title: Tera-1 rep1

description: SAMPLE 2

value: testicular embryonal germ cell tumor


title: GSC03A_Differentiation_7day

status: Public on Jan 26 2013

type: RNA

city: kumamoto

first: norie

last: araki

department: tumor genetics and biology

country: Japan

institute: kumamoto university

hyb_protocol: After the labeled cRNA purification and fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: GIC03A cultured for 7 days with FCS

label_protocol: Biotinylated cRNA were prepared from 100 ng of total RNA according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Affymetrix, P/N 702232 Rev. 3).

growth_protocol: The GIC clones prepared from human glioma tissues were cultured in NSC medium; Neurobasal-A Medium (GIBCO/Invitrogen), B-27 (1:50; GIBCO/Invitrogen), heparin (5 g/ml; SIGMA), and GlutaMax-1 (GIBCO) containing recombinant hFGF-2 (20 ng/ml; PeproTech Inc), recombinant hEGF (20 ng/ml; PeproTech Inc), recombinant hLIF (20 ng/ml; Chemicon Inc), and insulin (10 ng/ml, SIGMA)

extract_protocol: Extraction of total RNA was performed with Quiagen RNAeasy according to the manufacturer's instructions.

treatment_protocol: The GICs were cultured in NSC medium with (differentiation condition) or without (sphere condition) 10% FCS for 2 days and 7 days after the sphere dispersion by Accumax (Innovative Cell Technologies).

tag: cell

value: Glioma initiating cell


title: whole blood, Carrier replicate 3

city: Memphis

first: Satya

last: Vemula

state: TN

address: 855 Monroe Avenue, Suite 415 Link Building

department: Neurology

country: USA

institute: University of Tennessee Health Science Center

description: Illumina HT-12 v4 expression arrays

hyb_protocol: Standard Illumina beadarray hybridization protocol for gene expression profiling (carried out at Genomics core located at Washington University Medical School at St. Louis).

scan_protocol: Standard Illumina beadarray scan protocol for gene expression profiling(carried out at Genomics core located at Washington University Medical School at St. Louis).

data_processing: Gene expression values derived from Illumina GenomeStudio software were subject to quantile normalization for statistical analysis.

label: Biotin

source_name: whole blood

label_protocol: Standard Illumina beadarray probe synthesis for gene expression profiling (carried out at Genomics core located at Washington University Medical School at St. Louis).

growth_protocol: Cells were propagated in RPMI-1640 medium (Sigma-Aldrich) supplemented with 20% fetal bovine serum (Sigma-Aldrich) and 2 mM L-glutamine at 37°C in 5% CO2

extract_protocol: Human peripheral blood mononuclear were used to establish lymphblastoid cell lines and extracted the total RNA was with Ambion’s TRI reagent kit.

treatment_protocol: Subjects included adult mutation carriers and normal controls with no mutations.

tag: Sex

value: Female

tag: tissue

value: whole blood

tag: disease state

value: mutation carrying dystonia


title: Nt2/D1 rep1

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

description: SAMPLE 1

hyb_protocol: RNA was quantified using Nanodrop and quality was checked by Agilent Total RNA 6000 chip. 400 ng of total RNA was amplified by Illumina® TotalPrep™ RNA Amplification Kit (Ambion). Amplified RNA was hybridized with HumanHT-12 gene expression array (Illumina)  according to Illumina protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: Data aquisition and analysis were done by GenomeStudio software (Illumina) using gene expression module (GSGX v.1.8).

source_name: cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion).

growth_protocol: Cells were grown on DMEM/F12 medium containing 10% fetal calf serum (Invitrogen) at 37°C and 5% CO2. Hippocampus sample was obtained postmortem and stored in RNAlater at -70°C.

extract_protocol: Total  RNA was extracted from samples  with Trizol reagent according to manufacture instruction.

tag: cell line

tag: cell type

value: partly-differentiated testicular germ cells with CNS-precursor cell characteristics


title: GSC03A_Sphere_2day

source_name: GIC03A cultured for 2 days without FCS


title: whole blood, Control replicate 4

description: Illumina HT-12 v4 expression arrays

value: normal control


title: whole blood, Control replicate 1

description: Illumina HT-12 v4 expression arrays

value: Male


title: GSC03A_Differentiation_2day

source_name: GIC03A cultured for 2 days with FCS


title: GSC03U_Differentiation_7day

source_name: GIC03U cultured for 7 days with FCS


title: GSC03U_Sphere_2day

source_name: GIC03U cultured for 2 days without FCS


title: whole blood, Carrier replicate 4

description: Illumina HT-12 v4 expression arrays


title: 126840 IC vs Broth

status: Public on Jan 25 2013

type: genomic

city: Stony brook

first: Cindy

middle: A.

last: Thomas

state: New York

address: 280 CMM

department: Molecular Genetics and Microbiology

institute: Stony brook University

hyb_protocol: cDNA with 200 pmol Cy3 and cDNA with 200 pmol Cy5 were included in hybridization solution. Hybridization was performed on a TEcan hyrbridization station.

scan_protocol: Arrays were scanned with an Agilent 2505B scanner with laser power set to 100% and PMT gains set to auto.

data_processing: GenePix Pro 6 was used to grid arrays. Lossless image files were stored for later analysis. The microarray data was analyzed using the Limma module of the Bioconductor package for the R statistical environment. The normexp method was used for background correction, followed by print tip loess normalization and between-array normalization of intensities. The microarray data for each gene were fitted to a linear model, and statistics were generated using the lmFit and eBayes functions. The P values displayed were adjusted for multiple testing using the Benjamini and Hochberg method within Limma. Genes with P values of <0.05 were considered differentially regulated. Annotations for microarray data were derived from TIGR gal files.

molecule: genomic DNA

organism: Francisella tularensis subsp. holarctica LVS

source_name: Broth

label_protocol: The cDNA of both the intracellular and broth-cultured LVS was synthsized from total RNA and labeled with cy3 or cy5, respectively.

growth_protocol: The F. tularensis LVS cultured in MH broth overnight was used to infect FL83B cells or harvested as Broth control.

extract_protocol: Intracellular bacteria were released by saponin in the presence of ethanol and phenol. Bacteria harvest from MH broth were treated the same way. Total RNA of bacteria were isolated with RNeasy Midi Kit.

treatment_protocol: The FL83B cells were co-incubated with the LVS for 24 h, washed, and incubate for another 24 h with gentamicin.

tag: sample type

value: Broth

tag: growth substrate

value: MH broth

source_name: Intracellular

value: Intracellular

value: hepatocytic cell line FL83B


title: GSC03U_Sphere_7day

source_name: GIC03U cultured for 7 days without FCS


title: whole blood, Control replicate 3

description: Illumina HT-12 v4 expression arrays


title: 126422 IC vs Broth


title: 126421 Broth vs IC


title: GSC03U_Differentiation_2day

source_name: GIC03U cultured for 2 days with FCS


title: 126849 Broth vs IC


title: GSC03A_Sphere_7day

source_name: GIC03A cultured for 7 days without FCS


title: whole blood, Control replicate 2

description: Illumina HT-12 v4 expression arrays


title: whole blood, Carrier replicate 2

description: Illumina HT-12 v4 expression arrays


title: whole blood, Carrier replicate 1

description: Illumina HT-12 v4 expression arrays


title: CCNY21_SNP

status: Public on Jan 24 2013

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina CytoSNP12 System Manual

data_processing: Raw data were normalized based on reference cluster file provided by Illumina using GenomeStudio software. Segmented DNA copy number was estimated by using CBS algorithm ("poor-functioning" probes designated by Illumina were removed). NaN indicates locus called as gap by the CBS algorithm.

source_name: Human intrahepatic cholangiocarcinoma

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, genomic DNA was extracted using QIAcube and QIAGEN spin columns (QIagen).

value: intrahepatic cholangiocarcinoma (ICC)

tag: icc subclass

value: Proliferation


title: CCNY26_SNP

scan_protocol: Refer to the Illumina CytoSNP12 System Manual


title: CCNY24_SNP

label_protocol: Refer to the Illumina CytoSNP12 System Manual


title: CCNY23_SNP


title: CCNY060_SNP


title: CCNY17_SNP


title: CCNY047_SNP


title: CCNY048_SNP


title: CCNY046_SNP


title: CCNY062_SNP


title: CCNY061_SNP


title: CCNY063_SNP


title: CCNY18_SNP


title: CCNY20_SNP


title: CCNY059_SNP


title: CCNY19_SNP


title: CCNY052_SNP


title: CCNY051_SNP

value: Inflammation


title: CCNY058_SNP


title: CCNY054_SNP


title: CCNY064_SNP


title: CCNY049_SNP


title: CCNY044_SNP


title: CCNY045_SNP


title: CCNY053_SNP


title: CCNY057_SNP


title: CCNY055_SNP


title: CCNY043_SNP


title: CCNY041_SNP


title: CCNY038_SNP


title: CCNY039_SNP


title: human breast cancer cell line IMR90-1

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

hyb_protocol: DNA was labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Genechip scanner 3000 using the latest version at that time of AGCC, v1.1.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Partek Genomic Suite.

source_name: human breast cancer cell line IMR90

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Blood and Cell Culture DNA Midi Kit (QIAGEN)

value: breast cancer


title: CCNY034_SNP


title: CCNY016_SNP


title: CCNY035_SNP


title: CCNY015_SNP


title: CCNY031_SNP


title: CCNY032_SNP


title: CCNY011_SNP


title: CCNY014_SNP


title: CCNY042_SNP


title: CCNY037_SNP


title: CCNY028_SNP


title: CCNY010_SNP


title: CCNY012_SNP


title: CCNY002_SNP


title: CCNY005_SNP


title: CCNY004_SNP


title: CCNY013_SNP


title: CCNY007_SNP


title: CCNY001_SNP


title: CCNY029_SNP


title: CCNY040_SNP


title: human breast cancer cell line MCF7-2

source_name: human breast cancer cell line MCF7


title: CCNY009_SNP


title: CCM070_SNP


title: human breast cancer cell line MCF7-1


title: CCM071_SNP


title: CCM065_SNP


title: CCM063_SNP


title: CCM072_SNP


title: CCM064_SNP


title: CCNY033_SNP


title: CCM060_SNP


title: human breast cancer cell line IMR90-2


title: CCM044_SNP


title: CCM056_SNP


title: CCM061_SNP


title: CCM050_SNP


title: CCM043_SNP


title: CCM054_SNP


title: CCM059_SNP


title: CCM058_SNP


title: CCM040_SNP


title: CCM046_SNP


title: CCM045_SNP


title: CCM049_SNP


title: CCM055_SNP


title: CCM053_SNP


title: CCM041_SNP


title: CCM051_SNP


title: CCM057_SNP


title: CCM036_SNP


title: CCM042_SNP


title: CCM048_SNP


title: CCM047_SNP


title: CCM062_SNP


title: CCM052_SNP


title: CCM038_SNP


title: CCM037_SNP


title: CCM032_SNP


title: CCM039_SNP


title: CCM031_SNP


title: CCM030_SNP


title: CCM033_SNP


title: CCM034_SNP


title: CCM026_SNP


title: CCM027_SNP


title: CCM029_SNP


title: CCM014_SNP


title: CCM018_SNP


title: CCM008_SNP


title: CCM023_SNP


title: CCM017_SNP


title: CCM019_SNP


title: CCM020_SNP


title: CCM021_SNP


title: CCM022_SNP


title: CCM002_SNP


title: CCM013_SNP


title: CCM005_SNP


title: CCM016_SNP


title: CCBCN24_SNP


title: CCBCN25_SNP


title: CCM004_SNP


title: CCM006_SNP


title: CCM012_SNP


title: CCM007_SNP


title: CCBCN16_SNP


title: CCBCN26_SNP


title: CCBCN21_SNP


title: CCBCN22_SNP


title: CCBCN27_SNP


title: CCBCN011_SNP


title: CCBCN006_SNP


title: CCM003_SNP


title: CCBCN004_SNP


title: CCBCN002_SNP


title: CCBCN013_SNP


title: CCM025_SNP


title: shESRP1 HCET doxycycline, biological rep4 [exon-level]

