title: Decidua P0, biological rep2 (Series 2)

source_name: Mouse decidual tissue at postnatal day 0, biological replicate 2


title: Decidua e8.5, biological rep1, technical rep1 (Series 2)

status: Public on Apr 23 2008

type: RNA

city: Stanford

first: Kirstin

last: Knox

state: CA

address: 300 Pasteur Dr.

department: Genetics

country: USA

institute: Stanford Univeristy

description: Gene expression data from maternal decidua at e8.5

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: In order to control for differences in overall strength of hybridization, all arrays were normalized to the same median intensity using the dCHIP invariant set method.  Modeling was performed using the dCHIP Perfect Match (PM) modeling algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 1, technical replicate 1

label_protocol: For each sample, labeled cRNA was prepared from 10 ug of starting RNA according to Affymetrix  protocols. Briefly, RNA was reverse transcribed and the resulting double stranded cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  The cDNA was used as a template for a biotin labeling in vitro transcription.  The resulting cRNA was purified using an Rneasy column, quantified, then fragmented using KOAc RNA fragmentation buffer.

growth_protocol: For all dissected samples, a minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage. The one exception is e8.5: for this experiment (Series 2) only one of the placenta_e8.5 sample is used (see extract protocol below).  For the two undissected samples, a single C57BL/6 female was sacrificed at e17.0 and two individual, undissected placentas were collected to generate two replicates.  In all cases, fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.

extract_protocol: Each sample was homogenized in Trizol with a rotor homogenizer.  RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated.  Note: Due to limited tissue availability, two of the full timecourse e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) included in Series 1 were homogenized in Ambion lysis buffer rather than Trizol and were purified with Ambion Rnaqueous rather than Quiagen Rneasy, so are not included in the Series 2 experiment.

treatment_protocol: For dissected samples, placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells.  Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation.  Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging.  For undissected samples, single undissected e17.0 placentas were flash frozen and stored at –80°  C until RNA isolation.

tag: Strain

value: Swiss Webster

tag: Tissue

value: decidua (maternal origin)


title: Decidua e10.5, biological rep1 (Series 2)

description: Gene expression data from maternal decidua at e10.5

source_name: Mouse decidual tissue at embryonic day 10.5, biological replicate 1


title: Placenta P0, biological rep2 (Series 2)

description: Gene expression data from fetal placenta at P0

source_name: Mouse placental tissue at postnatal day 0, biological replicate 2

value: placenta (fetal origin)


title: Decidua e8.5, biological rep2, technical rep1 (Series 2)

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 2, technical replicate 1


title: Placenta e19.0, biological rep2 (Series 2)

description: Gene expression data from fetal placenta at e19.0

source_name: Mouse placental tissue at embryonic day 19.0, biological replicate 2


title: Placenta P0, biological rep1 (Series 2)

source_name: Mouse placental tissue at postnatal day 0, biological replicate 1


title: Placenta e19.0, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 19.0, biological replicate 1


title: Placenta e17.0, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e17.0

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 3


title: Placenta e17.0, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 2


title: Placenta e15.0, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e15.0

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 3


title: Decidua e10.5, biological rep2 (Series 2)

source_name: Mouse decidual tissue at embryonic day 10.5, biological replicate 2


title: NA12155_CN2

status: Public on Apr 24 2008

type: genomic

city: Santa Clara

first: Fan

last: Shen

address: 3420 Central Expressway

institute: Affymetrix, Inc

description: Hapmap sample NA12155 was hybridized to Nsp CN arrays

hyb_protocol: The DNA samples are hybridized to the arrays at 49oC in a buffer that contains MES (58 mM), Denhardt's solution (2.5X), EDTA (6 mM), Herring Sperm DNA (0.12 mg/ml), Human Cot-1 DNA (0.01 mg/ml), Tween-20 (0.01%), DMSO (5 %), and TMACl (2.7M). The arrays are then washed using Wash A (6X SSPE, 0.01% Tween 20) at 25oC followed by washing with Wash B (0.6X SSPE, 0.01% Tween 20)at 45oC. The arrays are then stained with streptavidin conjugated to phycoerythrin (SAPE) for 10 minutes at 25oC, followed by staining with a biotinylated goat Anti-streptavidin antibody for 10 minutes at 25oC, followed by another stain with SAPE at 25oC. There is then a final wash with Wash A at 30oC.

scan_protocol: The arrays are scanned on a GCS3000 scanner (Affymetrix).

data_processing: Intensity data are extracted using Affymetrix Power Tool software package (http://www.affymetrix.com/support/developer/powertools/index.affx)

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository

label_protocol: Standard Affymetrix protocol.

extract_protocol: DNA from cell lines was purchased from the Coriell Institute for Medical Research (Camden, NJ).

tag: HapMap sample


title: Placenta e13.5, biological rep1 (Series 2)

description: Gene expression data from fetal placenta at e13.5

source_name: Mouse placental tissue at embryonic day 13.5, biological replicate 1


title: Placenta e15.0, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 2


title: Placenta e12.0, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e12.0

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 3


title: Placenta e10.5, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e10.5

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 3


title: Placenta e12.0, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 2


title: Placenta e17.0, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 1


title: NA12145_CN2

description: Hapmap sample NA12145 was hybridized to Nsp CN arrays


title: Placenta e13.5, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 13.5, biological replicate 2


title: NA12144_CN1

description: Hapmap sample NA12144 was hybridized to Nsp CN arrays


title: Placenta e12.0, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 12.0, biological replicate 1


title: Placenta e9.0, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e9.0

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 3


title: Placenta e10.5, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 1


title: Placenta e9.0, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 2


title: Placenta e9.0, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 9.0, biological replicate 1


title: Placenta e10.5, biological rep2 (Series 2)

source_name: Mouse placental tissue at embryonic day 10.5, biological replicate 2


title: NA10846_CN2

description: Hapmap sample NA10846 was hybridized to Nsp CN arrays


title: NA12144_CN2


title: NA10846_CN1


title: NA01416_Nsp_CN2_rep1

description: Sample NA01416 was hybridized to Nsp CN arrays in triplicates


title: 501_Dualchip

status: Public on Apr 22 2008

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description:
Images were processed by Adaptive method of QuantArray® 3.0 Analysis software (Perkin-Elmer) and mean signal and background intensities were calculated.
Probes for “internal standards”, “positive hybridization/orientation control” probes and “positive biotin detection control” spots were excluded from the following analysis because they do not represent any genomic sequence.

hyb_protocol: One µL of labeled DNA was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the specific activity of the labeled DNA was calculated. One µg of each cyanine 5- and cyanine 3-labeled samples were mixed with 50 ug of human Cot-1 DNA and 100 ug of yeast tRNA (Invitrogen Life Technologies) and ethanol-precipitated. The solution was rinsed twice in cold 70% ethanol and air-dried. Ten ul of HybriBuffer A and 40 µl of HybriBuffer B (both supplied with the Eppendorf DualChip® kit) were added to the dried labeled sample mixture, 50 µg of salmon sperm DNA (Eppendorf) and 100 µg of BSA (Promega). An appropriate volume of RNase-free water was added to bring a final volume of 100 µl. After denaturation at 95°C for 3 minutes, samples were pre-annealed at 37°C for 2 hours. Hybridization mixes were injected into hybridization frames according to the DualChip® manual and slides (DualChip® human cancer 1.1) were hybridized at 60°C for 12-16 hours in a ThermoMixer Plus (Eppendorf) with a mixing frequency of 1400 rpm. Washing steps were performed in glass dishes and with agitation according to the DualChip® manual.

scan_protocol: Spot fluorescences were measured by using a G2565BA scanner (Agilent Technologies, Santa Clara, CA) checking "flipping the tif-image", with 5 µm scan resolution, and both Red and Green PMTs set to 100%.

data_processing:
Spots with a Signal-to-Noise-Ratio (SNR) value < 2 on both channels were considered unreliable and were filtered out. Whenever a spot did not pass this criterion for only one channel, the spot was included in the analysis. The log-intensity of each spot was written as M = log2R - log2G (R and G: background-corrected red and green intensities for each spot). Log-intensity of each spot was written as A = ½ (log2R + log2G), a measure of the overall brightness of the spot. Background-subtracted fluorescence log-ratios were normalized within each array by using loess normalization (Smyth, G.K. and T.P. Speed. 2003. Normalization of cDNA microarray data. Methods. 31(4): 265-273) available in Bioconductor Limma package (http://www.bioconductor.org; Smyth, G.K., Michaud, J., and H.S. Scott. 2005. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics. 21(9): 2067-2075), in order to correct the log-ratios for both spatial variation and intensity-based trends. The loess curve was constructed by a series of local regressions, one for each point in the MA-plot (Dudoit, S. Yang, Y.H., Callow, M.J., and T.P. Speed. 2002. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica. 12: 111-140), for 120 invariant genes known to be not gained not lost in the tumor sample.
A threshold method was then applied to automatically classify gene gains or losses (Scaruffi, P. Moretti, S., Coco, S., Mazzocco, K., Defferrari, R., Albino, D., Bonassi, S., and G.P. Tonini. 2006. Oligonucleotide array Comparative Genomic Hybridization profiling of neuroblastoma tumours. Cancer Genomics & Proteomics. 3: 245-252). In each array, the normalized ratios corresponding to the 120 reference genes were plotted to a normal quantile-quantile (QQ) plot to establish the threshold bounds for gain/loss assessment. Based on the proportion of ratios which lay on the line passing through the first and third quartiles in all QQ plots, for each array j, the two thresholds, c+j and c–j, were computed, such that c+j = Meanj + StDevj and c-j = Meanj - StDevj where Meanj and StDevj were the mean and the standard deviation of ratio distribution of spots corresponding to the 120 control genes on the j-th array, respectively. Then, those probes whose ratio on each array j was greater than c+j were scored as gain. Conversely, those probes whose ratio on the array j was lower than the c–j were scored as loss. Each gene was classified as lost or gained when at least 2 out of the 3 corresponding replicated probes were scored as loss or gain, respectively.

