: GFs+OHT rep 1

description: GF (IGF+EGF) + tamoxifen treated replicate 1

source_name: Control replicate 1, total RNA from vehical treated MCF7.SH cells


title: Strain S22 Tachyzoite_1

description: PDS X CEP F1 Progeny clone S22 biological replicate 1


title: wild-type+ 0.5% methylcellulose, rep3


title: Strain CL15 Tachyzoite

description: PDS X CTG F1 Progeny clone CL15


title: PPARa-null+1mg/kg PFOA, rep3


title: PPARa-null+50mg/kg Wy14,643, rep2


title: wild-type+1mg/kg PFOA, rep2


title: Strain S28 Tachyzoite

description: PDS X CTG F1 Progeny clone S28


title: GFs+ICI rep 3

description: GF (IGF+EGF) + ICI treated replicate 3

source_name: MCF7.SH cells, GF+ICI treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 50 μg/ml EGF and 50 μg/ml IGF-I  + 100 nM ICI182,780 (ICI). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: Strain S30 Tachyzoite

description: PDS X CTG F1 Progeny clone S30


title: Strain S23 Tachyzoite_2

description: PDS X CEP F1 Progeny clone S23 biological replicate 2


title: Strain S25 Tachyzoite

description: PDS X CTG F1 Progeny clone S25


title: GFs+ICI rep 2

description: GF (IGF+EGF) + ICI treated replicate 2


title: Strain S23 Tachyzoite_3

description: PDS X CEP F1 Progeny clone S23 biological replicate 3


title: Strain S27 Tachyzoite

description: PDS X CTG F1 Progeny clone S27


title: Strain S23 Tachyzoite

description: PDS X CTG F1 Progeny clone S23


title: GFs rep 2

description: GF (IGF+EGF) treated replicate 2

source_name: MCF7.SH cells, GF treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 50 μg/ml EGF and 50 μg/ml IGF-I. 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: GFs rep 3

description: GF (IGF+EGF) treated replicate 3


title: Strain S23 Tachyzoite_1

description: PDS X CEP F1 Progeny clone S23 biological replicate 1


title: GFs+ICI rep 1

description: GF (IGF+EGF) + ICI treated replicate 1


title: Strain CTG Tachyzoite_3

description: CTG biological replicate 3


title: Strain S22 Tachyzoite

description: PDS X CTG F1 Progeny clone S22


title: PPARa-null+0.5% methylcellulose, rep2


title: Strain CTG Tachyzoite_2

description: CTG biological replicate 2


title: Strain S23 Tachyzoite_4

description: PDS X CEP F1 Progeny clone S23 biological replicate 4


title: wild-type+0mg/kg PFOA, rep2


title: Strain CTG Tachyzoite_1

description: CTG biological replicate 1


title: wild-type+ 0.5% methylcellulose, rep2


title: wild-type+3mg/kg PFOA, rep2


title: Strain S21 Tachyzoite

description: PDS X CTG F1 Progeny clone S21


title: cAMP+OHT rep 3

description: cAMP+tamoxifen treated replicate 3

source_name: MCF7.SH cells, cAMP+OHT treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 1mM 8-Br-cAMP (cAMP) + 100 nM 4-hydroxytamoxifen (OHT). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: GFs rep 1

description: GF (IGF+EGF) treated replicate 1


title: Strain PDS Tachyzoite_2

description: PDS biological replicate 2


title: wild-type+50mg/kg Wy14,643, rep2


title: PPARa-null+50mg/kg Wy14,643, rep1


title: PPARa-null+3mg/kg PFOA, rep2


title: PPARa-null+1mg/kg PFOA, rep2


title: Strain S29 Tachyzoite

description: PDS X CTG F1 Progeny clone S29


title: Strain CL19 Tachyzoite

description: PDS X CTG F1 Progeny clone CL19


title: Strain CL16 Tachyzoite

description: PDS X CTG F1 Progeny clone CL16


title: cAMP+OHT rep 2

description: cAMP+tamoxifen treated replicate 2


title: Strain CL13 Tachyzoite

description: PDS X CTG F1 Progeny clone CL13


title: cAMP+ICI rep 3

description: cAMP+ICI treated replicate 3

source_name: MCF7.SH cells, cAMP+ICI treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 1mM 8-Br-cAMP (cAMP) + 100 nM ICI182,780 (ICI). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: cAMP+OHT rep 1