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression data from doxycycline treated shRNA-ESRP1 knock down HCET cell

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix hGlue3_0 transcriptome array.  GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: The arrays were scanned using Affymetrix Fluidics Station FS450 and GeneChip Scanner 30007G.

data_processing: Affymetrix Power Tools (APT) was applied for data processing.  Arrays were RMA-background-corrected, quantile-normalized and summarized into exon/gene expression using median-polish approaches.  The probe group file is hGlue3_0.r1.pgf, and the meta-probeset file is hGlue3_0.r1.TC.mps

source_name: ESRP1 knock down HCET cell treated with doxycycline

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip WT Terminal Labeling Kit protocol from 100 ng total RNA.

growth_protocol: HCET cells were cultured in DMEM/F12 medium containing 5% FBS , 5 μg/mL insulin, 0.1 μg/mL cholera toxin, 10 ng/mL human epidermal growth factor (hEGF) and 0.5% dimethyl sulfoxide (DMSO). The stable cells were selected and maintained with 2 ug/ml of puromycin.

extract_protocol: Total RNA was isolated with the RNeasy Plus Mini Kit and treated with RNase-free DNase I (Qiagen).

treatment_protocol: Parental HCET (control), shRNA-PNN HCET knock down, shRNA-ESRP1 HCET knock down cells with/without doxycycline treatment

tag: shRNA


title: shPNN HCET doxycycline, biological rep4 [exon-level]

description: Gene expression data from doxycycline treated shRNA-PNN knock down HCET cell

source_name: PNN knock down HCET cell treated with doxycycline

value: shRNA-PNN


title: shPNN HCET doxycycline, biological rep3 [exon-level]


title: shESRP1 HCET doxycycline, biological rep3 [exon-level]


title: shESRP1 HCET doxycycline, biological rep2 [exon-level]


title: shESRP1 HCET control, biological rep3 [exon-level]

description: Gene expression data from shRNA-ESRP1 knock down HCET cell

source_name: ESRP1 knock down HCET cell


title: shPNN HCET control, biological rep3 [exon-level]

description: Gene expression data from shRNA-PNN knock down HCET cell

source_name: PNN knock down HCET cell


title: shESRP1 HCET doxycycline, biological rep1 [exon-level]


title: shPNN HCET control, biological rep1 [exon-level]


title: shESRP1 HCET doxycycline, biological rep4 [gene-level]


title: shESRP1 HCET doxycycline, biological rep2 [gene-level]


title: shPNN HCET doxycycline, biological rep2 [exon-level]


title: Parental HCET doxycycline, biological rep4 [exon-level]

description: Gene expression data from doxycycline treated parental HCET cell

source_name: Parental HCET cell treated with doxycycline

value: parental


title: Parental HCET doxycycline, biological rep2 [exon-level]


title: shESRP1 HCET doxycycline, biological rep3 [gene-level]


title: Parental HCET control, biological rep2 [exon-level]

description: Gene expression data from parental HCET cell

source_name: Parental HCET cell


title: shESRP1 HCET control, biological rep2 [exon-level]


title: shPNN HCET control, biological rep4 [exon-level]


title: shPNN HCET control, biological rep2 [exon-level]


title: shESRP1 HCET control, biological rep1 [exon-level]


title: shESRP1 HCET control, biological rep4 [exon-level]


title: shESRP1 HCET doxycycline, biological rep1 [gene-level]


title: Parental HCET control, biological rep3 [exon-level]


title: Parental HCET control, biological rep4 [exon-level]


title: shPNN HCET doxycycline, biological rep1 [exon-level]


title: Parental HCET control, biological rep1 [exon-level]


title: Parental HCET doxycycline, biological rep1 [exon-level]


title: CCBCN005_SNP


title: Parental HCET doxycycline, biological rep3 [exon-level]


title: shESRP1 HCET control, biological rep3 [gene-level]


title: shESRP1 HCET control, biological rep1 [gene-level]


title: shPNN HCET doxycycline, biological rep1 [gene-level]


title: shESRP1 HCET control, biological rep4 [gene-level]


title: shPNN HCET doxycycline, biological rep3 [gene-level]


title: shPNN HCET control, biological rep1 [gene-level]


title: Parental HCET doxycycline, biological rep4 [gene-level]


title: shPNN HCET doxycycline, biological rep4 [gene-level]


title: CCBCN003_SNP


title: shPNN HCET control, biological rep4 [gene-level]


title: Parental HCET doxycycline, biological rep2 [gene-level]


title: Parental HCET doxycycline, biological rep1 [gene-level]


title: shPNN HCET doxycycline, biological rep2 [gene-level]


title: shPNN HCET control, biological rep2 [gene-level]


title: shPNN HCET control, biological rep3 [gene-level]


title: Parental HCET control, biological rep3 [gene-level]


title: Parental HCET control, biological rep4 [gene-level]


title: Parental HCET doxycycline, biological rep3 [gene-level]


title: shESRP1 HCET control, biological rep2 [gene-level]


title: Parental HCET control, biological rep2 [gene-level]


title: Parental HCET control, biological rep1 [gene-level]


title: Fibroblast_30 µM daidzein + 30 µM genistein_48h_rep3

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description:
48h30D/G_3
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package (gene expression module version 1.9.0).

source_name: HDFa fibroblasts, 30 µM daidzein + 30 µM genistein, 48h

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays.

growth_protocol: Fibroblasts were cultured from cryo-preserved cells in Dulbecco's Modified Eagle's Medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80%.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with the Quant iT RiboGreen Assay Kit.

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05% or 30, 60 or 100 µM kaemferol; 60 or 100 µM daidzein; 30 µM + 30 µM kaemferol/genistein; 30 µM + 30 µM daidzein/genistein concentrations, with 0.05% DMSO. The experimental treatment was carried out for 24 h and 48 h periods.

value: HDFa

value: normal fibroblasts

tag: treatment

value: 30 µM daidzein + 30 µM genistein

tag: treatment duration


title: Fibroblast_30 µM kaemferol + 30 µM genistein_48h_rep3

description:
48h30K/G_3
Replicate 3

source_name: HDFa fibroblasts, 30 µM kaemferol + 30 µM genistein, 48h

value: 30 µM kaemferol + 30 µM genistein


title: Fibroblast_0.05%DMSO_48h_rep3

description:
48hDMSO_3
Replicate 3

source_name: HDFa fibroblasts, 0.05%DMSO, 48h


title: Fibroblast_60 µM daidzein_48h_rep3

description:
48h60D_3
Replicate 3

source_name: HDFa fibroblasts, 60 µM daidzein, 48h

value: 60 µM daidzein


title: Fibroblast_60 µM kaemferol_48h_rep3

description:
48h60K_3
Replicate 3

source_name: HDFa fibroblasts, 60 µM kaemferol, 48h

value: 60 µM kaemferol


title: Fibroblast_0.05%DMSO_24h_rep3

description:
24hDMSO_3
Replicate 3

source_name: HDFa fibroblasts, 0.05%DMSO, 24h


title: Fibroblast_100 µM kaemferol _48h_rep3

description:
48h100K_3
Replicate 3

source_name: HDFa fibroblasts, 100 µM kaemferol, 48h

value: 100 µM kaemferol


title: Fibroblast_30 µM daidzein + 30 µM genistein_24h_rep3

description:
24h30D/G_3
Replicate 3

source_name: HDFa fibroblasts, 30 µM daidzein + 30 µM genistein, 24h


title: Fibroblast_100 µM daidzein_24h_rep3

description:
24h100D_3
Replicate 3

source_name: HDFa fibroblasts, 100 µM daidzein, 24h

value: 100 µM daidzein


title: Fibroblast_100 µM daidzein_48h_rep3

description:
48h100D_3
Replicate 3

source_name: HDFa fibroblasts, 100 µM daidzein, 48h


title: Fibroblast_60 µM daidzein_24h_rep3

description:
24h60D_3
Replicate 3

source_name: HDFa fibroblasts, 60 µM daidzein, 24h


title: Fibroblast_60 µM kaemferol_24h_rep3

description:
24h60K_3
Replicate 3

source_name: HDFa fibroblasts, 60 µM kaemferol, 24h


title: Fibroblast_0.05%DMSO_48h_rep2

description:
48hDMSO_2
Replicate 2


title: Fibroblast_100 µM kaemferol _24h_rep3

description:
24h100K_3
Replicate 3

source_name: HDFa fibroblasts, 100 µM kaemferol, 24h


title: Fibroblast_60 µM daidzein_48h_rep2

description:
48h60D_2
Replicate 2


title: Fibroblast_30 µM daidzein + 30 µM genistein_48h_rep2

description:
48h30D/G_2
Replicate 2


title: Fibroblast_100 µM daidzein_48h_rep2

description:
48h100D_2
Replicate 2


title: Fibroblast_30 µM kaemferol + 30 µM genistein_24h_rep2

description:
24h30K/G_2
Replicate 2

source_name: HDFa fibroblasts, 30 µM kaemferol + 30 µM genistein, 24h


title: Fibroblast_100 µM kaemferol _24h_rep2

description:
24h100K_2
Replicate 2


title: Fibroblast_60 µM kaemferol_48h_rep2

description:
48h60K_2
Replicate 2


title: Fibroblast_100 µM daidzein_24h_rep2

description:
24h100D_2
Replicate 2


title: Fibroblast_0.05%DMSO_24h_rep2

description:
24hDMSO_2
Replicate 2


title: Fibroblast_30 µM kaemferol + 30 µM genistein_48h_rep2

description:
48h30K/G_2
Replicate 2


title: Fibroblast_100 µM kaemferol _48h_rep2

description:
48h100K_2
Replicate 2


title: Fibroblast_30 µM kaemferol_48h_rep2

description:
48h30K_2
Replicate 2

source_name: HDFa fibroblasts, 30 µM kaemferol, 48h

value: 30 µM kaemferol


title: Fibroblast_60 µM daidzein_24h_rep2

description:
24h60D_2
Replicate 2


title: Fibroblast_30 µM kaemferol_24h_rep3

description:
24h30K_3
Replicate 3

source_name: HDFa fibroblasts, 30 µM kaemferol, 24h


title: Fibroblast_30 µM kaemferol_24h_rep2

description:
24h30K_2
Replicate 2


title: Fibroblast_60 µM kaemferol_24h_rep2

description:
24h60K_2
Replicate 2


title: Fibroblast_30 µM daidzein + 30 µM genistein_24h_rep2

description:
24h30D/G_2
Replicate 2


title: Fibroblast_30 µM kaemferol + 30 µM genistein_24h_rep1

description:
24h30K/G_1
Replicate 1


title: Fibroblast_60 µM kaemferol_24h_rep1

description:
24h60K_1
Replicate 1


title: Fibroblast_60 µM daidzein_48h_rep1

description:
48h60D_1
Replicate 1


title: Fibroblast_100 µM daidzein_48h_rep1

description:
48h100D_1
Replicate 1


title: Fibroblast_30 µM kaemferol + 30 µM genistein_48h_rep1

description:
48h30K/G_1
Replicate 1


title: Fibroblast_100 µM kaemferol _24h_rep1

description:
24h100K_1
Replicate 1


title: Fibroblast_30 µM daidzein + 30 µM genistein_48h_rep1

description:
48h30D/G_1
Replicate 1


title: Fibroblast_60 µM kaemferol_48h_rep1

description:
48h60K_1
Replicate 1


title: Fibroblast_30 µM daidzein + 30 µM genistein_24h_rep1

description:
24h30D/G_1
Replicate 1


title: Fibroblast_30 µM kaemferol_48h_rep1

description:
48h30K_1
Replicate 1


title: Fibroblast_100 µM kaemferol _48h_rep1

description:
48h100K_1
Replicate 1


title: Fibroblast_0.05%DMSO_48h_rep1

description:
48hDMSO_1
Replicate 1


title: Fibroblast_0.05%DMSO_24h_rep1

description:
24hDMSO_1
Replicate 1


title: Fibroblast_60 µM daidzein_24h_rep1

description:
24h60D_1
Replicate 1


title: Fibroblast_30 µM kaemferol + 30 µM genistein_24h_rep3

description:
24h30K/G_3
Replicate 3


title: Oral mucosal tissue 2

city: Chiyoda-ku

first: Hodaka

last: Sasaki

address: 2-9-18, Kandamisaki-cho

department: Dept. of Oral and Maxillofacial Implantology

institute: Tokyo Dental College

description: Gene expression data from oral mucosal tissue

hyb_protocol: Following fragmentation, aRNA products (15 μg) were hybridized on GeneChip® Rat Genome 230 2.0 Array Chips (Affymetrix) for 16 h at 45°C in a GeneChip® Hybridization Oven 640 (Affymetrix).