source_name: normal female DNA

label_protocol: Two µg of reference DNA were digested with AluI/RsaI restriction enzyme (5 U each) mix (Promega, Madison, WI) at 37°C for 2 hours in a ThermoStat heating block (Eppendorf). Two µl of digested genomic DNA were run on a 0.8% agarose gel stained with SYBR SafeTM (Invitrogen Life Technologies, Carlsbad, CA) to assess the completeness of digestion. The average size of fragments was between 200 and 500 bp. Digested DNA was concentrated to a final volume of 21 µl in a Concentrator 5301 (Eppendorf) at 30°C. DNA was labeled with Cy3-dCTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction contained dATP, dGTP and dTTP (120 uM each), dCTP (60 uM) and Cy3-dCTP (60 uM). After incubation with Klenow Fragment (40 U) at 37°C for 2 hours, the enzyme was inactivate by heating at 65°C for 20 minutes. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) by using 1X TE (pH 8.0) buffer, according to manufacturer’s protocol.

extract_protocol: Commercial DNA

tag: Female genomic DNA

source_name: #501 tumor DNA

label_protocol: Two µg of test DNA were digested with AluI/RsaI restriction enzyme (5 U each) mix (Promega, Madison, WI) at 37°C for 2 hours in a ThermoStat heating block (Eppendorf). Two µl of digested genomic DNA were run on a 0.8% agarose gel stained with SYBR SafeTM (Invitrogen Life Technologies, Carlsbad, CA) to assess the completeness of digestion. The average size of fragments was between 200 and 500 bp. Digested DNA was concentrated to a final volume of 21 µl in a Concentrator 5301 (Eppendorf) at 30°C. DNA was labeled with Cy5-dCTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction contained dATP, dGTP and dTTP (120 uM each), dCTP (60 uM) and Cy5-dCTP (60 uM). After incubation with Klenow Fragment (40 U) at 37°C for 2 hours, the enzyme was inactivate by heating at 65°C for 20 minutes. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) by using 1X TE (pH 8.0) buffer, according to manufacturer’s protocol.

extract_protocol: Total genomic DNA was extracted from the tumor sample according to Sambrook et al. (Sambrook J, Fritsch EF and Maniatis T: Molecular Cloning. A Laboratory Manual. Second edition. Cold Spring Harbor Laboratory Press, 1989)

tag: Human primary neuroblastoma tumor sample (frozen).

tag: The surgically resected tumor was handled according to guidelines by the International Neuroblastoma Pathology Committee (Shimada H, Umehara S, Monobe Y, Hachitanda Y, Nakagawa A, Goto S, Gerbing RB, Stram DO, Lukens JN, Matthay KK. International neuroblastoma pathology classification for prognostic evaluation of patients with peripheral neuroblastic tumors

value: a report from the Children's Cancer Group. Cancer 2001;92:2451-61) and tumor cell content was evaluated. The sample was classified as "Neuroblastoma Schwannian stroma poor tumor" containing more than 80% malignant neuroblasts and having diploid DNA. According to the criteria of the International Neuroblastoma Staging System, the tumor was classified as stage 4 neuroblastoma.


title: Decidua e8.5, biological rep2, technical rep2 (Series 2)

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 2, technical replicate 2


title: 2270_Dualchip

source_name: #2270 tumor DNA

value: a report from the Children's Cancer Group. Cancer 2001;92:2451-61) and tumor cell content was evaluated. The sample was classified as "Neuroblastoma Schwannian stroma poor tumor" containing more than 80% malignant neuroblasts and having diploid DNA. According to the criteria of the International Neuroblastoma Staging System, the tumor was classified as stage 4S neuroblastoma.


title: NA15510_Nsp_CN2_rep1

description: Sample NA15510 was hybridized to Nsp CN arrays in triplicates

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository


title: NA10831_CN2

description: Hapmap sample NA10831 was hybridized to Nsp CN arrays


title: Dicer1-null 27H10 overexpressing Dnmt3a,3b versus Dicer1-null 27H10 cells 2

city: Madrid

first: Roberta

last: Benetti

address: Calle Melchor Fernandez Almagro

country: Spain

institute: CNIO

description:
no additional information
Dye swap technical replicate of MT3a3b / Null27h10

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 825 ng. Duration: 17 hours.Volume: 100 uL.Temperature (ºC): 65.

scan_protocol: Scanned on an G2565BA DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 9.5.1).

data_processing:
Per Spot: Divide by control channel. Each gene's measured intensity was divided by its control channel value in each sample; if the control channel was below 0 then 0 was used instead. If the control channel and the signal channel were both below 0 then no data was reported.
Per Chip: Normalize to 50th percentile. Each measurement was divided by the 50,0th percentile of all measurements in that sample.The percentile was calculated using only genes marked present.

label_protocol: Amount of nucleic acid labeled: 2ug.Amplification: by RNA polymerases.Commercial "Two-Color Microarray-Based Gene Expression Analysis" kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.5 Feb 2007. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Cell lines wild type and Dicer-1 (cultures 27G5 and 27H10) or Dicer-1 null (27G5 or 27H10) + DNMT1 and Dicer-1 null (27G5 and 27H10) + DNMT3a3b, were cultivated on gelatin-coated plates with media supplemented with Leukemia Inhibitory Factor.

extract_protocol: Commercial RNeasy kit (Qiagen) was used in spin-column format by following manufacturer instructions. Total RNA was analysed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Samples' RNA Integrity Numbers were in the range 8.0 to 9.5

treatment_protocol: No special treatment were applied, cells were growth in appropriate conditions (see growth protocol) and harvested to prepare RNA.

tag: Dicer1-null 27H10 overexpressing Dnmt3a and 3b

source_name: Dicer Null 27H10

tag: Dicer-1 null  27H10 cells


title: Dicer1-null 27H10 cells overexpressing Dnmt1 versus Dicer1-null 27H10 cells 2

description:
no additional information
Dye swap technical replicate of MT1 / Null27h10

tag: Dicer-1 null culture 27H10


title: KOPTK1 CompE 24h rep2

city: New York

first: Adolfo

middle: A

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Standard Affymetrix procedure

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Affymetrix Microarray Suite Version 5 followed by  Dchip data normalization for adjustment of interarray intensity differences and calculation of  model based expression (VALUE).

source_name: KOPTK1 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

label_protocol: Approx. 10micrograms of total RNA was processed to produce biotinylated cRNA targets

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% fetal bovine serum plus antibiotics (pen/strep) in a humidified incubator with 5% CO2 atmosphere at 37C

extract_protocol: RNA was extracted with RNAqueous minikit (Ambion) following the manufacturer’s instructions

treatment_protocol: Compound E (CompE) [ (2S)-2-{[ (3,5-Difluorophenyl)acetyl]amino}-N-[(3S)-1-methyl-2-oxo-5-phenyl-2,3-dihydro-1H-1,4-benzodiazepin-3-yl] propanamide] (Alexis Biochemicals) a cell permeable, potent, selective, non-transition state and non-competitive inhibitor of gamma-secretase treatment at 500nM in DMSO for 24h.

tag: T-cell acute lymphoblastic leukemia cell line


title: DND41 CompE 24h rep2

description: Standard Affymetrix procedure

source_name: DND41 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: Dicer1-null 27G5 versus wild-type ES cells 1

description: no additional information

source_name: wtEstCells

tag: ES wild type cell line

source_name: DicerNull27 g5

tag: Dicer-1 null  27G5 cells


title: Placenta e8.5, biological rep3 (Series 2)

description: Gene expression data from fetal placenta at e8.5

source_name: Mouse placental tissue at embryonic day 8.5, biological replicate 3


title: CUTLL1 CompE 24h rep1

description: Standard Affymetrix procedure

source_name: CUTLL1 Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

tag: T-cell acute lymphoblastic lymphoma cell line


title: Placenta e15.0, biological rep1 (Series 2)

source_name: Mouse placental tissue at embryonic day 15.0, biological replicate 1


title: 2270_Agilent

description: Microarray images were processed by Feature Extraction software (version 8.1, Agilent Technologies).

hyb_protocol: Dye incorporations of post-labelling products were measured by ND-1000 spectrophotometer (NanoDrop Technologies) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul. Fluorescent-labelled reference and tumour DNAs (1 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies), 100 ug of yeast tRNA (Invitrogen Life Technologies), control targets (Agilent Technologies) and were hybridized to Human Genome CGH Microarray 44A (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65° C for 40 hrs. After hybridization the slides were washed with 0.5x SSC and 0.005% Triton X-102 at room temperature for 5 min and with 0.1x SSC and 0.005% Triton X-102 at 37o C for 5 min. Slides were air dried.

scan_protocol: Slides were scanned at 10 µm resolution by using the Agilent G2565BA Scanner. Scan Settings: • Scan region was set to Scan Area (61 × 21.6 mm). • Green PMT was set to 100%. • Red PMT was set to 100%.

data_processing: Array CGH analysis was performed by using the aCGH Analytics Software (version 3.2.32, Agilent Technologies). A statistical analysis based on hypergeometric Z-scores was used to identify all aberrant regions in each sample. The scoring method has two steps. First, it identifies the total number of probes with log ratios significantly different from zero in a normal sample. These probes are referred to as aberrant probes and the normal sample is referred to as calibration sample. These statistics can be calculated using a sample with no genetic abnormalities or they can be calculated from the test array itself, which is the recommended procedure and the method used in this study.  The log ratios from each sample are converted to normalized log ratios. In the normalization step, the expected mean log ratio is subtracted from all log ratios, and these modified log ratios are divided by the estimated variance of the log ratios. In this case, the expected mean is set to 0 and variance is computed as the Derivative Log Ratio Spread (DLRSpread) of the array. Chromosomes X and Y are not included in the estimation of mean and variance as differences between arrays in these probes may offset the statistics. The number of probes for which normalized log ratios are above and below the user specified thresholds (2.0, in this case) are counted and reported as the calibration statistics. In the second step, aberrant regions are identified by comparing the proportion of aberrant probes identified in a given region of the genome in the test sample as compared to that calculated in the first step. If significantly more probes are detected as aberrant in a given genomic region in the test sample then this region gets a higher score and is called as an aberrant region. In this step the over or under abundance of aberrant log ratios is analyzed for each sample using the user specified window size. In this case, a moving window of size 2 Mb is used. For each position of this window, the number of probes with log ratios above and below the user specified cut off of 2.0 is calculated. Then, a z-score is computed that measures the over or under abundance of aberrant positive log ratios in that particular position of 2 Mb window using an equation that reflects a hypergeometric distribution. The score is assigned to the probe in the middle of that window. This score identifies statistically significant groups of probes that appear to deviate from the typical distribution of log ratios around the mean for the given microarray and provides predictive power to make calls of gain/amplification or deletion events. Probes with a log ratio value > 2 were considered as amplified.

