title: HEMn Agilent-014706 1 of 2 G4489A

type: genomic

city: Copenhagen

first: Christina

last: Dahl

address: Strandboulevarden 49

country: Denmark

institute: Danish Cancer Society

hyb_protocol: Equal amounts of labeled DNA from the enriched and the reference samples were combined (2.5-4 µg each) and hybridized to the Human Promoter Array 244K (Agilent Technologies).

scan_protocol: Array scanning with Agilent G2565BA Microarray Scanner

data_processing: Data extraction and normalization were performed using the Feature extraction 9.5.3.1 software (Agilent technologies). DNA methylation levels were evaluated using the DNA analytics program (Agilent technologies), the UCSC database (http://genome.ucsc.edu) and the Galaxy tool (http://galaxy.psu.edu).

molecule: genomic DNA

source_name: Human Epidermal Melanocytes, neonatal

label_protocol: Reference and immunoprecipitated DNA were primed with 5µl Random Primers (supplied with Agilent Genomic DNA labeling kit PLUS) and incubated with 19µl Labeling Master Mix (Agilent) at 37°C for 2h. Immunoprecipitated methylated DNA was labeled with Cy5 fluorophore and the input genomic DNA was labeled with Cy3 fluorophore (Agilent Technologies).

growth_protocol: Melanoma cells were routinely cultured as monolayers in RPMI 1640 medium containing 10% fetal bovine serum and antibiotics at 37°C and 5% CO2. Primary human melanocytes (Invitrogen) were maintained in Medium 254 containing Human Melanocyte Growth Supplement 2 (Invitrogen) at 37°C and 5% CO2

extract_protocol: Genomic DNA was isolated using the Qiagen Mini Prep kit (Qiagen) and sonicated using a Bioruptor (Diagenode) to generate 200 to 600 bp fragments. Fragmented DNA (1.6 µg) was used as reference sample, while the remaining was subjected to immunoprecipitation. DNA was denatured for 5 min at 95°C and immunoprecipitated for 4 h at 4°C with 10 µg of monoclonal mouse antibody against 5-methylcytosine (Clone 33D3; 1 mg/mL; Eurogentec) bound to pan-mouse IgG Dynal magnetic beads (Invitrogen).

treatment_protocol: No treatment

value: HEMn

tag: sample type

value: genomic DNA Input

value: MeDIP-DNA


title: pTH2804_HK_8mer_599

status: Public on Aug 01 2014

type: protein

city: Cincinnati

first: Matthew

middle: Tyson

last: Weirauch

state: OH

address: 3333 Burnet Avenue

country: USA

institute: Cincinnati Children's Hospital

hyb_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate. After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution.  Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low).  The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used.   Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: Rarb_HK design

label_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as SacI–BamHI fragments into pTH5325, a modified T7-driven GST expression vector, in most cases.  See paper supplemental web site (http://hugheslab.ccbr.utoronto.ca/supplementary-data/CisBP/) for exceptions.

tag: dbd

tag: platform_id_id design

value: HK

tag: dbd source organism


title: FM79 Agilent-014706 1 of 2 G4489A

organism: Homo sapiens

source_name: Melanoma Cell line

tag: cell line


title: pTH2673_HK_8mer_597

source_name: Foxc1_HK design

extract_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.


title: LP1 JQ1 Treated - 8 hours - mAdbID:117875

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 117875

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

molecule: total RNA

source_name: LP1 JQ1 Treated - 8 hours

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

treatment_protocol:
Treatment type: small molecule
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 8 hours

tag: cell type

value: multiple myeloma cells

tag: disease state

value: multiple myeloma

source_name: LP1 DMSO Treated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol: Agent: DMSO (Dimethyl sulfoxide)


title: LP1 JQ1 Treated - 3 hours - mAdbID:117874

description: mAdb experiment ID: 117874

source_name: LP1 JQ1 Treated - 3 hours

treatment_protocol:
Treatment type: small molecule
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 3 hours


title: SK-MEL-28 Agilent-014706 1 of 2 G4489A


title: tumor tissue at age36-45 years (SA-BC9)

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

department: Biostatistics, Epidemiology and Scientific Computing

country: Saudi Arabia

institute: KFSHRC

description:
SA-BC9.CEL
Gene expression data from tumor tissue at age36-45 years

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the standardized protocol from Affymetrix on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed in the Affymetrix automated fluidic station and scanned with Affymetrix G7 3000 scanner.

scan_protocol: GeneChips were scanned using  Affymetrix G7 3000 scanner.

data_processing: The open source  R/Bioconductor  packages, (Fred Hutchinson Cancer Research Center, Seattle, WA, USA)were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. The CEL files or CEL/CHP files were utilized for further analysis using dChip, MEV,  and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

label: biotin

source_name: tumor tissue at age36-45 years

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

growth_protocol: Tumors and adjacent disease free tissues obtained at time of surgical resection, according to institutional review board approved protocols.

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

tag: sample id

tag: tumor/normal

value: T

tag: grade

tag: er

tag: pr

tag: type

value: IDC

tag: age (years)


title: tumor tissue at age36-45 years (40T)

description:
40T.CEL
Gene expression data from tumor tissue at age36-45 years


title: tumor tissue at age36-45 years (38T)

description:
38T.CEL
Gene expression data from tumor tissue at age36-45 years


title: HBL1 JQ1 Treated - 3 hours - mAdbID:117870

description: mAdb experiment ID: 117870

source_name: HBL1 JQ1 Treated - 3 hours

value: ABC DLBCL cells

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HBL1 DMSO Treated


title: tumor tissue at age36-45 years (SA-BC012)

description:
SA-BC012.CEL
Gene expression data from tumor tissue at age36-45 years


title: HBL1 JQ1 Treated - 24 hours - mAdbID:117872

description: mAdb experiment ID: 117872

source_name: HBL1 JQ1 Treated - 24 hours

treatment_protocol:
Treatment type: small molecule
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 24 hours


title: LP1 JQ1 Treated - 1 hour - mAdbID:117873

description: mAdb experiment ID: 117873

source_name: LP1 JQ1 Treated - 1 hour

treatment_protocol:
Treatment type: small molecule
Agent: JQ1
Treatment dose: 100 nM
Treatment time: 1 hour


title: tumor tissue at age36-45 years (SA-BC011)

description:
SA-BC011.CEL
Gene expression data from tumor tissue at age36-45 years


title: tumor tissue at age36-45 years (SA-BC7)

description:
SA-BC7.CEL
Gene expression data from tumor tissue at age36-45 years


title: HBL1 JQ1 Treated - 8 hours - mAdbID:117871

description: mAdb experiment ID: 117871

source_name: HBL1 JQ1 Treated - 8 hours


title: Cmah KO_liver _3

city: Seoul

first: Deug-Nam

last: Kwon

address: 1 hwayang-dong, Kwangjin-gu

country: South Korea

institute: Konkuk University

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

organism: Mus musculus

source_name: liver from Cmah KO mouse

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted and purified from the liver, lung, kidney, and heart of WT and Cmah-null mice using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol.

tag: strain

tag: genotype

value: Cmah knockout

tag: tissue

value: liver

tag: age

value: 12 weeks


title: pTH1294_ME_8mer_462

source_name: Setbp1_ME design

tag: dbd

value: ME


title: tumor tissue at age36-45 years (SA-BC010)

description:
SA-BC010.CEL
Gene expression data from tumor tissue at age36-45 years


title: FM55M2 Agilent-014706 1 of 2 G4489A

tag: sample type


title: Cmah KO_liver _1

description: replicate 1


title: pTH1294_HK_8mer_593

source_name: Setbp1_HK design

tag: platform_id_id design

tag: dbd source organism


title: FM 6 Agilent-014706 1 of 2 G4489A

tag: cell line

value: FM 6


title: Wild type_liver _3

description: replicate 3

source_name: liver from control mouse

value: wildtype


title: Wild type_liver _1

description: replicate 1


title: HBL1 JQ1 Treated - 1 hour - mAdbID:117869

description: mAdb experiment ID: 117869

source_name: HBL1 JQ1 Treated - 1 hour

tag: cell type

tag: disease state


title: Cmah KO_liver _2

description: replicate 2


title: Wild type_liver _2

description: replicate 2


title: Cnah KO_heart_3

description: replicate 3

source_name: heart from Cmah KO mouse

value: heart


title: Tbx3_n6

city: Leiden

first: Henk

last: Buermans

state: ZH

address: Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Biological replicate 6 of 6. Tbx3 overexpressing Atria.

hyb_protocol: Standard Illumina conditions

scan_protocol: Standard Illumina protocol

data_processing: VSN normalized data; standard parameters

label_protocol: 250ng totRNA Illumina RNA amplification kit (Ambion)

extract_protocol: Macherey-Nagel nucleospin column

tag: labeled (total) RNA from left atria of 4 weeks old double-transgenic male FVB mice (N=6)

tag: expressing human TBX3 upon Cre-recombinase mediated activation


title: Wild type_heart_3

description: replicate 3

source_name: heart from control mouse


title: Cnah KO_heart_2

description: replicate 2


title: Wild type_heart_1

description: replicate 1


title: Control_n2

description: Biological replicate 2 of 6. Control Atria.

tag: labeled (total) RNA from left atria of 4 weeks old male FVB mice (N=6)

tag: containing the atrium specific Nppa-Cre4 transgene


title: Cmah KO_kidney_3

description: replicate 3

source_name: kidney from Cmah KO mouse

value: kidney


title: normal tissue at age36-45 years (SA-BC27)

description:
SA-BC27.CEL
Gene expression data from normal tissue at age36-45 years

source_name: normal tissue at age36-45 years

tag: sample id

tag: tumor/normal

value: N

tag: grade

tag: er

tag: pr

tag: type

value: NORMAL


title: Tbx3_n4

description: Biological replicate 4 of 6. Tbx3 overexpressing Atria.