scan_protocol: Hybridized arrays were washed and stained by using a Gene Chip® Fluidics station 450 (Affymetrix), and the images were scanned by using a Genechip® scanner 3,000 (Affymetrix).

data_processing: CEL files were generated using the GeneChip® Operating Software version 1.2 (Affymetrix). Data analysis and normalization were performed using GeneSpring® GX software version 12 (Agilent Technologies, Foster City, CA, USA).

organism: Rattus norvegicus

source_name: Tooth extraction only

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled aRNA.

growth_protocol: Four-week-old male Sprague-Dawley rats were obtained from Japan SLC Inc.( Tokyo, Japan). After surgery the animals were housed in a room with controlled temperature and humidity and a 12 h light dark cycle and given freely water and diet until sacrificed after 4 weeks.

extract_protocol: Total RNA was extracted from peri-implant soft tissue and oral mucosal tissue using an RNeasy® Mini kit (QIAGEN, Alameda, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Both side upper first molars of rats were extracted and titanium alloy implants were placed only in the left extraction socket. Four weeks after surgery, peri-implant soft tissue from the left side and oral mucosal tissue from the site of healing after tooth extraction on the right side were harvested under a dissecting microscope.

tag: strain

value: Sprague Dawley

tag: gender

value: male

value: Tooth extraction only

value: oral mucosal tissue


title: Peri-implant soft tissue 3

description: Gene expression data from peri-implant soft tissue

source_name: Tooth extraction and implant placement

value: Tooth extraction and implant placement

value: peri-implant soft tissue


title: Ctrl_3

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. After subtracting background signal intensities, data were then normalized using the cubic spline algorithm.

source_name: Human normal biliary epithelial cells

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

value: normal biliary epithelial cells


title: Peri-implant soft tissue 1


title: Ctrl_5

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: Fibroblast_30 µM kaemferol_24h_rep1_rep1

description:
24h30K_1
Replicate 1


title: Ctrl_5_2

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: Oral mucosal tissue 1


title: Fibroblast_100 µM daidzein_24h_rep1

description:
24h100D_1
Replicate 1


title: Ctrl_6


title: Ctrl_1


title: Ctrl_2


title: Oral mucosal tissue 3


title: CCNY21

source_name: Human intrahepatic cholangiocarcinoma

value: intrahepatic cholangiocarcinoma

value: Proliferation


title: CCNY19


title: CCNY18


title: CCNY058


title: CCNY064


title: CCNY063


title: CCNY055


title: CCNY062


title: Peri-implant soft tissue 2


title: CCNY059


title: CCNY054


title: CCNY060


title: CCNY17


title: CCNY061


title: CCNY20


title: CCNY057


title: CCNY052


title: CCNY053


title: CCNY049


title: CCNY048


title: CCNY051

value: Inflammation


title: CCNY046


title: CCNY047


title: CCNY045


title: CCNY041


title: CCNY042


title: CCNY040


title: Fibroblast_30 µM kaemferol_48h_rep3

description:
48h30K_3
Replicate 3

value: HDFa

value: normal fibroblasts


title: CCNY039


title: CCNY044


title: CCNY043


title: CCNY033


title: CCNY038


title: CCNY036


title: CCNY026


title: CCNY029


title: CCNY037


title: CCNY032


title: CCNY012


title: CCNY014


title: CCNY027


title: CCNY028


title: CCNY035


title: CCNY011


title: CCNY034


title: CCNY023


title: CCNY024


title: CCNY005


title: CCNY016


title: CCNY013


title: CCNY031


title: CCNY010


title: CCNY002


title: CCNY004


title: CCNY009


title: CCNY001


title: CCM28


title: CCM072


title: CCNY007


title: CCNY015


title: CCM071


title: CCM070


title: CCM068


title: CCM066


title: CCM067


title: CCM061


title: CCM065


title: CCM060


title: CCM063


title: CCM055


title: CCM054


title: CCM059


title: CCM064


title: CCM051


title: CCM053


title: CCM047


title: CCM056


title: CCM046


title: CCM058


title: CCM049


title: CCM062


title: CCM043


title: CCM052


title: CCM069


title: CCM045


title: CCM057


title: CCM044


title: CCM050


title: CCM048


title: CCM041


title: CCM040


title: CCM042


title: CCM039


title: CCM038


title: CCM036


title: CCM037


title: CCM031


title: CCM030


title: CCM033


title: CCM032


title: CCM027


title: CCM034


title: Tot2_MSCV-IRF8-rep2

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

institute: Yokohama City University

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90040, Version 6.5, May 2010).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-60502) at 100% in Green channel, with a scan resolution of 3um.

data_processing: Data are extracted with Agilent Feature Extraction Software. Each measurement was divided by the 75th percentile of all measurements in that sample for normalization. Microarray data in two replications was further processed with analyzed by NIA Array Analysis software (http://lgsun.grc.nia.nih.gov/ANOVA/).

organism: Mus musculus

source_name: Tot2 cells, MSCV-IRF8 transuced, Day4, replicate 2

label_protocol: Total RNA was labeled using the Agilent Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

growth_protocol: Myeloid progenitor cell line Tot2 cells derived from Irf8 knockout mouse were cultured in RPMI1640 supplemented with 2 mM L-Glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 20% fetal bovine serum and 5.0 ng/ml granulocyte-macrophage colony stimulating factor.

extract_protocol: Total RNA was extracted from cells using RNAiso Plus reagent (Takara) and further purified using RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions.

treatment_protocol: Retroviral preparation and transduction with control MSCV-puro, MSCV-IRF8FLAG or MSCV-KLF4FLAG were performed as described previously (Tamura et al. Blood 106: 1938, 2005). Cells were transduced by spinoculation in a retroviral supernatant supplemented with cytokines and 4 μg/ml polybrene. Transduced cells were selected with 2 μg/ml puromycin 48 hr after spinoculation. At 4 days after the transduction, the cells were harvested for RNA isolation.

value: Myeloid progenitor cell line Tot2 (derived from Irf8 knockout mouse)

tag: treatment period

value: 4 days

tag: culture condition

value: MSCV-IRF8 transduced


title: CCM026


title: CCM018


title: CCM023


title: CCM021


title: Tot2_MSCV-rep2

source_name: Tot2 cells, MSCV transuced, Day4, replicate 2

value: MSCV transduced


title: CCM029


title: CCM017


title: CCM022


title: Tot2_MSCV-IRF8-rep1

source_name: Tot2 cells, MSCV-IRF8 transuced, Day4, replicate 1


title: CCM024


title: CCM019


title: CCM016


title: CCM020


title: CCM015


title: Tot2_MSCV-KLF4-rep2

source_name: Tot2 cells, MSCV-KLF4 transuced, Day4, replicate 2

value: MSCV-KLF4 transduced


title: CCM025


title: Tot2_MSCV-rep1

source_name: Tot2 cells, MSCV transuced, Day4, replicate 1


title: Tot2_MSCV-KLF4-rep1

source_name: Tot2 cells, MSCV-KLF4 transuced, Day4, replicate 1


title: CCM014


title: CCM013


title: CCM011


title: CCM012


title: CCM009


title: CCM010


title: CCM007


title: Sham Control 7d 4

city: Louisville

first: Kalina

last: Andreeva

address: 500 S.Preston Street

institute: University of Louisville

description: Gene expression at time point 7d after sham surgery

hyb_protocol: 1.65ug labeled with Cy3 for each sample was fragmented, denatured and then hybridized to Agilent 4x44 rat shole genome micrarray slides for 17 hours at 65C. Slides were then washed according to the protocol.

scan_protocol: Microarrays were scanned with Agilent Technologies Scanner (G2505B US45102880) at 5um resolution at 100% PTM. The images were then imported into Agilent Feature Extraction Software.

data_processing: The raw data files extracted from Agilent Feature extraction software are processed and analyzed by GeneSpring GX10 software. The raw data were at first normalized with the following conditions and then filtered by the flag using GeneSpring GX10 software. The Normalization included log2 transformation, per chip normalization to 75% quantile and per gene normalization to median. Filtered on the Flag included Entities(transcripts) where at least 100 percent of samples in any 1 out of 1 conditions have flags in Present or Marginal. Select the flag values that an entity must satisfy to pass the filter by defining the acceptable flags (Present or Marginal present). We retain entities in which at least 6 genes in 1 out of 6 conditions (3 Sham controls and 3 Ischemia Reperfusion with 6 replicates) have acceptable values, which contain total 23897 transcripts.

source_name: Retina, Sham Control 7d replication 4

label_protocol: Following Agilent One-Color Microarray-Based Gene Expression protocol of the Low RNA Input Fluoresent Linear Amplification Kit Plus (Agilent, Santa Clara, CA), 200ng RNA with the addition of One-Color Spike Mix was denatured and incubate with T7 Promoter perimer. Synthesis of cDNA followed with the addition of First-Strand buffer, DTT, dNTP mix, MMLV-RT and RNAse Out and incubation at 40C for 2 hours. Transcription of the product incorporated the Cyanine 3-CTP in the master Mix with incubation at 40C for 2 hours.

growth_protocol: Long Evan's hooded male rats (Harlan, Indianapolis, IN) weighing 250 to 300 g were used. All animals were housed on a 12-hour light- dark cycle with food and water. The treatment and care of all animals used in this study were approved by the University of Louisville Institutional Animal Care and Use Committee (IACUC) and were performed in accordance with the ARVO Statement for the Use and Care of Animals in Ophthalmic and Vision Research.