label_protocol: Three ug of reference genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). After purification with QIAprep MiniPrep kit (Qiagen GmbH, Hilden, Germany), fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy3-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy3-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.

label_protocol: Three ug of test genomic DNAs were digested with AluI/RsaI restriction enzyme mix (Promega, Madison, WI). After purification with QIAprep MiniPrep kit (Qiagen GmbH, Hilden, Germany), fragmented DNA was labelled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labelled with Cy5-dUTP (Perkin Elmer, Wellesley, MA) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies, Carlsbad, CA). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 uM each), dUTP (60 uM) and Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore, Billerica, MA) according to the manufacturer protocol.


title: Keratinocyte Untreated

city: Miami

first: Jie

last: Li

state: FL

address: 1600 NW 10th Avenue, RMSB2049A

department: Department of Dermatology and Cutaneous Surgery

institute: University of Miami Miller School of Medicine

hyb_protocol: Standard Affymetrix hybridization protocol following Affymetrix Technical Manual

scan_protocol: Affymetrix GC 3000 Scanner, factory settings

data_processing: Affymetrix MAS 5.0, Target Normalization intensity of 500

source_name: Normal Human Keratinocytes

label_protocol: Standard Affymetrix IVT following Affymetrix Technical Manual

growth_protocol: Normal human keratinocytes were maintained in growth medium of EpiLife (Cascade Biologics, Portland, Oregon) with human keratinocyte growth supplement at concentration of 0.2% v/v of bovine pituitary extract, 5 ug/ml bovine insulin, 0.18 ug/ml hydrocortisone, 5 ug/ml bovine transferrin, 0.2 ng/ml human epidermal growth factor (Cascade Biologics, Portland, Oregon), plus antibiotics of 100 U/ml penicillin G and 100 ug/ml streptomycin at 37ºC and 5% CO2. Media were changed every 24 hours.

extract_protocol: RNA was isolated from cells using an RNeasy Mini RNA Isolation Kit (Qiagen Sciences, Germantown, Maryland), and converted to double stranded cDNA using a cDNA RT Kit (Applied Biosystems, Foster City, California)

treatment_protocol: Normal human epidermal keratinocytes were maintained in 35-mm cell culture dishes and in EpiLife at 37ºC and 5% CO2. Keratinocytes were maintained in growth media and grown to confluency. At time 0, a cross-shaped wound gap or cell-free zone was made among confluent monolayer cells in the center of the culture dish, and detached cells were washed off with PBS and then replaced with growth medium. This control group received no treatment and was placed in the cell culture hood at temperatures of 31±2ºC for one hour. This group was performed in triplicates, and the cultures were combined at the end for RNA extraction.

tag: Normal Human Keratinocytes


title: Dicer1-null 27G5 cells overexpressing Dnmt3a,3b versus Dicer1-null 27G5 cells 1

description: no additional information

source_name: Dicer Null 27G5

source_name: 27 g5+DNMT3a,3b

tag: Dicer1-null 27G5 cells overexpressing Dnmt3a and 3b


title: Keratinocyte EMF treated

source_name: Normal Human Keratinocytes, EMF Treated 1 Hour

treatment_protocol: Normal human epidermal keratinocytes were maintained in 35-mm cell culture dishes and in EpiLife at 37ºC and 5% CO2. Keratinocytes were maintained in growth media and grown to confluency. At time 0, a cross-shaped wound gap or cell-free zone was made among confluent monolayer cells in the center of the culture dish, and detached cells were washed off with PBS and then replaced with growth medium. This treatment group was treated using a induced electromagnetic field device (Field Therapy Accelerator; Advatech, Miami, Florida) for 1 hour immediately after wounding, at a frequency of 2080 cycles/second, electric field strength of 20mV/cm, and duty cycle of 90%. The temperature was maintained at 31±2ºC for one hour. This group was performed in triplicates, and the cultures were combined at the end for RNA extraction.


title: CCRF-CEM CompE 24h rep1

description: Standard Affymetrix procedure

source_name: CCRF-CEM Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: Dicer1-null 27G5 cells overexpressing Dnmt1 versus Dicer1-null 27G5 cells 2

description:
no additional information
Dye swap technical replicate of MT1 / Null27g5

source_name: 27 g5+DNMT1


title: Dicer1-null 27H10 cells overexpressing Dnmt1 versus Dicer1-null 27H10 cells 1

description: no additional information


title: RPMI8402 CompE 24h rep1

description: Standard Affymetrix procedure

source_name: RPMI8402 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h

label_protocol: Approx. 10 micrograms of total RNA was processed to produce biotinylated cRNA targets


title: Dicer1-null 27H10 versus wild-type ES cells 2

description:
no additional information
Dye swap technical replicate of Null27h10 / wt

source_name: DicerNull27 h10


title: RPMI8402 CompE 24h rep2

description: Standard Affymetrix procedure


title: NA12156_CN2

description: Hapmap sample NA12156 was hybridized to Nsp CN arrays

source_name: DNA was obtained from NIGHS Human Genetic Cell Repository


title: CUTLL1 CompE 24h rep2

description: Standard Affymetrix procedure

tag: Human T-cell lymphoblastic lymphoma cell line


title: 501_Agilent

source_name: normal female DNA

source_name: #501 tumor DNA


title: HPB-ALL CompE 24h rep1

description: Standard Affymetrix procedure

source_name: HPB-ALL human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: ALLSIL CompE 24h rep2

description: Standard Affymetrix procedure

source_name: ALL-SIL Human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: Dicer1-null 27H10 versus wild-type ES cells 1

description: no additional information

source_name: wtEstCells

tag: Dicer-1 null 27H10 cells


title: HPB-ALL CompE 24h rep2

description: Standard Affymetrix procedure


title: Dicer1-null 27G5 versus wild-type ES cells 2

description:
no additional information
Dye swap technical replicate of Null27g5 / wt

source_name: DicerNull27 g5


title: DND41 CompE 24h rep1

description: Standard Affymetrix procedure

source_name: DND41 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: CCRF-CEM CompE 24h rep2

description: Standard Affymetrix procedure


title: Attachment-Detachment-1

status: Public on Apr 19 2008

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

data_processing: LimmaGUI, http://bioconductor.org/

organism: Dreissena polymorpha

source_name: Attached zebra mussel feet

tag: Zebra mussels stayed attached in water for 48 hours.

source_name: Detached zebra mussel feet

tag: Zebra mussels stayed detached in water for 48 hours.


title: Dicer1-null 27H10 overexpressing Dnmt3a,3b versus Dicer1-null 27H10 cells 1

description: no additional information

source_name: Dicer Null 27H10


title: Attachment-Detachment-3

tag: Zebra mussels stayed attached in water for 48 hours


title: Detachment-Attachment-4

tag: Zebra mussels stayed detached in water for 48 hours


title: KOPTK1 CompE 24h rep1

description: Standard Affymetrix procedure

source_name: KOPTK1 human T-cell lymphoblastic cell line gamma-secretase inhibitor (CompE 500nM) treatment 24h


title: BR2 5/20 CD34- vs. BR2 5/20 CD34+  Cy3: BR2 5/20 CD34-  Cy5: BR2 5/20 CD34+

status: Public on Apr 21 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.    For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.    Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).

data_processing: Agilent Feature Extraction protocol for 44K arrays, log2ratio Treated/Control

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 0.5µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.

extract_protocol: The CD34+ and CD34- cells were pelleted and lysed in 1 ml lysis buffer with beta-mercaptoethanol (Qiagen Rnasesy kit), then total RNA extracted following manufacturer’s protocol.

treatment_protocol: Keratinocytes were harvested from adult mouse skin (7 weeks of age) following digestion in 0.25% trypsin for 2 hours at 32 C. Single cell preparations were made after epidermal cells were scraped into fresh media (SMEM supplemented with 10% fetal bovine serum and 1X gentamicin). Cells were stained with antibodies to CD34 (rat anti-mouse CD34 RAM clone and rat anti-human alpha-6 integrin) and sorted into alpha6+CD34+ (stem and progenitor cells) and alpha6+CD34- (basal cells) using fluorescence activated cell sorting (FACS).

tag: control

tag: treated


title: CD 34- vs. CD 34+  Cy3: CD 34-  Cy5: CD34+

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.5).


title: Detachment-Attachment-2


title: Dicer1-null 27G5 cells overexpressing Dnmt1 versus Dicer1-null 27G5 cells 1

description: no additional information

source_name: Dicer Null 27G5


title: BR1 5/19 CD34- vs. BR1 5/19 CD34+  Cy3: BR1 5/19 CD34+  Cy5: BR1 5/19 CD34-


title: A549 WT vivo 4

status: Public on Apr 18 2008

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: See manuscript for additional details.

hyb_protocol: Microarrays were hybridized 12-16 hours at 45 C under standard conditions (Affymetrix).

scan_protocol: Microarrays were scanned under standard conditions (Affymetrix).

data_processing: RMA normalization using the ArrayAssist (Stratagene).

source_name: xenograft A549 cells

label_protocol: Total RNA samples were converted into biotin-labeled cRNA using standard protocols recommended by Affymetrix (Santa Clara, CA).

growth_protocol: Animal care was in accordance with NIH and institutional guidelines. For the A549 xenograft model, 1.7 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation (Sirotnak, et al., 2000). For the A549 rho zero xenograft model, 1.5 million cells were used. Tumor and body weight measurements (6 or 7 mice per group) were performed three times per week once tumors became palpable. This occurred 41 versus 9 days post-implantation in (rho zero) and wildtype A549 xenograft models, respectively. Tumor volume was calculated using the equation V (mm3) = a × b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed.

extract_protocol: To perform gene expression profiling, tumors (4 tumors per group) were harvested and snap frozen immediately on dry ice when the tumor size reached 500-800 mm3. Tumor tissue was dissected, homogenized in Trizol, and total RNA was isolated.


title: BR1 5/19 CD34- vs. BR1 5/19 CD34+  Cy3: BR1 5/19 CD34-  Cy5: BR1 5/19 CD34+


title: Dicer1-null 27G5 cells overexpressing Dnmt3a,3b versus Dicer1-null 27G5 cells 2

description:
no additional information
Dye swap technical replicate of MT3a3b / Null27g5

source_name: 27 g5+DNMT3a,3b


title: CD 34- vs. CD 34+  Cy3: CD 34+  Cy5: CD34-


title: A549 WT vivo 2

description: See manuscript for additional details.

