title: fibroblast-like synoviocytes transfected with mimic-miR-23b

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: FLS transfected with mimic-miR-23b

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

growth_protocol: fibroblast-like synoviocytes were maintained in DME supplemented with 10% (vol/vol) FBS (Hyclone), 100 µg/ml penicillin G, and 100 µg/ml streptomycin.

treatment_protocol: fibroblast-like synoviocytes were transfected with mimic-NC or mimic-miR-23b by Lipofactamin 2000 for two times.

tag: cell origin

value: rheumatoid arthritis (RA) patients

value: fibroblast-like synoviocytes

tag: transfected with


title: fibroblast-like synoviocytes transfected with mimic-NC

status: Public on May 15 2012

type: RNA

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

country: China

institute: Renji Hospital, JiaoTong University School of Medicine

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: FLS transfected with mimic-NC

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

tag: cell type

value: mimic-NC


title: wt-rite-H3-T7-1-b

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

molecule: nuclear RNA

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

tag: strain

source_name: refpool

value: refpool


title: Flp-FBXO25-WT_24 h _ rep1

city: Ribeirão Preto

first: Ana

middle: Carolina

last: Humanes

state: SP

address: Avenida Bandeirantes, 3900

department: Bioquímica e Imunologia

country: Brazil

institute: Universidade de São Paulo

description:
252665213786_GE2-v5_95_Feb07_1_1
Biological replicate 1 of 2.  Flp-In-293-WT-FBXO25 , untreated or treated with tetracyclin for 24 hours.

hyb_protocol: 825 ng of each labeled cRNA was mixed with Agilent Fragmentation Mix and incubated at 60 °C for 30 minutes. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 110 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in Agilent G2545A Hybridization Oven set to 65 °C for 17 hours. Microarray slides were washed according to Agilent’s instruction.

scan_protocol: Scanned on GenePix 4000B microarray scanner (Molecular Devices, USA

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction. Data were processed using TIGR platform. Data were visualized and statistically analysed (t test) using TMeV from TIGR.

source_name: Flp-FBXO25-WT_24 h treated

label_protocol: cDNA was synthesized from 1 µg of total RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for tetracycline treated samples) for 2 hours at 40 ºC.

growth_protocol: Flp-In-293-WT-FBXO25 and Flp-In-293-∆F-FBXO25 cells were grown in DMEM supplemented with 10% fetal bovine serum and the antibodies  Hygromicin and Blasticidin (for clonal selection) at 37ºC in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using Rnaeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Flp-In-293-WT-FBXO25 and Flp-In-293-∆F-FBXO25 cells were treated with tetracycline for 24 and 48 hours to induce Fbxo25 (wild type or mutant) expression

source_name: Flp-FBXO25-WT_ untreated


title: Part 2: MCF 1 day time point rep2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.1, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.1, Biobase_2.8.0

source_name: MCF cells, 24 hour post treatment with 10µM concentration of erlotinib

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

growth_protocol: 1x10^6 cells were plated in a 10 cM dish in media containing 10% FBS, and allowed to adhere for 24 hours before treatment with erlotinib.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was DNAseI treated and further purified using the QIAgen Rneasy mini columns

treatment_protocol: Erlotinib was added to a final concentration of 10µM

tag: time post treatment

value: 24 hours

tag: treatment

value: 10 µM erlotinib

tag: cell line

value: MCF


title: Part 2: MCF 1 day time point rep1


title: Part 2: MCF 0 minute time point rep1

source_name: MCF cells, 0 minutes post treatment with 10µM concentration of erlotinib

value: 0 minutes


title: Part 2: MCF 0 minute time point rep2


title: Part 1: MD 1 day time point rep1

source_name: MDA-MB-453 cells, 24 hours post treatment with 10µM concentration of erlotinib


title: Part 1: MD 1 day time point rep2


title: Part 2: MCF 1 day time point rep3


title: Part 2: MCF 0 minute time point rep3


title: Yra1_intron_B2

city: Ithaca

first: Jeffrey

middle: A

last: Pleiss

state: NY

address: 451 Biotech

department: Molecular Biology and Genetics

institute: Cornell University

hyb_protocol: qPCR was performed using SYBR green as the intercalating dye

scan_protocol: qPCR data was obtained on a Roche 480 LightCycler machine

data_processing: A normalization constant was calculated based on the expression levels of six genes (Scr1, Faa1, U1, Tef5 exon, Tub1 and Srb2 exon) in each of the 5500 mutants, then this value was applied to calculate the normalized levels in each strain. For each primer pair, [ng(xi)] represents the relative nanogram quantity calculated for an individual sample and are presented as raw data files. These values have been extrapolated based on the Cp values and standard curves for each primer pair (to be found in Figure S8, PMID: 22479188). The Sample data table contains the relative amount of RNA in a given strain [RNArel(xi)] values.

label: SYBR green

source_name: Yra1_intron_mid-log phase yeast cells

label_protocol: cDNA was generated using random ninemers

growth_protocol: A collection of deletion and temperature sensitive S. cerevisiae strains were grown in rich media supplemented with 2% glucose to saturation, then back-diluted and grown until they reached mid-log phase. The deletion mutants were grown at 30C, while the temperature sensitive strains were initially grown to saturation at 25C, the shifted to 30C after the back dilution.

extract_protocol: Phenol/Chloroform extraction, followed by DNase I treatment

tag: strains

value: 5500 yeast mutants

tag: target rna


title: Yra1_intron_B1


title: Part 1: MD 0 minute time point rep1

source_name: MDA-MB-453 cells, 0 minutes post treatment with 10µM concentration of erlotinib


title: Part 1: MD 1 day time point rep3


title: Part 1: MD 0 minute time point rep3


title: Part 1: MD 0 minute time point rep2


title: Yra1_intron_A1


title: 1057_MOMA2

type: genomic

city: Cold Spring Harbor

first: Kazimierz

middle: O.

last: Wrzeszczynski

address: One Bungtown Rd.

institute: Cold Spring Harbor Laboratory

description: Genomic DNA was first digested with MspI and ligated with adaptors; for ch1 the sample was then subjected to McrBC treatment while mock treatment for ch2, both followed by PCR amplification. Then a dye (label) swap was performed on the split sample (mock digestion is 635nm_Cy5 in dye swap experiments).

hyb_protocol: The primary restriction endonuclease used is MspI. After the digestion the following linkers were ligated: MspI24mer CAGCATCGAGACTGAACGCAGCAG, and MspI12mer CGCTGCTGCGTT. The 12 mer is not phosphorylated and does not ligate. After ligation the material is cleaned by phenol chloroform, precipitated, centrifuged, and resuspended. The material is divided in two, half being digested by the endonuclease McrBC and the other half being mock digested according to specification by New England Biolabs. The digestion time is 3 hours. As few as four 250-μL tubes were used for each sample pair for amplification of the representation in a 100ul volume reaction.  The cycle conditions were 95°C for 1 min, 72°C for 3 min, for 15 cycles, followed by a 10-min extension at 72°C. The contents of the tubes for each pair were pooled when completed. Representations were cleaned by phenol-chloroform extraction, precipitated, resuspended, and the concentration determined. Representations were run on a gel to check for content, the McrBC digested representation being approximately 100-150bp shorter on average than the mock. DNA was labeled as described with minor changes (Lucito, Healy et al. 2003). Briefly, 2μg of DNA template was placed (dissolved in TE at pH 8) in a 0.2-mL PCR tube. 5 μL of random nanomers (Sigma Genosys) were added brought up to 25 μL with dH2O, and mixed. The tubes were placed in Tetrad at 100°C for 5 min, then on ice for 5 min.  To this 5 μL of NEB Buffer2, 5 μL of dNTPs (0.6nm dCTP, 1.2nm dATP, dTTP, dGTP), 5 μL of label (Cy3-dCTP or Cy5-dCTP) from GE Healthcare, 2 μL of NEB Klenow fragment, and 2 μL dH2O was added. Procedures for hybridization and washing were followed as reported previously (Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ) with the exception that the oven temperature for hybridization was increased to 50°C.  This procedure was performed in duplicate with a dye-swap for the second experiment. The labels were swapped bettween the McrBC treated and Mocks samples, therefore 635nm_Cy5 in channel 1 and 532nm_Cy3 in channel 2, both .ftr raw data files are provided for each sample. For each probe, the geometric mean of the ratios (GeoMeanRatio) of McrBc and control treated samples were then calculated for each experiment and its associated dye swap.

scan_protocol: Microarray Images were scanned on GenePix 4000B scanner and data extracted using Nimblescan software (Nimblegen Systems Inc).

data_processing: For each probe, the geometric mean of the ratios (GeoMeanRatio) of McrBc and control treated samples were then calculated for each experiment and its associated dye swap. The GeoMeanRatios of all the samples in a dataset were then normalized using quantile normalization method (Bolstad, B.M., Irizarry, R.A., Astrand, M. and Speed, T.P. (2003) Bioinformatics, 19, 185-193).

molecule: genomic DNA

source_name: Ovarian Normal/McrBC restriction enzyme

label_protocol: Take 5ug of DNA template and place in a 0.2mL PCR tube and add 5uL of primer solution and bring volume up to 40uL with diH20, mix gently and quickly spin. Then place the tubes in thermal cycler at 100 C for 5 minutes, quickly spin and immediately place on ice for 5 minutes. After this add 6uL of Klenow Buffer, 4uL Cy3-dCTP and 4uL Cy5-dCTP, 2uL klenow fragment, 6uL dNTPs and 2uL diH2O in a total volume of 60uL. Mix by pipetting, quickly spin and incubate at 37 C for 2 hours in thermal cycler. After the incubation combine the labeled samples into one Eppendorf tube and add 50uL Human Cot-I DNA, 10uL yeast tRNA and 200uL low TE. Load this into a Microcon YM-30 filter and spin at 12,600 rcf for 10 minutes. Discard deep purple flow through and add 450uL low TE and spin again. Repeat this until flow through is clear and then invert filter into new tube and spin for 2 minutes. Transfer the sample into a new 0.2mL PCR tube and adjust volume to 10uL with low TE.

extract_protocol: DNA was extracted by first homogenizing tissue in lysis buffer and incubating for 60 minutes followed by 3 phenol extractions and precipitation.

tag: gender

value: female

tag: tissue

value: normal ovary

source_name: Ovarian Normal/Mock digestion control

value: female, ovarian, normal


title: Part 1: BT20 6 hour time point rep3

source_name: BT20 cells, 6 hour post treatment with 10µM concentration of erlotinib

value: 6 hours


title: 1056_MOMA2


title: Part 1: BT20 6 hour time point rep2


title: 1054_MOMA2


title: 1055_MOMA2


title: Ubc13_intron_B1

source_name: Ubc13_intron_mid-log phase yeast cells


title: Yra1_intron_A2


title: 1052_MOMA2


title: Ubc13_intron_A2


title: Ubc13_intron_B2


title: 1053_MOMA2


title: 4879_MOMA2

source_name: Ovarian Tumor/McrBC restriction enzyme

value: ovarian tumor

source_name: Ovarian Tumor/Mock digestion control


title: Part 1: BT20 0 minute time point rep4

source_name: BT20 cells, 0 minutes post treatment with 10µM concentration of erlotinib


title: 1050_MOMA2


title: U3_intron_A1

source_name: U3_intron_mid-log phase yeast cells


title: Part 1: BT20 6 hour time point rep1


title: Ubc13_intron_A1


title: 1048_MOMA2


title: U1_B2

source_name: U1_mid-log phase yeast cells


title: U1_B1


title: U3_intron_B1


title: U3_intron_B2


title: U1_A2


title: U3_intron_A2


title: 5025_MOMA2


title: Part 1: BT20 1 day time point rep2

source_name: BT20 cells, 24 hour post treatment with 10µM concentration of erlotinib


title: Part 1: BT20 30 minute time point rep3

source_name: BT20 cells, 30 minutes post treatment with 10µM concentration of erlotinib

value: 30 minutes


title: Part 1: BT20 1 day time point rep3


title: U1_A1


title: 4936_MOMA2


title: Part 1: BT20 30 minute time point rep2


title: Part 1: BT20 1 day time point rep1


title: 4861_MOMA2


title: Tub3_intron_B1

source_name: Tub3_intron_mid-log phase yeast cells


title: Tub3_intron_A2


title: 4870_MOMA2


title: Tub3_intron_B2


title: 0591_MOMA2


title: Part 1: BT20 30 minute time point rep1


title: Tub1_B2

source_name: Tub1_mid-log phase yeast cells


title: 4779_MOMA2


title: Tub1_B1


title: DES UM3

city: Saint Louis

first: Yan

last: Yin

state: MO

address: 660 S. Euclid Ave. CB8123

department: Medicine

institute: Washington University in St. Louis

description: P5 DES-treated uterine mesenchyme pool3

hyb_protocol: Hybridization was performed by the Genome Technology Access Center (GTAC) at Washington University in St. Louis. Protocol is available upon request.