extract_protocol: Retinas were homogenized in lysis/binding buffer (Ambion, Inc.) using a motorized rotor-stator homogenizer. Total RNA was isolated using mirVana™ miRNA Isolation Kit (Ambion, Inc, Austin TX). The quality of the RNA was checked with the aid of the spectrophotometer (NanoDrop Technologies, Wilmington, DE). The RNA integrity numbers (RIN) for all samples were greater than 8

treatment_protocol: To induce ischemia, rats were first anesthetized with sodium pentobarbital (50 mg/kg, i.p.). Tetracaine hydrochloride 0.5% and tropicamide 1% ophthalmic drops were administered to provide local anesthesia and mydriasis, respectively. For induction of high intra-ocular pressure (IOP) the anterior chamber of one eye was cannulated with a 30 gauge needle attached to an elevated 1L sterile saline reservoir. High IOP of 110 mmHg was maintained for 60 min. Reperfusion proceeded for the 3 time points: 0h, 24h and 7 days after which animals were euthanized and tissues were collected. The same procedures were administered to rats receiving sham surgeries except that high IOP was not induced. IOP was measured in mmHg at 15, 30 and 60min using a TonoLab tonometer device (Colonial Medical Supply, Franconia, NH). Retinas were dissected from each eye, flash frozen in liquid nitrogen, and stored in -80°C for subsequent use.

value: Sham control


title: Sham Control 0h 6

description: Gene expression at time point 0h after sham surgery

source_name: Retina, Sham Control 0h replication 6


title: Sham Control 24h 3

description: Gene expression at time point 24h after sham surgery

source_name: Retina, Sham Control 24h replication 3


title: Sham Control 7d 3

source_name: Retina, Sham Control 7d replication 3


title: Sham Control 24h 5

source_name: Retina, Sham Control 24h replication 5


title: CCM006


title: Sham Control 0h 4

source_name: Retina, Sham Control 0h replication 4


title: CCM005


title: CCM008


title: Sham Control 7d 1

source_name: Retina, Sham Control 7d replication 1


title: Sham Control 7d 2

source_name: Retina, Sham Control 7d replication 2


title: Sham Control 24h 6

source_name: Retina, Sham Control 24h replication 6


title: Ischemia Reperfusion 7d 6

description: Gene expression at time point 7d post-ischemia (60 min)

source_name: Retina, Experimental sample_7d replication 6

value: Ischemia reperfusion


title: Sham Control 0h 1

source_name: Retina, Sham Control 0h replication 1


title: Ischemia Reperfusion 7d 5

source_name: Retina, Experimental sample_7d replication 5


title: Sham Control 24h 2

source_name: Retina, Sham Control 24h replication 2


title: Sham Control 24h 4

source_name: Retina, Sham Control 24h replication 4


title: Sham Control 0h 2

source_name: Retina, Sham Control 0h replication 2


title: Sham Control 0h 5

source_name: Retina, Sham Control 0h replication 5


title: Sham Control 7d 6

source_name: Retina, Sham Control 7d replication 6


title: CCM004

source_name: Human intrahepatic cholangiocarcinoma


title: Sham Control 0h 3

source_name: Retina, Sham Control 0h replication 3


title: Sham Control 24h 1

source_name: Retina, Sham Control 24h replication 1


title: Sham Control 7d 5

source_name: Retina, Sham Control 7d replication 5


title: CCM003


title: Ischemia Reperfusion 7d 1

source_name: Retina, Experimental sample_7d replication 1


title: Ischemia Reperfusion 7d 3

source_name: Retina, Experimental sample_7d replication 3


title: Ischemia Reperfusion 7d 4

source_name: Retina, Experimental sample_7d replication 4


title: Ischemia Reperfusion 24h 6

description: Gene expression at time point 24h post-ischemia (60 min)

source_name: Retina, Experimental sample_24h replication 6


title: Ischemia Reperfusion 24h 5

source_name: Retina, Experimental sample_24h replication 5


title: CCBCN31


title: Ischemia Reperfusion 0h 4

description: Gene expression at time point 0h post-ischemia (60 min)

source_name: Retina, Experimental sample_0h replication 4


title: Ischemia Reperfusion 0h 1

source_name: Retina, Experimental sample_0h replication 1


title: Ischemia Reperfusion 24h 1

source_name: Retina, Experimental sample_24h replication 1


title: CCM002


title: Ischemia Reperfusion 7d 2

source_name: Retina, Experimental sample_7d replication 2


title: CCBCN30


title: Ischemia Reperfusion 24h 2

source_name: Retina, Experimental sample_24h replication 2


title: Ischemia Reperfusion 24h 4

source_name: Retina, Experimental sample_24h replication 4


title: Ischemia Reperfusion 24h 3

source_name: Retina, Experimental sample_24h replication 3


title: Ischemia Reperfusion 0h 3

source_name: Retina, Experimental sample_0h replication 3


title: CCBCN18

source_name: Human intrahepatic cholangiocarcinoma


title: Ischemia Reperfusion 0h 6

source_name: Retina, Experimental sample_0h replication 6


title: CCBCN16


title: Ischemia Reperfusion 0h 2

source_name: Retina, Experimental sample_0h replication 2


title: CCBCN22


title: CCBCN24


title: CCBCN17


title: CCBCN21


title: CCBCN20


title: CCBCN26


title: CCBCN25


title: CCBCN27


title: Ischemia Reperfusion 0h 5

source_name: Retina, Experimental sample_0h replication 5


title: CCBCN013


title: CCBCN011


title: CCBCN014


title: CCBCN006


title: CCBCN012


title: CCBCN002


title: CCBCN001


title: Int_WT_1

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: based on Affymetrix protocols

scan_protocol: based on Affymetrix protocols

data_processing: Data was processed/normalized by RMA algorithm using Affymetrix Expression Console version 1.1.

source_name: Klf5wt/wtShhEGFP/Cre+ , E14.5 Intestine

label_protocol: based on Affymetrix protocols

extract_protocol: Total RNA was isolated from dissected intestine segments using the Qiagen MicroRNA Kit.

value: mixed (part C57Bl/6)

value: Intestine

tag: genotype

tag: age

value: E14.5 embryos


title: Gli1-/- mouse fundus (3 mice per group) rep2

city: Ann Arbor

first: Mohamad

last: El-Zaatari

address: 1150 W Medical Ctr Dr

institute: University of Michigan

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 PM plate arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Plate arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).

growth_protocol: Mice were housed at the University of Michigan animal facility.

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

treatment_protocol: Stomachs were opened along the greater curvature, pinned out, the fundi dissected out and directly homogenized in Trizol.  Homogenates were stored at -80C.  RNA was extracted and cleaned up at a later date.

value: Trizol homogenized gastric fundus

value: 6 months old


title: CCBCN004

value: intrahepatic cholangiocarcinoma


title: Gli1-/- + H. felis (6mo) mouse fundus (3 mice per group) rep2


title: Gli1-/- mouse fundus (3 mice per group) rep1


title: Int_KO_klf5_1

source_name: Klf5 knockout, E14.5 Intestine


title: CCBCN005

value: Proliferation


title: Int_KO_klf5_3


title: Int_WT_2


title: Int_WT_3


title: Gli1-/- + H. felis (6mo) mouse fundus (3 mice per group) rep1


title: WT + H. felis (6mo) mouse fundus (3 mice per group) rep2


title: E13.5 germ cell rep2

city: Singapore

first: Vibhor

last: Kumar

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

country: Singapore

institute: Genome Institute of Singapore

description: Biological replicate 2

hyb_protocol: 1.5 µg of biotin-labelled cDNA was hybridized to microarrays (MouseWG-6 Expression BeadChip version 2.0) at 48 °C, according to NuGEN’s recommendation.

scan_protocol: Illumina Mouse-6 Expression BeadChip v2.0 were washed and stained with streptavidin-Cy3 before scanning using the Illumina Bead Reader.

data_processing: The data were analyzed using Bead Array suite software. Rank invariant normalization method was used to obtain the signal intensity.

source_name: FACS-purified Pou5f1-GFP-positive germ cells

label_protocol: Biotin-labelling was performed by incubating 5 µg of the amplified cDNA with UNG enzyme (Epicentre Biotechnologies) at 50 °C for 30 min. Labelling buffer (0.952 M acetic acid and 28 mM MgCl2) and ARP solution (Molecular Probes) was added and the mixture was incubated at 50 °C for 1 h, followed by a final purification using the Zymo Research DNA Clean & Concentrator-25 kit.

extract_protocol: RNA was extracted from FACS-purified cells using the Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) with on-column DNase treatment to eliminate potential DNA contamination. RNA quality was assessed using the RNA 6000 Pico LabChip Kit (Agilent) and quantitated using the Quant-iT RiboGreen RNA Reagent (Invitrogen). 10 ng of good-quality RNA, as defined by RIN value greater than 8.0, was amplified using the Ovation RNA Amplification System V2 (NuGEN) and purified using the Zymo Research DNA Clean & Concentrator-25 kit.

tag: developmental stage

value: male

value: gonad

value: (CBA/CaJ X C57BL/6J)F16+ X Hsd:ICR(CD-1)


title: E13.5 germ cell rep1

description: Biological replicate 1

tag: tissue


title: Non-germ cell control rep2

description: Biological replicate 2

source_name: FACS-purified Pou5f1-GFP-negative cells


title: E15.5 germ cell rep2

description: Biological replicate 2


title: CCBCN003

tag: disease state


title: E15.5 germ cell rep1

description: Biological replicate 1


title: HeLa cells-MHT 3h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

description: HeLa cells treated with heat stress at 41°C and cultured for 3 h

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite

source_name: Human cervical squamous cell carcinoma cell line HeLa

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle’s Medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: MHT treatment was carried out by immersing plastic culture vessels containing the attached cells in a water bath at 41°C for 30 min. After heat treatment, the cells were incubated for 0-3 h at 37°C.

tag: cell line

value: HeLa

value: female

value: 31 years

value: cervix

tag: life span

value: infinite

tag: morphology

value: epithelial-like


title: WT mouse fundus (3 mice per group) rep2

source_name: WT mouse fundus (3 mice per group) rep2


title: E13.5 germ cell rep3

description: Biological replicate 3


title: Int_KO_klf5_2


title: Non-germ cell control rep1

description: Biological replicate 1


title: WT + H. felis (6mo) mouse fundus (3 mice per group) rep1


title: E15.5 germ cell rep3

description: Biological replicate 3


title: WT mouse fundus (3 mice per group) rep1

source_name: WT mouse fundus (3 mice per group) rep1


title: E11.5 germ cell rep1

description: Biological replicate 1

value: male/female


title: HeLa cells-MHT 0h

description: HeLa cells treated with heat stress at 41°C and cultured for 0 h


title: HeLa (MCB2281)

status: Public on Jan 23 2013

city: Dresden

first: Zoltan

last: Maliga

address: Pfotenhauer Str 108

country: Germany

institute: MPI-CBG

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture. The samples were then hybridized to 4x44K Agilent Whole Human Genome Oligo Microarrays (AMADID 014850) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa_human MYH6-LAP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug total RNA using the One-Color Microarray-Based Gene Expression Analysis v5.5 protocol (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: grown to confluence in DMEM-GlutaMAX, 10% FCS, penicillin/streptomycin with supplemental glutamine

extract_protocol: Total RNA was isolated by suspending PBS-rinsed adherent HeLa cells in Trizol and following the manufacturer's instructions for isolation of total RNA

tag: cell type

value: HeLa-kyoto cells

tag: stably transfected with

value: human MYH6-LAP BAC transgene


title: HeLa (MCB2264)

source_name: HeLa_human KIF9-LAP

value: human KIF9-LAP BAC transgene


title: HeLa (MCB2280)

source_name: HeLa_human MYH4-LAP

value: human MYH4-LAP BAC transgene


title: HeLa (MCB2282)

source_name: HeLa_human MYH8-LAP

value: human MYH8-LAP BAC transgene


title: E11.5 germ cell rep3

description: Biological replicate 3


title: HeLa cells-control

description: HeLa cells (control)


title: DC_BC656

description: SAMPLE 5

source_name: activated dendritic cells (DCs)

growth_protocol: Monocytes were isolated from resuspended  peripheral blood mononuclear cells from the buffy coats (BC) of anonymous blood donors (aged 30-35) using MACS® CD14 microbeads, resuspended in medium for macrophage or dendritic cell differentiation, as described below, and seeded at a density of 2,5x10^6 cells/well in 6-well dishes.