treatment_protocol: Animal care was in accordance with NIH and institutional guidelines. For the A549 xenograft model, 1.7 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation (Sirotnak, et al., 2000). For the A549 rho zero xenograft model, 1.5 million cells were used. Tumor and body weight measurements (6 or 7 mice per group) were performed three times per week once tumors became palpable. This occurred 41 versus 9 days post-implantation in (rho zero) and wildtype A549 xenograft models, respectively. Tumor volume was calculated using the equation V (mm3) = a × b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed.


title: A549 WT vivo 1

description: See manuscript for additional details.

tag: Animal care was in accordance with NIH and institutional guidelines. For the A549 xenograft model, 1.7 million A549 cells were injected subcutaneously/intramuscularly into the right hind flank of 6 week old CD-1 nude mice that had been irradiated with 4 Gy of total body irradiation from a 137Cs radiation source one day prior to tumor implantation (Sirotnak, et al., 2000). For the A549 rho zero xenograft model, 1.5 million cells were used. Tumor and body weight measurements (6 or 7 mice per group) were performed three times per week once tumors became palpable. This occurred 41 versus 9 days post-implantation in (rho zero) and wildtype A549 xenograft models, respectively. Tumor volume was calculated using the equation V (mm3) = a × b2/2, where a is the largest diameter and b is the smallest diameter. No significant body weight loss was observed.


title: BR2 5/20 CD34- vs. BR2 5/20 CD34+  Cy3: BR2 5/20 CD34+  Cy5: BR2 5/20 CD34-


title: July 2007 Sewage sample hybridization unto virus microarray

type: mixed

city: East Lansing

first: Mark

last: Wong

state: MI

address: 3 Natural Resources

department: Crops and Soil Sciences

description: Arrays were scanned and washed at several different wash temperatures to ensure that probe signals behaved appropriately and were not artifacts of the hybridization.

hyb_protocol: Hybridization was carried out in 50 ul hybridization buffer at 20 degrees Celsius using a microfluidic hybridization wash station. Hybridization was allowed to proceed for at least 17 hours before washing and scanning.

scan_protocol: Arrays were scanned in a Genepix 4000B microarray scanner at PMT values of appoximately 700.

data_processing: Signal values were derived from the RAW data files by extracting the median foreground intensity for each given spot.

organism: Viruses

source_name: July 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

label_protocol: Total nucleic acid extract was treated with DPN II restriction enzyme for 1 hr. Labeled with Cy3 using Klenow fragment and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.

growth_protocol: Buffalo Green Monkey cells were coated with 12 ml virus concentrate and allowed to contact for 2 hrs with occassional rocking.

extract_protocol: Viral DNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.

treatment_protocol: Virus was concentrated through organic flocculation with 15% Beef extract supplemented with glycine and concentrated by centrifugation. Viruses were resuspended in Sodium phosphate buffer and stored prior to cell culture

tag: Source - Virus concentrate from Sewage

tag: Culture - Buffalo Green Monkey cells (BGMK)

tag: Time of infection - approximately 48 for CPE development

tag: Label - Cy3 dye

source_name: July 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells

label_protocol: Total RNA was labeled with Cy5 using Sensicript III reverse transcriptase and random hexamer primers. Cyanine dye was indirectly coupled via amino allyl-dUTP.

extract_protocol: Viral RNA extracted using QIAGEN viral RNA extraction kit following manufacturer's protocol.

tag: Label - Cy5 dye


title: ALLSIL CompE 24h rep1

description: Standard Affymetrix procedure

tag: T-cell acute lymphoblastic leukemia cell line


title: March 2007 Sewage sample hybridization unto virus microarray

source_name: March 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: March 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: June 2007 Sewage sample hybridization unto virus microarray

source_name: June 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: June 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: developmental liver sample at T165, biological rep2

city: Boston

first: Hasan

middle: Huseyin

last: Otu

state: MA

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

description: Gene expression data from 16.5 dpc mouse embryonic liver sample.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Mouse Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip using smoothing spline invariant set method with the model based expression algorithm following the perfect match (PM)-mismatch (MM) difference model. In the dChip analysis, array outliers are not treated as missing expression values and no truncation on signal values is applied.

source_name: Liver sample from mouse embryo liver at 16.5 days post conception (dpc)

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

growth_protocol: All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center. A maximum of five minutes was allowed to elapse between sacrifice and liver harvest to prevent RNA degradation and transcriptional changes.

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

treatment_protocol: Pregnant CD-1 females were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation. The abdomen was opened and the uterus removed. After removal of the uterine musculature, embryos were removed from the yolk sacs and livers microdissected, taking care to remove all extraneous tissue including the retrohepatic vena cava.

tag: Genotype

value: CD-1 mouse embryo

tag: Age


title: May 2007 Sewage sample hybridization unto virus microarray

source_name: May 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: May 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: A549 WT vitro 3

description: See manuscript for additional details.

source_name: cultured cells

growth_protocol: A549 cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).

extract_protocol: A549 or A549 rho zero human lung cancer cells (1 x 10^5 cells per T-25 flask in 7 mL complete RPMI 1640 medium) were seeded 8 days prior to RNA isolation. Each experiment was performed in triplicate. After incubation, all cultures were washed twice with HBSS supplemented with 0.5% BSA and total RNA was isolated using the RNA Stat-60 reagent (Tel-Test, Inc., Friendswood, TX).


title: August 2007 Sewage sample hybridization unto virus microarray

source_name: August 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: August 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: A549 rho vivo 1

description: See manuscript for additional details.

source_name: xenograft A549 rho zero cells


title: A549 rho vivo 3

description: See manuscript for additional details.


title: A549 rho vivo 2

description: See manuscript for additional details.


title: developmental liver sample at T135, biological rep2

description: Gene expression data from 13.5 dpc mouse embryonic liver sample.

source_name: Liver sample from mouse embryo liver at 13.5 days post conception (dpc)


title: A549 WT vivo 3

description: See manuscript for additional details.


title: February 2007 Sewage sample hybridization unto virus microarray

source_name: February 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: February 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: developmental liver sample at T145, biological rep1

description: Gene expression data from 14.5 dpc mouse embryonic liver sample.

source_name: Liver sample from mouse embryo liver at 14.5 days post conception (dpc)


title: April 2007 Sewage sample hybridization unto virus microarray

source_name: April 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: April 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: A549 rho vivo 4

description: See manuscript for additional details.


title: developmental liver sample at T145, biological rep2


title: developmental liver sample at T135, biological rep1


title: developmental liver sample at T125, biological rep1

description: Gene expression data from 12.5 dpc mouse embryonic liver sample.

source_name: Liver sample from mouse embryo liver at 12.5 days post conception (dpc)


title: A549 WT vitro 1

description: See manuscript for additional details.

treatment_protocol: A549 cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).


title: December 2006 Sewage sample hybridization unto virus microarray

source_name: December 2006 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: December 2006 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: A549 rho vitro 3

description: See manuscript for additional details.

growth_protocol: A549 rho zero cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).


title: developmental liver sample at T165, biological rep1


title: January 2007 Sewage sample hybridization unto virus microarray

source_name: January 2007 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: January 2007 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: A549 rho vitro 2

description: See manuscript for additional details.

treatment_protocol: A549 rho zero cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).


title: developmental liver sample at T125, biological rep2


title: November 2006 Sewage sample hybridization unto virus microarray

source_name: November 2006 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: November 2006 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: developmental liver sample at T105, biological rep2

description: Gene expression data from 10.5 dpc mouse embryonic liver sample.

source_name: Liver sample from mouse embryo liver at 10.5 days post conception (dpc)


title: A549 rho vitro 1

description: See manuscript for additional details.

source_name: cultured cells

tag: A549 rho zero cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).


title: October 2006 Sewage sample hybridization unto virus microarray

source_name: October 2006 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: October 2006 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: baseline liver sample at T0, biological rep1

description: Gene expression data from 10-week-old normal female liver sample.

source_name: 10-week-old normal female liver sample

growth_protocol: All experiments used CD-1 mice obtained from Charles River Laboratories (Wilmington, MA) or our own breeding colony. Animals were maintained in a pathogenfree facility administered by Harvard Medical School in accordance with the institutional guidelines of Harvard Medical School and Beth Israel Deaconess Medical Center.

treatment_protocol: After anesthesia with 100 mg/kg ketamine and 10 mg/kg Xylazine, the abdomen was prepped with alcohol and betadyne. Aftermidline laparotomy, the tip of the xiphoid was resected, and the liver exteriorized. A silk tie was placed around the three anterior lobes of the liver, including the gallbladder, and the 2/3 hepatectomy with cholecystectomy was completed. The liver was returned to the abdominal cavity and the abdomen closed in two layers. Postoperative analgesia consisted of Buprenorphine 0.05-0.1 mg/kg twice daily for 48 hours or until sacrifice. At harvest,mice were sacrificed with carbon dioxide asphyxiation followed by cervical dislocation.

value: Female CD-1 mouse

value: 10 week


title: developmental liver sample at T115, biological rep1

description: Gene expression data from 11.5 dpc mouse embryonic liver sample.

source_name: Liver sample from mouse embryo liver at 11.5 days post conception (dpc)


title: 60_G_CD34_rep2

status: Public on Apr 17 2008

city: Amsterdam

first: Stephan

middle: Henrik

last: Schirmer

address: Meibergdreef 9

department: Cardiology

country: Netherlands

institute: Academic Medical Center

hyb_protocol: According to beadchip array manufacturer's protocol

data_processing: Array data were extracted using Illumina's BeadStudio software. One mislabeled array and ten low-signal arrays (corresponding to seven unique samples and one triplicate sample) with less than 30% of the probes having a detection p-value <0.01 were removed, leaving a total of 151 arrays for analysis (including 39 technical replicates). From the CD34+ cell samples, 38 arrays were analyzed, including 8 technical replicates. Normalization and statistical analysis of the bead summary data from the arrays was carried out using the limma package14 and in-house scripts in R/Bioconductor. Bead summary intensities were log2-transformed and then normalized using quantile normalization. To find differentially expressed genes, we performed a linear model analysis. Technical replicates were handled by estimating a common value for the intra-replicate correlation and including it in the linear model. Differential expression between the treatments of interest was assessed using a moderated t-test. This test is similar to a standard t-test for each probe except that the standard errors are moderated across genes to ensure more stable inference for each gene. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate.