scan_protocol: Scanning was performed by the Genome Technology Access Center (GTAC) at Washington University in St. Louis. Protocol is available upon request.

data_processing: Data processing was performed by the Genome Technology Access Center (GTAC) at Washington University in St. Louis. Protocol is available upon request. Briefly, Average normalization is used to rescale intensities across multiple arrays and chips. This algorithm is an appropriate choice for experiments that employ a large number of arrays with differences in overall intensity. For average normalization, a scaling factor, Si, is calculated by dividing the average intensity of the virtual array by the average intensity for all arrays in a group.  The bead-type intensities of all arrays in the experiment are normalized by Si. Ipi(norm) = IpiSi Each probe is indexed by p and the number of probes ranges from 1 to n. Each array is indexed by i and the number of arrays ranges from 1 to m (more at http://www.illumina.com/documents/products/technotes/technote_beadstudio_normalization.pdf).

organism: Mus musculus

source_name: uterine mesenchyme isolated from P5 DES-treated uteri

label_protocol: Labeling was performed by the Genome Technology Access Center (GTAC) at Washington University in St. Louis. Protocol is available upon request.

extract_protocol: whole uteri were dissected from P5 mice of the same treatment group and pooled accordingly. Each uterine horn was cut into 3-4 mm pieces and rinsed in Ca2+-, Mg2+-free Hank’s Balanced Salt Solution (HBSS). Tissues were digested in 1% Trypsin in HBSS at 4°C for 1 hour on a rotating platform. An equal volume of 5 mg/ml Bovine Serum Albumin (BSA) was added to stop the digestion. Gentle pressure was applied along each piece with tweezers to squeeze out the epithelia, which were transferred to 1.5 ml tubes by pipetting. The epithelial cells were collected by low-speed centrifugation. The remaining uterine tissue containing mostly mesenchymal cells were transferred to 1.5 ml tubes and spun down. Total RNA was isolated from the cell/tissue pellets with RNA Stat-60 (Tel-Test, Inc., Friendswood, TX) following manufacture’s instruction.

treatment_protocol: DES was dissolved in 100% ethanol to 10mg/ml and further diluted in corn oil to a final concentration of 100 ng/ul. Neonatal female CD1 pups received daily subcutaneous injections of either 20ul oil (control) or 20 ul DES from postnatal day 1 (P1) to P5.

tag: age

value: postnatal day5

value: uterine mesenchyme (UM)

tag: treated with

value: 20ul of 100 ng/ul DES for 5d (P1-P5)


title: 4818_MOMA2


title: Part 1: BT20 0 minute time point rep3


title: 4789_MOMA2


title: 4740_MOMA2


title: Tub1_A2


title: Oil UM3

description: P5 Oil-treated uterine mesenchyme pool3

source_name: uterine mesenchyme isolated from P5 oil-treated uteri

value: 20ul of vehicle (oil) for 5d (P1-P5)


title: Part 1: BT20 0 minute time point rep1


title: control vs MeHg exposure rep 4

city: Eggenstein-Leopoldshafen

first: Jessica

last: Legradi

state: Baden-Wuerttemberg

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genomics ITG

country: Germany

institute: Karlsruhe Institute of Technology

description: biological repeat

hyb_protocol: The hybridistaion of labelled probes was performed following Agilent Microarray hyridisation Kit.

scan_protocol: Samples were scanned on Axon 4000B scanner and the images analysed used GenePix Pro 61

data_processing: The data was analysed using Matlab R2009b, data is background substracted, log2-values calculated and LOWESS- and centering normalized was perfomed. Dye-swaps were combined.  Samples were labeled with Cy5 exposed, Cy3 control.  Reverse is true for _swap.gpr raw data files.

label: Cy3, Cy5

organism: Danio rerio

source_name: whole organism

label_protocol: 2 µg of total RNA from each sample (exposure and control embryos) was labelled with Cyanine3 and Cyanine 5-CTP according to Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: adult fish were maintained in fish water at 28.5 °C, subjected to a photoperiod of 10 hours light and 14 hours dark, and fed with dry flake food and brine shrimp. Embryos were kept in embryo medium.

extract_protocol: Total RNA extraction following Rneasy Mini Kit (Qiagen)

treatment_protocol: 24 hpf embryos were exposed for 24 hours with 60µg/l MeHg and embryos were maintained in fish medium at 28.5 °C as control

value: wild type AB, Tübingen

value: whole embryos

tag: developmental stage

value: 4 dpf

value: fish medium (control)

label: Cy5, Cy3

value: exposed to 3-4 dpf to 60µg/l MeHg


title: Part 1: BT20 0 minute time point rep2

value: 0 minutes

value: 10 µM erlotinib


title: DES UM1

description: P5 DES-treated uterine mesenchyme pool1

value: female


title: Tub1_A1

value: 5500 yeast mutants


title: Tef5_intron_B2

source_name: Tef5_intron_mid-log phase yeast cells


title: 4704_MOMA2


title: control vs MeHg exposure rep 3

description: biological repeat


title: 4661_MOMA2


title: 4713_MOMA2


title: Oil UM1

description: P5 Oil-treated uterine mesenchyme pool1


title: DES UM2

description: P5 DES-treated uterine mesenchyme pool2


title: DES UE3

description: P5 DES-treated uterine epithelium pool3

source_name: uterine epithelium isolated from P5 DES-treated uteri

value: uterine epithelium (UE)


title: 4737_MOMA2


title: Tub3_intron_A1


title: control vs MeHg exposure rep 2

description: biological repeat


title: 4762_MOMA2


title: 4641_MOMA2


title: Tef5_intron_A1


title: 4600_MOMA2


title: Oil UM2

description: P5 Oil-treated uterine mesenchyme pool2


title: DES UE2

description: P5 DES-treated uterine epithelium pool2


title: Tef5_intron_A2


title: 4656_MOMA2


title: control vs MeHg exposure rep 1

description: biological repeat


title: 4589_MOMA2


title: DES UE1

description: P5 DES-treated uterine epithelium pool1


title: Tef5_exon_B1

source_name: Tef5_exon_mid-log phase yeast cells


title: Oil UE3

description: P5 Oil-treated uterine epithelium pool3

source_name: uterine epithelium isolated from P5 oil-treated uteri


title: Tef5_exon_A2


title: Oil UE2

description: P5 Oil-treated uterine epithelium pool2


title: Tef5_exon_A1


title: Gill_tissue_K+12_Rep4_msh5

city: Bloomington

first: Claire

last: Burns

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

hyb_protocol: Microarray slides were blocked prior to hybridisation with 5xSSC, 0.1%SDS, 0.1mg.ml-1 BSA at 42oC for 45 min, after which slides were rinsed twice in room temperature 0.1xSSC for 5 min each, followed by a final 10s rinse in water.  Slides were dried by centrifugation for 1min in a Labnet C1303 slide spinner. Arrays were placed in Corning hybridization chambers and mSeries Lifterslips (Erie Scientific) placed over the array grids.  Labelled cDNAs were combined in 50μl with 30% deionized formamide (Ambion), 5xSSPE, 0.2% SDS, 1μg.μl-1 tRNA (Invitrogen), 40ng.μl-1 oligo dA (Invitrogen).  The hybridization mixture was heated at 100oC for 2min, cooled to 25oC, and applied to the microarray slide.  Slides were hybridised for 16 hours at 42oC, then washed for 5 min each in 1xSSC, 0.03%SDS (37oC), then 0.2xSSC (ambient temperature), and finally 0.1xSSC (ambient temperature).  Slides were dried by centrifugation, as previously, and scanned immediately.

scan_protocol: Microarray slides were scanned using a GenePix 4200A scanner (Molecular Devices).  PMT settings were adjusted so the dye channels were balanced, with a few saturated spots, to maximize data capture.  Spots were identified using GenePix Pro software (Molecular Devices) and manual inspection. Scans were quality assessed using the Basic Hybridization Analysis R script (http://cgb.indiana.edu/downloads/1). Spots were manually flagged to be excluded from analysis if there were areas of poor quality such as scratches or dust.  Spots were also flagged for omission, using GenePix software, if they fulfilled any of the following criteria: manually flagged, buffer only spots, spots not found, percentage of saturated pixels in both channels > 3,  spot pixels < 40.

data_processing: Data normalization and filtering were performed using the Bioconductor package (http://www.bioconductor.org/) within the R statistical framework (http://www.r-project.org/).  The OLIN package was used for intra-slide normalization and log2 transformation.  Data were included in further analysis if two of the four replicates were not flagged.  Ratio values were exported for further analysis, with individual flagged ratio values omitted.  Statistical significance of changing expression was assessed using the one class function in Significance Analysis of Microarrays (SAM) software

label: Alexa fluor 647

organism: Coprinopsis cinerea

source_name: C. cinerea excised gill tissue, 12 hours after karyogamy

label_protocol: 20ug of total RNA were reverse transcribed and labelled with Alexa fluor using the Invitrogen Superscript Indirect labeling kit.

growth_protocol: Dikaryotic strains wre grown at 37 C for two days and then moved to 25 C with a cycle of 8 hours dark, 16 hours light.

extract_protocol: At the pertinent timepoint, gill tissue from 7-10 mushrooms was separated from the mushroom stipe, and the veil removed.  Gill tissue was immediately frozen in liquid nitrogen. RNA was extracted from all the tissue collected using RNeasy Plant mini-prep kit.

treatment_protocol: no treatments

value: gill

tag: timepoint

value: 12 hrs after karyogamy

label: Alexa fluor 555

value: Java;5-5 x Java;5-4


title: Tef5_exon_B2


title: 4455_MOMA2

source_name: Ovarian Tumor/McrBC restriction enzyme

value: ovarian tumor


title: 4633_MOMA2

source_name: Ovarian Tumor/Mock digestion control


title: Srb2_exon_B2

source_name: Srb2_exon_mid-log phase yeast cells


title: 4275_MOMA2


title: 4398_MOMA2


title: Tef5_intron_B1


title: Srb2_exon_B1


title: Gill_tissue_K+12_Rep2_msh5


title: Gill_tissue_K+9_Rep4_msh5

source_name: C. cinerea excised gill tissue, 9 hours after karyogamy

value: 9 hrs after karyogamy


title: Gill_tissue_K+12_Rep3_msh5


title: 4203_MOMA2


title: Gill_tissue_K+12_Rep1_msh5


title: Srb2_exon_A2


title: CD27- NK cells rep3

city: Montréal

first: Sylvie

last: Lesage

address: 5415, boul. de l'Assomption

country: Canada

institute: Hopital Maisonneuve-Rosemont

description: SAMPLE 9

hyb_protocol: Standard Illumina hybridation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were log2-transformed and quantile normalized in R using limma package

source_name: CD27- NK cells

label_protocol: Biotinylated cRNA

extract_protocol: RNA was extracted with trizol reagents, followed by purification with Quiagen column clean-up. Quality control and integry checks of RNA samples with Bioanalyser 2100 (Agilent).