extract_protocol: Cells rinsed with warm phosphate-buffered saline, resuspended in Trizol (Invitrogen) and total RNA was isolated using the manufacturer's protocol.

treatment_protocol: Macrophages were obtained by culture of monocytes in DMEM GlutaMAX (Invtirogen) supplemented with L-glutamine, penicillin/streptomycin, 20% FCS and 10% HS. Medium was replaced at day 1 and 5. Cells were harvested after 7 days. Immature dendritic cells (DCs) were obtained by culturing monocytes for 6 days in RPMI supplemented with 3% FCS, L-glutamine, penicillin/streptomycin, 50 ng/ml GM-CSF (R&D Systems) and 10 ng/ml IL-4 (R&D Systems). This medium was exchanged for RPMI supplemented with 5% FCS, L-glutamine, 10 ng/ml lipopolysaccharide and 100 U/ml interferon gamma and incubated for 24 hours to prepare the mature DCs.

tag: tissue origin

value: primary human monocytes

tag: buffy coat


title: HeLa cells-MHT 1h

description: HeLa cells treated with heat stress at 41°C and cultured for 1 h

tag: treatment


title: DC_BC950

description: SAMPLE 6


title: HeLa (MCB2256)

source_name: HeLa_human KIF2B-LAP

value: human KIF2B-LAP BAC transgene


title: macrophage_BC123

description: SAMPLE 7

source_name: activated macrophages

value: male


title: HeLa (MCB2274)

source_name: HeLa_human MYH13-LAP

value: human MYH13-LAP BAC transgene


title: macrophage_BC950

description: SAMPLE 9


title: monocyte_BC656

description: SAMPLE 2

source_name: monocyte


title: DC_BC123

description: SAMPLE 4


title: monocyte_BC123

description: SAMPLE 1


title: HeLa (MCB3115)

source_name: HeLa_human KIF16-LAP

value: human KIF16-LAP BAC transgene


title: macrophage_BC656

description: SAMPLE 8


title: CD4M_BC970b_stimulated_rep2

description: SAMPLE 16

growth_protocol: CD4+ T-cells were isolated using a primary negative depletion of peripheral blood mononuclear cells from the buffy coats (BC) of anonymous blood donors (aged 30-35) using MACS® Naïve CD4+ T Cell Isolation Kit II or Memory CD4+ T Cell Isolation Kit II, followed by secondary negative depletion with CD25 Microbeads (Miltenyi Biotec) to remove regulatory T-cells. The resulting naïve or memory T-cells were resuspended in X-Vivo medium supplemented with 10 % HS, seeded 200,000 cells/well in 96-well plates (Corning V-plates).

treatment_protocol: T-cells were stimulated with Dynabeads CD3/CD28 T-cell expander (Invitrogen) for 3 days.

value: Primary human memory CD4+CD25- T-cells

tag: stimulation

value: ex vivo stimulated with CD3-CD28 Dynabeads


title: FBR macrophages from 3-days implants, biological rep1

city: Leuven

first: Lindsay

last: Mesure

address: Minderbroedersstraat 17

department: Cardiovascular Diseases

country: Belgium

institute: KULeuven

description:
Gene expression data from freshly isolated macrophages from 3-days implants in rats
Macrophages_C3-1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr to Rat 230 2.0 GeneChips. Arrays were washed and stained with streptavidin-phycoerythrin, biotinylated anti-streptavidin.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Arrays were analyzed independently of each other with Microarray Suite version 5.0 (MAS 5.0). Only probe sets that were present (p<0.04) in all 3 arrays representing 1 sample type were retained for further multiple array data analysis. In the comparison analysis, the Robust Multichip Analysis (RMA) algorithm was used.

source_name: FBR macrophages from 3-days implants

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

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

value: foreign body reaction


title: monocyte_BC950

description: SAMPLE 3

tag: gender


title: FBR macrophages from 3-days implants, biological rep3

description:
Gene expression data from freshly isolated macrophages from 3-days implants in rats
Macrophages_C3-3


title: E11.5 germ cell rep2

description: Biological replicate 2

value: gonad

tag: strain

value: (CBA/CaJ X C57BL/6J)F16+ X Hsd:ICR(CD-1)


title: CD4M_BC970b_resting_rep2

description: SAMPLE 15

value: female

value: no stimulation


title: CD4N_BC725b_stimulated_rep2

description: SAMPLE 14

value: Primary human naïve CD4+CD25- T-cells


title: FBR macrophages from 3-days implants, biological rep2

description:
Gene expression data from freshly isolated macrophages from 3-days implants in rats
Macrophages_C3-2


title: CD4N_BC725b_resting_rep2

description: SAMPLE 13


title: CD4M_BC881_stimulated

description: SAMPLE 12


title: CD4M_BC970_stimulated_rep1

description: SAMPLE 8


title: ATP11B-SiRNA-A2780-CP20cell-1

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression beadchip 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.

source_name: Ovarian cancer 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 protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: chemoresistance

value: cisplatin-resistant

value: ATP11B siRNA


title: CD4M_BC656_resting

description: SAMPLE 9


title: Ctr-siRNA-A2780-CP20cell-3

value: control siRNA


title: CD4M_BC656_stimulated

description: SAMPLE 10


title: Fibrinogen activated macrophages, biological rep1

description:
Gene expression data from rat blood macrophages activated during 3 days on fibrinogen coated PTFE
Macrophages_C2-1

source_name: Fibrinogen activated macrophages

value: blood


title: ATP11B-SiRNA-A2780-CP20cell-2


title: CCBCN015

source_name: Human intrahepatic cholangiocarcinoma

value: intrahepatic cholangiocarcinoma

value: Inflammation


title: CD4M_BC970_resting_rep1

description: SAMPLE 7


title: CD4N_BC656_resting

description: SAMPLE 5

value: male


title: Fibrinogen activated macrophages, biological rep2

description:
Gene expression data from rat blood macrophages activated during 3 days on fibrinogen coated PTFE
Macrophages_C2-2


title: Blood macrophages, biological rep1

description:
Gene expression data from freshly isolated rat blood macrophages
Macrophages_C1-1

source_name: Blood macrophages


title: Ctr-siRNA-A2780-CP20cell-2


title: Fibrinogen activated macrophages, biological rep3

description:
Gene expression data from rat blood macrophages activated during 3 days on fibrinogen coated PTFE
Macrophages_C2-3


title: Blood macrophages, biological rep2

description:
Gene expression data from freshly isolated rat blood macrophages
Macrophages_C1-2


title: CD4N_BC881_resting

description: SAMPLE 3


title: CD4N_BC881_stimulated

description: SAMPLE 4


title: Blood macrophages, biological rep3

description:
Gene expression data from freshly isolated rat blood macrophages
Macrophages_C1-3


title: ATP11B-SiRNA-A2780-CP20cell-3


title: Ctr-siRNA-A2780-CP20cell-1


title: CD4N_BC656_stimulated

description: SAMPLE 6


title: CD4M_BC881_resting

description: SAMPLE 11


title: HeLa (MCB3112)

description: gene expression in HeLa-kyoto cells stably transfected with a human MYO1H-LAP BAC transgene

source_name: HeLa-Kyoto_human MYO1H-LAP

growth_protocol: Cells were grown to confluence in DMEM-GlutaMAX, 10% FCS, penicillin/streptomycin with supplemental glutamine.

extract_protocol: Total RNA was isolated by suspending PBS-rinsed adherent HeLa cells in Trizol and following the manufacturer's instructions for isolation of total RNA.

value: HeLa-kyoto cells

tag: transfected with

value: human MYO1H-LAP BAC transgene

tag: facs-isolated clone

value: no


title: CD4N_BC725_resting_rep1

description: SAMPLE 1


title: Cortical neurons-NMDA-24h-Rep 2

city: Hobart

first: Minghui Jessica

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description: Replicate 2 of 3

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a pmt value=478.

data_processing:
The data were normalised using median normalisation with GeneSpring Ver 7.3.

Non-normalized data is available in the 'GSE16035_non-normalized_data.txt' file, which is linked to the GSE16035 record.

source_name: Murine primary cortical neurons, NMDA, 24h

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

growth_protocol: Neocortical neurons (gestational days 15 or 16) obtained from foetal cortices of Swiss albino mice were used to prepare the primary cultures employing previous described procedures with modifications [Cheung NS, Beart PM, Pascoe CJ, John CA, Bernard O. Human Bcl-2 protects against AMPA receptor-mediated apoptosis. J Neurochem. 2000; 74: 1613-1620.].

extract_protocol: RNA was extracted and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Anhydrous form of NaHS and NMDA (Sigma, Louis, MO) were freshly prepared in water upon usage to get a stock concentration of 100 mM respectively. Desired concentrations were achieved through dilution with NB medium. Day 7 cultured murine cortical neurons were treated with 200uM NMDA or 200uM NaHS over a time course of 5h, 15h and 24h. Neuronal samples were then collected for global gene expression analyses.

value: Swiss Albino

tag: age

value: Gestation day 15-16

value: Primary cortical neurons

tag: age of  culture

value: Day 7

value: NMDA

tag: treatment time-point


title: HeLa (MCB3114) clone 4

description: gene expression in FACS-isolated single clones of HeLa-kyoto cells stably transfected with a human MYO19-LAP BAC transgene

source_name: HeLa-Kyoto_human MYO19-LAP

value: human MYO19-LAP BAC transgene

value: yes


title: CD4N_BC725_stimulated_rep1

description: SAMPLE 2

value: female

tag: tissue

value: Primary human naïve CD4+CD25- T-cells

value: ex vivo stimulated with CD3-CD28 Dynabeads


title: ATP11B-SiRNA-A2780-PARcell-1

value: cisplatin-sensitive

value: ATP11B siRNA


title: ATP11B-SiRNA-A2780-PARcell-2


title: HeLa (MCB3393) clone 2

description: gene expression in FACS-isolated single clones of HeLa-kyoto cells stably transfected with a mouse MYO1B-LAP BAC transgene

source_name: HeLa-Kyoto_mouse MYO1B-LAP

value: mouse MYO1B-LAP BAC transgene


title: Cortical neurons-NMDA-24h-Rep 1

description: Replicate 1 of 3


title: HeLa (MCB2283)

description: gene expression in HeLa-kyoto cells stably transfected with a human MYH9-LAP BAC transgene

source_name: HeLa-Kyoto_human MYH9-LAP

value: human MYH9-LAP BAC transgene


title: Cortical neurons-NMDA-15h-Rep 3

description: Replicate 3 of 3

source_name: Murine primary cortical neurons, NMDA, 15h


title: Ctr-siRNA-A2780-PARcell-2

value: control siRNA


title: ATP11B-SiRNA-A2780-PARcell-3


title: Cortical neurons-NMDA-24h-Rep 3

description: Replicate 3 of 3


title: HeLa (MCB3118)

description: gene expression in HeLa-kyoto cells stably transfected with a human KIF26A-LAP BAC transgene

source_name: HeLa-Kyoto_human KIF26A-LAP

value: HeLa-kyoto cells

value: human KIF26A-LAP BAC transgene


title: HeLa (MCB3119)

description: gene expression in HeLa-kyoto cells stably transfected with a human KIF26B-LAP BAC transgene

source_name: HeLa-Kyoto_human KIF26B-LAP

value: human KIF26B-LAP BAC transgene

value: no


title: Cortical neurons-NMDA-15h-Rep 1

description: Replicate 1 of 3

value: Swiss Albino

value: Gestation day 15-16

value: Primary cortical neurons


title: Ctr-siRNA-A2780-PARcell-3


title: HeLa

description: gene expression in HeLa-kyoto cells

source_name: HeLa-kyoto


title: Cortical neurons-NMDA-5h-Rep 3

description: Replicate 3 of 3

source_name: Murine primary cortical neurons, NMDA, 5h

value: Day 7

value: NMDA


title: Ctr-siRNA-A2780-PARcell-1


title: Cortical neurons-NO-24h-Rep 1

description: Replicate 1

hyb_protocol: 15μg of fragmented cRNA produced above was hybridized to the GeneChip Mouse Genome 430 2.0 arrays for 16h at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The hybridized arrays were washed, stained, and scanned using the Hewlett-Packard GeneArray Scanner G2500A according to the manufacturer’s instructions.