label: biotin, Cy3

source_name: stem cells

label_protocol: Total RNA samples fwere amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX).

growth_protocol: Using immunomagnetic beads (Dynabeads, Invitrogen, Carlsbad, CA), CD14+ monocytes as well as CD34+ stem cells were positively isolated for direct cell lysis, while negatively isolated monocytes were split into two fractions for stimulation with 10 ng/ml lipopolysaccharide (LPS) for 3h, or for 20h cell culture towards macrophages.

extract_protocol: Positively isolated monocytes and stem cells as well as cultured stimulated monocytes and macrophages were lysed and total RNA was isolated (Absolutely RNA Microprep Kit, Stratagene, La Jolla, CA)

tag: GAR

tag: CFI

tag: patientID

tag: age

tag: sex

value: M


title: 42_G_CD34

scan_protocol: According to beadchip array manufacturer's protocol


title: 18_G_CD34


title: 33_G_CD34


title: 21_G_CD34_rep2


title: August 2006 Sewage sample hybridization unto virus microarray

source_name: August 2006 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: August 2006 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: baseline liver sample at T0, biological rep2


title: 15_B_CD34

value: F


title: 41_B_CD34

tag: BAR


title: 62_B_CD34_rep2


title: 47_B_CD34_rep2


title: A549 WT vitro 2

description: See manuscript for additional details.

tag: A549 cells cultured in RPMI 1640 medium supplemented with 20 mM HEPES, 2 mM L-glutamine, 10% heat inactivated fetal bovine serum (Hyclone) and antibiotics (200 U/mL penicillin and 200 μg/mL streptomycin).


title: 31_B_CD34


title: 46_G_CD34


title: developmental liver sample at T115, biological rep2


title: 37_G_CD34_rep2


title: developmental liver sample at T105, biological rep1


title: 45_B_CD34


title: September 2006 Sewage sample hybridization unto virus microarray

source_name: September 2006 Sewage sample, Cy 3 Labeled virus DNA extracted from Cell culture on BGM cells

source_name: September 2006 Sewage sample, Cy 5 Labeled virus RNA extracted from Cell culture on BGM cells


title: 53_G_CD34


title: 47_B_CD34


title: 49_G_CD34


title: 37_G_CD34


title: 32_B_CD34


title: 8_B_CD34


title: 29_B_CD34


title: 25_G_CD34


title: 5_B_CD34


title: 21_G_CD34


title: 38_G_CD34


title: 49_G_CD34_rep2


title: 16_B_CD34


title: 39_B_CD34


title: 34_G_CD34


title: 60_G_CD34


title: 1_G_CD34


title: 23_B_CD34


title: 39_B_CD34_rep2


title: 36_G_CD34


title: 62_B_CD34


title: 30_B_CD34


title: 13_B_CD34


title: 31_B_3h

source_name: stim. monocyes


title: 51_G_20h_rep2

source_name: macrophages


title: 3_B_3h


title: 42_G_CD34_rep2


title: 23_B_20h


title: 49_G_3h_rep2


title: 43_B_CD14_rep2

source_name: resting monocyes


title: 51_G_20h


title: 47_B_CD14


title: 44_B_3h_rep2


title: 11_G_3h


title: 48_B_CD34


title: 4_G_CD14


title: 39_B_3h


title: 36_G_20h_rep3


title: 21_G_CD14


title: 43_B_3h


title: 33_G_3h


title: 45_B_CD14_rep3


title: 37_G_20h_rep2


title: 11_G_CD14


title: 13_B_CD14_rep3


title: 46_G_3h_rep2


title: 51_G_3h_rep2


title: 48_B_3h_rep2


title: 15_G_3h_rep2


title: 31_B_20h


title: 45_B_20h


title: 21_G_CD14_rep2


title: 13_B_3h_rep2


title: 25_G_CD14_rep2


title: 8_B_3h_rep2


title: 22_G_20h


title: 19_B_20h


title: 49_G_20h


title: 5_B_3h


title: 47_B_3h_rep2


title: 23_B_CD14


title: 34_G_20h_rep2


title: 10_G_20h


title: 43_B_20h_rep3


title: 19_B_3h_rep2


title: 12_B_20h


title: 8_B_20h


title: 48_B_CD14


title: 36_G_3h


title: 33_G_20h


title: 30_B_CD14


title: 48_B_3h


title: 34_G_3h_rep2


title: 34_G_20h_rep3


title: 12_B_CD14


title: 33_G_CD14


title: 51_G_CD14


title: 34_G_3h


title: 48_B_20h


title: 11_G_20h


title: 42_G_20h


title: 18_G_3h


title: 41_B_20h

tag: CFI: 0.1


title: 36_G_20h


title: 19_B_3h


title: 25_G_20h


title: 34_G_CD14


title: 8_B_CD14


title: 49_G_CD14


title: 16_B_3h


title: 43_B_20h_rep2


title: 33_G_20h_rep2


title: 4_G_20h


title: 49_G_3h


title: 38_G_CD14


title: 38_G_3h


title: 17_B_CD14


title: 10_G_3h


title: 5_B_20h


title: 43_B_20h


title: 45_B_3h


title: 23_B_3h


title: 31_B_3h_rep2


title: 12_B_3h


title: 13_B_3h


title: 37_G_CD14


title: 8_B_3h


title: 13_B_20h


title: 44_B_3h


title: 1_G_CD14


title: 48_B_CD14_rep2


title: 7_B_CD14_rep2


title: 25_G_3h


title: 39_B_CD14


title: 44_B_CD14


title: 38_G_3h_rep2


title: Bradyrhizobium japonicum wild-type strain USDA110spc4, rep_4

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: B. japonicum wild-type strain grown aerobically

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 2–2.5 µg of labeled cDNA were used in a total volume of 150 µl hybridization solution, which contained 7% DMSO (Sigma-Aldrich, St. Louis, USA) in addition to the described composition. Hybridization was done overnight at 48°C.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with the Affymetrix gene chip operating software version 1.2 (GCOS; Affymetrix) using the algorithms described in the Affymetrix statistical algorithms description document (http://www.affymetrix.com). Data were globally scaled to a target intensity of 500, and default statistical parameters of GCOS (α1 = 0.05, α2 = 0.065, τ =0.015, γ1H = 0.002,γ1L = 0.002, γ2H = 0.002667, γ2L = 0.002667, Perturbation1.1) were applied. Signal values from the arrays were then processed using Genespring GX 7.3 (Agilent Technologies,CA, USA). The experiment was normalized with the default settings for Affymetrix arrays, i.e., first data transformation to set measurements of below 0.01 to 0.01 followed by a per-chip normalization to the 50th percentile and a per-gene normalization to median. For statistical comparisons, the student t-test with a P value threshold of 0.01 was applied. Genes were considered as differentially expressed if the fold change (FC) was higher than 2 when comparing the different strains.

organism: Bradyrhizobium japonicum

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP in a final volume of 50 µl using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA.

growth_protocol: Cells were grown to mid-exponential phase (OD600 of 0.4-0.5). For harvesting, cultures were rapidly transferred to cold tubes containing one tenth of the culture volume of “stop solution” (10% Tris-HCl-buffered phenol [pH 8] in ethanol), centrifuged for 5 min (10,800 × g; 4°C), the supernatant was decanted, and cells were frozen in liquid nitrogen and stored at −80°C.

extract_protocol: Total RNA was isolated using the hot phenol extraction procedure described previously (Babst et al. 1996). RNA integrity was checked by agarose gel electrophoresis. Precipitated RNA (100 µg) was treated with 20 units of RQ1 DNase I (Promega, Madison, USA) for 30 min at 37°C in a reaction volume of 200 µl. SUPERase•InTM (100 units; Ambion,Huntingdon, UK) was included in the reaction to inhibit potential RNase activity. RNA samples were cleaned up with RNeasy spin columns (Qiagen). cDNA was synthesized according to the Affymetrix antisense genome array protocol for E. coli (http://www.affymetrix.com). For reverse transcription, MMLV reverse transcriptase RNase H minus (Promega, Madison, USA) was used in the supplied reaction buffer. The resulting cDNA was spectrophotometrically quantified and fragmented according to the Affymetrix manual except that the time for fragmentation by DNase I was shortened to 3 min. For control, 200 ng of DNase I-treated cDNA were separated on a 2% agarose gel and stained with SYBR green II (Molecular Probes, Inc., Eugene, OR, USA). Ideally, the fragmented cDNA migrated in a range that corresponded to 50–200 bp of the 50-bp ladder (Fermentas International Inc., Burlington, Canada).

tag: Growth condition

value: aerobic

tag: Medium

value: PSY


title: 16_B_20h


title: Bradyrhizobium japonicum wild-type strain USDA110spc4, rep_2

source_name: B. japonicum wild-type strain grown aerobically


title: Bradyrhizobium japonicum wild-type strain USDA110spc4, rep_3


title: 46_G_CD14_rep2


title: 18_G_CD14


title: Bradyrhizobium japonicum pmtA mutant strain 5569, rep_5

description: B. japonicum pmtA mutant strain grown aerobically


title: Bradyrhizobium japonicum wild-type strain USDA110spc4, rep_1


title: 41_B_3h


title: Bradyrhizobium japonicum pmtA mutant strain 5569, rep_3

source_name: B. japonicum pmtA mutant strain grown aerobically


title: Bradyrhizobium japonicum pmtA mutant strain 5569, rep_2


title: 40_G_20h_rep2


title: Bradyrhizobium japonicum pmtA mutant strain 5569, rep_4


title: 14_G_CD14_rep2


title: Bradyrhizobium japonicum pmtA mutant strain 5569, rep_1


title: 9_B_CD14


title: 37_G_3h


title: 1_G_3h


title: 9_B_20h


title: 51_G_3h


title: 7_B_CD14


title: 14_G_CD14


title: 47_B_3h


title: 12_B_20h_rep2


title: Bradyrhizobium japonicum wild-type strain USDA110spc4, rep_5


title: 37_G_20h


title: 39_B_20h


title: 19_B_CD14


title: 32_B_3h


title: 29_B_CD14


title: 46_G_3h


title: 29_B_20h


title: 21_G_20h


title: 30_B_3h


title: 29_B_3h


title: 13_B_CD14


title: 25_G_CD14


title: 15_G_3h


title: 15_G_CD14


title: 43_B_CD14


title: 15_G_20h


title: 40_G_CD14


title: 32_B_20h


title: 14_G_3h


title: 45_B_CD14


title: 46_G_20h


title: 34_G_20h


title: 17_B_20h


title: 36_G_20h_rep2


title: 33_G_20h_rep3


title: 32_B_CD14


title: 40_G_3h


title: 44_B_20h_rep2


title: 10_G_CD14


title: 13_B_CD14_rep2


title: 41_B_CD14


title: 30_B_20h


title: 46_G_CD14


title: 42_G_3h


title: Gene expression after infection of mice with Y. enterocolitica pYV+, lethal dose