description: cAMP+tamoxifen treated replicate 1


title: Strain CL11 Tachyzoite

description: PDS X CTG F1 Progeny clone CL11

source_name: Tachyzoites


title: Strain CL12 Tachyzoite

description: PDS X CTG F1 Progeny clone CL12

source_name: empty pBluescript vector, in vitro transcribed


title: cAMP+ICI rep 1

description: cAMP+ICI treated replicate 1


title: Strain PDS Tachyzoite_1

description: PDS biological replicate 1


title: cAMP rep 3

description: cAMP treated replicate 3

source_name: MCF7.SH cells, cAMP treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 1mM 8-Br-cAMP (cAMP). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: Strain CL18 Tachyzoite

description: PDS X CTG F1 Progeny clone CL18


title: PPARa-null+0.5% methylcellulose, rep1


title: cAMP rep 2

description: cAMP treated replicate 2


title: wild-type+0mg/kg PFOA, rep1


title: Sca-1_High_6d

first: Hannah

middle: H.

last: Chang

address: 1 Blackfan Circle

department: Vascular Biology

institute: Childrens Hospital Boston, Harvard Medical School

description: For complete protocol, see www.illumina.com

hyb_protocol: 1.5 ug of cRNA was hybirdized using the Whole-Genome Gene Expression Direct Hibridization Assay to Mouse -6 v1.1 micro-bead chips according to manufecturere's instructions (Illumina)

scan_protocol: Micro-bead ships were scanned with the Illumina BeadArray scanner

data_processing: Rank-invariant normalization was performed with BeadStudio 3.0 software provided by the manufecturer (Illumina)

source_name: EML cell line

label_protocol: 10-100 ng of total RNA were amplified into cRNA using the Ilumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: 8-20 millions cells were used to extract total RNA using the Rneasy Mini RNA isolation kit from Qiagen.

treatment_protocol: Untreated

tag: Highest 15% Sca-1 fraction


title: cAMP+ICI rep 2

description: cAMP+ICI treated replicate 2


title: Non_sorted

tag: Unsorted


title: D7_Epo

treatment_protocol: Treated with Erythropoietin for 7 days


title: wild-type+3mg/kg PFOA, rep1


title: PPARa-null+0mg/kg PFOA, rep1


title: Sca-1_Mid_6d

tag: Middle 15% Sca-1 fraction


title: Strain CL17 Tachyzoite

description: PDS X CTG F1 Progeny clone CL17


title: wild-type+ 0.5% methylcellulose, rep1


title: OHT rep 3

description: tamoxifen treated replicate 3

source_name: MCF7.SH cells, OHT treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 100 nM 4-hydroxytamoxifen (OHT). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: cAMP rep 1

description: cAMP treated replicate 1


title: Sca-1_Low_6d

tag: Lowest 15% Sca-1 fraction


title: wild-type+50mg/kg Wy14,643, rep1


title: Strain S2T Tachyzoite

description: PDS X CTG F1 Progeny clone S2T


title: PPARa-null+1mg/kg PFOA, rep1


title: OHT rep 2

description: tamoxifen treated replicate 2


title: Strain S1T Tachyzoite

description: PDS X CTG F1 Progeny clone S1T


title: OHT rep 1

description: tamoxifen treated replicate 1


title: Sca-1_High_0d


title: PCA_wt_omcF_BR2A

city: Amherst

first: Derek

last: Lovley

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV north room 202

department: Microbiology

institute: University of Massachusetts Amherst

description: total RNA was directly labeled with the Micromax ASA labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work.  Background signal was calculated from a set of negative control spots incorporated into the array.  As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest.  To avoid this issue the negative control spots were ranked according to their total intensity.  The average of the lowest 30% was calculated.  Background signal was calculated as this mean + 2 standard deviations.  The background signal was then subtracted from the total intensity for each spot.  Probes whose signal was not greater than zero after background subtraction were omitted from further analysis.  For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3)  LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes.  Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001.  Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1.	Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2.	Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3.	Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: OmcF-deficient mutant grown on fumarate