data_processing: The data from each array were collected and initially analyzed using Affymetrix Microarray Suite 5.0 software. For comparison of multiple arrays, the signal intensity of each array was scaled to 500. The regulated genes were filtered on fold change 1.5 fold against controls in at least one of three time-points. One-way ANOVA (p<0.05) approach was used to find differentially expressed genes using GeneSpring™ GX 7.3 software (Agilent Technologies, CA, USA).

source_name: Murine primary cortical neurons

label_protocol: According to technical manual form Affymetrix, 7μg of extracted total RNA was used for cDNA synthesis. Double-stranded cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) with a T7-dT24 primer. After cleanup, Biotin-labeled cRNA was synthesized by in vitro transcription (Enzo Diagnostic, Inc., NY, USA) and fragmented subsequently.

extract_protocol: RNA from samples was extracted using RNeasy Mini Kit (Qiagen Cat. No. 74104) according to the manufacturer’s instructions. 1.5μl of the RNA sample was aliquoted for spectrophotometric quantification using Nanodrop ND-1000 Version 3.2.1 and 1μl for RNA quality analysis using E-gene HDAGT12 genetic analyzer.

treatment_protocol: NO donor, NOC-18, was prepared as 100mM aqueous stock solution containing 0.01M sodium hydroxide (NaOH) and stored at -20°C. Desired concentrations were achieved by dilution with serum-free NB. On day 7 in vitro, the cultured neurons were treated with NOC-18 in NB medium.

value: Swiss Albino mice

tag: time point

tag: agent


title: PP during Fusion

city: Suita

first: Takayoshi

last: Sakai

state: Osaka

address: 1-8 Yamadaoka

department: Oral-Facial Disorders

institute: Osaka Univ Grad Sch Dent

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings with no scaling (scale factor set to 1).

source_name: embryonic palate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (One-Cycle Target Labeling, Expression Analysis Technical Manual).

growth_protocol: The maxillary portion was removed from each fetus at E14. Explants were grown with BGJB medium containing 1% penicillin/streptomycin and 95%O2/5%CO2 at 37C.

extract_protocol: The extraction of total RNA was performed with RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: For microarray analysis, the edge of the palatal processes was microdissected and collected using a microscope and forceps at the each stage of palatal development (before, during and after fusion) .

tag: strain background

value: ICR

value: female

tag: developmental stage

value: fetus at E14

value: embryonic palate during fusion


title: Cortical neurons-NO-15h-Rep 3

description: Replicate 3


title: PP before Fusion

value: embryonic palate before fusion


title: Cortical neurons-NMDA-5h-Rep 2

description: Replicate 2 of 3


title: PP after Fusion

value: embryonic palate after fusion


title: Cortical neurons-NMDA-15h-Rep 2

description: Replicate 2 of 3


title: Cortical neurons-NO-24h-Rep 3

description: Replicate 3


title: Cortical neurons-NaHS-24h-Rep 3

description: Replicate 3 of 3

source_name: Murine primary cortical neurons, NaHS, 24h

value: NaHS


title: Cortical neurons-NO-15h-Rep 1

description: Replicate 1


title: Cortical neurons-NMDA-5h-Rep 1

description: Replicate 1 of 3


title: Cortical neurons-NO-15h-Rep 2

description: Replicate 2


title: Cortical neurons-NO-24h-Rep 2

description: Replicate 2


title: Cortical neurons-NaHS-24h-Rep 2

description: Replicate 2 of 3


title: Cortical neurons-NO-8h-Rep 2

description: Replicate 2


title: Cortical neurons-NaHS-24h-Rep 1

description: Replicate 1 of 3


title: Cortical neurons-NaHS-15h-Rep 1

description: Replicate 1 of 3

source_name: Murine primary cortical neurons, NaHS, 15h


title: Cortical neurons-Ctrl-Rep 1

description: Replicate 1

value: Ctrl

value: vehicle-treated control


title: Cortical neurons-NO-8h-Rep 3

description: Replicate 3


title: Cortical neurons-Ctrl-Rep 2

description: Replicate 2


title: Cortical neurons-Ctrl-Rep 5

description: Replicate 5


title: Cortical neurons-NaHS-15h-Rep 2

description: Replicate 2 of 3


title: Cortical neurons-NO-8h-Rep 1

description: Replicate 1


title: Cortical neurons-NaHS-15h-Rep 3

description: Replicate 3 of 3


title: Cortical neurons-Ctrl-Rep 4

description: Replicate 4


title: Cortical neurons-Ctrl-Rep 3

description: Replicate 3


title: Cortical neurons-Ctrl-Rep 5

description: Replicate 5 of 6

source_name: Murine primary cortical neurons, control

value: ctrl


title: Th2 vector (12hr)

city: St Louis

first: K. Scott

last: Weber

state: MO

address: 425 South Euclid Ave

institute: Washington University in St. Louis

description: Gene expression data from Th2 cells - vector only

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was normalized and modeled using dChip software.

source_name: Th2 cells infected with vector only

label_protocol: standard Affymetrix protocol

growth_protocol: T cells polarized to Th1 or Th2 cells for two weeks.

treatment_protocol: Depending on the sample - Thy1 siRNA, Trpm4 siRNA, Vector only or DN Trpm4 vector.

tag: time

value: 12 hour stimulation

tag: cell type

value: vector only


title: Cortical neurons-NaHS-5h-Rep 3

description: Replicate 3 of 3

source_name: Murine primary cortical neurons, NaHS, 5h

value: Swiss Albino

value: Gestation day 15-16

tag: treatment


title: ECC-1 cell, treated with DEHP rep1

city: seoul

first: hyunhee

last: cho

address: seochogu banpodong

country: South Korea

institute: catholic university medical colleage

description: DEHP T_1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

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: DEHP treated ECC-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The ECC-1 cell line was donated from St. Vincent Hospital of Catholic University Medical college, Suwon, and was maintained under a humidified atmosphere of 5% CO2 and 95% air at 37℃. The culture medium was RPMI supplemented with 5% fetal bovine serum (GIBCO, Invitrogen Co., USA) and penicillin . The culture medium was refreshed every 2 to 3 days.

treatment_protocol: ECC-1 cells were seeded in a 100-mm dish at a density of 1.24 × 106 cells/ml. After incubation for 24 h at 37 °C, the cells were treated with 50 μM (The 20% inhibitory concentration (IC20)) di-(2-ethylhexyl) phthalate (DHEP) for 48 h.

tag: cell line

value: endometrial cancer cell line (ECC-1)


title: Th2 DN Trpm4 (12hr)

description: Gene expression data from Th2 cells - DN Trpm4

source_name: Th2 cells infected with dominant negative Trpm4

value: dominant negative Trpm4


title: Cortical neurons-NaHS-5h-Rep 2

description: Replicate 2 of 3

value: Primary cortical neurons

value: Day 7


title: Th1 vector (12hr)

description: Gene expression data from Th1 cells - vector only

source_name: Th1 cells infected with vector only


title: Cortical neurons-Ctrl-Rep 3

description: Replicate 3 of 6


title: Th1-Thy1 siRNA

description: Gene expression data from Th1 cells with Thy1 siRNA

source_name: Th1 cells with Thy1 siRNA

value: Thy1 siRNA


title: Th1-Trpm4 siRNA

description: Gene expression data from Th1 cells with Trpm4 siRNA

source_name: Th1 cells with Trpm4 siRNA

value: Trpm4 siRNA


title: Cortical neurons-NaHS-5h-Rep 1

description: Replicate 1 of 3


title: Th2 vector (4hr)

value: 4 hour stimulation


title: Th2-Trpm4 siRNA

description: Gene expression data from Th2 cells with Trpm4 siRNA

source_name: Th2 cells with Trpm4 siRNA


title: Th1 vector (4hr)


title: Th1 DN Trpm4 (12hr)

description: Gene expression data from Th1 cells - DN Trpm4

source_name: Th1 cells infected with dominant negative Trpm4


title: Cortical neurons-Ctrl-Rep 1

description: Replicate 1 of 6


title: Released rep2

status: Public on Jan 22 2013

city: Tsukuba

first: Chikako

last: Nishitani

state: Ibaraki

institute: National Institutes of Fruit Tree Science

hyb_protocol: The labeled samples were hybridized to the oligoarray slides using Gene Expression Hybridization Kit (Agilent, Palo Alto, CA) as a hybridization buffer at 65°C for 17 h in a hybridization chamber. After hybridization, arrays were washed with Gene Expression Wash Buffer (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

scan_protocol: The dried slides were scanned by Agilent scanner. Raw data from scanning of the array was captured using Agilent Feature Extraction Ver. 9.5.3.1 or 10.7.1.1(with Linear & Lowess normalization).

data_processing: Normalization was performed by GeneSpring Ver. 7.3.1 (Agilent, Palo Alto, CA). Expression for each gene was calculated as the mean value of two to three biological replicates for all time points and the standard error of the mean. Per-chip and per-gene normalization was performed.

organism: Pyrus pyrifolia

source_name: leaf bud

label_protocol: Reverse transcription of mRNA in the total RNA samples and composition of labeled cDNA was performed using Low RNA Input Linear Amplification Kit PLUS, One-Color (Agilent, Palo Alto, CA) according to the manufacturer’s instructions.

growth_protocol: Pear trees were managed according to standard orchard practices.

extract_protocol: Total RNAs were extracted from each sample using the method described in Wan et al. (1994). Isolated RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and the quality and purity were checked using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). RNA was ethanol precipitated and resuspended to 500 ng/μl.

treatment_protocol: Not treated.

tag: cultivar

value: pear cv.Kosui

value: leaf bud

value: breaking stage


title: Cortical neurons-Ctrl-Rep 4

last: Chen

description: Replicate 4 of 6

tag: strain


title: Th2-Thy1 siRNA

description: Gene expression data from Th2 cells with Thy1 siRNA

source_name: Th2 cells with Thy1 siRNA


title: ECC-1 cell, control group rep2

description: DEHP C_2

source_name: Solvent(DMSO) treated ECC-1


title: Released rep1


title: Released rep3


title: Cortical neurons-Ctrl-Rep 6

description: Replicate 6 of 6


title: Cortical neurons-Ctrl-Rep 2

description: Replicate 2 of 6


title: Th2

description: Gene expression data from Th2 cells

source_name: Th2 cells


title: ECC-1 cell, treated with DEHP rep2

description: DEHP T_2


title: Th1

description: Gene expression data from Th1 cells

source_name: Th1 cells


title: Th1 DN Trpm4 (4hr)


title: Th2 DN Trpm4 (4hr)


title: ECC-1 cell, control group rep1

description: DEHP C_1


title: OS_Resection_99_pair (miRNA)

city: Boston

first: Katherine

last: Hill

state: MA

address: 330 Brookline Avenue, DA-679

department: Medicine

institute: Beth Israel Deaconess Medical Center

hyb_protocol: Standard Illumina hybridization protocol. Arrays were washed and stained with strepatavidin-Cy3, and then scanned in the array reader.