value: male

value: 7-10 weeks old

value: 10 pooled spleens ex vivo

value: CD27- NK cells


title: 4305_MOMA2


title: CD27- NK cells rep2

description: SAMPLE 8


title: Oil UE1

description: P5 Oil-treated uterine epithelium pool1

value: postnatal day5

value: 20ul of vehicle (oil) for 5d (P1-P5)


title: CD27- NK cells rep1

description: SAMPLE 7

value: 8 pooled spleens ex vivo


title: Gill_tissue_K+9_Rep1_msh5


title: Gill_tissue_K+9_Rep3_msh5


title: Srb2_exon_A1


title: Gill_tissue_K+9_Rep2_msh5


title: Gill_tissue_K+6_Rep4_msh5

source_name: C. cinerea excised gill tissue, 6 hours after karyogamy

value: 6 hrs after karyogamy


title: Scr1_B2

source_name: Scr1_mid-log phase yeast cells


title: Gill_tissue_K+6_Rep3_msh5


title: 4124_MOMA2


title: CD27+ NK cells rep3

description: SAMPLE 6

source_name: CD27+ NK cells

value: CD27+ NK cells


title: Scr1_B1


title: CD27+ NK cells rep2

description: SAMPLE 5


title: Scr1_A2


title: Gill_tissue_K+6_Rep2_msh5


title: B220+ NK cells rep3

description: SAMPLE 3

source_name: B220+ NK cells

value: B220+ NK cells


title: 4126_MOMA2

value: female


title: 4164_MOMA2


title: CD27+ NK cells rep1

description: SAMPLE 4


title: Gill_tissue_K+3_Rep4_msh5

source_name: C. cinerea excised gill tissue, 3 hours after karyogamy

value: 3 hrs after karyogamy


title: Rpl31B_intron_A2

source_name: Rpl31B_intron_mid-log phase yeast cells

value: 5500 yeast mutants


title: Scr1_A1


title: B220+ NK cells rep2

description: SAMPLE 2


title: 4087_MOMA2


title: Rpl31B_intron_B1


title: Gill_tissue_K+6_Rep1_msh5

value: gill


title: Gill_tissue_K+3_Rep2_msh5

value: Java;5-5 x Java;5-4


title: Gill_tissue_K+3_Rep3_msh5


title: B220+ NK cells rep1

description: SAMPLE 1


title: 4114_MOMA2

value: ovarian tumor


title: 4047_MOMA2


title: Rpl31B_intron_A1


title: Rpl31B_intron_B2


title: Rec107_B2

source_name: Rec107_mid-log phase yeast cells


title: Gill_tissue_K+3_Rep1_msh5


title: Gill_tissue_K_Rep3_msh5

source_name: C. cinerea excised gill tissue, at karyogamy

value: at karyogamy


title: Gill_tissue_K_Rep4_msh5


title: Rec107_A2


title: Rec107_A1


title: 4064_MOMA2


title: Gill_tissue_K-3_Rep4_msh5

source_name: C. cinerea excised gill tissue, 3 hours before karyogamy

value: 3 hrs before karyogamy


title: Faa1_B2

source_name: Faa1_mid-log phase yeast cells


title: Gill_tissue_K-3_Rep3_msh5


title: Gill_tissue_K-3_Rep2_msh5


title: Gill_tissue_K_Rep2_msh5


title: Gill_tissue_K_Rep1_msh5


title: Faa1_B1


title: 4044_MOMA2


title: Rec107_B1


title: Faa1_A2


title: Gill_tissue_K-3_Rep1_msh5


title: 3942_MOMA2


title: Gill_tissue_K+12_Rep3_rad50

value: 12 hrs after karyogamy


title: 4035_MOMA2


title: 3935_MOMA2


title: Gill_tissue_K+12_Rep2_rad50


title: Gill_tissue_K+12_Rep4_rad50


title: Faa1_A1


title: 4078_MOMA2


title: Gill_tissue_K+12_Rep1_rad50


title: 3917_MOMA2


title: 3887_MOMA2


title: 4004_MOMA2


title: Du_552-8_CMV-WT_Rep3_ATH1

city: Loughborough

first: nasc

last: nasc

address: Sutton bonington Campus

department: Plant&Crop Sciences

country: United Kingdom

institute: NASC

description: Four days in dark at 4 celsius degree  Plants were grown on 4:1 soil/sand mixture, amended with 0.002% (w/v) intercept 5GR. They were maintained at 21 degrees celsius in a custom built growth room, under cycles of 8 hours light/16 hours dark and at 60% relative humidity.  Levington M3 compost (Scotts, Chilworth, Ipswich, UK)  Watered daily until soil was moist 21 °C average, 21 °C day, 21 °C night 60 % average, 60 % day, 60 % night

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system

organism: Arabidopsis thaliana

source_name: CMV-WT

label_protocol: Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"

extract_protocol: Qiagen RNAeasy kit protocol

tag: ecotype

value: Aerial tissues


title: Gill_tissue_K+9_Rep4_rad50

value: 9 hrs after karyogamy


title: Du_552-7_Mock-At_Rep3_ATH1

source_name: Mock-At


title: Du_552-9_CMV-A2b_mutant_Rep3_ATH1


title: Gill_tissue_K+9_Rep3_rad50


title: Du_552-6_CMV-A2b_mutant_Rep2_ATH1


title: 3998_MOMA2

source_name: Ovarian Tumor/McrBC restriction enzyme


title: Gill_tissue_K+9_Rep2_rad50


title: Du_552-5_CMV-WT_Rep2_ATH1


title: 4015_MOMA2

source_name: Ovarian Tumor/Mock digestion control


title: 3684_MOMA2


title: Gill_tissue_K+9_Rep1_rad50


title: Du_552-4_Mock-At_Rep2_ATH1


title: Gill_tissue_K+6_Rep4_rad50


title: 3658_MOMA2


title: 3666_MOMA2


title: rice (IKP)-root-3weeks-replicate2

city: Louvain-la-Neuve

first: Stanley

last: Lutts

address: Croix du sud 4-5 bte L7.07.13

department: Earth and Life Institute

country: Belgium

institute: Université catholique de Louvain

description: biological replicate 2 of 2

hyb_protocol: Hybridization of the labeled cDNA (0.3 microg per sample) were added to hybridization buffer (Agilent In Situ Hybridization Kit Plus)  and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially according to Agilent instructions.

scan_protocol: Scanned on an Agilent Scanner G2565B Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

label: Alexa Fluor 555

organism: Oryza sativa

source_name: IKP-control_root_3 wks

label_protocol:
First strand cDNA was synthetized from 10 microg RNA. Synthesized cDNA were purified and labeled with Alexa Fluor 555 and Alexa Fluor 647. Experiments were carried out according to instructions of the Superscript Plus Indirect cDNA Labeling system (Invitrogen).
The quality of the labeled cDNA and its concentration were respectively measured with the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA) and ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: plants where grown in hydroponic solution (Yoshida, 1976) in greenhouse (heated and extra lighting  to expose plants to a minimum 12 h day length at a minimum PAR of 150 µmol m-2 s-1 at the top of the canopy).

extract_protocol: Total RNA was prepared from 100 mg of roots or shoots (of pooled plants) using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron ( FeSO4•7H2O) for 3 days and 3 weeks in hydroponic culture

tag: cultivar

value: I Kong Pao

value: 25 days old

tag: sample type

value: control (no treatment)

tag: treatment duration

value: 3 weeks

label: Alexa Fluor 647

source_name: IKP-iron_root_3 wks

value: 125 ppm ferrous iron


title: Du_552-3_CMV-A2b_mutant_Rep1_ATH1


title: 3872_MOMA2


title: 3635_MOMA2


title: Gill_tissue_K+6_Rep3_rad50

value: 6 hrs after karyogamy


title: rice (IKP)-shoot-3weeks-replicate2

description: biological replicate 2 of 2

source_name: IKP-control_shoot_3 wks

source_name: IKP-iron_shoot_3 wks


title: 3630_MOMA2

value: female


title: Du_552-1_Mock-At_Rep1_ATH1


title: Du_552-2_CMV-WT_Rep1_ATH1


title: rice (IKP)-root-3days-replicate2

description: biological replicate 2 of 2

source_name: IKP-control_root_3 days

value: 3 days

source_name: IKP-iron_root_3 days


title: 3581_MOMA2


title: Gill_tissue_K+6_Rep1_rad50

source_name: C. cinerea excised gill tissue, 6 hours after karyogamy


title: Gill_tissue_K+6_Rep2_rad50


title: erf6-1 mutant HL treated sample

city: Kaifeng

first: Chun-Peng

last: Song

state: Henan

address: 85 Minglun street

institute: Henan University

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: three week oldseedlings

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

treatment_protocol: 2000 umol m-2s-1 illumination for 2 h

value: young seedling

value: 2000 umol m-2s-1 illumination for 2 h

tag: genetic background

tag: genotype


title: rice (IKP)-shoot-3days-replicate2

description: biological replicate 2 of 2


title: wild-type HL treated sample

value: wild type


title: 3376_MOMA2

value: ovarian tumor


title: rice (IKP)-root-3weeks-replicate1

description: biological replicate 1 of 2


title: 3654_MOMA2


title: rice (IKP)-root-3days-replicate1

description: biological replicate 1 of 2


title: Gill_tissue_K+3_Rep4_rad50

source_name: C. cinerea excised gill tissue, 3 hours after karyogamy

tag: strain

value: gill

value: 3 hrs after karyogamy

value: Java;5-5 x Java;5-4


title: erf6-1 mutant untreated sample

tag: treatment

value: control


title: 3417_MOMA2


title: wild-type untreated sample


title: Gill_tissue_K+3_Rep3_rad50


title: renal biopsy samples from eight SLE individual_8

description:
Test
SLE-08

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous housekeeping MammU6. [delta] CT =  CTsample - CTreference.

label: FAM

source_name: renal biopsy samples from SLE patient

label_protocol: Individual TaqMan® MicroRNA Assays cards were performed for miRNA profiling following the Manufacturer’s instructions .Reverse transcription was performed from 50ng total RNA per sample using Megaplex™ RT Pools(Applied Biosystems). Then add Megaplex™ PreAmp Primers(Applied Biosystems) for additional assay sensitivity. Quantitative real-time PCR were performed on an AbiPrism 7900 HT cycler (Applied Biosystems) with 1 cycle at 50℃ for 2 minutes and 95℃ for 10 minutes and 40 cycles at 94℃ for 15 seconds and 60℃ for 60 seconds.

tag: tissue source

value: systemic lupus erythematosus (SLE) patient

value: kidney


title: rice (IKP)-shoot-3days-replicate1

description: biological replicate 1 of 2

source_name: IKP-control_shoot_3 days

value: I Kong Pao

value: 25 days old

source_name: IKP-iron_shoot_3 days


title: Gill_tissue_K+3_Rep1_rad50


title: Gill_tissue_K+3_Rep2_rad50


title: renal biopsy samples from eight SLE individual_7

description:
Test
SLE-07


title: 3546_MOMA2


title: Gill_tissue_K_Rep4_rad50

source_name: C. cinerea excised gill tissue, at karyogamy

value: at karyogamy


title: renal biopsy samples from eight SLE individual_6

description:
Test
SLE-06


title: 3337_MOMA2


title: rice (IKP)-shoot-3weeks-replicate1

description: biological replicate 1 of 2

value: control (no treatment)

value: 3 weeks

value: 125 ppm ferrous iron


title: Gill_tissue_K_Rep3_rad50


title: renal biopsy samples from eight SLE individual_5

description:
Test
SLE-05


title: 3331_MOMA2

value: female


title: 3482_MOMA2


title: Brain_Schizophrenia_subject12

city: Belmont

first: Sarah

last: Mauney

address: 115 Mill St.

institute: McLean Hospital

description:
S12
Used for analysis

hyb_protocol: Labeled aRNA underwent hybridization as explained in the TURBO Biotin labeling™ kit (end-labeling; Life Technologies Corporation). Gene expression profiling was performed using the Affymetrix Human X3P GeneChip®, which possesses an extreme 3' bias in its probe design and hence is particularly suitable for samples that are prone to RNA degradation, such as postmortem human brain tissue. The hybridization and scanning procedures were performed at the Partners HealthCare Center for Personalized Genetic Medicine (Cambridge, MA).

scan_protocol: The scanning procedures were performed at the Partners HealthCare Center for Personalized Genetic Medicine (Cambridge, MA).

data_processing: Each array was scanned twice and the Affymetrix Microarray Suite 5.1 software averaged the two images to compute an intensity value for each probe cell within each probe set. For the quality control step, we employed the dChip and Partek® software’s built-in function (Copyright, Partek Inc., St. Louis, MO). We then normalized all data with Partek’s standard normalization method (i.e. data has a mean of zero and a variance of one, and each column for each sample was divided by the average of all control samples). After a principal component analysis revealed the contribution of batch effect (scan date) to the observed variance, an Analysis of Covariance (ANCOVA) was performed with diagnosis and batch effect as covariates and the false discovery rate set at 10%. Differentially expressed genes were visualized by performing unsupervised hierarchical clustering as stringency of the filtering criteria (i.e. fold-change and p-value) was being varied to determine a representative gene list for pathway analyses. We employed three approaches to explore the biological significance of our expression data. First, differentially expressed genes were manually grouped to elucidate gene families that appeared to be dysregulated in schizophrenia. Second, pathway analyses were performed with two web-based algorithms, Ingenuity Pathway Analysis (Ingenuity® Systems) and MetaCore from GeneGo Inc. to map the differentially expressed genes onto biological functions and canonical pathways. With Ingenuity, the significance for each of the identified pathways was determined via a Fisher’s exact test, whereas GeneGo makes use of their algorithm for hypergeometric distribution, identifying pathways overrepresented with significant genes. Third, literature mining was performed to elucidate which of these pathways or gene families might be particularly pertinent for pyramidal neuronal functions and dendritic/synaptic architecture and plasticity. We also made note of differentially expressed genes that have been implicated as schizophrenia risk genes.