city: Tuebingen

first: Erwin

last: Bohn

address: Elfriede-Aulhorn-Strasse 6

department: Institutefor Medical Microbiology and Hygiene

country: Germany

institute: University of Tuebingen

description: CD11b+ cells of infected mice; Mice were infected with a lethal dose of Yersinia enterocolitica WA-314 (pYV+) for one day

hyb_protocol: Standard procedure; Affymetrix protocol

scan_protocol: Standard procedure; Affymetrix protocol

data_processing: Affymetrix ExpressionStat 5.0

source_name: CD11b+ cells of the spleen, infected of mice with Y. enterocolitica pYV+, lethal dose

label_protocol: Standard procedure; Affymetrix protocol

extract_protocol: Total RNA was extracted from CD11b+ cells using the RNAeasy mini-kit following the manufacturer´s instructions (Qiagen, Hilden, Germany). Generation of fragmented cRNA was performed as recently described [38] and used for hybridization onto MG-U74Av2 from Affymetrix (Affymetrix, High Wycombe, UK). Genechips were washed, stained with streptavidin–phycoerythrin and read using a GeneChip Scanner 2500 (Affymetrix) at the IZKF microarray facility, Tübingen.

treatment_protocol: Mice were infected intravenously with 50000 Y. enterocolitica WA-314 (pYV+), lethal dose, for one day. After one day, five to ten mice per group were sacrificed by CO2 asphyxiation.  The spleens  were removed and placed in ice-cold HBSS (Ca2+ and Mg2+ free Hanks’ balanced salt solution [HBSS; BioWhittaker,Walkersville, MD.] supplemented with 2% FCS [HyClone, Logan, Utah] and 10 mM HEPES buffer). The spleens were forced with a 5 ml syringe pestle through a 100 µm-pore nylon mesh cell strainer (Falcon; BD Biosciences). Red blood cells were lysed from spleen samples by incubating the cell suspensions for 5 min at room temperature in erythrocyte lysis buffer (170 mM Tris, 160 mM NH4Cl, pH 7,4) followed by two washes in ice-cold HBSS. CD11b+ cells were purified by positive selection using MACS® CD11b MicroBeads (Miltenyi Biotec) according to the manufacturer´s instructions. To ensure enrichment values of 96-98% purity, the magnetic separation was performed twice. Cell viability and number were assessed by trypan blue exclusion.

value: 6-8 weeks old

tag: Gender

value: female

tag: Strain

value: C57BL/6 mice

tag: infected with Y. enterocolitica WA-314 (pYV+), lethal dose for one day


title: 22_G_3h


title: Gene expression after infection with Y. enterocolitica YopH mutant, sublethal

description: CD11b+ cells of infected mice; Mice were infected with a sublethal dose of Yersinia enterocolitica YopH deletion mutant(delta YopH) for one day

source_name: CD11b+ cells of the spleen, infected with Y. enterocolitica YopH mutant, sublethal

treatment_protocol: Mice were infected intravenously with 50000 Y. enterocolitica YopH deletion mutant (DeltaYopH), sublethal dose, for one day. After one day, five to ten mice per group were sacrificed by CO2 asphyxiation.  The spleens  were removed and placed in ice-cold HBSS (Ca2+ and Mg2+ free Hanks’ balanced salt solution [HBSS; BioWhittaker,Walkersville, MD.] supplemented with 2% FCS [HyClone, Logan, Utah] and 10 mM HEPES buffer). The spleens were forced with a 5 ml syringe pestle through a 100 µm-pore nylon mesh cell strainer (Falcon; BD Biosciences). Red blood cells were lysed from spleen samples by incubating the cell suspensions for 5 min at room temperature in erythrocyte lysis buffer (170 mM Tris, 160 mM NH4Cl, pH 7,4) followed by two washes in ice-cold HBSS. CD11b+ cells were purified by positive selection using MACS® CD11b MicroBeads (Miltenyi Biotec) according to the manufacturer´s instructions. To ensure enrichment values of 96-98% purity, the magnetic separation was performed twice. Cell viability and number were assessed by trypan blue exclusion.

value: 6-8 weeks old female

tag: infected with a sublethal dose of Y. enterocolitica YopH deletion mutant (delta YopH)


title: 40_G_20h


title: 7_B_3h


title: Gene expression after infection of mice with Y. enterocolitica deltaYopH, lethal dose

description: CD11b+ cells of infected mice; Mice were infected with a lethal dose of Yersinia enterocolitica YopH deletion mutant(delta YopH) for one day

source_name: CD11b+ cells of the spleen, infected of mice with Y. enterocolitica deltaYopH, lethal dose

treatment_protocol: Mice were infected intravenously with 5000000 Y. enterocolitica YopH deletion mutant (DeltaYopH),lethal dose, for one day. After one day, five to ten mice per group were sacrificed by CO2 asphyxiation.  The spleens  were removed and placed in ice-cold HBSS (Ca2+ and Mg2+ free Hanks’ balanced salt solution [HBSS; BioWhittaker,Walkersville, MD.] supplemented with 2% FCS [HyClone, Logan, Utah] and 10 mM HEPES buffer). The spleens were forced with a 5 ml syringe pestle through a 100 µm-pore nylon mesh cell strainer (Falcon; BD Biosciences). Red blood cells were lysed from spleen samples by incubating the cell suspensions for 5 min at room temperature in erythrocyte lysis buffer (170 mM Tris, 160 mM NH4Cl, pH 7,4) followed by two washes in ice-cold HBSS. CD11b+ cells were purified by positive selection using MACS® CD11b MicroBeads (Miltenyi Biotec) according to the manufacturer´s instructions. To ensure enrichment values of 96-98% purity, the magnetic separation was performed twice. Cell viability and number were assessed by trypan blue exclusion.

tag: infected with 500000 Y. enterocolitica YopH deletion mutant (delta YopH), lethal dose


title: 45_B_CD14_rep2


title: 38_G_20h


title: 29_B_20h_rep2


title: 44_B_20h


title: Gene expression after infection with Y. enterocolitica pYV+, sublethal

description: CD11b+ cells of infected mice; Mice were infected with a sublethal dose of Yersinia enterocolitica WA-314 (pYV+) for one day

source_name: CD11b+ cells of the spleen, infected with Y. enterocolitica pYV+, sublethal

treatment_protocol: Mice were infected with 5000 Y. enterocolitica WA-314 (pYV+), sublethal dose, for one day. After one day, five to ten mice per group were sacrificed by CO2 asphyxiation.  The spleens  were removed and placed in ice-cold HBSS (Ca2+ and Mg2+ free Hanks’ balanced salt solution [HBSS; BioWhittaker,Walkersville, MD.] supplemented with 2% FCS [HyClone, Logan, Utah] and 10 mM HEPES buffer). The spleens were forced with a 5 ml syringe pestle through a 100 µm-pore nylon mesh cell strainer (Falcon; BD Biosciences). Red blood cells were lysed from spleen samples by incubating the cell suspensions for 5 min at room temperature in erythrocyte lysis buffer (170 mM Tris, 160 mM NH4Cl, pH 7,4) followed by two washes in ice-cold HBSS. CD11b+ cells were purified by positive selection using MACS® CD11b MicroBeads (Miltenyi Biotec) according to the manufacturer´s instructions. To ensure enrichment values of 96-98% purity, the magnetic separation was performed twice. Cell viability and number were assessed by trypan blue exclusion.

tag: Age

tag: infected with Y. enterocolitica strain WA-314 (pYV+) for one day


title: 42_G_CD14

tag: GAR


title: 5_B_CD14


title: Gene expression analysis of CD11b+ cells of the spleen; uninfected

description: CD11b+ cells of uninfected C57BL/6 mice

source_name: CD11b+ cells of the spleen, uninfected

treatment_protocol: Five to ten mice per group were sacrificed by CO2 asphyxiation.  The spleens  were removed and placed in ice-cold HBSS (Ca2+ and Mg2+ free Hanks’ balanced salt solution [HBSS; BioWhittaker,Walkersville, MD.] supplemented with 2% FCS [HyClone, Logan, Utah] and 10 mM HEPES buffer). The spleens were forced with a 5 ml syringe pestle through a 100 µm-pore nylon mesh cell strainer (Falcon; BD Biosciences). Red blood cells were lysed from spleen samples by incubating the cell suspensions for 5 min at room temperature in erythrocyte lysis buffer (170 mM Tris, 160 mM NH4Cl, pH 7,4) followed by two washes in ice-cold HBSS. CD11b+ cells were purified by positive selection using MACS® CD11b MicroBeads (Miltenyi Biotec) according to the manufacturer´s instructions. To ensure enrichment values of 96-98% purity, the magnetic separation was performed twice. Cell viability and number were assessed by trypan blue exclusion.

tag: CD11b+ cells of the spleen were isolated


title: Blood; Iberian; Female (BLOO_IB_F)

status: Public on Apr 16 2008

city: Bellaterra

first: Miguel

last: Perez-Enciso

address: Veterinary School

department: Animal Science

institute: Universitat Autonoma Barcelona

description: Blood; Iberian; Female

hyb_protocol: The hybridization was done according to Affymetrix standard protocols.