scan_protocol: Standard Illumina scanning protocol using the Illumina BeadArray Reader.

data_processing: Expression data were imported to the R environment and processed using the Illumina-specific package lumi. Variance-stabilizing transformation (VST) and quantile normalization were applied. VST is described in Lin SM, Du P, Huber W, Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008 36:e11 (PMID 18178591).

source_name: Osteosarcoma resection, pair 6

label_protocol: Total RNA underwent a reverse transcription reaction to generate double-stranded cDNA. Standard Illumina protocols followed (Whole-Genome DASL HT Assay Kits #'s DA-905-0024, DA-905-0096, DA-905-1024, DA-905-1096).

extract_protocol: RNA was extracted from FFPE blocks using the Qiagen RNeasy kit according to company protocol.

tag: gender

value: female

value: osteosarcoma

tag: biopsy/resection pair


title: OS_Resection_94_pair (miRNA)

source_name: Osteosarcoma resection, pair 11


title: OS_Resection_95_pair (miRNA)

source_name: Osteosarcoma resection, pair 10


title: OS_Resection_96_pair (miRNA)

source_name: Osteosarcoma resection, pair 13


title: OS_Resection_91_pair (miRNA)

source_name: Osteosarcoma resection, pair 12


title: OS_Resection_92_pair (miRNA)

source_name: Osteosarcoma resection, pair 2

value: male


title: OS_Resection_93_pair (miRNA)

source_name: Osteosarcoma resection, pair 8


title: Dormant rep1

value: early endodormancy


title: Dormant rep2


title: Dormant rep3


title: OS_Resection_84_pair (miRNA)

source_name: Osteosarcoma resection, pair 19


title: OS_Resection_86_pair (miRNA)

source_name: Osteosarcoma resection, pair 3


title: OS_Resection_85_pair (miRNA)

source_name: Osteosarcoma resection, pair 18


title: OS_Resection_83_pair (miRNA)

source_name: Osteosarcoma resection, pair 15


title: OS_Resection_82_pair (miRNA)

source_name: Osteosarcoma resection, pair 20


title: OS_Resection_97_pair (miRNA)

source_name: Osteosarcoma resection, pair 9


title: OS_Resection_89_pair (miRNA)

source_name: Osteosarcoma resection, pair 16


title: OS_Resection_79_pair (miRNA)

source_name: Osteosarcoma resection, pair 14


title: OS_Resection_81_pair (miRNA)

source_name: Osteosarcoma resection, pair 21


title: OS_Resection_80_pair (miRNA)

source_name: Osteosarcoma resection, pair 7


title: OS_Resection_88_pair (miRNA)

source_name: Osteosarcoma resection, pair 5


title: OS_Resection_98_pair (miRNA)

source_name: Osteosarcoma resection, pair 17


title: OS_Resection_72_pair (miRNA)

source_name: Osteosarcoma resection, pair 26


title: OS_Resection_75_pair (miRNA)

source_name: Osteosarcoma resection, pair 25


title: OS_Resection_71_pair (miRNA)

source_name: Osteosarcoma resection, pair 22


title: OS_Resection_76_pair (miRNA)

source_name: Osteosarcoma resection, pair 24


title: OS_Resection_69_pair (miRNA)

source_name: Osteosarcoma resection, pair 23


title: OS_Resection_87_pair (miRNA)

source_name: Osteosarcoma resection, pair 1


title: OS_Biopsy_66_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 25

value: 25 years

tag: chemotherapy

value: MAP 2 pre-surgery, 3 post

tag: percent necrosis

value: 20% necrosis

tag: recurrence

value: Y

tag: death

tag: time until first recurrence or latest follow-up (months)


title: OS_Biopsy_51_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 16

tag: age

value: 9 years

value: 50% necrosis

tag: tissue


title: OS_Biopsy_64_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 23

value: 59 years

value: AP 2 pre-surgery, 3 post

value: 20-25% necrosis

value: N


title: OS_Biopsy_65_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 24

value: 27 years


title: OS_Biopsy_63_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 22

value: 33 years

value: 5% necrosis


title: OS_Biopsy_59_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 21

value: 12 years

value: female

value: 80% necrosis


title: OS_Biopsy_58_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 20

value: male

value: 40% necrosis

value: osteosarcoma


title: OS_Biopsy_57_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 19

value: 17 years

value: MAP 2 pre-surgery, 3 post

value: 75-80% necrosis


title: OS_Biopsy_53_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 18

value: 13 years

value: 50% necrosis


title: OS_Biopsy_52_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 17

value: 20% necrosis

value: Y


title: OS_Biopsy_34_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 12

value: 15 years

value: 60-70% necrosis

value: N


title: OS_Biopsy_50_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 15

value: 11 years


title: OS_Biopsy_36_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 13

value: 23 years

value: >80% necrosis


title: OS_Biopsy_48_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 14

value: 7 years

value: female


title: OS_Biopsy_18_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 5

value: 70% necrosis


title: OS_Biopsy_33_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 11

value: 9 years

value: 40% necrosis

value: osteosarcoma


title: OS_Biopsy_28_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 10

value: MAP 2 pre-surgery, 3 post

value: 30% necrosis


title: OS_Biopsy_67_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 26

value: 71 years

value: male

value: AP 2 pre-surgery, 3 post

value: 50% necrosis


title: OS_Biopsy_19_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 6

value: 16 years

value: 80% necrosis


title: OS_Biopsy_16_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 3

value: 12 years

value: Y


title: OS_Biopsy_14_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 2

value: 60-70% necrosis

value: N


title: OS_Biopsy_17_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 4

value: 10 years

value: female

value: 10-20% necrosis


title: OS_Biopsy_7_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 1

value: 4 years

value: 60% necrosis


title: OS_Biopsy_67 (miRNA)

source_name: Osteosarcoma biopsy

value: osteosarcoma


title: OS_Biopsy_66 (miRNA)

value: 25 years

value: MAP 2 pre-surgery, 3 post

value: 20% necrosis


title: OS_Biopsy_65 (miRNA)

value: 27 years


title: OS_Biopsy_20_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 7

value: 13 years

value: male

value: 70% necrosis


title: OS_Biopsy_26_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 9

value: 11 years

value: 40% necrosis


title: OS_Biopsy_64 (miRNA)

value: 59 years

value: AP 2 pre-surgery, 3 post

value: 20-25% necrosis


title: OS_Biopsy_24_pair (miRNA)

source_name: Osteosarcoma biopsy, pair 8

value: female

value: 30% necrosis

value: N


title: OS_Biopsy_59 (miRNA)

value: 12 years

value: 80% necrosis

value: Y


title: OS_Biopsy_62 (miRNA)

value: 17 years

value: MAP 2 pre-surgery, 3 post

value: 90-95% necrosis

value: osteosarcoma


title: OS_Biopsy_56 (miRNA)

value: 15 years

value: male


title: OS_Biopsy_63 (miRNA)

value: 33 years

value: 5% necrosis


title: OS_Biopsy_60 (miRNA)

value: 23 years


title: OS_Biopsy_61 (miRNA)

value: 19 years


title: OS_Biopsy_57 (miRNA)

value: 75-80% necrosis


title: OS_Biopsy_58 (miRNA)

value: 9 years

value: 40% necrosis


title: OS_Biopsy_52 (miRNA)

value: 13 years

value: 20% necrosis

value: N


title: OS_Biopsy_53 (miRNA)

value: 50% necrosis


title: OS_Biopsy_50 (miRNA)

value: 11 years

value: Y


title: OS_Biopsy_51 (miRNA)

value: female

value: MAP 2 pre-surgery, 3 post


title: OS_Biopsy_49 (miRNA)

value: 15 years

value: >90% necrosis

value: osteosarcoma


title: OS_Biopsy_47 (miRNA)

value: 3 years


title: OS_Biopsy_46 (miRNA)

value: 10 years

value: male

value: >95% necrosis


title: OS_Biopsy_43 (miRNA)


title: OS_Biopsy_55 (miRNA)

value: 9 years

value: 85% necrosis


title: OS_Biopsy_48 (miRNA)

value: 7 years


title: OS_Biopsy_54 (miRNA)

value: 8 years


title: OS_Biopsy_40 (miRNA)

value: 16 years

value: N


title: OS_Biopsy_39 (miRNA)

value: 80-90% necrosis


title: OS_Biopsy_42 (miRNA)

value: 4 years

value: 90-95% necrosis


title: OS_Biopsy_38 (miRNA)

value: 11 years

value: female

value: MAP 2 pre-surgery, 3 post

value: 20-25% necrosis

value: Y


title: OS_Biopsy_37 (miRNA)

value: osteosarcoma


title: OS_Biopsy_36 (miRNA)

value: 23 years

value: >80% necrosis


title: OS_Biopsy_35 (miRNA)

value: >95% necrosis


title: OS_Biopsy_34 (miRNA)

value: 15 years

value: 60-70% necrosis


title: OS_Biopsy_31 (miRNA)

value: 13 years

value: >99% necrosis


title: OS_Biopsy_32 (miRNA)

value: 8 years

value: male

value: 30% necrosis

value: N


title: OS_Biopsy_45 (miRNA)

value: 9 years

value: 98% necrosis


title: OS_Biopsy_30 (miRNA)

value: 14 years

value: female

value: MAP 2 pre-surgery, 3 post

value: 0% necrosis


title: OS_Biopsy_33 (miRNA)

value: 40% necrosis

value: Y

value: osteosarcoma


title: OS_Biopsy_28 (miRNA)


title: OS_Biopsy_27 (miRNA)

value: 12 years

value: 100% necrosis


title: OS_Biopsy_23 (miRNA)

value: 16 years

value: 85% necrosis


title: OS_Biopsy_41 (miRNA)

value: 5 years

value: >99% necrosis


title: OS_Biopsy_26 (miRNA)

value: 11 years


title: OS_Biopsy_25 (miRNA)

value: male

value: 20% necrosis

value: N


title: OS_Biopsy_29 (miRNA)

value: 15 years

value: 85-90% necrosis


title: OS_Biopsy_24 (miRNA)

value: female

value: MAP 2 pre-surgery, 3 post

value: 30% necrosis


title: OS_Biopsy_21 (miRNA)

value: 80% necrosis


title: OS_Biopsy_18 (miRNA)

value: 7 years

value: 70% necrosis

value: Y

value: osteosarcoma


title: OS_Biopsy_19 (miRNA)

value: 16 years


title: OS_Biopsy_17 (miRNA)

value: 10 years

value: 10-20% necrosis


title: OS_Biopsy_22 (miRNA)

value: 11 years

value: 80-90% necrosis


title: OS_Biopsy_20 (miRNA)

value: 13 years

value: male


title: OS_Biopsy_44 (miRNA)

value: 50-60% necrosis


title: OS_Biopsy_13 (miRNA)

value: 12 years

value: 98% necrosis

value: N


title: OS_Biopsy_12 (miRNA)

value: MAP 2 pre-surgery, 3 post

value: 90-95% necrosis


title: OS_Biopsy_11 (miRNA)

value: 5 years

value: >99% necrosis


title: OS_Biopsy_16 (miRNA)

value: 50% necrosis

value: Y


title: OS_Biopsy_10 (miRNA)