title: tumor tissue at age36-45 years (SA-BC1)

description:
SA-BC1.CEL
Gene expression data from tumor tissue at age36-45 years

tag: age (years)


title: normal tissue at age36-45 years (349 N)

description:
349 N.CEL
Gene expression data from normal tissue at age36-45 years


title: Tbx3_n2

description: Biological replicate 2 of 6. Tbx3 overexpressing Atria.


title: Wild type_heart_2

description: replicate 2

tag: strain

tag: genotype

tag: tissue

tag: age


title: normal tissue at age36-45 years (385 N)

description:
385 N.CEL
Gene expression data from normal tissue at age36-45 years


title: Control_n4

description: Biological replicate 4 of 6. Control Atria.


title: Cmah KO_kidney_1

description: replicate 1


title: normal tissue at age36-45 years (366 N)

description:
366 N.CEL
Gene expression data from normal tissue at age36-45 years


title: Control_n6

description: Biological replicate 6 of 6. Control Atria.


title: Cmah KO_kidney_2

description: replicate 2


title: Cnah KO_heart_1

description: replicate 1


title: normal tissue at age36-45 years (SA_BC290N)

description:
SA_BC290N.CEL
Gene expression data from normal tissue at age36-45 years


title: normal tissue at age36-45 years (355 N)

description:
355 N.CEL
Gene expression data from normal tissue at age36-45 years


title: Wild type_kidney_3

description: replicate 3

source_name: kidney from control mouse


title: Tbx3_n5

description: Biological replicate 5 of 6. Tbx3 overexpressing Atria.


title: ME180 6 hours rep 3

city: Washington

first: Tabari

middle: M

last: Baker

state: District of Columbia

address: 3970 Reservoir Rd. NW

department: Oncology

institute: Georgetown University

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Gene specific bead intensities were background corrected and quantile normalized using the variance-stabilizing transformation (VST) from the R package limma.   Log2 expression levels were calculated using the R package limma.

label: Biotin

source_name: ME180 cells, 10μM ATRA, 6 hours

label_protocol: Biotinylated cRNA was generated using the Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Cells were grown in Iscove's Modified Dulbecco's Modified Eagle Medium (IMDM) supplemented with 10% fetal bovine serum(FBS)

extract_protocol: Total RNA was isolated using RNA-Stat 60 (Tel-Test; Friendswood, TX), resuspended in DNase, RNase free water, and stored at -80 C until use.  Two step quality control was performed using an Agilent Bioanalyzer and Quant-IT RiboGreen RNA Assay according to manufacturer's instructions.

treatment_protocol: Cells were treated with either DMSO (vehicle) or 10μM ATRA for 1, 3, and 6 hours.

tag: cell line

value: cervix; derived from metastatic site:omentum

tag: disease

value: epidermoid carcinoma

tag: organism

value: Homo sapiens, human

tag: drug treatment

value: 10μM ATRA

tag: treatment time

value: 6 hours


title: Control_n5

description: Biological replicate 5 of 6. Control Atria.

tag: labeled (total) RNA from left atria of 4 weeks old male FVB mice (N=6)

tag: containing the atrium specific Nppa-Cre4 transgene


title: normal tissue at age36-45 years (SA_BC384N)

description:
SA_BC384N.CEL
Gene expression data from normal tissue at age36-45 years

tag: sample id

tag: tumor/normal


title: normal tissue at age36-45 years (342 N)

description:
342 N.CEL
Gene expression data from normal tissue at age36-45 years

tag: grade

tag: er


title: ME180 6 hours rep 4

description: Replicate 4


title: Tbx3_n3

description: Biological replicate 3 of 6. Tbx3 overexpressing Atria.

tag: labeled (total) RNA from left atria of 4 weeks old double-transgenic male FVB mice (N=6)

tag: expressing human TBX3 upon Cre-recombinase mediated activation


title: Control_n1

description: Biological replicate 1 of 6. Control Atria.


title: Wild type_kidney_2

description: replicate 2

tag: strain


title: ME180 6 hours rep 2

description: Replicate 2


title: Wild type_kidney_1

description: replicate 1

tag: genotype


title: Tbx3_n1

description: Biological replicate 1 of 6. Tbx3 overexpressing Atria.


title: cDNA from sth1-3 cells_37C rep1

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

department: Chromosome segregation

country: United Kingdom

institute: Canser Research UK

description:
cDNA from sth1-3 cells
4343/37°C

hyb_protocol: Hybridization was performed following the manufacturers instructions (Affymetrix). Samples were hybridized in buffer containing SSPE, TritonX-100, denatured salmon sperm DNA and biotin-labelled control oligonucleotide, oligo B2. Samples were denatured at 95ºC for 10 minutes before being hybridized to the arrays for 16 hours at 42ºC in a GeneChip Hybridization Oven 640.

scan_protocol: The washing and scanning protocol (FlexMini_euk2v3_450), provided by Affymetrix, was performed automatically on a GeneChip Fluidics Station 450. Arrays were scanned using the GeneChip Scanner 3000 7G, and primary analysis of the chip data was performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data provided was pre-processed and normalised using the standard RMA procedure, as provided by the affy package in Bioconductor 2.11.

organism: Saccharomyces cerevisiae

source_name: sth1-3 cells_37C

label_protocol: 10 mg of dscDNA was digested with DNase I and end-labeled using biotin-N6-ddATP using terminal transferase TdT (Roche, 400 U/µl) and Biotin-N6-ddATP (Enzo Life Sciences).

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0.25 and then the temperature shifted from 25°C to 37°C for two hours.

extract_protocol: Total RNA was extracted following the manufacturers instructions (QUIAGEN). dscDNA was amplified using IVT (Invitrogen).

treatment_protocol: Exponentially growing cells were harvested.

tag: genotype/variation

value: MATα, sth1-3ts, Scc2-Pk9::TRP1


title: cDNA from scc2-4 cells_37C rep2

description:
cDNA from scc2-4 cells
4251/37°C

source_name: scc2-4 cells_37C

value: MATa, scc2-4, Scc1-Pk9::TRP1, Sth1-9myc::URA3


title: cDNA from sth1-3 cells_37C rep2

description:
cDNA from sth1-3 cells
4343/37°C


title: Control_n3

description: Biological replicate 3 of 6. Control Atria.


title: cDNA from scc2-4 cells_37C rep1

description:
cDNA from scc2-4 cells
4251/37°C


title: Cmah KO_lung_3

description: replicate 3

source_name: lung from Cmah KO mouse

value: Cmah knockout

tag: tissue

value: lung

tag: age


title: normal tissue at age36-45 years (SA_BC141N)

description:
SA_BC141N.CEL
Gene expression data from normal tissue at age36-45 years

tag: pr

tag: type

tag: age (years)


title: Cmah KO_lung_1

description: replicate 1

value: 12 weeks


title: ME180 6 hours rep 1

description: Replicate 1

tag: cell line

tag: disease

tag: organism

tag: drug treatment

tag: treatment time


title: cDNA from wild type cells_37C rep2

description:
cDNA from wild type cells
K700/37°C

source_name: wild type cells_37C


title: normal tissue at age36-45 years (SA_BC169N)

description:
SA_BC169N.CEL
Gene expression data from normal tissue at age36-45 years

tag: sample id

tag: tumor/normal

tag: grade


title: Cmah KO_lung_2

description: replicate 2


title: Wild type_lung_3

description: replicate 3

source_name: lung from control mouse


title: ME180 3 hours rep 3

description: Replicate 3

source_name: ME180 cells, 10μM ATRA, 3 hours

value: 3 hours


title: normal tissue at age36-45 years (SA-BC26)

description:
SA-BC26.CEL
Gene expression data from normal tissue at age36-45 years

tag: er


title: ME180 3 hours rep 2

description: Replicate 2


title: normal tissue at age36-45 years (277N)

description:
277N.CEL
Gene expression data from normal tissue at age36-45 years


title: cDNA from wild type cells_37C rep1

description:
cDNA from wild type cells
K700/37°C

tag: strain


title: ME180 3 hours rep 4

description: Replicate 4


title: ME180 1 hour rep 4

description: Replicate 4

source_name: ME180 cells, 10μM ATRA, 1 hour

value: 1 hour


title: Wild type_lung_2

description: replicate 2

tag: genotype

value: wildtype


title: Wild type_lung_1

description: replicate 1


title: ME180 1 hour rep 3

description: Replicate 3


title: ME180 3 hours rep 1

description: Replicate 1


title: normal tissue at age36-45 years (180N)

description:
180N.CEL
Gene expression data from normal tissue at age36-45 years


title: normal tissue at age36-45 years (SA-BC23)

description:
SA-BC23.CEL
Gene expression data from normal tissue at age36-45 years


title: Dsky1 cisplatin, biological rep2

city: A Coruña

first: M Esperanza

last: Cerdan

state: A Coruña

address: Campus de A Zapateira

department: Biología Celular y Molecular

country: Spain

institute: Universidad de A Coruña

description:
Sample name: SAMPLE 11
Raw file: 14_(Yeast_2).CEL

hyb_protocol: Hybridization, washes and staining were done with the GeneChip® HT Hybridization, Wash and Stain Kit. (Manufactured for Affymetrix, Inc. by Ambion, Inc.Affymetrix)

scan_protocol: Image caption and preliminary data analysis were carried out with Affymetrix® Expression Console™ software (v.1.1)

data_processing:
Array data were normalized and summarized using the RMA algorithm from Affymetrix. The data were analyzed using the web suite Babelomics (version 4.3) (Medina et al., 2010). Statistical analysis to identify DEGs were made by using the LIMMA (Linear models for microarray data) test (Smyth, 2005), a moderated t-test.
The FDR (False Discovery Rate) was estimated to correct values for multiple comparison (Benjamini and Hochberg, 1995), using a adjusted p-value of 0.05.
REFERENCES:
Benjamini Y, and Hochberg, Y (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society, Series B, 57(1): 289–300.
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tarraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, Garcia F, Marba M, Montaner D, Dopazo J: Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res 2010, 38(Web Server issue):W210-3.
Rodríguez Lombardero S, Vizoso Vázquez A, Rodríguez Belmonte E, González Siso  MI, Cerdán ME. SKY1 and IXR1 interactions, their effects on cisplatin and spermine resistance in Saccharomyces cerevisiae. Can J Microbiol. 2012, 58(2):184-188.
Smyth, G K (2005). Limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds.), Springer, New York, pages 397–420
Zitomer RS, Hall BD (1976) Yeast cytochrome c messenger RNA. In vitro translation and specific immunoprecipitation of the CYC1 gene product. J Biol Chem 1976, 251(20):6320-6326.