source_name: pyramidal neurons layer 3 STG_schizophrenia

label_protocol: The TURBO Biotin labeling™ kit (end-labeling; Life Technologies Corporation) was used to label the aRNA obtained from amplified samples (~15 μg).

extract_protocol: RNA extraction and isolation was performed using the Picopure™ RNA Isolation kit (Life Technologies Corporation), with a DNase step (Qiagen Inc., CA). This typically resulted in approximately 1-25 ng of total RNA. Total RNA integrity was evaluated by inspection of the 18S/28S peaks of the electropherograms and virtual gel generated by Experion™ HighSens LabChip (Bio-Rad, CA) and the RNA Quality Indicator (RQI). If there was evidence of significant degradation, as indicated by a large area under the curve or if the peaks were not visible, the cells were re-captured from tissue sections stored at -80°C. The extracted RNA underwent two rounds of linear amplification using the RiboAmp® kit (Life Technologies Corporation, CA). A dilution of the resulting aRNA (approximately 250 ng/µl) was used to determine the mRNA transcript length with the StdSens Labchip (Experion, Bio-Rad, CA). The concentration and purity were determined by NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE) analysis at an optical density of A260 and A280. Only samples with transcript lengths extending past 600 nucleotides (eFigure 1) and an optical density ratio of higher than 1.8 were labeled for gene expression profiling

treatment_protocol: Liquid nitrogen vapor fresh-frozen blocks containing the superior temporal gyrus (STG) from subjects were cut on a cryostat at 8μm. These sections were stained with the Histogene™ quick staining kit (Life Technologies Corporation, CA) and identified in layer 3 of the STG strictly according to the following criteria: (1) cells with pyramidal morphology and (2) clearly identifiable proximal apical and basal dendrites. Approximately 500 neurons per subject were extracted from the surrounding tissue via laser capture microdissection (Arcturus XT™ system, Life Technologies Corporation, CA).

tag: post mortem interval (pmi)

value: brain

value: superior temporal gyrus (STG)

tag: cell type

value: pyramidal cells in layer III of the STG


title: Brain_Schizophrenia_subject11

description:
S11
Used for analysis

tag: gender

value: male


title: Brain_Schizophrenia_subject8

description:
S8
Used for analysis

tag: tissue


title: 3329_MOMA2

value: ovarian tumor


title: Brain_Schizophrenia_subject6

description:
S6
Used for analysis

tag: age


title: 3122_MOMA2


title: renal biopsy samples from eight SLE individual_2

description:
Test
SLE-02


title: 3328_MOMA2


title: 3137_MOMA2


title: renal biopsy samples from eight SLE individual_3

description:
Test
SLE-03


title: 3159_MOMA2


title: Brain_Schizophrenia_subject5

description:
S5
Used for analysis


title: renal biopsy samples from eight SLE individual_4

description:
Test
SLE-04


title: Gill_tissue_K_Rep1_rad50

value: gill


title: renal biopsy samples from eight SLE individual_1

description:
Test
SLE-01


title: 3118_MOMA2


title: Gill_tissue_K_Rep2_rad50

value: Java;5-5 x Java;5-4


title: siFOXM1_Dox_2

city: Houston

first: Yun-Yong

last: Park

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: UT, MD Anderson Cancer Center

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48803 probes on the Human-Ht12 beadChip ver. 3 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to a ver. 3 of the Illumina Human-Ht-12 BeadChip (48K) according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

source_name: MDA-MB-231 Breast Cacner Cell

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina?? TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana?? RNA Isolation labeling kit (Ambion Inc) according to the manufacturer¢®?s protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: cell line

tag: transfection

value: doxycline + doxorubicin


title: siFOXM1_Dox_1


title: Rif1-depleted HeLa_rep2

city: Setagaya-ku

first: Satoshi

last: Yamazaki

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Genome Dynamics Project

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: For each two-color comparison, Cy3- and Cy5-labeled DNA were mixed and fragmented using the Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit protocol. Hybridizations were performed for 24 hours at 65ºC at 20 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with a Laser Scanner GenePix 4000B (Molecular Devices) using appropriate gains on the PMT in both channels, with a scan resolution of 5µm.

data_processing: All data were obtained from two independent biological replicates in which early and late replicating DNA were labeled reciprocally in each experiment. Agilent Feature Extraction Software (v 9.5.1.1) was used for quantification of images, background subtraction and linear normalization. Raw early / late (log2 ratio) data were calculated using the combining algorithm. Smoothed replication-timing profiles were processed by triangular algorithm with a moving average of 100-kb windows (Genomic workbench software, Agilent).

source_name: Early-replicating DNA of Rif1-depleted HeLa cells

label_protocol: 2µg of DNA sample was labeled using the Agilent Genomic DNA Enzymatic Labeling Kit according to the manufacturer's protocol.

growth_protocol: HeLa (human cervical cancer) cells were maintained in Dulbecco's modified Eagle's Medium supplemented with 10 % fetal bovine serum at 37°C.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to Agilent oligonucleotide arrays, as described in Ryba et al [2011]. Briefly, HeLa cells were pulse-labeled with BrdU and sorted into two gates in S-phase by FACS Aria III (early and late-S-phase). Isolation of BrdU-labeled DNA with immunoprecipitation has also been described in Ryba et al. Nascent DNA was amplified in the linear range (20 cycles) by using a WGA2 kit (whole-genome amplification; Sigma-Aldrich) according to the protocol provided by the supplier and the unbiased amplification products were then purified with a PCR cleanup kit (QIAGEN).

treatment_protocol: HeLa cells were transfected with control and Rif1 siRNA for 72hrs using transfection reagent (Oligofectamine: Invitorgen)

value: HeLa

value: Rif1 siRNA

tag: time point

value: early-replicating

source_name: Late-replicating DNA of Rif1-depleted HeLa cells

value: late-replicating


title: tumor adjacent kidney tissues from kidney cancer individual_4

description:
Control
Nor-04

source_name: tumor-adjacent kidney tissues from kidney cancer patient

value: kidney cancer patient

value: kidney


title: Brain_Schizophrenia_subject1

description:
S1
Used for analysis


title: 3079_MOMA2

source_name: Ovarian Tumor/McrBC restriction enzyme

source_name: Ovarian Tumor/Mock digestion control


title: 3338_MOMA2


title: 3097_MOMA2


title: siFOXM1_Dox_3


title: siLuc1_Dox_3

value: siLuc


title: Brain_Schizophrenia_subject2

description:
S2
Used for analysis


title: Brain_Schizophrenia_subject3

description:
S3
Used for analysis


title: tumor adjacent kidney tissues from kidney cancer individual_2

description:
Control
Nor-02


title: tumor adjacent kidney tissues from kidney cancer individual_3

description:
Control
Nor-03


title: tumor adjacent kidney tissues from kidney cancer individual_1

description:
Control
Nor-01


title: 3113_MOMA2


title: 2857_MOMA2


title: 2853_MOMA2


title: Rif1-depleted HeLa_rep1


title: HeLa_rep1

source_name: Early-replicating DNA of HeLa cells

value: control siRNA

source_name: Late-replicating DNA of HeLa cell


title: Flax_outer_rep2_25-mers arrays

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité scientifique

country: France

institute: University Lille 1

description: This sample is of flax stem outer tissues. It is the second of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.

hyb_protocol: Microarrays were hybridized at 38°C (25-mers arrays) and at 42°C (60-mers arrays) during 16 to 18h with 6µg of Cy3 labelled ds-cDNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5µm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix Pro 6.0 software (Axon).

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Linum usitatissimum

source_name: Flax stem outer tissues

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 10 µg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 250 ng random hexamer primers. ds-cDNA was cleaned and labeled in accordance with the Nimblegen Gene Expression Analysis protocol (Nimblegen Systems, Inc., Madison, WI, USA).

growth_protocol: Linum usitatissimum (var. Diane) plants were grown in a growth chamber (light/night cycles 16h (22°C)/8h (19°C), 50% humidity and light intensity of 400 µE s-1 m-2) and harvested after nine weeks of grown. The outer fiber-bearing tissues were peeled off and inner tissues (xylem) from a 15 cm long stem section were cut into short fragments before both tissues were frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated from the collected tissues. 100 mg of frozen stem tissues were ground in liquid nitrogen using the Trizol method (Invitrogen, Carlsbad, CA). Total RNAs were purified using the RNeasy Plant kit (Qiagen) according to the manufacturer's instructions. The genomic DNA was eliminated after treatment with Dnase I for 20 min at 37°C using the DNA-free kit (Ambion, Austin, TX, USA). RNA was checked for purity and degradation by capillary electrophoresis using the Bio-Analyzer Experion (Bio-Rad; RNA Standard Sens kit; RNA StdSens chips).

tag: tissues

value: outer stem tissues

tag: array type

value: Nimblegen 25-mers


title: siFOXM1_3

value: doxycline


title: Brain_Schizophrenia_subject4

description:
S4
Used for analysis

value: female

value: brain

value: superior temporal gyrus (STG)

value: pyramidal cells in layer III of the STG


title: HeLa_rep2


title: siLuc1_Dox_2


title: Brain_Control_subject12

description:
C12
Used for analysis

source_name: pyramidal neurons layer 3 STG_control


title: siLuc1_Dox_1


title: siFOXM1_2


title: Flax_outer_rep1_25-mers arrays

description: This sample is of flax stem outer tissues. It is the first of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.


title: siLuc_3


title: Brain_Control_subject10

description:
C10
Used for analysis


title: Flax_outer_rep3_25-mers arrays

description: This sample is of flax stem outer tissues. It is the third of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.


title: Brain_Control_subject6

description:
C6
Used for analysis


title: Brain_Control_subject5

description:
C5
Used for analysis

value: male


title: siFOXM1_1


title: 2801_MOMA2

value: ovarian tumor


title: siLuc_2


title: Brain_Control_subject4

description:
C4
Used for analysis


title: Brain_Control_subject8

description:
C8
Outlier-excluded after normalization; ignored for analysis


title: Brain_Control_subject11

description:
C11
Used for analysis


title: Brain_Control_subject1

description:
C1
Used for analysis


title: Flax_inner_rep3_25-mers arrays

description: This sample is of flax stem inner tissues. It is the third of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.

source_name: Flax stem inner tissues

value: inner stem tissues


title: Flax_inner_rep2_25-mers arrays

description: This sample is of flax stem inner tissues. It is the second of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.


title: Brain_Control_subject2

description:
C2
Used for analysis


title: CONTROL_M_M1

status: Public on May 14 2012

city: La Jolla

first: Kristopher

middle: L.

last: Nazor

state: CA

address: 10550 North Torrey Pines Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Genome Studio software v2010.3, Normalization method: Average beta values are range scaled.

source_name: Methylated control

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: sample type

value: Methylated control_Replicate 2


title: CONTROL_M_M3

value: Methylated control_Replicate 4


title: CONTROL_M_M2

value: Methylated control_Replicate 3


title: Flax_inner_rep1_25-mers arrays

description: This sample is of flax stem inner tissues. It is the first of three technical replicates used in this experiment. Hybridization was on 25-mers arrays.