value: 4 years

value: female

value: 94% necrosis

value: osteosarcoma


title: OS_Biopsy_14 (miRNA)

value: 16 years

value: 60-70% necrosis


title: OS_Biopsy_6 (miRNA)

value: 13 years

value: 95% necrosis


title: OS_Biopsy_4 (miRNA)

value: 14 years


title: OS_Biopsy_7 (miRNA)

value: male

value: 60% necrosis


title: OS_Biopsy_9 (miRNA)

value: 11 years

value: MAP 2 pre-surgery, 3 post

value: >90% necrosis

value: N


title: OS_Biopsy_2 (miRNA)

value: >95% necrosis


title: OS_Biopsy_5 (miRNA)

value: 15 years

value: >98% necrosis


title: OS_Biopsy_1 (miRNA)

value: 6 years


title: OS_Biopsy_15 (miRNA)

value: female

value: 70% necrosis


title: OS_Resection_90_pair (miRNA)

source_name: Osteosarcoma resection, pair 4

value: osteosarcoma


title: OS_Resection_82_pair (mRNA)

source_name: Osteosarcoma resection, pair 3


title: OS_Biopsy_48_pair (mRNA)

value: 7 years

value: 50% necrosis

value: Y


title: OS_Resection_90_pair (mRNA)

source_name: Osteosarcoma resection, pair 1


title: OS_Resection_72_pair (mRNA)

source_name: Osteosarcoma resection, pair 5


title: OS_Biopsy_67 (mRNA)

value: 71 years

value: AP 2 pre-surgery, 3 post


title: OS_Biopsy_58_pair (mRNA)

value: 9 years

value: male

value: 40% necrosis


title: OS_Biopsy_66 (mRNA)

value: 25 years

value: MAP 2 pre-surgery, 3 post

value: 20% necrosis


title: OS_Biopsy_63_pair (mRNA)

value: 33 years

value: 5% necrosis


title: OS_Resection_79_pair (mRNA)

source_name: Osteosarcoma resection, pair 2


title: OS_Biopsy_63 (mRNA)


title: OS_Biopsy_58 (mRNA)

value: N


title: OS_Biopsy_48 (mRNA)

value: female


title: OS_Biopsy_43 (mRNA)

value: 13 years

value: >90% necrosis


title: OS_Biopsy_17_pair (mRNA)

value: 10 years

value: 10-20% necrosis

value: osteosarcoma


title: OS_Biopsy_57 (mRNA)

value: 17 years

value: 75-80% necrosis

value: Y


title: OS_Biopsy_52 (mRNA)

value: male


title: OS_Biopsy_53 (mRNA)

value: 50% necrosis


title: OS_Biopsy_51 (mRNA)

value: 9 years


title: OS_Biopsy_67_pair (mRNA)

source_name: Osteosarcoma biopsy, pair 5

value: 71 years

value: AP 2 pre-surgery, 3 post


title: OS_Biopsy_46 (mRNA)

value: MAP 2 pre-surgery, 3 post

value: >95% necrosis


title: OS_Biopsy_37 (mRNA)

value: 8 years

value: N


title: OS_Biopsy_36 (mRNA)

value: 23 years

value: female

value: >80% necrosis


title: OS_Resection_71_pair (mRNA)


title: OS_Biopsy_41 (mRNA)

value: 5 years

value: >99% necrosis


title: OS_Biopsy_50 (mRNA)

value: 11 years

value: 20% necrosis

value: osteosarcoma


title: OS_Biopsy_45 (mRNA)

value: 98% necrosis


title: OS_Biopsy_40 (mRNA)

value: 16 years

value: male


title: OS_Biopsy_38 (mRNA)

value: 20-25% necrosis

value: Y


title: OS_Biopsy_35 (mRNA)

value: 4 years

value: MAP 2 pre-surgery, 3 post


title: OS_Biopsy_34 (mRNA)

value: 15 years

value: 60-70% necrosis


title: OS_Biopsy_33 (mRNA)

value: 9 years

value: 40% necrosis

value: N


title: OS_Biopsy_25 (mRNA)

value: 12 years


title: OS_Biopsy_31 (mRNA)

value: 13 years

value: female

value: >99% necrosis


title: OS_Biopsy_14 (mRNA)

value: osteosarcoma


title: OS_Biopsy_9 (mRNA)

value: 11 years

value: >90% necrosis


title: OS_Biopsy_12 (mRNA)

value: male

value: 90-95% necrosis


title: OS_Biopsy_13 (mRNA)

value: 98% necrosis


title: OS_Biopsy_10 (mRNA)

value: 4 years

value: 94% necrosis


title: OS_Biopsy_26 (mRNA)

value: MAP 2 pre-surgery, 3 post

value: Y


title: OS_Biopsy_19 (mRNA)

value: 16 years

value: 80% necrosis


title: OS_Biopsy_11 (mRNA)

value: 5 years

value: N


title: OS_Biopsy_16 (mRNA)

value: 12 years

value: 50% necrosis


title: OS_Biopsy_28 (mRNA)

value: 9 years

value: female

value: 30% necrosis


title: Semen 3

city: Daejon

first: Seon-Young

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human semen

label_protocol: Illumina TotalPrep RNA Amplification kit (Ambion)

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit or QIAGEN RNeasy Protect Saliva mini kit (saliva) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Experion (BIO-RAD).

tag: physiological specimen

value: Semen

tag: ethnic group

value: Korean


title: Semen 5

description: replicate 5

value: male


title: Semen 6

description: replicate 6


title: OS_Biopsy_20 (mRNA)

value: 13 years

value: 70% necrosis

value: osteosarcoma


title: Saliva 3

description: replicate 3

source_name: Human saliva

value: Saliva


title: OS_Biopsy_18 (mRNA)

value: 7 years

value: MAP 2 pre-surgery, 3 post

value: Y


title: Saliva 2

description: replicate 2


title: Semen 1

description: replicate 1


title: Saliva 6

description: replicate 6


title: Blood 6

description: replicate 6

source_name: Human blood

value: Blood


title: OS_Biopsy_17 (mRNA)

value: 10 years

value: 10-20% necrosis

value: N


title: Blood 5

description: replicate 5


title: Saliva 5

description: replicate 5


title: Semen 4

description: replicate 4


title: Saliva 1

description: replicate 1


title: Saliva 4

description: replicate 4


title: Semen 2

description: replicate 2


title: Blood 4

description: replicate 4


title: OS_Biopsy_7 (mRNA)

value: 4 years

value: 60% necrosis


title: Blood 1

description: replicate 1


title: PHB vs 960 replicate 2

city: Beijing

first: Hailong

last: Liu

address: West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: compare gene expression profiles of ΔphaEC strain with wild-type strain

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

organism: Haloarcula hispanica

source_name: PHB

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: The wild-type strain and ΔphaEC strain were were cultivated at 37°C to mid exponential phase in MG medium containing 10 g/L glucose as carbon source.

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

treatment_protocol: The wild-type strain and ΔphaEC strain were harvested at mid exponential phase.

tag: genotype/variation

value: ΔphaEC mutant

tag: medium

value: MG

tag: Stage

value: middle exponential stage

value: wild-type

tag: tag


title: Vaginal swab 6

description: replicate 6

source_name: Human vaginal swab

value: Vaginal swab

value: Korean

value: female


title: PHB vs 960 replicate 3


title: Vaginal swab 1

description: replicate 1


title: Blood 3

description: replicate 3


title: Blood 2

description: replicate 2


title: Vaginal swab 3

description: replicate 3


title: Vaginal swab 5

description: replicate 5


title: Vaginal swab 4

description: replicate 4


title: Vaginal swab 2

description: replicate 2


title: PHB vs 960 replicate 1


title: MG vs 168 replicate 3

description: compare gene expression profiles of wild-type strain cultured in MG medium with 168 medium

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, lowess normalized log2 ratio (test/control) was calculated.

source_name: wild-type strain from MG medium

growth_protocol: The wild-type strain was cultivated in MG medium or 168 medium at 37°C to mid exponential phase.

treatment_protocol: The wild-type strains from both media were harvested at mid exponential phase.

source_name: wild-type strain from 168 medium


title: MG vs 168 replicate 1


title: MG vs 168 replicate 2


title: Awia_1c9 (clone m)

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: gene expression data from Awia_1c9 (clone m)

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Arrays were scanned with a GeneChip3000 7G scanner.

data_processing: Probe level quantile normalisation and robust multi-array analysis on the raw CEL files were performed using the Affymetrix package of the Bioconductor project. Differentially expressed probe sets were identified using SAM with the fold-change threshold set to 1.5 and the FDR (the q-value) below 1%.

source_name: Wp restricted clone

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10ug total RNA

growth_protocol: Cells were maintained in exponential growth in RPMI1640 medium containing 10% foetal calf serum and 2mM glutamine.

extract_protocol: Total RNA was prepared using Trizol according to the manufacturer's instructions. RNA quality was confirmed with an Agilent 2100 BioAnalyser and all samples had RIN values >9.8.

tag: cell line

value: Awia-BL

tag: cell type

value: Burkitt lymphoma

tag: ebv status

value: Positive

tag: ebv latency

value: Wp restricted


title: Awia_1e9 (clone p)

description: gene expression data from Awia_1e9 (clone p)


title: Awia_1g6 rep1 (clone w)

description: gene expression data from Awia_1g6 rep1 (clone w)

source_name: EBV negative clone

value: Negative


title: s.c.adiposetissue_subject372

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: Gene expression data from white adipose tissue.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridization, the arrays were scanned using an Affymetrix confocal laser scanner (GeneArray scanner GCS3000) and visualized using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method of Probe Logarithmic Intensity Error (PLIER) based on perfect match only (pm-only) calculation (Affymetrix). The robust quantile method was applied to get normalized expression values.

source_name: subcutaneous adipose tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was prepared using the RNeasy Lipid Tissue Kit (Qiagen).

treatment_protocol: Tissues were snap frozen in liquid nitrogen.

value: subcutaneous adipose tissue

tag: Sex

value: male


title: s.c.adiposetissue_subject367


title: s.c.adiposetissue_subject374


title: Awia_5e10 rep1 (clone z)

description: gene expression data from Awia_5e10 rep1 (clone z)


title: s.c.adiposetissue_subject365


title: Awia_5e10 rep2 (clone z')

description: gene expression data from Awia_5e10 rep2 (clone z')


title: s.c.adiposetissue_subject369


title: s.c.adiposetissue_subject368


title: s.c.adiposetissue_subject375


title: s.c.adiposetissue_subject373


title: Awia_1h11 (clone q)

description: gene expression data from  Awia_1h11 (clone q)


title: Awia_20 (clone d)

description: gene expression data from Awia_20 (clone d)

source_name: Latency I clone

value: Latency I


title: Awia_33b (clone c)

description: gene expression data from Awia_33b (clone c)


title: Awia_9 (clone a)

description: gene expression data from Awia_9 (clone a)


title: s.c.adiposetissue_subject370


title: Awia_1g6 rep2 (clone w')

description: gene expression data from Awia_1g6 rep2 (clone w')


title: s.c.adiposetissue_subject371


title: Awia_15 (clone b)

description: gene expression data from Awia_15 (clone b)


title: Awia_1b12 (clone n)

description: gene expression data from Awia_1b12 (clone n)


title: s.c.adiposetissue_subject360


title: s.c.adiposetissue_subject366


title: s.c.adiposetissue_subject361


title: s.c.adiposetissue_subject364


title: s.c.adiposetissue_subject363


title: s.c.adiposetissue_subject362


title: s.c.adiposetissue_subject358


title: s.c.adiposetissue_subject359