source_name: Dsky1  mutant treated with cisplatin in DMSO

label_protocol: 10 ng of total RNA from each sample were used for successive cDNA, aRNA generation, labeling with biotin and fragmentation using the GeneChip 3' IVT Express Kit. RNA fragmentation was monitored with the 2100 Bioanalyzer (Agilent Technologies, Inc. Santa Clara, CA 95051-7201USA), selecting conditions producing fragments from 35-200 nt with a majority among 100-120 nt.

growth_protocol: W303-Dsky1 cells grown in complete synthetic medium and treated with 600 microM cisplatin in DMSO

extract_protocol: RNA was extracted from a number of cells corresponding to OD 600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturer's instructions. Concentration and purity of RNA was evaluated by measuring the ratio R= A 260 /A 280 (always in the range 1.7<R<2.1). RNA integrity was evaluated by the RIN parameter (RNA Integrity Number) evaluated with the 2100 Bioanalyzer (Agilent Technologies, Inc. Santa Clara, CA 95051-7201USA) according with manufacturer instructions. RIN was near to the value 9 in all the samples.

tag: agent

value: cisplatin


title: Dsky1 cisplatin, biological rep3

description:
Sample name: SAMPLE 12
Raw file: 22_(Yeast_2).CEL


title: wt cisplatin, biological rep 3

description:
Sample name: SAMPLE 9_reanalyzed
Re-analysis of SAMPLE9
Raw file: 21_(Yeast_2).CEL

source_name: wild-type S. cerevisiae treated with cisplatin in DMSO

growth_protocol: W303 cells grown in complete synthetic medium and treated with 600 microM cisplatin in DMSO


title: Dsky1 cisplatin, biological rep1

description:
Sample name: SAMPLE 10
Raw file: 6_(Yeast_2).CEL


title: ME180 DMSO rep 2

description: Replicate 2

source_name: ME180 cells, DMSO-treated

tag: tissue

value: DMSO (Vehicle)


title: ME180 DMSO rep 4

description: Replicate 4


title: ME180 1 hour rep 2

description: Replicate 2


title: epidermis_REDD1_KO_treated_FA_1

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

hyb_protocol: RNA amplification, labeling, hybridization with the Mouse Whole-Genome Gene Expression BeadChips (Illumina), and data analysis were performed at the Genomics Core Facility at the Center for Genetic Medicine at Northwestern University according to the DNA chip manufacturer's protocols.

data_processing: The data underwent background subtraction and quantile normalization using the neqc function from limma package in R

source_name: Epidermis from posterior ear lobe

extract_protocol: Total RNA from murine epidermis was isolated with RiboPure kit (Ambion). Total RNA from murine s.c. adipose was isolated with RNeasy Lipid Tissue Kit (Qiagen). The RNA samples were treated with TURBOTM DNase (Ambion). Purity of RNA samples isolated from epidermis and s.c. fat was confirmed by the expression of adipose and keratinocyte cell markers.

treatment_protocol: Seven wk old B6D2 females in the telogen stage of the hair cycle were shaved, and treated 3 days later. Glucocorticoid FA was applied topically (2 ug/animal) in 200 ul acetone to the back skin once or up to four applications every third day as described previously (Chebotaev et al., 2007b). Control animals were treated with acetone only.

tag: treatment status

value: 2 ug/animal Glucocorticoid FA

tag: phenotype


title: wt cisplatin, biological rep 1

description:
Sample name: SAMPLE 7_reanalyzed
Re-analysis of SAMPLE7
Raw file: 5_(Yeast_2).CEL


title: ME180 DMSO rep 1

description: Replicate 1


title: tumor tissue at age > 55 years (564 T)

description:
564 T.CEL
Gene expression data from tumor tissue at age > 55 years

source_name: tumor tissue at age > 55 years

value: T

tag: pr

tag: type

value: DCIS


title: normal tissue at age36-45 years (SA_BC40N)

description:
SA_BC40N.CEL
Gene expression data from normal tissue at age36-45 years

value: N

value: NORMAL

tag: age (years)


title: normal tissue at age36-45 years (SA-BC22)

description:
SA-BC22.CEL
Gene expression data from normal tissue at age36-45 years


title: ME180 DMSO rep 3

description: Replicate 3

tag: cell line

value: cervix; derived from metastatic site:omentum

tag: disease

value: epidermoid carcinoma

value: Homo sapiens, human


title: epidermis_REDD1_KO_treated_FA_2

scan_protocol: RNA amplification, labeling, hybridization with the Mouse Whole-Genome Gene Expression BeadChips (Illumina), and data analysis were performed at the Genomics Core Facility at the Center for Genetic Medicine at Northwestern University according to the DNA chip manufacturer's protocols.


title: cDNA from wild type cells_25C

description:
cDNA from wild type cells
K700/25°C

source_name: wild type cells_25C

tag: genotype/variation


title: wt cisplatin, biological rep 2

description:
Sample name: SAMPLE 8_reanalyzed
Re-analysis of SAMPLE8
Raw file: 13_(Yeast_2).CEL


title: normal tissue at age36-45 years (SA_BC018N)

description:
SA_BC018N.CEL
Gene expression data from normal tissue at age36-45 years


title: wt cisplatin, biological rep_3

description:
Sample name: SAMPLE 9
Re-analyzed by SAMPLE 9_reanalyzed
Raw file: 21_(Yeast_2).CEL


title: ME180 1 hour rep 1

description: Replicate 1

tag: organism

tag: drug treatment

value: 10μM ATRA

tag: treatment time


title: normal tissue at age36-45 years (289N)

description:
289N.CEL
Gene expression data from normal tissue at age36-45 years

tag: sample id

tag: tumor/normal

tag: grade


title: epidermis_REDD1_KO_2

label_protocol: RNA amplification, labeling, hybridization with the Mouse Whole-Genome Gene Expression BeadChips (Illumina), and data analysis were performed at the Genomics Core Facility at the Center for Genetic Medicine at Northwestern University according to the DNA chip manufacturer's protocols.

value: untreated

tag: strain


title: normal tissue at age36-45 years (38N)

description:
38N.CEL
Gene expression data from normal tissue at age36-45 years

tag: er


title: tumor tissue at age 46 to 55 years (562 T)

description:
562 T.CEL
Gene expression data from tumor tissue at age 46 to 55 years

source_name: tumor tissue at age 46 to 55 years

value: IDC


title: epidermis_REDD1_KO_1


title: wt cisplatin, biological rep_2

description:
Sample name: SAMPLE 8
Re-analyzed by SAMPLE 8_reanalyzed
Raw file: 13_(Yeast_2).CEL

tag: agent


title: epidermis_wildtype_treated_FA_2

tag: treatment status


title: normal tissue at age36-45 years (SA-BC21)

description:
SA-BC21.CEL
Gene expression data from normal tissue at age36-45 years

source_name: normal tissue at age36-45 years


title: wt non treated, biological rep_3

description:
Sample name: SAMPLE 3_reanalyzed
Re-analysis of SAMPLE3
Raw file: 17_(Yeast_2).CEL

source_name: control, wild-type S. cerevisiae treated with DMSO

growth_protocol: W303 cells grown in complete synthetic medium suplemented with DMSO

value: control


title: epidermis_wildtype_1

tag: phenotype


title: HCT116 3BKO  5-Aza-CdR D54_2

city: Los Angeles

first: Xiaojing

last: Yang

state: CA

address: 1441 Eastlake Ave, Room 7336

institute: USC/Norris Comprehensive Cancer Center

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
replicate 2

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.12.0) and GenomeStudio.

source_name: Colon

label_protocol: standard as recommended by illumina

growth_protocol: Standard as recommended by ATCC

extract_protocol: standard as recommended by illumina

treatment_protocol: Cells were treated with 5-Aza-CdR and RNA were collected at indicated time points after treatment.

tag: genotype

value: DNMT3B KO

tag: treatment

tag: time


title: tumor tissue at age > 55 years (446 T)

description:
446 T.CEL
Gene expression data from tumor tissue at age > 55 years

tag: pr

tag: type

tag: age (years)


title: wt cisplatin, biological rep_1

description:
Sample name: SAMPLE 7
Re-analyzed by SAMPLE 7_reanalyzed
Raw file: 5_(Yeast_2).CEL


title: epidermis_wildtype_treated_FA_1


title: tumor tissue at age > 55 years (39 T)

description:
39 T.CEL
Gene expression data from tumor tissue at age > 55 years


title: tumor tissue at age > 55 years (546 T)

description:
546 T.CEL
Gene expression data from tumor tissue at age > 55 years


title: HCT116 3BKO  5-Aza-CdR D42_2

tag: cell line


title: tumor tissue at age 46 to 55 years (434 T)

description:
434 T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: wt non treated, biological rep_2

description:
Sample name: SAMPLE 2_reanalyzed
Re-analysis of SAMPLE2
Raw file: 9_(Yeast_2).CEL


title: Macrophages rep3

city: Boston

first: Niroshana

last: Anandasabapathy

state: MA

address: 221 Longwood Ave. EBRC 513

department: Department of Dermatology

institute: Brigham and Women’s Hospital

description: SAMPLE 22

data_processing: The data were normalized using quantile normalization in Genespring v12.5 (Agilent).