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: Ambion RiboPure-Bacteria

tag: Geobacter sulfurreducens was grown anaerobically in steady-state chemostats with fumarate as the terminal electron acceptor and acetate as the electron donor.

source_name: wildtype grown on fumarate

extract_protocol: Ambion Ribopure-Bacteria kit


title: ICI rep 3

description: ICI treated replicate 3

source_name: MCF7.SH cells, ICI treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 100 nM ICI182,780 (ICI). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: wild-type+1mg/kg PFOA, rep1

source_name: Male adult liver, 129SV background


title: PPARa-null+3mg/kg PFOA, rep1


title: Sca-1_Mid_0d


title: Sca-1_Low_0d


title: Sca-1_High_0d_a


title: Sca-1_Mid_0d_a


title: Sca-1_Low_0d_a


title: ICI rep 2

description: ICI treated replicate 2


title: PCA_wt_omcF_BR3B

description: total RNA was directly labeled with the Micromax ASAP labeling kit, using 10 ug total RNA for each sample.

label_protocol: MicroMax ASAP direct RNA labeling protocol

extract_protocol: Ambion RiboPure-Bacteria Kit

label_protocol: Micromax ASAP direct DNA labeling protocol

extract_protocol: Ambion Ribopure-Bacteria Kit


title: Strain PDS Tachyzoite_1

description: PDS biological replicate 1


title: Strain PDS Tachyzoite_3

description: PDS biological replicate 3


title: Strain PDS Tachyzoite_2

description: PDS biological replicate 2


title: ICI rep 1

description: ICI treated replicate 1


title: Strain CTG Tachyzoite_3

description: CTG biological replicate 3


title: Strain CTG Tachyzoite_2

description: CTG biological replicate 2


title: E2 rep 3

description: Estrogen treated replicate 3

source_name: MCF7.SH cells, E2 treatment, 4 hours

treatment_protocol: Cells were treated for 4 hours with 100 nM 17β-estradiol (E2). 24 hours prior to treatment, cells were starved of serum. 30 min prior to induction, 50 µg/ml cycloheximide was added to all cultures.


title: E2 rep 1

description: Estrogen treated replicate 1


title: PCA_wt_omcF_BR3A


title: E2 rep 2

description: Estrogen treated replicate 2


title: Strain CTG Tachyzoite_1

description: CTG biological replicate 1


title: PCA_wt_omcF_BR1B


title: PCA_wt_omcF_BR2B


title: SF539 Poly 7gy6h_2

status: Public on May 21 2008

type: other

city: Gaithersburg

first: Shuping

last: Zhao

address: 8717 Grovemont Circle

department: Radiation Oncology Branch

institute: NCI

description: Tumor cell lines had a biological replicate, and each replicate was run on duplicate slides.

scan_protocol: Hybridized arrays were scanned with 10-Am resolution on a GenePix 4000A scanner (Axon Instruments, Inc., Foster City, CA) at wavelengths 635 and 532 nm for Cy5- and Cy3-labeled probes, respectively. The resulting TIFF images were analyzed by GenePix Pro 4.0 software (Axon Instruments).

data_processing: The ratios of the sample intensity to the reference [green (Cy3)/red (Cy5)] intensity for all targets were determined, and ratio normalization was done to normalize the center of ratio distribution to 1.0.

source_name: tumor cell line SF539; polysomal RNA; irradiated

label_protocol: Amplified RNA (1.5-3.0 Ag) was labeled with Cy3-dUTP (experimental RNA) or Cy5-dUTP (Stratagene Universal Reference, La Jolla, CA) using Superscript II Reverse Transcriptase (Invitrogen, Carlsbad, CA). Each cDNA microarray chip contained 7680 human cDNA clones (National Cancer Institute ROSP 8K Human Array), and methods for microarray hybridization and washing were described previously (Chuang YY, Chen Y, Gadisetti, et al. Gene expression after treatment with hydrogen peroxide, menadione, or t –butyl hydroperoxide in breast cancer cells. Cancer Res 2002;62:6246–54.16).