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray expression data were generated with GeneChip Operating Software (GCOS)

organism: Sus scrofa

source_name: Blood; Iberian; Female

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

growth_protocol: Pigs with one month of age were housed simultaneously, fed the same diets during the fattening period, that lasted two months.

extract_protocol: Total RNA was extracted from 100 mg tissue using the RiboPure™ kit (Ambion, Austin, USA) according to the manufacturer’s protocol.

treatment_protocol: At necropsy, samples of 16 tissues were collected, snap frozen in liquid nitrogen and stored at -80 ºC, until de RNA extraction.

tag: weight

value: 89 days


title: 14_G_20h

tag: patientID

tag: age


title: Blood; Large Wite; Female (BLOO_LW_F)

description: Blood; Large Wite; Female

source_name: Blood; Large Wite; Female

value: 87 days


title: Blood; Iberian; Male (BLOO_IB_M)

description: Blood; Iberian; Male

source_name: Blood; Iberian; Male


title: Ileum; Iberian; Male (ILEU_IB_M)

description: Ileum; Iberian; Male

source_name: Ileum; Iberian; Male


title: Ileum; Iberian; Female (ILEU_IB_F)

description: Ileum; Iberian; Female

source_name: Ileum; Iberian; Female


title: Ileum; Large Wite; Female (ILEU_LW_F)

description: Ileum; Large Wite; Female

source_name: Ileum; Large Wite; Female


title: Blood; Large Wite; Male (BLOO_LW_M)

description: Blood; Large Wite; Male

source_name: Blood; Large Wite; Male


title: Liver; Iberian; Male (LIVR_IB_M)

description: Liver; Iberian; Male

source_name: Liver; Iberian; Male


title: Stomach; Iberian; Male (STOM_IB_M)

description: Stomach; Iberian; Male

source_name: Stomach; Iberian; Male


title: Liver; Large Wite; Female (LIVR_LW_F)

description: Liver; Large Wite; Female

source_name: Liver; Large Wite; Female


title: Liver; Iberian; Female (LIVR_IB_F)

description: Liver; Iberian; Female

source_name: Liver; Iberian; Female


title: Liver; Large Wite; Male (LIVR_LW_M)

description: Liver; Large Wite; Male

source_name: Liver; Large Wite; Male


title: Stomach; Large Wite; Male (STOM_LW_M)

description: Stomach; Large Wite; Male

source_name: Stomach; Large Wite; Male


title: Abdominal fat tissue; Large Wite; Male (FATA_LW_M)

description: Abdominal fat tissue; Large Wite; Male

source_name: Abdominal fat tissue; Large Wite; Male


title: Biceps femoris muscle; Iberian; Female (BIFE_IB_F)

description: Biceps femoris muscle; Iberian; Female

source_name: Biceps femoris muscle; Iberian; Female


title: Back fat tissue; Iberian; Male (FATB_IB_M)

description: Back fat tissue; Iberian; Male

source_name: Back fat tissue; Iberian; Male


title: Abdominal fat tissue; Iberian; Male (FATA_IB_M)

description: Abdominal fat tissue; Iberian; Male

source_name: Abdominal fat tissue; Iberian; Male


title: Abdominal fat tissue; Large Wite; Female (FATA_LW_F)


title: Biceps femoris muscle; Iberian; Male (BIFE_IB_M)

description: Biceps femoris muscle; Iberian; Male

source_name: Biceps femoris muscle; Iberian; Male


title: Back fat tissue; Large Wite; Male (FATB_LW_M)

description: Back fat tissue; Large Wite; Male

source_name: Back fat tissue; Large Wite; Male


title: Abdominal fat tissue; Iberian; Female (FATA_IB_F)

description: Abdominal fat tissue; Iberian; Female

source_name: Abdominal fat tissue; Iberian; Female


title: Ileum; Large Wite; Male (ILEU_LW_M)

description: Ileum; Large Wite; Male

source_name: Ileum; Large Wite; Male


title: Stomach; Large Wite; Female (STOM_LW_F)

description: Stomach; Large Wite; Female

source_name: Stomach; Large Wite; Female


title: Back fat tissue; Iberian; Female (FATB_IB_F)

description: Back fat tissue; Iberian; Female

source_name: Back fat tissue; Iberian; Female


title: Back fat tissue; Large Wite; Female (FATB_LW_F)

description: Back fat tissue; Large Wite; Female

source_name: Back fat tissue; Large Wite; Female


title: Biceps femoris muscle; Large Wite; Male (BIFE_LW_M)

description: Biceps femoris muscle; Large Wite; Male

source_name: Biceps femoris muscle; Large Wite; Male


title: Biceps femoris muscle; Large Wite; Female (BIFE_LW_F)


title: Diaphragm muscle; Large Wite; Male (DIAP_LW_M)

description: Diaphragm muscle; Large Wite; Male

source_name: Diaphragm muscle; Large Wite; Male


title: Diaphragm muscle; Iberian; Male (DIAP_IB_M)

description: Diaphragm muscle; Iberian; Male

source_name: Diaphragm muscle; Iberian; Male


title: Diaphragm muscle; Large Wite; Female (DIAP_LW_F)

description: Diaphragm muscle; Large Wite; Female

source_name: Diaphragm muscle; Large Wite; Female


title: Adrenal medulla; Iberian; Male (ADGM_IB_M)

description: Adrenal medulla; Iberian; Male

source_name: Adrenal medulla; Iberian; Male


title: Thyroid gland; Large Wite; Male (THYG_LW_M)

description: Thyroid gland; Large Wite; Male

source_name: Thyroid gland; Large Wite; Male


title: Adrenal medulla; Large Wite; Female (ADGM_LW_F)

description: Adrenal medulla; Large Wite; Female

source_name: Adrenal medulla; Large Wite; Female


title: Adrenal medulla; Large Wite; Male (ADGM_LW_M)

description: Adrenal medulla; Large Wite; Male

source_name: Adrenal medulla; Large Wite; Male


title: Thyroid gland; Iberian; Male (THYG_IB_M)

description: Thyroid gland; Iberian; Male

source_name: Thyroid gland; Iberian; Male


title: Thyroid gland; Large Wite; Female (THYG_LW_F)

description: Thyroid gland; Large Wite; Female

source_name: Thyroid gland; Large Wite; Female


title: Adrenal medulla; Iberian; Female (ADGM_IB_F)

description: Adrenal medulla; Iberian; Female

source_name: Adrenal medulla; Iberian; Female


title: Thyroid gland; Iberian; Female (THYG_IB_F)

description: Thyroid gland; Iberian; Female

source_name: Thyroid gland; Iberian; Female


title: Diaphragm muscle; Iberian; Female (DIAP_IB_F)

description: Diaphragm muscle; Iberian; Female

source_name: Diaphragm muscle; Iberian; Female


title: Adrenal cortex; Iberian; Female (ADGC_IB_F)

description: Adrenal cortex; Iberian; Female

source_name: Adrenal cortex; Iberian; Female


title: Experiment 2a

city: Caen

first: Benoit

middle: Denis

last: Roussel

address: Bd Becquerel

department: GIP Cyceron

country: France

institute: INSERM

description: The level of expression of each gene was evaluated by calculating the mean ratio “signal/background” for each corresponding spot from the 2 dye-swap experiments. Genes were considered to be expressed if their mean ratio was higher or equal to 1.2. Genes with mean ratio <1.2 in the 2 conditions were not used for further analysis.

hyb_protocol: RNG-MRC_MM25k_EVRY microarrays (Le brigand et al., NAR, 2006) were first incubated in a humid chamber for 2 hours to rehydrate the spots then placed for 1 hour in a dessicator and blocked for 1 hour at room temperature in 50mM Sodium Borate pH 9, 0.003% ethanolamine. Slides were then washed 5 minutes with water and dried by centrifugation. Hybridizations were performed in 50% formamide, 5X Denhardt’s, 4x SSC and 0.1% SDS solution at 42°C for 16 hours. Microarrays were then washed at room temperature 5 minutes in 2X SSC, 0.1% SDS, 5 minutes in 1X SSC, 5 minutes in 0.2X SSC and 5 minutes in 0.05X SSC. Slides were finally dried by centrifugation 4 minutes at 900rpm.

scan_protocol: Microarray images were obtained using a ScanArray Gx scanner (Perkin Elmer). Median signal and median local background intensities were extracted from the images using Genepix 4.1 software (Axon Instruments).

data_processing: Filtered data were submitted to VARAN (http//:www. bionet. espci.fr) for lowess fit normalization and differential expression analysis (Golfier et al.,2004). Normalized log2ratio 21 months/4 months were then used for further statistical analysis by SAM software (Tusher et al., 2001) and t-test with a p-value equal to 5% using TIGR Multiexperiment Viewer (TM4:MeV, http://www.tm4.org/mev.html).

source_name: Neurons 15 DIV

label_protocol: 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy5 mono-Reactive Dye (GE Healthcare) according to the manusfacturer’s instructions. Labelled cDNAs were then purified on Qiaquick PCR prurification kit (Qiagen)

extract_protocol: Total RNAs were extracted from cultured cells or tissues by using the NucleoSpin® RNA II kit from Macherey-Nagel. The samples were lysed in RA1® buffer containing 1% of -mercaptoethanol. After filtration of the lysates on Nucleospin® filter units, total RNAs were purified on Nucleospin® RNA II columns according to the manufacturer’s instructions and eluted with RNase-free water.