source_name: Peritoneal

label_protocol: RNA was amplified and hybridized on the Illumina MouseRef-8 v2.0 Expression BeadChip

growth_protocol: C57BL/6 mice were injected for 12-14 days with human recombinant Flt3L (Celldex), skin draining LNs (inguinal , axillary, brachial, popliteal and cervical were pooled and DC were preapred by standard collagenase D isolation technique. For some samples mice were treated with 5ug of LPS IV and skin draining LN were harvested 24 hours later. Peritoneal macrophages were isolated from untreated mice

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Purity analysis was performed by nanodrop and Eukaryote Total RNA Pico Series II (Agilent)

tag: age

value: 8-12 weeks

tag: injected with

tag: cell subtype

value: Peritoneal macrophages


title: HCT116 3BKO  5-Aza-CdR D54_1

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
replicate 1


title: HCT116 3BKO  5-Aza-CdR D10_2


title: Macrophages rep2

description: SAMPLE 21


title: HCT116 3BKO  5-Aza-CdR D42_1


title: epidermis_wildtype_2

value: wildtype


title: tumor tissue at age > 55 years (347 T)

description:
347 T.CEL
Gene expression data from tumor tissue at age > 55 years

tag: sample id

tag: tumor/normal


title: Macrophages rep1

description: SAMPLE 20

tag: strain


title: wt non treated, biological rep_1

description:
Sample name: SAMPLE 1_reanalyzed
Re-analysis of SAMPLE1
Raw file: 1_(Yeast_2).CEL


title: tumor tissue at age 46 to 55 years (311 T)

description:
311 T.CEL
Gene expression data from tumor tissue at age 46 to 55 years

tag: grade

tag: er


title: HCT116 3BKO  5-Aza-CdR D10_1


title: Dsky1 non treated, biological rep3

description:
Sample name: SAMPLE 6
Raw file: 18_(Yeast_2).CEL

source_name: control, Dsky1  mutant treated with DMSO

growth_protocol: W303-Dsky1 cells grown in complete synthetic medium suplemented with DMSO

tag: agent


title: HCT116 3BKO Ctrl_2

value: baseline


title: DEC205+ DC LPS rep3

description:
SAMPLE 19
24 hours after intravenous injection of 5 ug of LPS

source_name: skin draining LN

value: 5ug of LPS IV

value: Dendritic cells (DCs)


title: Dsky1 non treated, biological rep2

description:
Sample name: SAMPLE 5
Raw file: 10_(Yeast_2).CEL


title: DEC205+ DC LPS rep2

description:
SAMPLE 18
24 hours after intravenous injection of 5 ug of LPS


title: tumor tissue at age > 55 years (333 T)

description:
333 T.CEL
Gene expression data from tumor tissue at age > 55 years

value: T


title: tumor tissue at age > 55 years (300 T)

description:
300 T.CEL
Gene expression data from tumor tissue at age > 55 years


title: wt non treated, biological rep 3

description:
Sample name: SAMPLE 3
Re-analyzed by SAMPLE 3_reanalyzed
Raw file: 17_(Yeast_2).CEL


title: HCT116 D42_2

description:
colorectal carcinoma cell line
replicate 2


title: wt non treated, biological rep 1

description:
Sample name: SAMPLE 1
Re-analyzed by SAMPLE 1_reanalyzed
Raw file: 1_(Yeast_2).CEL


title: wt non treated, biological rep 2

description:
Sample name: SAMPLE 2
Re-analyzed by SAMPLE 2_reanalyzed
Raw file: 9_(Yeast_2).CEL


title: HCT116 D14_2


title: DC-SIGN+ LPS rep3

description:
SAMPLE 16
24 hours after intravenous injection of 5 ug of LPS


title: DEC205+ DC LPS rep1

description:
SAMPLE 17
24 hours after intravenous injection of 5 ug of LPS


title: tumor tissue at age 46 to 55 years (28 T)

description:
28 T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: Dsky1 non treated, biological rep1

description:
Sample name: SAMPLE 4
Raw file: 2_(Yeast_2).CEL


title: HCT116 D24_2


title: tumor tissue at age 46 to 55 years (SA_BC382T)

description:
SA_BC382T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: DC-SIGN+ LPS rep1

description:
SAMPLE 14
24 hours after intravenous injection of 5 ug of LPS


title: HCT116 3BKO Ctrl_1

description:
colorectal carcinoma cell line;HCT116 derivative cell lines with a genetic knockout of DNMT3B
replicate 1


title: tumor tissue at age > 55 years (338T)

description:
338T.CEL
Gene expression data from tumor tissue at age > 55 years


title: tumor tissue at age 46 to 55 years (SA_BC378T)

description:
SA_BC378T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: DC-SIGN+ LPS rep2

description:
SAMPLE 15
24 hours after intravenous injection of 5 ug of LPS


title: tumor tissue at age 46 to 55 years (SA_BC376T)

description:
SA_BC376T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: Langerin-CD11b- migratory DC rep4

description: SAMPLE 13

value: human recombinant Flt3L with 12-14 days (intraperitoneal)

value: Langerin-CD11b- migratory DC


title: HCT116 D42_1

description:
colorectal carcinoma cell line
replicate 1


title: HCT116 Ctrl_2 (2)


title: tumor tissue at age > 55 years (312T)

description:
312T.CEL
Gene expression data from tumor tissue at age > 55 years


title: Langerin-CD11b- migratory DC rep2

description: SAMPLE 11


title: HCT116 D24_1


title: HCT116 D5_2


title: HCT116 D5_1


title: tumor tissue at age 46 to 55 years (285T)

description:
285T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: Langerin-CD11b- migratory DC rep1

description: SAMPLE 10


title: IKKbetaSA,T45m,CD40L:6

city: Yokohama

first: Hisaaki

last: Shinohara

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

description:
two biological replicates
Replicate 1 raw data = CEL file ending in .r01; Replicate 2 raw data = CEL file ending in .r02

hyb_protocol: Affymetrix standard procedures

scan_protocol: using GeneChip Scanner 3000

data_processing:
CEL files were processed by RMA method to obtain normalized gene expression level.
Data in table represents merging of both replicates.

organism: Gallus gallus

source_name: DT40 B cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: DT40 B Cells were cultured with RPMI containing 10% FBS

extract_protocol: TotalRNA was purified using the Qiagen RNeasy mini kit.

treatment_protocol: WT cells or MEK Inh. (MEK inhibitor;U0126 5mM, 30min pretreated) or IKKbetaSA (S176/181A knock-in) Cells were stimulated with 0.1, 1, 10 µg/ml of anti-IgM (M4) or 1, 3, 6  µg/ml of CD40ligand (CD40L) for 0, 15, 30, 45, 60 or 90min.

tag: cell type

value: B cell


title: Langerin-CD11b+ migratory DC rep2

description: SAMPLE 8

value: Langerin-CD11b+ migratory DC


title: IKKbetaSA,T60m,CD40L:6


title: Langerin-CD11b+ migratory DC rep3

description: SAMPLE 9


title: Langerin-CD11b+ migratory DC rep1

description: SAMPLE 7


title: HCT116 Ctrl_1 (2)


title: IKKbetaSA,T90m,CD40L:6


title: IKKbetaSA,T15m,CD40L:6


title: tumor tissue at age > 55 years (275T)

description:
275T.CEL
Gene expression data from tumor tissue at age > 55 years


title: MEK Inh.,T90m,CD40L:6


title: IKKbetaSA,T30m,CD40L:6


title: MEK Inh.,T60m,CD40L:6


title: Langerin+CD103+ migratory DC rep3

description: SAMPLE 6

value: Langerin+CD103+ migratory DC


title: tumor tissue at age 46 to 55 years (SA_BC273T)

description:
SA_BC273T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: HCT116 D14_1


title: tumor tissue at age 46 to 55 years (267T)

description:
267T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: tumor tissue at age > 55 years (SA_BC279T)

description:
SA_BC279T.CEL
Gene expression data from tumor tissue at age > 55 years


title: Trunk NCC3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: Trunk EGFP+

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Microsoft Excel was used for the normalization.

source_name: mouse E12.5 embryo, trunk NCC

label_protocol: Amino Allyl aRNA was synthesized by using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed according to  the protocol supplied by TORAY Industries, Inc.

growth_protocol: Single cells from E12.5 embryos were sorted by flow cytometry in regard to intensity of EGFP.

extract_protocol: RNA samples were extracted from sorted cells using the miRNeasy mini kit (Qiagen).

value: trunk neural crest cell

tag: developmental stage

value: E12.5 embryo


title: tumor tissue at age > 55 years (SA_BC220T)

description:
SA_BC220T.CEL
Gene expression data from tumor tissue at age > 55 years

value: IDC


title: Langerin+CD103+ migratory DC rep2

description: SAMPLE 5


title: tumor tissue at age > 55 years (225T)

description:
225T.CEL
Gene expression data from tumor tissue at age > 55 years


title: MEK Inh.,T45m,CD40L:6


title: Craniofacial NCC2

description: Craniofacial EGFP+

source_name: mouse E12.5 embryo, craniofacial NCC

value: craniofacial neural crest cell


title: tumor tissue at age > 55 years (196T)

description:
196T.CEL
Gene expression data from tumor tissue at age > 55 years


title: CD8a cDC rep3

description: SAMPLE 3

value: CD8a cDC


title: WT,T90m,CD40L:6


title: Langerin+CD103+ migratory DC rep1

description: SAMPLE 4

value: 8-12 weeks


title: WT,T60m,CD40L:6


title: Trunk non NCC2

description: Trunk EGFP-

source_name: mouse E12.5 embryo, trunk non-NCC

value: trunk non-neural crest cell


title: Trunk NCC2

description: Trunk EGFP+


title: MEK Inh.,T15m,CD40L:6


title: Craniofacial NCC1

description: Craniofacial EGFP+


title: CD8a cDC rep1

description: SAMPLE 1


title: Colon goblet cell 4

city: ROCHESTER

first: Kathryn

middle: A

last: Knoop

state: MN

address: 2511 Boulder Ridge Dr NW

department: Internal Medicine, Gastroenterology Division

institute: Mayo Clinic

description: SAMPLE 8

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

source_name: Colon goblet cells

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

extract_protocol: Cells were sorted directly into Qiagen buffer RLT. RNA was extracted using a Qiagen RNAeasy mini kit.