growth_protocol: SF539 cells were grown in RPMI 1640 containing glutamate (5 mmol/L) and 10% fetal bovine serum(FBS)

extract_protocol: Polysomes were isolated using sucrose-gradient fractionation basically as described by Galban et al. Cells were grown to 80% confluence in 150-mm2 tissue culture dishes and incubated in 100 Ag of cycloheximide/mL for 15 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1 mL of polysome buffer [10 mmol/L Tris-HCl (pH 8), 140 mmol/L NaCl, 1.5 mmol/L MgCl2, 0.5% NP40, 10 mmol/L DTT, 100 Ag/mL cycloheximide, 500 Ag/mL heparin, 1 mmol/L phenylmethanesulfonyl fluoride, and 500 units/mL RNasin (Promega, Madison, WI)]. After 10 minutes on ice, lysates were centrifuged (10,000 _ g for 10 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 _ g for 3 hours at 4C and 1-mL fractions collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIZOL and used for Northern analysis, or fractions 5 to 11 (corresponding to polysome-bound RNA) were pooled and subjected to microarray analysis.

treatment_protocol:
Treatment:
Monolayer cultures were irradiated using a Pantak X-ray source at a dose rate of 1.55 Gy/min.

tag: Polysome RNA from irradiated Human Brain Tumor Cell line SF539

source_name: Human Reference RNA

growth_protocol: reference to the manufacturer

extract_protocol:
PROTOCOL
Universal Human Reference RNA is provided in a solution of 70% ethanol and 0.1 M sodium acetate. Prepare the Reference RNA for
use as follows:
1. Centrifuge the tube at 12,000 × g for 15 minutes at 4°C.
2. Carefully remove the supernatant.
3. Wash the pellet in 70% ethanol.
4. Centrifuge the tube at 12,000 × g for 15 minutes at 4°C.
5. Carefully remove the supernatant and air-dry the pellet at room temperature for 30 minutes to remove retained ethanol.
6. Resuspend the pellet in RNase-free water to the desired concentration.

treatment_protocol: no treatment

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines. The reference RNA is designed to

tag: be used as a reference for microarray gene-profiling experiments.


title: SF539 Total 7gy6h_1

hyb_protocol: methods for microarray hybridization and washing were described previously (Chuang YY, Chen Y, Gadisetti, et al. Gene expression after treatment with hydrogen peroxide, menadione, or t –butyl hydroperoxide in breast cancer cells. Cancer Res 2002;62:6246–54.16).

source_name: tumor cell line SF539; total RNA; irradiated

extract_protocol: Cells were scraped from tissue culture flasks, and total RNA was extracted from each sample using TRIZOL reagent (Invitrogen, Carlsbad, CA) passed through an RNeasy spin column (Qiagen, Valencia, CA) and then amplified using RiboAmp RNA kits (Arcturus, Mountain View, CA) according to manufacturer’s protocol.

tag: irradiated Human Brain Tumor Cell line SF539


title: Mll5 KO LSK Rep1

city: San Francisco

first: Yan

last: Zhang

address: 513 Parnassus Ave, HSE1001B

institute: University of California, San Francisco

description: Bone marrow cells were pooled from eight week-old Mll5-/- mice and sex-matched wild-type littermates (pools of six mice; two pools per genotype).

hyb_protocol: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent)

data_processing: raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent,)

source_name: MII5 KO deficient mouse

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)

extract_protocol: Total RNA was extracted form FACS sorted mouse bone marrow LSK (Lin-, Sca-1+, C-Kit+) cells by RNeasy Mini kit  (Qiangen)

tag: Lin−ScaI+c-Kit+ (LSK) cells from Mll5-/- mice


title: SF539 Poly 7gy6h_1

tag: Polysome RNA from Human Brain Tumor Cell Line SF539 as control


title: SF539 Poly Control_1

source_name: tumor cell line SF539; polysomal RNA; untreated

treatment_protocol: No treatment as control grown in the same condition as irradiated SF539 cells


title: SF539 Total Control_1

source_name: tumor cell line SF539; total RNA; untreated

treatment_protocol: no treatment as control grown in the same condition as irradiated SF126 cells