value: Human, Stage :15 DIV, Tissue :neurons in vitro

source_name: ARNu

label_protocol: 5µg of total RNA were reverse-transcribed in the presence of 7.5µM random hexamers (GE Healthcare), 75µM aa-dUTP (Sigma-Aldrich) and 100U Rtases Reverse-iT Blend (Thermo scientific) overnight at 37°C. Aminoallyl cDNAs were labelled with Cy3 mono-Reactive Dye (GE Healthcare) according to the manusfacturer’s instructions. Labelled cDNAs were then purified on Qiaquick PCR prurification kit (Qiagen)

extract_protocol: Purchased from Stratagene

tag: Universal Human Reference RNA


title: Neurohypophisis; Iberian; Female (PHYP_IB_F)

description: Neurohypophisis; Iberian; Female

source_name: Neurohypophisis; Iberian; Female


title: Experiment 2b


title: Adrenal cortex; Large Wite; Female (ADGC_LW_F)

description: Adrenal cortex; Large Wite; Female

source_name: Adrenal cortex; Large Wite; Female


title: Adrenal cortex; Large Wite; Male (ADGC_LW_M)

description: Adrenal cortex; Large Wite; Male

source_name: Adrenal cortex; Large Wite; Male


title: Adrenal cortex; Iberian; Male (ACGC_IB_M)

description: Adrenal cortex; Iberian; Male

source_name: Adrenal cortex; Iberian; Male


title: Neurohypophisis; Iberian; Male (PHYP_IB_M)

description: Neurohypophisis; Iberian; Male

source_name: Neurohypophisis; Iberian; Male


title: Adenohypophisis; Iberian; Female (AHYP_IB_F)

description: Adenohypophisis; Iberian; Female

source_name: Adenohypophisis; Iberian; Female


title: Pineal gland; Iberian; Male (PING_IB_M)

description: Pineal gland; Iberian; Male

source_name: Pineal gland; Iberian; Male


title: Adenohypophisis; Iberian; Male (AHYP_IB_M)

description: Adenohypophisis; Iberian; Male

source_name: Adenohypophisis; Iberian; Male


title: Neurohypophisis; Large Wite; Male (PHYP_LW_M)

description: Neurohypophisis; Large Wite; Male

source_name: Neurohypophisis; Large Wite; Male


title: Dye-swap_1

source_name: 2 DIV

value: Human, Stage :2 DIV, Tissue :neurons in vitro


title: Neurohypophisis; Large Wite; Female (PHYP_LW_F)

description: Neurohypophisis; Large Wite; Female

source_name: Neurohypophisis; Large Wite; Female


title: Pineal gland; Iberian; Female (PING_IB_F)

description: Pineal gland; Iberian; Female

source_name: Pineal gland; Iberian; Female


title: Experiment 1

source_name: Neurons 2 DIV

tag: Universal Human reference RNA


title: Adenohypophisis; Large Wite; Male (AHYP_LW_M)

description: Adenohypophisis; Large Wite; Male

source_name: Adenohypophisis; Large Wite; Male


title: Stomach; Iberian; Female (STOM_IB_F)

description: Stomach; Iberian; Female

source_name: Stomach; Iberian; Female


title: Adenohypophisis; Large Wite; Female (AHYP_LW_F)

description: Adenohypophisis; Large Wite; Female

source_name: Adenohypophisis; Large Wite; Female


title: Pineal gland; Large Wite; Male (PING_LW_M)

description: Pineal gland; Large Wite; Male

source_name: Pineal gland; Large Wite; Male


title: Pineal gland; Large Wite; Female (PING_LW_F)

description: Pineal gland; Large Wite; Female

source_name: Pineal gland; Large Wite; Female


title: normal 3370

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: Cancer Insitute

description: normal lung 3370

source_name: primary normal lung tissue 3370

source_name: lung reference


title: normal 2911

description: normal lung 2911

source_name: primary normal lung tissue 2911


title: normal 2841

description: normal lung 2841

source_name: primary normal lung tissue 2841


title: normal 2266

description: normal lung 2266

source_name: primary normal lung tissue 2266


title: ASK cells, ISAV isolate 2, day 3 post-infection

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: We have investigated intracellular responses during cytopathic ISAV infection in the macrophage-like Atlantic salmon kidney (ASK) cell line by microarray analysis (1.8K SFA2.0 immunochip) and a functional assay for glutathione.

scan_protocol: Scanning was performed with GSI Lumonics ScanArray 4000 (Packard Biosciences/PerkinElmer) and images were processed with GenePix 6.0 (Axon Instruments).

data_processing: Low-quality spots marked by GenePix were excluded from the analyses. After subtraction of background and normalization with Lowess, the differential expression was assessed by difference of the mean log-ER (Expression Ratio) from zero (six spot replicates of each gene, Student’s t-test).

label: Cy3 dUTP

organism: Salmo salar

source_name: Control cells

label_protocol: Control and test samples (10 µg RNA in each) were labeled with respectively Cy3-dUTP and Cy5-dUTP (Amersham Biosciences, UK) using the SuperScript™ Indirect cDNA Labeling System (Invitrogen). The cDNA synthesis was performed at 46 °C for 3 h in a 20 µl reaction volume, followed by RNA degradation with 0.2 M NaOH at 37 °C for 15 min and alkaline neutralization with 0.6 M hepes buffer. Labeled cDNA was purified with Microcon YM-30 (Millipore, MA, US). The slides were pretreated with 1 % BSA fraction V, 5 × SSC, 0.1 % SDS (30 min at 50 °C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60 °C in a cocktail containing 1.3 × Denhardt’s, 3 × SSC, 0.3 % SDS, 0.67 µg/µl polyadenylate and 1.4 µg/µl yeast tRNA. After hybridization slides were washed at room temperature in 0.5 SSC and 0.1 % SDS (15 min), 0.5 SSC and 0.01 % SDS (15 min), and twice in 0.06 SSC (3 min each).

growth_protocol: Atlantic salmon kidney (ASK) cells were kindly provided by B. Krossøy (Department of Fisheries and Marine Biology, University of Bergen, Norway). Passages 40-70 were routinely split and cultured in L-15 medium (Cambrex Bio Sciences, Verviers, Belgium) supplemented with 50 μg ml-1 gentamicin, 4 mM L-glutamine, 40 μM β-mercaptoethanol and 10 % fetal calf serum. Cells were mock-infected and incubated at 15 °C in 75 cm2 culture flasks, and harvested at 1, 3, and 5 days post-infection for immediate RNA isolation.

extract_protocol: Total RNA was extracted and purified using combined Trizol/PureLink micro-midi kit (Invitrogen, CA, USA), quantified by Nanodrop (Thermo Fisher Scientific, USA) and checked by gel-electrophoresis. Samples for qPCR were DNAse-treated using Turbo DNA-freeTM (Ambion, TX, USA) according to manufacturer’s instructions. cDNA was synthesized from 1 μg total RNA using random hexamer primers and TaqMan® Reverse Transcription reagents (Applied Biosystems, CA, USA) according to manufacturer’s protocol.

tag: ASK cells, mock infected, day 3

label: Cy5 dUTP

source_name: Infected cells

treatment_protocol: Atlantic salmon kidney (ASK) cells were kindly provided by B. Krossøy (Department of Fisheries and Marine Biology, University of Bergen, Norway). Passages 40-70 were routinely split and cultured in L-15 medium (Cambrex Bio Sciences, Verviers, Belgium) supplemented with 50 μg ml-1 gentamicin, 4 mM L-glutamine, 40 μM β-mercaptoethanol and 10 % fetal calf serum. Cells were infected at MOI = 1 with ISAV isolates I2 (Mjaaland et al., 2005) and I4 (Glesvaer 2/90 strain). Infection was performed at 15 °C in 75 cm2 culture flasks as described (Jorgensen et al., 2006b), and cells were harvested at 1, 3, and 5 days post-infection for immediate RNA isolation

tag: ASK cells, isolate 2 infected, day 3


title: ASK cells, ISAV isolate 2, day 5 post-infection

hyb_protocol: The slides were pretreated with 1 % BSA fraction V, 5 × SSC, 0.1 % SDS (30 min at 50 °C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60 °C in a cocktail containing 1.3 × Denhardt’s, 3 × SSC, 0.3 % SDS, 0.67 µg/µl polyadenylate and 1.4 µg/µl yeast tRNA. After hybridization slides were washed at room temperature in 0.5 SSC and 0.1 % SDS (15 min), 0.5 SSC and 0.01 % SDS (15 min), and twice in 0.06 SSC (3 min each).

treatment_protocol: Atlantic salmon kidney (ASK) cells were kindly provided by B. Krossøy (Department of Fisheries and Marine Biology, University of Bergen, Norway). Passages 40-70 were routinely split and cultured in L-15 medium (Cambrex Bio Sciences, Verviers, Belgium) supplemented with 50 μg ml-1 gentamicin, 4 mM L-glutamine, 40 μM β-mercaptoethanol and 10 % fetal calf serum. Cells were mock-infected and incubated at 15 °C in 75 cm2 culture flasks, and harvested at 1, 3, and 5 days post-infection for immediate RNA isolation.

tag: ASK cells, mock infected, day 5

tag: ASK cells, isolate 2 infected, day 5


title: Hypothalamus; Iberian; Male (HYPT_IB_M)

description: Hypothalamus; Iberian; Male

source_name: Hypothalamus; Iberian; Male


title: normal 1502

description: normal lung 1502

source_name: primary normal lung tissue 1502


title: Hypothalamus; Iberian; Female (HYPT_IB_F)

description: Hypothalamus; Iberian; Female

source_name: Hypothalamus; Iberian; Female


title: normal 1473

description: normal lung 1473

source_name: primary normal lung tissue 1473


title: normal 3208

description: normal lung 3208

source_name: primary normal lung tissue 3208


title: 14_G_20h_rep2

source_name: macrophages

tag: sex


title: normal 1546

description: normal lung 1546

source_name: primary normal lung tissue 1546


title: normal 1345

description: normal lung 1345

source_name: primary normal lung tissue 1345


title: Hypothalamus; Large Wite; Male (HYPT_LW_M)

description: Hypothalamus; Large Wite; Male

source_name: Hypothalamus; Large Wite; Male


title: ASK cells, ISAV isolate 4, day 5 post-infection

tag: ASK cells, isolate 4 infected, day 5


title: normal 1361

description: normal lung 1361

source_name: primary normal lung tissue 1361


title: Olfactory bulb; Iberian; Male (OLFB_IB_M)

description: Olfactory bulb; Iberian; Male

source_name: Olfactory bulb; Iberian; Male


title: normal 1455

description: normal lung 1455

source_name: primary normal lung tissue 1455

source_name: lung reference


title: normal 1144

description: normal lung 1144

source_name: primary normal lung tissue 1144


title: Hypothalamus; Large Wite; Female (HYPT_LW_F)

description: Hypothalamus; Large Wite; Female

source_name: Hypothalamus; Large Wite; Female


title: Olfactory bulb; Iberian; Female (OLFB_IB_F)

description: Olfactory bulb; Iberian; Female

source_name: Olfactory bulb; Iberian; Female


title: normal 1319

description: normal lung 1319

source_name: primary normal lung tissue 1319


title: ASK cells, ISAV isolate 4, day 1 post-infection

source_name: Control cells

tag: ASK cells, mock infected, day 1

source_name: Infected cells

tag: ASK cells, isolate 4 infected, day 1


title: normal 1112

description: normal lung 1112

source_name: primary normal lung tissue 1112


title: ASK cells, ISAV isolate 4, day 3 post-infection

tag: ASK cells, isolate 4 infected, day 3