tag: tissue

value: colon

value: isolated epithelial cells

value: FACS sorted goblet cells (CD45-CD24-CK18+UEA-I+ cells)


title: tumor tissue at age > 55 years (217T)

description:
217T.CEL
Gene expression data from tumor tissue at age > 55 years


title: Craniofacial non NCC2

description: Craniofacial EGFP-

source_name: mouse E12.5 embryo, craniofacial non-NCC

value: craniofacial non-neural crest cell


title: tumor tissue at age 46 to 55 years (207T)

description:
207T.CEL
Gene expression data from tumor tissue at age 46 to 55 years

value: T


title: MEK Inh.,T30m,CD40L:6


title: WT,T30m,CD40L:6


title: tumor tissue at age > 55 years (SA-BC17)

description:
SA-BC17.CEL
Gene expression data from tumor tissue at age > 55 years


title: WT,T45m,CD40L:6


title: CD8a cDC rep2

description: SAMPLE 2

value: human recombinant Flt3L with 12-14 days (intraperitoneal)


title: tumor tissue at age > 55 years (178T)

description:
178T.CEL
Gene expression data from tumor tissue at age > 55 years


title: tumor tissue at age 46 to 55 years (191T)

description:
191T.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: Langerin-CD11b- migratory DC rep3

description: SAMPLE 12

value: Langerin-CD11b- migratory DC


title: Craniofacial nonNCC1

description: Craniofacial EGFP-


title: Colon goblet cell 3

description: SAMPLE 7


title: WT,T90m,CD40L:3

value: B cell


title: Colon goblet cell 2

description: SAMPLE 6


title: Trunk NCC1

description: Trunk EGFP+


title: Colon goblet cell 1

description: SAMPLE 5


title: WT,T60m,CD40L:3


title: WT,T15m,CD40L:6


title: tumor tissue at age > 55 years (SA-BC16)

description:
SA-BC16.CEL
Gene expression data from tumor tissue at age > 55 years


title: tumor tissue at age > 55 years (SA-BC13)

description:
SA-BC13.CEL
Gene expression data from tumor tissue at age > 55 years


title: Trunk nonNCC1

description: Trunk EGFP-


title: tumor tissue at age > 55 years (SA-BC15)

description:
SA-BC15.CEL
Gene expression data from tumor tissue at age > 55 years


title: WT,T30m,CD40L:3


title: tumor tissue at age > 55 years (SA-BC11)

description:
SA-BC11.CEL
Gene expression data from tumor tissue at age > 55 years


title: WT,T45m,CD40L:3

description:
two biological replicates
Replicate 1 raw data = CEL file ending in .r01; Replicate 2 raw data = CEL file ending in .r02


title: MEF Trp53-/-, LMP sh.Trp53.703, high-copy

city: Cold Spring Harbor

first: Christof

last: Fellmann

state: NY

address: 1 Bungtown Road

institute: Mirimus Inc

description: RNAi off-target effects dependent gene expression changes

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Annotation information was used from the R / Bioconductor release via Affymetrix package: mogene10sttranscriptcluster.db as well as mogene10stprobeset.db. Details can be found at this link: http://www.bioconductor.org/packages/devel/data/annotation/. The data was normalized using the RMA method from the package Affy in R statistical programming language. We treated the MEF Trp53-/- wt and MEF Trp53-/- LMP miR30 (empty) as replicates for no shRNA (negative control). For analyses where we studied high-copy vs. low-copy off-target effects, we took ALL samples at high-copy as one set of replicates, and ALL samples at low-copy as another replicate. For analyses where we studied sequence-specific off-target effects, we took wt and LMP miR30 (empty) as negative control replicates, and then did an individual comparison of each sample with the negative control to see which genes (if any) are commonly up- or down-regulated, or are specifically deregulated in JUST that one shRNA (sample) but are NOT present in any other sample as differentially regulated.

source_name: MEF Trp53-/-

label_protocol: standard Affymetrix protocol

growth_protocol: Trp53-/- MEFs were grown in DMEM supplemented with 10% FBS, at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted from at least 5x10^6 cells per sample using TRIzol (Invitrogen), followed by acidic phenol:chloroform:IAA (125:24:1, pH 4.5, Ambion) purification and isopropanol precipitation. All samples were DNase I (Roche) treated and again purified by acid phenol:chloroform:IAA extraction and isopropanol precipitation.

treatment_protocol: Microarray analysis was performed on Trp53-/- MEFs not expressing any shRNA (wt and empty vector) or transduced at single- or high-copy with one of 6 Trp53 shRNAs.

tag: viral transduction

value: high-copy

value: MEFs

tag: genotype


title: MEF Trp53-/-, LMP sh.Trp53.1404, high-copy


title: Small Intestine goblet cell 1

description: SAMPLE 1

source_name: Small Intestine goblet cells

value: small intesine


title: tumor tissue at age > 55 years (SA-BC8)

description:
SA-BC8.CEL
Gene expression data from tumor tissue at age > 55 years

source_name: tumor tissue at age > 55 years

tag: pr

tag: type


title: WT,T90m,CD40L:1

tag: cell line


title: Small Intestine goblet cell 2

description: SAMPLE 2


title: MEF Trp53-/-, LMP sh.Trp53.393, high-copy


title: MEF Trp53-/-, LMP sh.Trp53.1090, high-copy


title: MEF Trp53-/-, LMP sh.Trp53.1525, high-copy


title: Small Intestine goblet cell 4

description: SAMPLE 4


title: tumor tissue at age > 55 years (SA-BC6)

description:
SA-BC6.CEL
Gene expression data from tumor tissue at age > 55 years

tag: age (years)


title: MEF Trp53-/-, LMP sh.Trp53.814, high-copy


title: tumor tissue at age 46 to 55 years (SA-BC10)

description:
SA-BC10.CEL
Gene expression data from tumor tissue at age 46 to 55 years


title: Small Intestine goblet cell 3

description: SAMPLE 3


title: Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep4

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description:
E12.5 placenta_Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep4
SAMPLE 12

data_processing: The data were log2 transformed and normalised using quantile normalisation with lumi in R

source_name: E12.5 placenta

label_protocol: Performed by Genome Quebec (Montreal, Qc, Canada)

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) followed by DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Quantification by Nanodrop.

value: placenta


title: WT,T60m,CD40L:1


title: Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep3

description:
E12.5 placenta_Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep3
SAMPLE 11


title: MEF Trp53-/-, LMP sh.Trp53.1525, single-copy

value: single-copy


title: tumor tissue at age > 55 years (SA-BC5)

description:
SA-BC5.CEL
Gene expression data from tumor tissue at age > 55 years

value: IDC


title: Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep1

description:
E12.5 placenta_Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep1
SAMPLE 9


title: Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep2

description:
E12.5 placenta_Map2k1flox/-Makp2k2+/-Tg+/Sox2Cre_rep2
SAMPLE 10


title: Map2k1+/-Makp2k2+/-_rep1

description:
E12.5 placenta_Map2k1+/-Makp2k2+/-_rep1
SAMPLE 5


title: MEF Trp53-/-, LMP sh.Trp53.1090, single-copy


title: MEF Trp53-/-, LMP sh.Trp53.1404, single-copy


title: WT,T15m,CD40L:1


title: MEK Inh.,T45m,M4:10


title: MEF Trp53-/-, LMP sh.Trp53.393, single-copy


title: WT,T30m,CD40L:1


title: normal tissue at age > 55 years (275N)

description:
275N.CEL
Gene expression data from normal tissue at age > 55 years

source_name: normal tissue at age > 55 years

value: N

value: NORMAL


title: MEK Inh.,T90m,M4:10


title: MEK Inh.,T60m,M4:10


title: Map2k1+/-Makp2k2+/-_rep4

description:
E12.5 placenta_Map2k1+/-Makp2k2+/-_rep4
SAMPLE 8


title: normal tissue at age 46 to 55 years (SA_BC273N)

description:
SA_BC273N.CEL
Gene expression data from normal tissue at age 46 to 55 years

source_name: normal tissue at age 46 to 55 years


title: WT,T45m,CD40L:1


title: Map2k1+/+Map2k2+/+_rep4

description:
E12.5 placenta_Map2k1+/+Map2k2+/+_rep4
SAMPLE 4


title: Map2k1+/-Makp2k2+/-_rep3

description:
E12.5 placenta_Map2k1+/-Makp2k2+/-_rep3
SAMPLE 7


title: MEF Trp53-/-, LMP sh.Trp53.814, single-copy


title: MEF Trp53-/-, LMP miR30 (empty), single-copy


title: Map2k1+/-Makp2k2+/-_rep2

description:
E12.5 placenta_Map2k1+/-Makp2k2+/-_rep2
SAMPLE 6


title: normal tissue at age 46 to 55 years (SA_BC216N)

description:
SA_BC216N.CEL
Gene expression data from normal tissue at age 46 to 55 years


title: Mouse liver, control vs. hydrogen treatment

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Liver, control (control gas and water for 3 weeks)

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Livers from control and hydrogen-treated mice were immersed in RNAlater solution (Ambion, Austin, TX) for several days at 4°C and then total RNA was isolated using RNeasy mini kit (Qiagen, Hilden, Germany) from the livers.