title: 2834_MOMA2


title: 0668_MOMA2


title: CONTROL_U_U1

source_name: Unmethylated control

value: Unmethylated control _Replicate 2


title: CONTROL_H_H1

source_name: Partially methylated control

value: Partially methylated control_Replicate 2


title: CONTROL_M_M

value: Methylated control_Replicate 1


title: CONTROL_H_H2

value: Partially methylated control_Replicate 3


title: 2842_MOMA2


title: Somatic.Tissue___Ureter_Adult__Patient1_Male_92.29.1.2

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

value: stem cell matrix version 342

tag: tissue type

value: Ureter

tag: fetal vs adult tissue

value: Adult

tag: patient id

value: Male


title: CONTROL_U_U2

value: Unmethylated control _Replicate 3


title: CONTROL_U_U3

value: Unmethylated control _Replicate 4


title: CONTROL_U_U

value: Unmethylated control _Replicate 1


title: siLuc_1

value: siLuc

tag: treatment

value: doxycline


title: CONTROL_H_H3

value: Partially methylated control_Replicate 4


title: Somatic.Tissue___Pancreas_Adult__Patient1_Male_220.29.1.6

value: Pancreas


title: Somatic.Tissue___Spleen_Adult__Patient1_Male_91.29.1.7

value: Spleen


title: Somatic.Tissue___Stomach_Adult__Patient1_Male_101.29.1.5

value: Stomach


title: Somatic.Tissue___Small.intestine_Fetal_15wk_Patient30_Male_146.412.1.1

value: Fetal

tag: gestational age


title: Somatic.Tissue_Prostate___Adult__Patient1_Male_ILMN.4

tag: cell type

value: Prostate


title: Somatic.Tissue___Lung_Adult__Patient1_Male_94.29.1.7

value: Lung

tag: gender


title: Somatic.Tissue_Heart___Adult__Patient1_Male_102.29.1.6

value: Heart


title: Somatic.Tissue___Lung_Fetal_15wk_Patient30_Male_94.412.1.1

value: stem cell matrix version 342


title: Somatic.Tissue___Brain_Fetal_15wk_Patient30_Male_21.412.1.1

value: Brain


title: Somatic.Tissue___Bladder_Adult__Patient1_Male_99.29.1.7

value: Bladder

value: Adult


title: CONTROL_H_H

value: Partially methylated control_Replicate 1


title: Somatic.Tissue___Adrenal_Fetal_15wk_Patient30_Male_95.412.1.2

value: Adrenal

value: Male


title: Somatic.Tissue___Lymph.Node_Adult__Patient1_Male_100.29.1.3


title: Somatic.Tissue___Tongue_Fetal_14wk_Patient26_Female_139.407.1.2

value: Tongue

value: Female


title: Somatic.Tissue___Adrenal_Adult__Patient1_Male_95.29.1.7


title: Somatic.Tissue_Aorta___Adult__Patient1_Male_96.29.1.7

value: Aorta


title: Somatic.Tissue_Skin___Adult__Patient2_Female_103.30.1.1

value: Skin


title: Somatic.Tissue___Pancreas_Adult__Patient2_Female_220.30.1.1

value: Pancreas


title: Somatic.Tissue___Diaphragm_Adult__Patient1_Male_93.29.1.6

value: Diaphragm


title: Somatic.Tissue___Spleen_Adult__Patient2_Female_91.30.1.1

value: Spleen


title: Somatic.Tissue___Spleen_Fetal_14wk_Patient32_Female_91.414.1.1

value: Fetal


title: Somatic.Tissue_Colon___Adult__Patient1_Male_ILMN.2

value: Colon


title: Somatic.Tissue___Stomach_Fetal_14wk_Patient32_Female_101.414.1.1

value: Stomach


title: Somatic.Tissue___Adipose_Adult__Patient1_Male_98.29.1.5

value: stem cell matrix version 342

value: Adipose


title: Somatic.Tissue___Stomach_Fetal_14wk_Patient26_Female_101.407.1.2


title: Somatic.Tissue___Lung_Fetal_14wk_Patient32_Female_94.414.1.1

value: Lung


title: Somatic.Tissue___Skeletal.muscle_Adult__Patient1_Male_97.29.1.7

value: Adult


title: Somatic.Tissue___Lymph.Node_Adult__Patient2_Female_100.30.1.1


title: Somatic.Tissue___Liver_Fetal_14wk_Patient32_Female_147.414.1.1

value: Liver


title: Somatic.Tissue___Lung_Adult__Patient2_Female_94.30.1.1


title: Somatic.Tissue_Ovary___Adult__Patient2_Female_ILMN.3

value: Ovary


title: Somatic.Tissue___Stomach_Fetal_15wk_Patient30_Male_101.412.1.1

value: Male


title: Somatic.Tissue___Heart_Fetal_14wk_Patient32_Female_111.414.1.1

value: Heart


title: Somatic.Tissue___Ovary_Adult__Patient2_Female_106.30.1.1

value: Female


title: Somatic.Tissue_Brain___Adult__Patient74_Female_21.628.2.3

value: Brain


title: Somatic.Tissue___Duodenum_Adult__Patient2_Female_104.30.1.1

value: Duodenum


title: Somatic.Tissue___Gallbladder_Adult__Patient2_Female_105.30.1.1

value: Gallbladder


title: Somatic.Tissue___Diaphragm_Adult__Patient2_Female_93.30.1.1

value: Diaphragm


title: Somatic.Tissue___Brain_Adult__Patient71_Female_21.625.2.3


title: Somatic.Tissue___Blood_Adult__Patient5_Female_107.362.1.2

value: Blood


title: Somatic.Tissue___Blood_Adult__Patient6_Female_107.363.2.2


title: Somatic.Tissue___Adipose_Adult__Patient2_Female_98.30.1.1


title: Somatic.Tissue_Breast___Adult__Patient2_Female_ILMN.1

value: Breast


title: Somatic.Tissue___Adrenal_Adult__Patient2_Female_95.30.2.1

value: Adrenal


title: Somatic.Tissue___Bladder_Adult__Patient2_Female_99.30.1.1

value: Bladder


title: Somatic.Tissue___Adrenal_Fetal_14wk_Patient32_Female_95.414.1.1

value: stem cell matrix version 342

value: Fetal


title: Somatic.Primary_SC23NSC______Male_62.225.3.1


title: Somatic.Primary_HANSE21______Male_191.296.1.4


title: Somatic.Tissue_Aorta___Adult__Patient2_Female_96.30.1.1

value: Aorta


title: Somatic.Primary_SM3______Male_71.236.3.1


title: Somatic.Primary_SC31MSC______Male_64.227.3.1


title: Somatic.Primary_SC27NSC______Female_125.375.1.2


title: Somatic.Primary_HANSE20H______Male_190.295.1.4


title: Somatic.Tissue___Kidney_Fetal_15wk_Patient30_Male_143.412.1.1

value: Kidney


title: Somatic.Primary_SC41MSC______Female_66.229.4.1


title: Somatic.Primary_HMSCbm252______Female_218.571.1.1


title: Somatic.Primary_NUFF______Male_6.16.2.2

value: NUFF


title: Somatic.Primary_SC11GLIA______Male_67.230.3.1


title: Somatic.Primary_HRPTEpiC257______Male_209.562.1.1


title: Somatic.Primary_HMSCad251______Male_219.572.1.1


title: Somatic.Primary_SM2______Female_72.237.2.1


title: Somatic.Primary_HANSE19H______Female_189.294.1.4


title: Somatic.Primary_NUFF______Male_6.17.2.2


title: Somatic.Primary_NUFF______Male_6.325.1.3


title: Somatic.Primary_KDIB2______Male_251.669.1.2


title: Somatic.Primary_KERA1______Male_137.400.3.1


title: Somatic.Primary_SC01GLIA______Male_61.224.3.1


title: Somatic.Primary_HREpiC256______Male_211.564.1.1


title: Somatic.Primary_MRC5______Male_312.891.3.1


title: Somatic.Primary_HIBEpiC254______Male_213.566.1.1


title: Somatic.Primary_HPLF260______Male_206.559.1.1


title: Somatic.Primary_HDF.HSP______Male_40.167.1.1


title: Somatic.Primary_HRCEpiC255______Male_210.563.1.1


title: Somatic.Primary_HESMC267______Male_207.560.1.1


title: Somatic.Primary_HDF.HSP______Male_40.166.1.1


title: Somatic.Primary_HDF.HSP______Male_40.168.1.1


title: Somatic.Primary_HDF.HSP______Male_40.165.1.1


title: Somatic.Primary_HCF1______Male_215.568.1.1


title: Somatic.Primary_HCFaa1______Male_216.569.1.1


title: Somatic.Tissue__Adipose__Female_Adult__Patient2_98.30.1.1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2010.3

label: Cy5 and Cy3

value: Adipose

value: Adult


title: Somatic.Tissue___Skeletal.muscle_Adult__Patient2_Female_97.30.1.1


title: Somatic.Tissue___Ureter_Adult__Patient2_Female_92.30.1.1

value: Ureter


title: Somatic.Primary_HDF.HSP______Male_40.164.1.1

value: Male


title: Somatic.Primary_HBVSMC266______Male_203.556.1.1


title: Somatic.Primary_HUVECBF4______Female_169.250.2.1

value: Female


title: Somatic.Primary_HDF.HSP______Male_40.163.1.1


title: Somatic.Tissue__Adipose__Male_Adult__Patient1_98.29.1.5


title: Somatic.Primary_HBdSMC265______Male_212.565.1.1


title: Somatic.Tissue___Kidney_Fetal_14wk_Patient32_Female_143.414.1.1


title: Somatic.Primary_HDK85______Female_257.689.1.1


title: Somatic.Primary_IMR90______Female_129.382.3.1


title: Somatic.Primary_HDF69______Female_201.544.1.1


title: Somatic.Primary_HUVECBF5______Female_170.251.2.1


title: Somatic.Primary_HDF51______Female_166.411.1.2


title: Somatic.Primary_HSkMC268______Female_208.561.1.1


title: Somatic.Primary_CCD1079SK______Male_128.380.3.1


title: Somatic.Primary_HDF68______Female_200.543.1.1


title: ES.parthenote_LLC6_passage16_____Female_43.172.1.5

value: parthenogentic embryonic stem cell, undifferentiated

tag: passage number


title: Somatic.Primary_HDF258______Female_204.557.1.1


title: ES.parthenote_LLC9_passage20_____Female_46.175.1.5


title: Somatic.Primary__HDF259_____Female_205.558.1.1


title: Somatic.Primary_ASTRO1______Female_253.675.3.1


title: ES.parthenote_LLC2_passage24_____Female_42.171.1.5


title: Somatic.Primary_HPAv263______Female_217.570.1.1


title: ES.parthenote_LLC15_passage45_____Female_317.905.1.3


title: ES.parthenote_LLC8_passage18_____Female_45.174.1.5


title: Somatic.Primary_HDF51______Female_166.436.1.2


title: ES.parthenote_LLC7_passage16_____Female_44.173.1.5


title: iPS_HDF51IPS5_passage34_____Female_156.646.1.1

value: induced pluripotent stem cell, undifferentiated


title: Somatic.Tissue__Kidney__Female_Fetal_20wk_Patient250_143.1442.1.1


title: iPS_HDF51IPS6_passage33_____Female_157.647.1.2


title: iPS_HDF51IPS3_passage34_____Female_155.645.1.4


title: iPS_HDF51IPS7_passage33_____Female_158.648.1.1


title: iPS_HDF51IPS9_passage33_____Female_160.649.1.3


title: ES.parthenote_LLC6_passage45_____Female_43.904.1.3


title: iPS_HDF51IPS11_passage33_____Female_162.650.1.1


title: iPS_HDF51IPS10_passage37_____Female_161.900.1.2


title: Mock 24hr pool vs. 8:0 24hr 2 (251485029602_1_2)

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.
Data matrix preparation for GEO submission
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the normalized data matrix, the limma package was used. Background correction was not performed (method=none)
Data was normalized within arrays with the loess method. Log2 ratios were calculated log2(Cy5/Cy3)

source_name: Mock 24hr pool

label_protocol: The Agilent Two-color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including cDNA probe preparation, hybridization and array washing. Cy3- and Cy5-labeled cRNA probes were generated using the Agilent low RNA input linear amplification kit.

growth_protocol: A549 cells were propagated in DMEM supplemented with 10% FBS and penicillin-streptomycin. Cells were seeded onto six-well plates and used the second day. Mock-infected  controls were treated only with DMEM containing 0.3% bovine serum albumin. Cells were infected with indicated viruses at an MOI of 2 in 500  l of DMEM for 1 h and washed. DMEM (2 ml) with 0.3% bovine serum albumin was added to each well. Cells were lysed in 0.5 ml of solution D at 2, 6, and 24 h postinfection.

extract_protocol: Total RNA was isolated using Qiagen RNAsy columns according to the manufacter's instructions.

treatment_protocol: Cells were lysed in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M beta-mercaptoethanol) at 2, 6, and 24 h postinfection.