tag: Human Brain Tumor Cell line SF539 as control


title: SF539 Total 7gy6h_2


title: WT LSK Rep2

source_name: wild type mouse

tag: Lin−ScaI+c-Kit+ (LSK) cells from wild type mouse


title: SF126 Poly 7gy6h_1

source_name: tumor cell line SF126; polysomal RNA; irradiated

growth_protocol: SF126 cells were grown in RPMI 1640 containing glutamate (5 mmol/L) and 10% fetal bovine serum(FBS)

tag: Polysome RNA from irradiated SF126 cells


title: SF539 Poly Control_2


title: Mll5 KO LSK Rep2


title: WT LSK Rep1


title: SF539 Total Control_2


title: A549 vs. WI38VA13 (LC-sense DNA Chip)

city: Gyeongju-si

first: Kyung-Oh

last: Doh

state: Gyeongsangbuk-do

address: 707 Seokjang-dong

department: Physiology

country: South Korea

institute: Dongguk University

description: Spotted by Takara Korea (Seoul, Korea)

hyb_protocol: Hybridization was conducted at 66 degrees C for 16 hours in a humidified chamber. After hybridization, the slides were washed once each in 2xSSC/0.2% SDS for 5 minutes at 55 degrees C, 2xSSC/0.2% SDS for 5 minutes at 65 degrees C, 2xSSC for 5 minutes at room temperature, and 0.05xSSC for 5 minutes at room temperature, then spin-dried in a centrifuge prior to image scanning.

scan_protocol: The slides were scanned by an Affymetrix 428 Array Scanner (Affymetrix).

data_processing: global normalization

source_name: WI38VA13 labeded with cy3

label_protocol: Total RNA sample (30 ug) from WI38VA13 cells was reverse-transcribed with oligo-dT primers in the presence of Cy3-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.

extract_protocol: Total RNA preparation was conducted with Welprep RNA isolation reagent (Welgene), in accordance with the protocol recommended by the manufacturer. The quality of purified RNA was verified from the OD 260/280 ratios and via electrophoresis using agarose gels stained with ethidium bromide.

tag: lung fibroblast cell line

source_name: A549 labeled with cy5

label_protocol: Total RNA sample (30 ug) from A549 cells was reverse-transcribed with oligo-dT primers in the presence of Cy5-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.

tag: lung cancer celline


title: SF126 Poly Control_2

source_name: tumor cell line SF126; polysomal RNA; untreated

treatment_protocol: No treatment as control grown in the same condition as irradiated SF126 cells


title: SF126 Total Control_2

source_name: tumor cell line SF126; total RNA; untreated

tag: Human Brain Tumor Cell line SF126 as control


title: SF126 Poly Control_1

tag: Polysome RNA from Human Brain Tumor Cell Line SF126 as control


title: U87 Poly 7gy6h_2

source_name: tumor cell line U87; polysomal RNA; irradiated

growth_protocol: U87 cells were grown in DMEM containing glutamate (5 mmol/L) and 10% fetal bovine serum(FBS)

tag: Polysome RNA from irradiated U87 cells


title: SF126 Total 7gy6h_1

source_name: tumor cell line SF126; total RNA; irradiated

tag: irradiated Human Brain Tumor Cell line SF126


title: SF126 Total 7gy6h_2


title: SF126 Poly 7gy6h_2


title: U87 Poly 7gy6h_1


title: SF126 Total Control_1


title: WI38VA13 vs. A549 (LC-sense 5K dyeswap)

description: Spotted by Genocheck (Ansan, Korea)

scan_protocol: The slides were scanned by GenePix 4000B (Molecular Devices).

data_processing: Intensity dependent(loess) normalization applied

source_name: A549 labeded with cy3

label_protocol: Total RNA sample (30 ug) from A549 cells was reverse-transcribed with oligo-dT primers in the presence of Cy3-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.

source_name: WI38VA13 labeded with cy5

label_protocol: Total RNA sample (30 ug) fromWI38VA13 cells was reverse-transcribed with oligo-dT primers in the presence of Cy5-dUTP. The labeled cDNA was then purified using a microcon-30 column. The cDNAs from the two samples were combined and precipitated with ethanol; the pellets were resuspended in a hybridization buffer.


title: A549 vs. WI38VA13 (takara chip)

description: purchased from Takara Bio (Kyoto, Japan)