treatment_protocol: control group: fed with control water and air for 3 weeks

value: BALB/c

tag: gender

value: male

tag: age

value: 10 weeks

value: liver

source_name: Liver, hydrogen-treated (H2 gas and H2-rich water for 3 weeks)

treatment_protocol: hydrogen-treated group: fed with hydrogen-rich water (0.7mM dissolved hydrogen) and hydrogen-containing air (2% hydrogen/98% air) for 3 weeks


title: MEK Inh.,T15m,M4:10

description:
two biological replicates
Replicate 1 raw data = CEL file ending in .r01; Replicate 2 raw data = CEL file ending in .r02


title: tumor tissue at age > 55 years (27T)

description:
27T.CEL
Gene expression data from tumor tissue at age > 55 years

tag: sample id


title: MEK Inh.,T30m,M4:10


title: MEF Trp53-/-, LMP sh.Trp53.703, single-copy

description: RNAi off-target effects dependent gene expression changes


title: normal tissue at age > 55 years (196N)

description:
196N.CEL
Gene expression data from normal tissue at age > 55 years

tag: tumor/normal


title: Map2k1+/+Map2k2+/+_rep3

description:
E12.5 placenta_Map2k1+/+Map2k2+/+_rep3
SAMPLE 3

tag: strain


title: MEF Trp53-/-, wt, none


title: WT,T15m,CD40L:3


title: normal tissue at age > 55 years (225N)

description:
225N.CEL
Gene expression data from normal tissue at age > 55 years

tag: grade


title: IKKbetaSA,T90m,M4:10


title: normal tissue at age 46 to 55 years (SA_BC191N)

description:
SA_BC191N.CEL
Gene expression data from normal tissue at age 46 to 55 years

tag: er


title: normal tissue at age > 55 years (SA_BC338N)

description:
SA_BC338N.CEL
Gene expression data from normal tissue at age > 55 years


title: Map2k1+/+Map2k2+/+_rep2

description:
E12.5 placenta_Map2k1+/+Map2k2+/+_rep2
SAMPLE 2


title: Mouse  recovered kupffer cells  (KCR)- replicate 3

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: Gene expression of KCR

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean, all were done by Partek Genomics suite (version 6.6).

source_name: Macrophages,recovered kupffer cells isolated at 72hrs following injury

growth_protocol: Isolation of hepatic nonparenchymal cells (NPCs): Perfused livers isolated from Cx3cr1(gfp/+) mice were cut into small fragments and incubated (37 degrees c, 250rpm, 40min) with 5ml of digestion buffer [5% FBS, 0.5mg/ml Collagenase VIII (Sigma Aldrich) and 0.1mg/ml DNase I (Roche) in PBS+/+]. This was followed by three cycles of washings with PBS-/- at 400rpm from which the supernatant was taken omitting the parenchymal cell pellet. The supernatant cell pellet was then lysed for erythrocytes by 2min incubation with ACK buffer (0.15M NH4Cl, 0.1M KHCO3, 1mM).   Flow Cytometry Analysis, Sorting of Liver-MF Subsets and ELISA  Abs used for liver-macrophage characterization included: CD45 (30-F11), CD45.2 (104), CD45.1 (A20), Ly6C (HK1.4), CD64 (X54-5/7.1), CD11c (N418), CD11b (M1/70), IAb (AF6-120.1), CD19 (HIB19), TCRβ (H57-597), B220 (RA3-6B2), and MPDCA1 (927) (all from BioLegend), NK1.1 (PK136) (BD Bioscience), F4/80 (CI: A3-1) (Serotec) and Ki67 (SolA15) (eBioscience). Kuppfer cells were defined as: CD45+CD11bintMHCII+F4/80+CD64+Cx3cr1(GFP)neg; Infiltrating Ly6Chi monocytes were defined as: CD11b+MHCIIneg,CD64+Cx3cr1(GFP)intLy6Chi and Ly6Clow monocyte-derived macrophages were defined as  CD45+CD11b+MHCII+F4/80+CD64+Cx3cr1(GFP)+. Cells were analyzed with LSRFortessa or FACSCanto-II flow cytometers and sorted with FACS Aria machine (BD). Flow cytometry analysis was performed using FlowJo software.

extract_protocol: RNA was prepared using the microRNeasy Kit (QIAGEN). RNA purity was assessed with ND-100 Nanodrop (Peqlab) and BioAnalyzer 2100 (Agilent). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

treatment_protocol: APAP induced acute liver injury   Mice were fasted overnight for 12hrs prior to administration of vehicle or 300mg/kg APAP (Tiptipot Novimol, 100mg Paracetamol/ml, CST) by oral gavage. Water was returned with APAP administration and the food 2hrs later.

tag: sample type

value: Recovered resident liver kupffer cells isolated at 72hrs following injury (recovery phase)

value: Recovered resident liver kupffer cells

tag: time

value: 72hrs following injury (recovery phase)

tag: genetic background


title: IKKbetaSA,T45m,M4:10

tag: cell type


title: Map2k1+/+Map2k2+/+_rep1

description:
E12.5 placenta_Map2k1+/+Map2k2+/+_rep1
SAMPLE 1

tag: developmental stage

tag: tissue


title: IKKbetaSA,T30m,M4:10


title: IKKbetaSA,T60m,M4:10


title: IKKbetaSA,T15m,M4:10


title: Mouse recovered kupffer cells  (KCR)- replicate 2

description: Gene expression of KCR

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: normal tissue at age > 55 years (SA-BC25)

description:
SA-BC25.CEL
Gene expression data from normal tissue at age > 55 years

tag: pr


title: 4x 4

city: Galway

first: Charles

last: Spillane

state: Galway

address: University Road

department: Botany and Plant Science

country: Ireland

institute: National University of Ireland, Galway

hyb_protocol: Affymetrix GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Fluidics protocol FS450_004 using Affymetric Fluidics station 450, Scanned using Affymetrix GeneChip Scanner 3000 7G, AGCC software

data_processing: Data was RMA normalized using R/Bioconductor

organism: Arabidopsis thaliana

label_protocol: Affymetrix 3' IVT express kit, biotin label

growth_protocol: 1x Murashige and Skoog medium, in a Percival growth chamber

extract_protocol: Trizol lysis followed by RNA extraction using Masherey-Nagel Nucleospin Total RNA plant.

value: two week old seedlings

tag: ploidy level

value: tetraploid


title: Mouse  Ly6CLow monocyte-derived macrophages - replicate 1

description: Gene expression of Ly6CLow

source_name: Macrophages, Ly6CLow, monocyte-derived Ly6CLow macrophages isolated 72hrs following injury

value: Ly6CLow monocyte-derived macrophages isolated at 72hrs following injury (recovery phase)

value: Ly6CLow monocyte-derived macrophages


title: 4x 1


title: Mouse  recovered kupffer cells (KCR)- replicate 1

description: Gene expression of KCR


title: Mouse  Ly6CLow monocyte-derived macrophages - replicate 2

description: Gene expression of Ly6CLow


title: MEF

city: La Jolla

first: Tariq

last: Rana

address: 9500 Gilman Drive, MC 0602

department: Pediatrics

institute: University of California, San Diego

description:
SAMPLE 10
Cell culture
Ref Sample_2

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Cell culture

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell population

value: MEF


title: 4x 3


title: 4x 2


title: WT,T90m,M4:10

source_name: DT40 B cell

tag: cell line

value: B cell


title: Mouse  Ly6CHi monocytes -  replicate 3

description: Gene expression of Ly6CHi

source_name: Ly6C(hi) monocytes isolated 24hrs following injury

value: Ly6CHi liver infiltrating monocytes isolated 24hrs following injury (inflammatory phase)

value: Ly6CHi liver infiltrating monocytes


title: 4x 5


title: normal tissue at age > 55 years (SA_BC133N)

city: Riyadh

first: Dilek

last: Colak

address: MBC03, PO Box 3354

institute: KFSHRC

description:
SA_BC133N.CEL
Gene expression data from normal tissue at age > 55 years

data_processing: The open source  R/Bioconductor  packages, (Fred Hutchinson Cancer Research Center, Seattle, WA, USA)were employed to normalize the data by GC Robust Multi-array Average (GC-RMA) algorithm. The CEL files or CEL/CHP files were utilized for further analysis using dChip, MEV,  and PARTEK Genomics Suite (Partek® software, Partek Inc., St. Louis, MO, USA.). We used MATLAB (The Math Works, Inc., Natic, MA) and PARTEK Genomics Suite for the statistical analysis.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms total RNA.

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

value: N

tag: type

tag: age (years)


title: mES_CCE

description:
SAMPLE 9
Cell culture
Ref Sample_1


title: Mouse  Ly6CLow monocyte-derived macrophages - replicate 3

description: Gene expression of Ly6CLow


title: normal tissue at age > 55 years (SA_BC64N)

description:
SA_BC64N.CEL
Gene expression data from normal tissue at age > 55 years

tag: sample id

value: NORMAL


title: SSEA1+DsRed-_rep#2

description:
SAMPLE 8
Cell culture
replicate 2


title: SSEA1+DsRed+_rep#2

description:
SAMPLE 7
Cell culture
replicate 2


title: Mouse  Ly6CHi monocytes - replicate 1

description: Gene expression of Ly6CHi

value: 24hrs following injury (inflammatory phase)


title: 3x(p) 4

source_name: paternal excess triploid_dscDNA

value: paternal excess triploid


title: Thy1-SSEA1-_rep#2

description:
SAMPLE 6
Cell culture
replicate 2


title: 3x(p) 5


title: Mouse steady state kupffer cells (KCSS), replicate 2

description: Gene expression of KCSS

source_name: Macrophages, KCSS, steady state resident liver kupffer cells

value: Resident liver KC isolated from steady state livers

value: Resident liver KC

value: control


title: Mouse  Ly6CHi monocytes - replicate 2

description: Gene expression of Ly6CHi


title: 3x(p) 3


title: 3x(p) 2


title: WT,T60m,M4:10


title: WT,T45m,M4:10


title: WT,T15m,M4:10


title: WT,T90m,M4:1


title: 3x(m) 5

source_name: maternal excess triploid_dscDNA

value: maternal excess triploid


title: 3x(p) 1


title: Mouse steady state kuppfer cells (KCSS), replicate 1

description: Gene expression of KCSS


title: SSEA1+DsRed-_rep#1

description:
SAMPLE 4
Cell culture
replicate 1


title: 3x(m) 4


title: tgTbr2GFP_1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 at the transcript level using the oligo package of Bioconductor