value: A549 cells

tag: virus infection

value: None- mock infected

tag: sample collection time post-infection

value: pool of 2hr, 6hr and 24hr cells

tag: biological replicate number

value: pool

value: r1918 infected


title: iPS_TH160OCT4SOX2BTHAL_passage38_____Male_311.890.3.1

value: stem cell matrix version 342

tag: cell line


title: iPS_HDF51IPS12_passage33_____Female_163.651.1.3


title: iPS_HDF51IPS1_passage25_____Female_153.738.1.1


title: Mock 24hr pool vs. 8:0 24hr 2 (251485029602_1_1)


title: Mock 24hr pool vs. 8:0 24hr 1 (251485029633_1_1)


title: iPS_HDF51IPS2_passage34_____Female_154.644.1.2


title: iPS_TH124SOX2BTHAL_passage34_____Male_309.888.3.1


title: Somatic.Tissue__Heart__Male_Adult__Patient1_111.29.1.6

value: Heart


title: iPS_TH152OCT4BTHAL_passage30_____Male_308.887.3.1


title: iPS_KIPS4F8_passage27_____Male_250.668.1.2


title: Mock 24hr pool vs. 7:1 24hr 3 (251485029632_1_2)

value: infected with r1918 virus containing the NS1 from A/Texas/36/91 (Tx/91)


title: Mock 24hr pool vs. 8:0 24hr 1 (251485029633_1_2)


title: iPS_NSC253I_passage23_____Male_314.893.3.1


title: iPS_GOTTESFELD4078.1B3_passage20_____Male_301.781.3.1


title: iPS_HDF51IPS13_passage34_____Female_164.652.1.1


title: Mock 24hr pool vs. 7:1 24hr 3 (251485029632_1_1)


title: Somatic.Primary__Chond1__Male____558.1451.1.1


title: iPS_HFIB2IPS5_passage69_____Male_85.420.1.3


title: Somatic.Primary__MRC5__Male____312.891.3.1


title: iPS_K4AMKIPS4F1_passage15_____Male_138.401.1.2


title: iPS_C14_passage32_____Male_310.889.3.1


title: Somatic.Tissue__Stomach__Male_Adult__Patient1_101.29.1.5

value: Stomach


title: iPS_IPS-Foreskin-CL1_passage18_____Male_130.384.3.1


title: iPS_IPS-Foreskin-CL2_passage17_____Male_131.387.3.1


title: iPS_IPS-Foreskin-CL4_passage18_____Male_133.390.3.1


title: iPS_IPS-Foreskin-CL3_passage19_____Male_132.389.3.1


title: Somatic.Primary__HPAv263__Female____217.570.1.1


title: Mock 24hr pool vs. 7:1 24hr 2 (251485029631_1_2)


title: iPS_IPS-IMR90C4_passage27_____Female_135.394.3.1


title: Mock 24hr pool vs. 7:1 24hr 2 (251485029631_1_1)


title: iPS_KIPS4F1_passage32_____Female_249.667.1.2


title: Mock 24hr pool vs. 7:1 24hr 1 (251485029630_1_1)


title: 8:0 6hr 2 vs. Mock 6hr pool (251485029151_1_4)

source_name: Mock 6hr pool


title: iPS_HDK68IPS1_passage5_____Female_221.574.1.1


title: iPS_GOTTESFELD4078.1A2_passage27_____Male_302.782.3.1


title: iPS_IPS-IMR90C2_passage27_____Female_134.392.3.1


title: Mock 24hr pool vs. 7:1 24hr 1 (251485029630_1_2)


title: 8:0 6hr 2 vs. Mock 6hr pool (251485029151_1_3)


title: iPS_HDF51IPS14_passage8_____Female_165.472.1.1


title: iPS_HDF68IPS4_passage4_____Female_230.596.1.1


title: iPS_HDF68IPS10_passage4_____Female_233.599.1.1


title: 8:0 6hr 2 vs. Mock 6hr pool (251485029151_1_2)


title: Somatic.Primary__HCFaa1__Male____216.569.1.1


title: Somatic.Primary__HIBEpiC254__Male____213.566.1.1


title: Somatic.Primary__HCF1__Male____215.568.1.1


title: iPS_GOTTESFELD8.2A4R_passage28_____Female_299.779.3.1


title: iPS_HDF51IPS14_passage27_____Female_165.592.1.2


title: 8:0 6hr 2 vs. Mock 6hr pool (251485029151_1_1)


title: 8:0 6hr 1 vs. Mock 6hr pool (251485029145_1_4)


title: iPS_GOTTESFELD3816.5_passage14_____Female_300.780.3.1


title: iPS_HDF51IPS9_passage7_____Female_160.473.1.1


title: iPS_HDF51IPS3_passage6_____Female_155.439.1.1


title: iPS_HDF51IPS6_passage5_____Female_157.441.1.1


title: 8:0 6hr 1 vs. Mock 6hr pool (251485029145_1_1)


title: iPS_HDF51IPS5_passage6_____Female_156.440.1.1


title: 8:0 6hr 1 vs. Mock 6hr pool (251485029145_1_2)


title: Somatic.Primary__HSkMC268__Female____208.561.1.1


title: iPS_HDF51IPS2_passage6_____Female_154.438.1.2


title: 8:0 6hr 1 vs. Mock 6hr pool (251485029145_1_3)


title: 8:0 2hr 3 vs. Mock 2hr pool (251485025521_1_4)

source_name: Mock 2hr pool


title: iPS_HDF51IPS1_passage6_____Female_153.437.1.2


title: iPS_HDF51IPS13_passage8_____Female_164.471.3.2


title: Somatic.Primary__HDF258__Female____204.557.1.1


title: ES_SIVF048_passage13_____Male_278.748.1.3

value: embryonic stem cell, undifferentiated


title: 8:0 2hr 3 vs. Mock 2hr pool (251485025521_1_3)


title: iPS_HDF51IPS11_passage8_____Female_162.475.3.2


title: Somatic.Primary__HDF259__Female____205.558.1.1


title: iPS_HDF51IPS7_passage5_____Female_158.442.1.1


title: ES_SIVF050_passage9_____Male_280.750.1.3


title: Somatic.Primary__HPLF260__Male____206.559.1.1


title: 8:0 2hr 3 vs. Mock 2hr pool (251485025521_1_2)


title: 8:0 2hr 3 vs. Mock 2hr pool (251485025521_1_1)


title: ES_SIVF045_passage13_____Male_286.756.1.3


title: ES_SIVF025_passage35_____Male_296.775.1.2


title: 8:0 2hr 2 vs. Mock 2hr pool (251485025520_1_4)


title: ES_SIVF044_passage13_____Male_285.755.1.3


title: ES_SIVF026_passage30_____Male_298.778.1.2


title: ES_SIVF043_passage12_____Male_284.754.1.3


title: iPS_HDF51IPS12_passage6_____Female_163.447.1.1


title: 8:0 2hr 2 vs. Mock 2hr pool (251485025520_1_3)


title: Somatic.Primary__HDF51__Female____166.436.1.3


title: Somatic.Primary__HDF51__Female____166.411.1.2


title: Somatic.Primary__CCD1079SK__Male____128.380.3.1


title: ES_SIVF022_passage48_____Male_121.768.1.3


title: ES_SIVF022_passage19_____Male_121.352.4.1


title: ES_SIVF021_passage19_____Male_120.351.4.1


title: 8:0 2hr 2 vs. Mock 2hr pool (251485025520_1_2)


title: ES_SIVF017_passage67_____Male_292.769.1.2


title: 8:0 2hr 2 vs. Mock 2hr pool (251485025520_1_1)


title: Mole__Hydatidiform.Complete.Mole__Male_Fetal__Patient67734_636.1804.1.1

value: Mole

value: Fetal


title: ES_SIVF017_passage43_____Male_116.346.4.1


title: 8:0 2hr 1 vs. Mock 2hr pool (251485025519_1_4)


title: Somatic.Primary__IMR90__Female____129.382.3.1


title: ES_SIVF015_passage18_____Male_274.744.1.2


title: ES_SIVF014_passage42_____Male_295.773.1.3


title: 8:0 2hr 1 vs. Mock 2hr pool (251485025519_1_2)


title: ES_SIVF002_passage50_____Male_290.763.1.3


title: ES_SIVF011_passage28_____Male_273.743.1.2


title: Mole__Hydatidiform.Complete.Mole__Male_Fetal__Patient65089_636.1783.1.1


title: ES_SIVF005_passage44_____Male_123.767.1.2


title: ES_MIZ4_passage65_____Male_37.157.1.1


title: Mole__Hydatidiform.Complete.Mole__Male_Fetal__Patient61655_636.1781.1.1


title: Mole__Hydatidiform.Complete.Mole__Male_Fetal__Patient68810_636.1805.1.1


title: iPS.diff_OPC.D42_iPS201B7_passage31_Female____511.1316.1.2

value: induced pluripotent stem cell, differentiated;OligodendrocyteProgenitors.day42


title: 8:0 2hr 1 vs. Mock 2hr pool (251485025519_1_3)


title: 8:0 2hr 1 vs. Mock 2hr pool (251485025519_1_1)


title: ES_SIVF002_passage17_____Male_136.398.3.1

value: Male


title: iPS_HDF51IPS10_passage6_____Female_161.445.1.1

value: Female


title: ES_MIZ4_passage63_____Male_37.152.1.1


title: Mole__Hydatidiform.Complete.Mole__Male_Fetal__Patient64055_636.1782.1.2


title: ES_SIVF021_passage49_____Male_120.764.1.2


title: 8:0 24hr 2 vs. Mock 24hr pool (251485029602_1_4)


title: 8:0 24hr 2 vs. Mock 24hr pool (251485029602_1_3)


title: ES_MIZ4_passage62_____Male_37.154.3.1


title: iPS.diff_OPC.D42_iPS414C.2_passage23_Female____510.1311.1.2


title: iPS.diff_NPC.D22_iPS201B7_passage31_Female____511.1314.1.2

value: induced pluripotent stem cell, differentiated;NeuralProgenitors.day23


title: ES_MIZ4_passage60_____Male_37.150.1.1


title: ES_MIZ4_passage53_____Male_37.148.1.1


title: ES_MEL1_passage59_____Male_35.128.4.1


title: ES_MIZ4_passage53_____Male_37.147.1.1


title: 8:0 24hr 1 vs. Mock 24hr pool (251485029633_1_3)


title: 8:0 24hr 1 vs. Mock 24hr pool (251485029633_1_4)


title: ES_MEL1_passage51_____Male_35.122.4.1


title: iPS.diff_NPC.D22_iPS201B7_passage31_Female____511.1313.1.2


title: ES_HUES16_passage21_____Male_70.233.3.1


title: ES_HES4_passage60_____Male_34.121.4.1


title: iPS__ChondiPS1_passage9_Male____606.1692.3.1

value: induced pluripotent stem cell, undifferentiated


title: ES_MEL1_passage59_____Male_35.125.4.1


title: iPS.diff_NPC.D22_iPS414C.2_passage23_Female____510.1309.1.2

value: induced pluripotent stem cell, differentiated;NeuralProgenitors.day22


title: 7:1 6hr 3 vs. Mock 6hr pool (251485029144_1_2)

value: A549 cells

value: None- mock infected


title: ES_HES4_passage57_____Male_34.117.4.1


title: 7:1 6hr 3 vs. Mock 6hr pool (251485029144_1_1)

value: pool of 2hr, 6hr and 24hr cells

value: pool


title: 7:1 6hr 3 vs. Mock 6hr pool (251485029144_1_4)


title: ES_FES22_passage44_____Male_23.92.1.1

value: stem cell matrix version 342


title: ES_HES4_passage56_____Male_34.116.4.1


title: ES_FES22_passage44_____Male_23.93.1.1


title: ES_ESI049_passage38_____Male_28.103.4.1


title: 7:1 6hr 2 vs. Mock 6hr pool (251485029143_1_4)


title: 7:1 6hr 3 vs. Mock 6hr pool (251485029144_1_3)


title: ES_WA09_passage51_____Female_87.302.3.1


title: iPS.diff_NPC.D22_iPS414C.2_passage23_Female____510.1310.1.2


title: ES_BG02_passage46_____Male_54.215.1.8


title: ES_WA09_passage49_____Female_87.146.4.1


title: iPS__ChondiPS3_passage9_Male____607.1693.3.1


title: ES_WA09_passage46_____Female_87.144.1.1


title: 7:1 6hr 2 vs. Mock 6hr pool (251485029143_1_3)