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Mouse Gene ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: Brains of adult (P35) animals (NesGFP,kiTbr2GFP,tgTbr2GFP,PomcGFP) were harvested and sliced at 750μm. DGs from dorsal and ventral regions were microdissected, dissociated into single cells and FACS-sorted (ARIA II) as described (Nelson et al., 2013; Nelson et al., 2011): one sister slice from each animal was live-cell MPM imaged. This generated ~3-5,000 cells per group. RNA was isolated, amplified and arrayed to Affymetrix Mouse Gene 1.0 ST arrays.

value: adult (P35)

tag: genotype/variation

value: tgTbr2GFP [Eomes (T-brain-2, Tbr2) BAC transgenic Green Fluorescent Protein (GFP) transgenic]

value: brain

value: DGs from dorsal and ventral regions


title: tgTbr2GFP_3


title: Thy1+SSEA1-_rep#2

description:
SAMPLE 5
Cell culture
replicate 2

tag: strain


title: WT,T30m,M4:10


title: WT,T30m,M4:1


title: WT,T45m,M4:1


title: SSEA1+DsRed+_rep#1

description:
SAMPLE 3
Cell culture
replicate 1


title: Thy1-SSEA1-_rep#1

description:
SAMPLE 2
Cell culture
replicate 1


title: PomcGFP_2

source_name: PomcGFP

value: PomcGFP [Pro-opiomelanocortin-alpha (Pomc) Green Fluorescent Protein (GFP) transgenic]


title: Thy1+SSEA1-_rep#1

description:
SAMPLE 1
Cell culture
replicate 1


title: tgTbr2GFP_2


title: 3x(m) 2

value: two week old seedlings


title: WT,T60m,M4:1

value: B cell


title: WT,T15m,M4:1


title: WT,T90m,M4:0.1


title: 2x 4

value: diploid


title: PomcGFP_1


title: 3x(m) 1


title: WT,T60m,M4:0.1


title: X756LN

city: Amsterdam

first: Philip

middle: C

last: Schouten

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

hyb_protocol: According to manufacterer's protocol (Nimblegen Roche)

scan_protocol: 2 um double pass

data_processing: Nimblescan, grid tiff files, generate pair reports followed by using the NimbleScan DNAcopy procedure at default settings

source_name: Breast Cancer Lymph Node Metastasis aCGH

label_protocol: With the ENZO 42760 labeling kit for array CGH: 20 uL primers (vial 1) with 500 ng of genomic tumor DNA or Promega Female reference DNA (GG1521) in 19 ul of nuclease free water for 10 minutes at 99 C in pcr machine, followed by 10 minutes of cooling to 4 degrees. Snap freeze and spin. While on ice add 11 ul Cy3 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to tumor DNA, and 11 ul Cy5 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to reference DNA and incubate in PCR machine for 4 hours at 37 C. Then add 5ul stop buffer (vial 5).  To remove excess nucleotides with Qiagen MinElute PCR purification kit add 275 uL binding buffer (PB) to sample and reference. Put on minElute column and spin 60 sec on 16000 rcf. Add 700 ul Wash Buffer (PE) and centrifuge 60 secs at 16000 rcf. Dry columns by spinning another 60 secs at 16000 rcf. Elute the DNA in 2 steps by adding 2x 10.5 ul of elution buffer (EB). Pool equal amounts of tumor and reference DNA and speedvac into a pellet.

extract_protocol: 10 x 10 u slices containing at least 60% tumour cells were cleared of paraffin (2 x 5 min xylene, 2 x 30 s 100% ethanol, 30s 90% ethanol, 30 s 70% ethanol, and rinsed with H2O), treated with 1 M NaSCN at 37 C overnight, and sections of interest (>70% tumour cells) were scraped in 200 ul buffer ATL (Qiagen, cat. no. 51304).  27 ul of proteinase K (15 ug/ull, Roche, cat. no.3115879001) was immediately added, as well as at the end of the day, and at the beginning and end of the next day; samples were constantly shaken at 37 C during the time of digestion. The following day, 40 ul RNase A (20 ug/ul, Sigma, cat. no. R5500) was added to the sample, vortexed, and incubated for 2 min at room temperature. 400 ul of buffer AL (Qiagen, cat.no.51304) was added and incubated for 10 min at 70 C. 420 ul of 100% ethanol was added and vortexed. The sample mixture was spun on a spincolumn (Qiagen, cat. no. 51304) for 1 min at 8,000 rpm. The column was sequentially washed with 500 ul of the following reagents and spun for 1 min at 8,000 rpm: AW1, AW2, and  twice with 80% ethanol. The column was spun dry for 3 min at 14,000 rpm. The sample was eluted with 50 ul of AE buffer by spinning for 1 min at 8,000 rpm.  (Joosse, SA et al, Breast Cancer Res Treat, 2009)

value: lymph node metastasis

tag: molecular subtype

tag: n stage

tag: t stage

tag: grade

source_name: Promega Female Reference genomic DNA G1574

tag: source

value: pooled Female Reference DNA


title: 2x 3


title: NesGFP_2

source_name: NesGFP

value: NesGFP [Nestin (Nes) Green Fluorescent Protein (GFP) transgenic]

tag: cell type


title: X630LN

tag: er

source_name: Promega Female Reference genomic DNA G1573


title: kiTbr2GFP_3

tag: developmental stage

value: kiTbr2GFP [Eomes (T-brain-2, Tbr2) knock-in Green Fluorescent Protein (GFP) transgenic]

tag: tissue


title: WT,T45m,M4:0.1


title: X421LN

tag: pr

source_name: Promega Female Reference genomic DNA G1571


title: NesGFP_3


title: WT,T15m,M4:0.1


title: 2x 1

tag: ploidy level


title: 3x(m) 3


title: X487LN

source_name: Promega Female Reference genomic DNA G1572


title: NesGFP_1


title: WT,T0

tag: cell line


title: 2x 2


title: MEK Inh.,T0


title: IKKbetaSA,T0


title: 347 mutant, biological rep 2

city: Rochester

first: Raul

last: Urrutia

address: 200 1st Street SW

department: Biochemistry & Molecular Biology

hyb_protocol: Fifteen micrograms of fragmented cRNA was hybridized for 16 h at 45°C with constant rotation (60 rpm).

scan_protocol: Intensity files were generated by Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA).

data_processing: Data analysis, hierarchical clustering, and ontology were performed with the OneChanelGUI to extend affylmGUI graphical interface capabilities and Partek Genomics Suite, version 6.6 (Partek Inc., St. Louis, MO).

source_name: Panc1 cells transduced with wild type 347 mutant

label_protocol: cDNA was in vitro transcribed using the T7 BioArray High Yield RNA Transcript Labeling Kit (Enzo Biochem, New York, N.Y.) to produce biotinylated cRNA.

growth_protocol: Standard cell culture conditions.

extract_protocol: RNA was prepared from pooled biological triplicates, technical duplicates.

treatment_protocol: Transduced with adenovirus for 48 hours prior to RNA harvest.

value: pancreatic epithelial cells

tag: transduction


title: EAPP mutant, biological rep 2

source_name: Panc1 cells transduced with wild type EAPP mutant


title: 347 mutant, biological rep 1


title: X412LN

source_name: Promega Female Reference genomic DNA G1568


title: 486 mutant, biological rep 2

source_name: Panc1 cells transduced with wild type 486 mutant


title: X847LN

source_name: Promega Female Reference genomic DNA G1564


title: X7LN

source_name: Promega Female Reference genomic DNA G1570


title: X350LN

source_name: Promega Female Reference genomic DNA G1567


title: kiTbr2GFP_2


title: WT,T30m,M4:0.1

source_name: DT40 B cell


title: X613LN

source_name: Promega Female Reference genomic DNA G1566


title: mESC_J1_treated with 2i_rep2

city: Tsukuba

first: Kuniya

last: Abe

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

description: Gene expression of undifferentiated mESCs.

hyb_protocol: One ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) for 16hours 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 immediately subjected to a microarray scanner.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner) using one color scan setting for 8x60k array slides ( Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters.

source_name: mESC, J1 treated with 2i, replicate 2

label_protocol: Twenty five nanogram of total RNA was labeled with Cy3-CTP with a Quick Amp Labeling Kit (Agilent Technologies). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: EpiSC lines were cultured in conventional medium, or in medium containing the Wnt signaling inhibitor. Murine ES cells were cultured in conventional medium or in medium containing 2i inhibitors.