title: 7:1 6hr 2 vs. Mock 6hr pool (251485029143_1_2)


title: iPS__ChondiPS2_passage6_Male____559.1452.1.1


title: ES_WA09_passage50_____Female_87.141.2.1


title: iPS__iPS201B7_passage31_Female____511.1312.1.2


title: ES_WA09_passage39_____Female_87.138.1.1


title: 7:1 6hr 2 vs. Mock 6hr pool (251485029143_1_1)


title: ES_WA09_passage40_____Female_87.137.1.1


title: ES_MIZ4_passage62_____Male_37.156.1.1


title: ES_WA09_passage43_____Female_87.521.1.1


title: 7:1 6hr 1 vs. Mock 6hr pool (251485029142_1_4)


title: iPS__HDF51IPS13_passage8_Female____164.471.3.2


title: 7:1 6hr 1 vs. Mock 6hr pool (251485029142_1_3)


title: iPS__iPS414C.2_passage23_Female____510.1308.1.2


title: ES_WA09_passage39_____Female_87.139.1.1


title: ES_WA09_passage41_____Female_87.304.7.1


title: iPS__HDF51IPS13_passage34_Female____164.652.1.1


title: ES_WA07_passage56_____Female_47.177.1.1


title: 7:1 6hr 1 vs. Mock 6hr pool (251485029142_1_2)


title: ES_WA09_passage39_____Female_87.142.1.1


title: iPS__HDF51IPS14_passage27_Female____165.592.1.2


title: 7:1 6hr 1 vs. Mock 6hr pool (251485029142_1_1)


title: iPS__HDF51IPS14_passage8_Female____165.472.1.1


title: ES_UC06_passage71_____Female_39.157.1.1


title: 7:1 2hr 3 vs. Mock 2hr pool (251485029155_1_4)


title: iPS__HDF51IPS12_passage33_Female____163.651.1.3


title: ES_SIVF049_passage9_____Female_279.749.1.3


title: ES_UC06_passage70_____Female_39.160.1.1


title: ES_UC06_passage61_____Female_39.158.1.1


title: ES_UC06_passage61_____Female_39.159.1.1


title: ES_UC06_passagexx_____Female_39.4.4.1

value: passagexx


title: 7:1 2hr 3 vs. Mock 2hr pool (251485029155_1_2)

value: infected with r1918 virus containing the NS1 from A/Texas/36/91 (Tx/91)


title: ES_SIVF046_passage11_____Female_287.757.1.3


title: 7:1 2hr 3 vs. Mock 2hr pool (251485029155_1_1)


title: 7:1 2hr 3 vs. Mock 2hr pool (251485029155_1_3)


title: iPS__HDF51IPS11_passage8_Female____162.475.3.2


title: iPS__HDF51IPS10_passage6_Female____161.445.2.1


title: iPS__HDF51IPS12_passage6_Female____163.447.1.1


title: iPS__HDF51IPS10_passage37_Female____161.900.1.2


title: ES_WA09_passage44_____Female_87.453.1.1


title: iPS__HDF51IPS11_passage33_Female____162.1568.1.2


title: ES_SIVF047_passage10_____Female_288.758.1.3


title: ES_SIVF028_passage28_____Female_276.746.1.3


title: ES_SIVF042_passage13_____Female_283.753.1.3


title: ES_SIVF041_passage17_____Female_282.752.1.3


title: ES_SIVF029_passage28_____Female_277.747.1.3


title: 7:1 2hr 2 vs. Mock 2hr pool (251485029154_1_3)


title: 7:1 2hr 2 vs. Mock 2hr pool (251485029154_1_4)


title: ES_SIVF027_passage31_____Female_297.777.1.3


title: iPS__HDF51IPS9_passage7_Female____160.473.1.1


title: 7:1 2hr 2 vs. Mock 2hr pool (251485029154_1_2)


title: iPS__ChondiPS2_passage9_Male____559.1691.3.1


title: iPS__HDF51IPS7_passage33_Female____158.648.1.1


title: ES_WA07_passage35_____Female_47.176.1.1


title: ES_SIVF024_passage28_____Female_294.774.1.3


title: ES_SIVF024_passage15_____Female_294.772.1.3


title: ES_SIVF040_passage17_____Female_281.751.1.3


title: iPS__HDF51IPS6_passage33_Female____157.647.1.2


title: iPS__HDF51IPS9_passage33_Female____160.649.1.3


title: 7:1 2hr 1 vs. Mock 2hr pool (251485029153_1_4)


title: ES_SIVF020_passage82_____Female_289.762.1.2


title: iPS__HDF51IPS6_passage5_Female____157.441.1.1


title: 7:1 2hr 2 vs. Mock 2hr pool (251485029154_1_1)


title: 7:1 2hr 1 vs. Mock 2hr pool (251485029153_1_3)


title: ES_SIVF019_passage67_____Female_118.776.1.3


title: ES_SIVF019_passage81_____Female_118.761.1.2


title: ES_UC06_passage70_____Female_39.156.1.1


title: ES_SIVF020_passage52_____Female_119.350.4.1


title: ES_SIVF018_passage44_____Female_117.347.4.1


title: ES_SIVF007_passage21_____Female_115.345.4.1


title: ES_SIVF016_passage19_____Female_275.745.1.3


title: ES_SIVF006_passage24_____Female_114.355.3.1


title: ES_SIVF018_passage72_____Female_293.770.1.2


title: 7:1 24hr 3 vs. Mock 24hr pool (251485029632_1_4)


title: ES_SIVF007_passage23_____Female_115.356.3.1


title: 7:1 2hr 1 vs. Mock 2hr pool (251485029153_1_2)


title: 7:1 2hr 1 vs. Mock 2hr pool (251485029153_1_1)


title: ES_SIVF006_passage22_____Female_114.344.4.1


title: iPS__HDF51IPS5_passage34_Female____156.646.1.1


title: ES_SIVF004_passage43_____Female_291.766.1.3


title: ES_SIVF003_passage22_____Female_113.343.4.1


title: 7:1 24hr 3 vs. Mock 24hr pool (251485029632_1_3)


title: iPS__HDF51IPS2_passage6_Female____154.438.1.2


title: ES_SIVF001_passage45_____Female_112.342.4.1


title: ES_SIVF001_passage18_____Female_112.396.3.1


title: ES_MIZ6_passage27_____Female_38.161.1.1


title: ES_MEL4_passage36_____Female_127.379.3.1


title: ES_MIZ6_passage27_____Female_38.162.1.1


title: ES_MIZ13_passage50_____Female_238.613.1.1


title: iPS__HDF51IPS2_passage34_Female____154.644.1.2


title: 7:1 24hr 2 vs. Mock 24hr pool (251485029631_1_4)


title: 7:1 24hr 1 vs. Mock 24hr pool (251485029630_1_3)


title: ES_SIVF001_passage39_____Female_112.340.4.1


title: 7:1 24hr 1 vs. Mock 24hr pool (251485029630_1_4)


title: iPS__HDF51IPS3_passage6_Female____155.439.1.1


title: ES_MEL4_passage35_____Female_127.378.3.1


title: ES_MEL2_passage15_____Female_36.133.4.1


title: ES_MEL3_passage34_____Female_126.376.3.1


title: ES.parthenote__LLC8_passage18_Female____45.174.1.4

value: parthenogentic embryonic stem cell, undifferentiated


title: iPS__HDF51IPS5_passage6_Female____156.440.1.1


title: 7:1 24hr 2 vs. Mock 24hr pool (251485029631_1_3)


title: iPS__HDF51IPS3_passage34_Female____155.645.1.3


title: iPS__HDF51IPS1_passage6_Female____153.437.1.1


title: ES_MEL2_passage13_____Female_36.131.4.1

value: embryonic stem cell, undifferentiated


title: iPS__HDF51IPS1_passage25_Female____153.738.1.1


title: ES_HES3_passage59_____Female_33.118.4.1


title: ES_HES3_passage54_____Female_33.112.4.1


title: ES_HES2_passage92_____Female_32.110.4.1


title: ES.parthenote__LLC7_passage16_Female____44.173.1.5


title: ES_HES3_passage31_____Female_33.276.1.1


title: ES.parthenote__LLC2_passage24_Female____42.171.1.5


title: Mock vs. WT 6hr (251485018219_1_3)

description:
251485018219_1_3
Polarity: +

hyb_protocol: The Agilent Two-color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including cDNA probe preparation, hybridization and array washing.

data_processing:
Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE2-v5_95_Feb07 extraction protocol.
Data matrix preparation for GEO submission
Agilent Feature extractor software:
platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package 'limma'
Description:
Package:       limma
Version:       3.6.9
Date:          2010/12/01version
For the creation of the nornalized data, the limma package was used. Background correction was not performed (method="none")
Data was normalized within arrays with the loess method. Log2 ratios were calculated log2(Cy5/Cy3)

source_name: Mock

growth_protocol: A549 cells were propagated in MEM supplemented with 10% FBS and penicillin-streptomycin. Cells at low passage were seeded onto six-well plates and infected 2 days later at a multiplicity of infection (MOI) of 2. Mock-infected controls were treated with allantoic fluid instead of virus. Virus was allowed to bind to cells for 1 h at 4°C in serum-free infection medium supplemented with trypsin (1  g/ml). Three replicate wells were used for each infection condition at each time point.

extract_protocol: Total RNA was isolated using Qiagen RNAsy columns according to the manufacter's instructions. For each experimental condition, equal masses of total RNA were pooled from each of the triplicate wells.

value: none- mock infected

tag: virus strain

source_name: WT 6hr

value: influenza infected


title: Mock vs. WT 2hr (251485018217_1_4)

description:
251485018217_1_4
Polarity: +

source_name: WT 2hr


title: Mock vs. WT 2hr (251485018217_1_3)

description:
251485018217_1_3
Polarity: +


title: ES_HES2_passage55_____Female_32.114.4.1


title: ES.parthenote__LLC6_passage16_Female____43.172.1.5


title: ES_HES2_passage91_____Female_32.275.1.1


title: ES_HES2_passage28_____Female_32.273.2.1


title: Mock vs. WT 24hr (251485018221_1_3)

description:
251485018221_1_3
Polarity: +

source_name: WT 24hr


title: ES_HES2_passage105_____Female_32.135.4.1


title: Mock vs. WT 24hr (251485018221_1_4)

description:
251485018221_1_4
Polarity: +


title: ES.parthenote__LLC15_passage45_Female____317.905.1.1


title: WT 6hr vs. Mock (251485018219_1_1)

description:
251485018219_1_1
Polarity: -


title: ES_FES30_passage26_____Female_22.91.1.1


title: ES_ESIH3_passagexx_____Female_31.106.1.1


title: WT 6hr vs. Mock (251485018219_1_2)

description:
251485018219_1_2
Polarity: -


title: ES_ESIH3_passage114_____Female_31.109.1.1


title: ES_ESI053_passage37_____Female_30.105.5.1


title: ES.diff_spontaneous.D3_WA09_passage39_Female____87.1436.2.1

value: embryonic stem cell, differentiated;spontaneous.day3


title: ES_ESI051_passage37_____Female_29.104.3.1


title: ES.parthenote__LLC9_passage20_Female____46.175.1.5


title: WT 2hr vs. Mock (251485018217_1_1)

description:
251485018217_1_1
Polarity: -


title: ES_ESI035_passage35_____Female_27.102.4.1


title: ES_CM8_passage12_____Female_241.619.1.1


title: ES_CSC14_passage26_____Female_197.524.1.2


title: ES_CSC14C1_passage26_____Female_202.550.1.1


title: WT 2hr vs. Mock (251485018217_1_2)

description:
251485018217_1_2
Polarity: -


title: ES.diff_spontaneous.D3_WA09_passage39_Female____87.1436.3.1


title: Mock vs. WT 6hr (251485018219_1_4)

description:
251485018219_1_4
Polarity: +


title: ES_CM8_passage25_____Female_241.618.1.1


title: ES.diff_OPC.D42_WA07_passage38_Female____47.1303.1.2

value: embryonic stem cell, differentiated;OligodendrocyteProgenitors.day42


title: WT 24hr  vs. Mock (251485018221_1_2)

description:
251485018221_1_2
Polarity: -


title: ES_CM7_passage19_____Female_243.621.1.1

value: Female


title: ES_CM2_passage17_____Female_245.623.1.1


title: WT 24hr vs. Mock (251485018221_1_1)

description:
251485018221_1_1
Polarity: -


title: ES_CM6_passage19_____Female_244.622.1.1


title: ES.diff_NPC.D22_WA07_passage38_Female____47.1301.1.2

value: embryonic stem cell, differentiated;NeuralProgenitors.day22


title: 1918 6hr vs. Mock (251485018220_1_1)

description:
251485018220_1_1
Polarity: -

value: Tx/91 with NS1 from r1921


title: ES_CM1_passage16_____Female_246.624.1.1


title: ES.diff_spontaneous.D3_WA09_passage39_Female____87.1436.1.1


title: ES_ESI017_passage24_____Female_26.101.3.1


title: ES_CM14_passage87_____Female_239.615.1.1


title: ES_CM14_passage21_____Female_239.616.1.1


title: ES_CM11_passage17_____Female_240.617.1.1


title: 1918 2hr vs. Mock (251485018218_1_2)

description:
251485018218_1_2
Polarity: -

value: Tx/91 with NS1 from r1918


title: 1918 24hr vs. Mock (251485018247_1_2)

description:
251485018247_1_2
Polarity: -

value: A549 cells


title: 1918 2hr vs. Mock (251485018218_1_1)

description:
251485018218_1_1
Polarity: -

value: Tx/91 with NS1 from r1919


title: HCC-1428/LTED, fulv, rep 3

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

institute: Vanderbilt Univ

description: Gene expression data from HCC-1428/LTED cells treated with 10% DCC-FBS + 1 uM fulvestrant x 48 hrs.

hyb_protocol: 15 ug biotinylated cRNA was fragmented and hybridizied to an Affymetrix GeneChip Human Genome U133 Plus 2.0 array.

scan_protocol: Hybridized cRNA was detected using streptavidin coupled to phycoerythrin. GeneChips were scanned using the GeneChip Scanner 3000 7G Plus 2 and GeneChip Operating System (Affymetrix).

data_processing: Default values were used to grid images (.DAT) and generate .CEL and .CHP files. Data were RMA-normalized using Expression Console (Affymetrix).

source_name: HCC-1428/LTED cells, fulvestrant

label_protocol: GeneChip One-Cycle Target Labeling and Control reagents kit (Affymetrix).

growth_protocol: MCF-7/LTED and HCC-1428/LTED cells were maintained in IMEM + 10% DCC-FBS (no phenol red).

extract_protocol: Trizol extraction followed by Qiagen RNeasy column clean-up with on-column DNase digestion.

treatment_protocol: Cells were seeded in 100-mm dishes in triplicate. The following day, cells were washed with PBS, and treated with IMEM + 10% DCC-FBS (no phenol red) containing 0.1% EtOH or 1 uM fulvestrant. Forty-eight hrs later, RNA was harvested.

value: breast cancer

value: fulvestrant


title: 1918 24hr vs. Mock (251485018247_1_1)

description:
251485018247_1_1
Polarity: -


title: ES_BG03_passage55_____Female_124.372.1.3

value: stem cell matrix version 342


title: HCC-1428/LTED, EtOH, rep 2

description: Gene expression data from HCC-1428/LTED cells treated with 10% DCC-FBS + 0.1% EtOH x 48 hrs.

source_name: HCC-1428/LTED cells, EtOH

value: ethanol


title: HCC-1428/LTED, EtOH, rep 1


title: HCC-1428/LTED, EtOH, rep 3


title: HCC-1428/LTED, fulv, rep 2


title: ES__WA09_passage41_Female____87.304.7.1


title: ES__HES2_passage105_Female____32.135.4.1


title: ES__WA07_passage35_Female____47.176.1.1


title: ES__HES4_passage57_Male____34.117.4.1

value: Male


title: ES__WA07_passage38_Female____47.1300.1.2


title: HCC-1428/LTED, fulv, rep 1


title: ES__MIZ6_passage27_Female____38.161.1.1


title: 1918 6hr vs. Mock (251485018220_1_2)

description:
251485018220_1_2
Polarity: -


title: Mock vs. 1918 6hr (251485018220_1_4)

description:
251485018220_1_4
Polarity: +


title: MCF-7/LTED, fulv, rep 3

description: Gene expression data from MCF-7/LTED cells treated with 10% DCC-FBS + 1 uM fulvestrant x 48 hrs.

source_name: MCF-7/LTED cells, fulvestrant


title: MCF-7/LTED, EtOH, rep 3

description: Gene expression data from MCF-7/LTED cells treated with 10% DCC-FBS + 0.1% EtOH x 48 hrs.

source_name: MCF-7/LTED cells, EtOH


title: Mock vs. 1918 2hr (251485018218_1_4)

description:
251485018218_1_4
Polarity: +


title: Mock vs. 1918 2hr (251485018218_1_3)

description:
251485018218_1_3
Polarity: +


title: ES__WA09_passage39_Female____87.1429.3.1


title: ES__SIVF025_passage35_Male____296.775.1.2


title: Mock vs. 1918 24hr (251485018247_1_3)

description:
251485018247_1_3
Polarity: +


title: ES.diff_NPC.D22_WA07_passage38_Female____47.1302.1.2


title: MCF-7/LTED, EtOH, rep 2


title: ES__MEL1_passage51_Male____35.122.4.1


title: 72hr_KO3

status: Public on May 13 2012

city: Cincinnati

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Cebpa d/d mice 72hrs after naphthalene injury.

hyb_protocol: Based on Affymetrix protocols.

scan_protocol: Based on Affymetrix protocols.

data_processing: RMA signal intensity calculation using GeneSpring GX.

source_name: Terminal bronchiolar epithelial cells, Cebpa d/d mice, 72hr

label_protocol: Based on Affymetrix protocols.

extract_protocol: Guanidinium thiocyanate (GITC).

tag: strain

value: mixture of FVB/N and C57BL/6

tag: genotype

value: Cebpa  d/d

tag: tissue

value: lung

value: terminal bronchiolar epithelial cells

value: naphthalene injury

tag: treatment duration


title: 3hr_KO3

description: Cebpa d/d mice 3hrs after naphthalene injury.

source_name: Terminal bronchiolar epithelial cells, Cebpa d/d mice, 3hr


title: ES__SIVF044_passage13_Male____285.755.1.3

tag: loring pipeline sample id

tag: loring pipeline stem cell matrix version

value: embryonic stem cell, undifferentiated


title: MCF-7/LTED, EtOH, rep 1


title: 3hr_KO2


title: Prunus armeniaca_Zhenkui_fruits_rep2

city: Nanjing

first: Jinggui

last: Fang

address: tongwei road 6

department: college of Horticulture

institute: Nanjing Agricultural University

description:
Gene expression in fruits of Prunus armeniaca
Array 2-4 Z2

hyb_protocol: 600  ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes,Add 25 µL 2x GEx Hybridization Buffer HI-RPMeaction,Mix well by careful pipetting. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.Place sample on ice and load onto the array as soon as possible.Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.Slowly dispense the volume of hybridization sample(40ul),Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”- labeled barcode is facing down and the numeric barcode is facing up. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Hand- tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. If necessary, tap the assembly on a hard surface to move stationary bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm when using 2x GEx Hybridization Buffer HI-RPM. Hybridize at 65°C for 17  hours in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K microarray formats array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with  Agilent Feature Extraction Software (v8.1) QC Report to Evaluate Microarray Performance (publication 5989- 3056EN), using default Default settings in FE 10.5.(GE1_105_Dec08 ) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Prunus armeniaca

source_name: Prunus armeniaca_Zhenkui_fruits_rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Agilent One-Color RNA Spike- In Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked Quantitate cRNA using NanoDrop ND- 1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Samples from two P. mume cultivars (‘Xiyeqing’ and ‘Ruantiaohongmei’) and two P. armeniaca cultivars (‘Manao’ and ‘Zhenkui’) were used in this study.  RNA was extracted from fruits at different stages (1 to 8), which collected every 7-10 d, from 3 weeks to 13 weeks after full bloom of P. mume and P. armeniaca.  It should be noted that the stage 1 to 4 was showing the first rapid increase of fruit, follwing by the slow increase from stage 5 or 6, also called stone hardening stage of the seeds, then it was showing the second rapid increase from stage 6 to 8.

extract_protocol: In order to prevent RNA enzyme contamination, all the centrifuge tubes and other consumables were soaked in 1% DEPC water for 48 h, then used after sterilization and drying.  Mortars and other ceramic equipment were baked at 180 ˚C for 6 h.  Total RNA from the selected fruits from each stage was extracted by using 2% CTAB (0.1 mol/L Tris-HCl (pH 8.0), 0.5 mol/L EDTA (pH 8.0), 1.4 mol/L NaCl, 2% CTAB (W/V), 2%PVP (W/V) 2%β- mercaptoethanol) respectively, and the steps were followed as done in Li et al (2010).  The quantity and integrity of RNA was first detected by BioPhotometer (Eppendorf, Gene Company Limited) and electrophoresis done on agarose with ethidium bromide.  Then the total RNA of different cultivars was assessed through QC methods by using RNA Nano 6000 Assay Kit and Agilent 2100 Bioanalyzer, with the samples meeting the QC criteria being selected, only R2, R4, X1, X3, M1, M2, Z1, Z2 were eligible and used for microarray construction as well as for reverse transcription quantitative PCR.  mRNA was puriﬁed using PolyATtract TM mRNA Isolation System kit (Promega, Madison, WI).

treatment_protocol: The samples were flash frozen in liquid nitrogen and stored at –40 ˚C until use.

value: fruit

tag: cultivar

value: Zhenkui

tag: developmental stage

value: mixed stages


title: MCF-7/LTED, fulv, rep 1

tag: treatment


title: Mock vs. 1918 24hr (251485018247_1_4)

description:
251485018247_1_4
Polarity: +

value: none- mock infected

value: influenza infected

value: Tx/91 with NS1 from r1921


title: 72hr_KO1

tag: cell type


title: 72hr_KO2


title: ES__SIVF002_passage50_Male____290.763.1.3

tag: gender


title: Prunus armeniaca_Zhenkui_fruits_rep1

description:
Gene expression in fruits of Prunus armeniaca
Array 2-3 Z1

source_name: Prunus armeniaca_Zhenkui_fruits_rep1


title: Prunus mume_Xiyeqing_fruits_rep2

description:
Gene expression in fruits of Prunus mume
Array 2-2 X3

organism: Prunus mume

source_name: Prunus mume_Xiyeqing_fruits_rep2

value: Xiyeqing


title: ES__SIVF050_passage9_Male____280.750.1.3

tag: passage number


title: MCF-7/LTED, fulv, rep 2

value: breast cancer

value: fulvestrant


title: 3hr_KO1


title: 0hr_KO3

description: Cebpa d/d mice 0hr after naphthalene injury.

source_name: Terminal bronchiolar epithelial cells, Cebpa d/d mice, 0hr


title: 0hr_KO2


title: ES__SIVF043_passage12_Male____284.754.1.3

value: stem cell matrix version 342


title: Prunus mume_Ruantiaohongmei_fruits_rep2

description:
Gene expression in fruits of Prunus mume
Array 1-4 R4

source_name: Prunus mume_Ruantiaohongmei_fruits_rep2

value: Ruantiaohongmei


title: Prunus mume_Xiyeqing_fruits_rep1

description:
Gene expression in fruits of Prunus mume
Array 2-1 X1

source_name: Prunus mume_Xiyeqing_fruits_rep1


title: 0hr_KO1

value: mixture of FVB/N and C57BL/6


title: Mock vs. 1918 6hr (251485018220_1_3)

description:
251485018220_1_3
Polarity: +

value: A549 cells

tag: virus infection


title: Prunus armeniaca_Manao_fruits_rep2

description:
Gene expression in fruits of Prunus armeniaca
Array 1-2 M2

source_name: Prunus armeniaca_Manao_fruits_rep2

value: Manao


title: 72hr_C3

description: Control mice 72hrs after naphthalene injury.

source_name: Terminal bronchiolar epithelial cells, control mice, 72hr

value: control

value: lung

value: terminal bronchiolar epithelial cells


title: Prunus armeniaca_Manao_fruits_rep1

description:
Gene expression in fruits of Prunus armeniaca
Array 1-1 M1

source_name: Prunus armeniaca_Manao_fruits_rep1

value: fruit


title: 72hr_C1

value: naphthalene injury