extract_protocol: Total RNAs were extracted from samples using an AllPrep DNA/RNA Micro Kit (Qiagen, Hilden, Germany). The quality of RNA samples was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: stem cells


title: mESC_R1_rep1

source_name: mESC, R1, replicate 1


title: mESC_J1_rep2

source_name: mESC, J1, replicate 2


title: X10LN

source_name: Breast Cancer Lymph Node Metastasis aCGH

source_name: Promega Female Reference genomic DNA G1565


title: X725LN

source_name: Promega Female Reference genomic DNA G1563


title: kiTbr2GFP_1


title: EAPP mutant, biological rep 1


title: X686LN

source_name: Promega Female Reference genomic DNA G1561


title: mESC_J1_treated with 2i_rep1

source_name: mESC, J1 treated with 2i, replicate 1


title: KLF11, biological rep 1

source_name: Panc1 cells transduced with wild type KLF11


title: KLF11, biological rep 2


title: X704LN

source_name: Promega Female Reference genomic DNA G1569


title: EV, biological rep 2

source_name: Panc1 cells transduced with EV

value: EV


title: X703LN

source_name: Promega Female Reference genomic DNA G1562


title: X527LN

source_name: Promega Female Reference genomic DNA G1560


title: mESC_R1_rep2

source_name: mESC, R1, replicate 2


title: X493LN

source_name: Promega Female Reference genomic DNA G1559


title: EV, biological rep 1


title: mESC_J1_rep1

source_name: mESC, J1, replicate 1


title: High Ca, control, 24h

city: Sendai

first: Kenshi

last: Yamasaki

address: Seiryo-machi 1-1, Aoba-ku

department: Deparment of Dermatology

institute: Tohoku University Graduate School of Medicine

description: Gene expression after 24 h in control of high calcium condition

hyb_protocol: Cy3-labeled cRNA (Cy3 incorporation >9.0 pmol/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containig 10× Blocking Agent, Nuclease-free water, and 25× Fragmentation Buffer following the manufature's instructions. On completion of the fragmentation reaction, 55 μl of 2× GE Hybridization Buffer (HI-RPM) was added to the fragmentation mixture and hybridized to 44K Agilent Whole Human Genome Oligo Microarays (G4112F) containing 45015 features representing 41000 biological probes for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minutes at room temparature with GE Wash Buffer 1 and 1 minute with 37°C GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: After washing according to manufacture's instructions, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4× 44K array slides (Scan Area 61 × 21.6 mm, Scan resolution 5 μm, Dye channel is set to Green, and eXtended Dynamic Range Scan Mode (Hi; 100%, Low;10%)).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent Technologies) using default parameters (protocol GE1-v1_95 and Grid: 014850_D_F_20060807). The data from all microarrays were analyzed using GeneSpring GX 12.6 (Agilent Technologies). Intensity value of green Processedsignal from the Feature Extraction was normalized per chip to the 75th percentile, and normalized to the median of the signal for each probe across the group, respectively. 41000 biological probes were used for analysis.

source_name: keratinocyte, High Ca, 24 h, control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 μg RNA using the Quick-Amp Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, USA). Dye incorporation and cRNA yield were checked with the Nanodrop spectrophotometer.

extract_protocol: Total RNA was extracted from NHEKs using RNeasy Mini Kits accoriding to the manufacture's instructions (Qiagen, Valecia, CA, USA). The concentration of the obtained total RNA was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). RNA quality was determined using the RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA) and an Agilent 2100 bioanalyzer (Agilent Technologies), and RNA was stored in RNase-free water at -80ºC. RNA with an RNA Integrity Number (RIN) of nine or more was used for experiments.

treatment_protocol: NHEKs were grown in serum-free medium supplemented with HuMedia-KG2 Growth Supplements (KURABO INDUSTRIES LTD., Tokyo, Japan). All cells were passed at 80% confluence in low calcium condition (0.05 mM), and keratinocytes in the third or fourth passages were used for experiments. NHEKs were cultured with or without LL37 stimulation for 12 h to 24 h at 37ºC, 5% CO2.

tag: treatment

value: High Ca control

tag: time

value: keratinocyte


title: Epiblast_ E6.5_rep1

description: Gene expression of dissected embryonic tissue

source_name: Epiblast, E6.5, replicate 1

value: embryonic epiblast


title: MCF-7 NC_(HuGene-1_0-st-v1).rma-gene-default-Signal

city: Beijing

first: Like

last: Qu

address: 52 Fucheng Road

country: China

institute: Peking Uiniversity Cancer Institute

description: MCF-7 cells infected with control lentivirus

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array in GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: RMA

source_name: MCF-7 NC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cell (ATCC) were maintained by standard proctocol.

extract_protocol: Trizol extraction of total RNA was performed according to standard protocol.

treatment_protocol: MCF-7 cells were infected with control and Naa10p-shRNA-expressing lentiviral vectors for 120 hr. The silencing efficiency of Naa10p was verified by RT-PCR and Western blot.

value: control


title: High Ca, treatment 1, 24h

description: Gene expression after 24 h in 2.56 mM LL37 treatment of high calcium condition

source_name: keratinocyte, High Ca, 24 h, LL37-2.56 mM

value: High Ca LL37-2.56 mM


title: High Ca, treatment 2, 24h

description: Gene expression after 24 h in 7.68 mM LL37 treatment of high calcium condition

source_name: keratinocyte, High Ca, 24 h, LL37-7.68 mM

value: High Ca LL37-7.68 mM


title: Epiblast_ E6.5_rep2

source_name: Epiblast, E6.5, replicate 2


title: EmbryonicEctoderm_E7.5_rep1

source_name: Embryonic Ectoderm, E7.5, replicate 1

value: embryonic ectoderm


title: X295LN

source_name: Breast Cancer Lymph Node Metastasis aCGH

source_name: Promega Female Reference genomic DNA G1558


title: EmbryonicEctoderm_E7.5_rep2

source_name: Embryonic Ectoderm, E7.5, replicate 2


title: Epiblast_ E5.5_rep1

source_name: Epiblast, E5.5, replicate 1


title: X268LN

source_name: Promega Female Reference genomic DNA G1556


title: X270LN

source_name: Promega Female Reference genomic DNA G1557


title: EpiSC line_ BNa17_rep2

description: Gene expression of undifferentiated EpiSCs.

source_name: EpiSC, BNa17, replicate 2

tag: method

value: established with Wnt inhibitor


title: X225LN

source_name: Promega Female Reference genomic DNA G1554


title: X258LN

source_name: Promega Female Reference genomic DNA G1555


title: Epiblast_ E5.5_rep2

source_name: Epiblast, E5.5, replicate 2


title: X209LN

source_name: Promega Female Reference genomic DNA G1553


title: X159LN

source_name: Promega Female Reference genomic DNA G1551


title: High Ca, treatment 2, 12h

description: Gene expression after 12 h in 7.68 mM LL37 treatment of high calcium condition

source_name: keratinocyte, High Ca, 12 h, LL37-7.68 mM


title: Tc-inducible FBL-kd ES_-Tc FBL-knock down_rep2.

first: Akira

last: Kurisaki

address: Tsukuba central 4, 1-1-1, Higashi

department: Research Center for Stem Cell Engineering

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of FBL-kd ES cells_rep2

hyb_protocol: 1.65 ug of Cy3-labelled cRNAs were fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Sureprint Whole Mouse Genome Microarrays (G4122F) 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile,  then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides..

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

source_name: ES cells, cultured without Tc for 2days

label_protocol: RNA was labeled using the ‘Low RNA Input Fluorescent Linear Amplification Kit ’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: Tc-inducible FBL-kd ES cells were maintained on gelatin-coated dish in the presence of LIF. 1000 ng/mL Tc was added to culture medium.

extract_protocol: Total RNAs were isolated from each samples using ISOGEN (Nippon Gene) according to the manufacture's recommendations. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Tc-inducible FBL-kd ES cells were cultured on gelatin-coated dish with (control) or without (FBL-kd) Tc for 2 days in the presence of LIF.

value: embryonic stem cells

tag: phenotype

value: FBL-knock down


title: High Ca, treatment 1, 12h

description: Gene expression after 12 h in 2.56 mM LL37 treatment of high calcium condition

source_name: keratinocyte, High Ca, 12 h, LL37-2.56 mM


title: High Ca, control, 12h

description: Gene expression after 12 h in control of high calcium condition

source_name: keratinocyte, High Ca, 12 h, control


title: Tc-inducible FBL-kd ES_-Tc FBL-knock down_rep1.

description: Gene expression of FBL-kd ES cells_rep1


title: EpiSC line_BNa17_rep1

source_name: EpiSC, BNa17, replicate 1


title: MCF-7 SA_(HuGene-1_0-st-v1).rma-gene-default-Signal

description: MCF-7 cells infected with shRNA-Naa10p lentivirus

source_name: MCF-7 SA


title: Tc-inducible FBL-kd ES_+Tc control_rep1.

description: Gene expression of Control ES cells_rep1

source_name: ES cells, cultured with Tc for 2days

value: FBL expressed


title: Low Ca, treatment 2, 24h

description: Gene expression after 24 h in 7.68 mM LL37 treatment of low calcium condition

source_name: keratinocyte, Low Ca, 24 h, LL37-7.68 mM

value: Low Ca LL37-7.68 mM


title: EpiSC line_ 129Ba2_rep2

source_name: EpiSC, 129Ba2, replicate 2


title: X25LN

source_name: Breast Cancer Lymph Node Metastasis aCGH

value: lymph node metastasis

tag: molecular subtype

source_name: Promega Female Reference genomic DNA G1548

value: pooled Female Reference DNA


title: EpiSC line_ 129Ba1_rep1

source_name: EpiSC, 129Ba1, replicate 1


title: X195LN

tag: n stage

source_name: Promega Female Reference genomic DNA G1552


title: EpiSC line_ 129Ba1_rep2

source_name: EpiSC, 129Ba1, replicate 2


title: X630

source_name: Breast Cancer aCGH

value: breast cancer

value: luminal

tag: t stage

value: Grade III

source_name: Promega Female Reference genomic DNA G1546


title: Low Ca, control, 24h

description: Gene expression after 24 h in control of low calcium condition

source_name: keratinocyte, Low Ca, 24 h, control

value: Low Ca control


title: Tc-inducible FBL-kd ES_+Tc control_rep2.

description: Gene expression of Control ES cells_rep2


title: 486 mutant, biological rep 1

source_name: Panc1 cells transduced with wild type 486 mutant

value: pancreatic epithelial cells


title: Low Ca, treatment 1, 24h

description: Gene expression after 24 h in 2.56 mM LL37 treatment of low calcium condition

source_name: keratinocyte, Low Ca, 24 h, LL37-2.56 mM

value: Low Ca LL37-2.56 mM

value: keratinocyte


title: X36LN

tag: grade

source_name: Promega Female Reference genomic DNA G1549


title: EpiSC line_ 129Ba2_rep1

source_name: EpiSC, 129Ba2, replicate 1

value: stem cells


title: Low Ca, treatment 1, 12h

description: Gene expression after 12 h in 2.56 mM LL37 treatment of low calcium condition

source_name: keratinocyte, Low Ca, 12 h, LL37-2.56 mM


title: EpiSC line_ 129C1_rep2

source_name: EpiSC, 129C1, replicate 2

value: established by the original protocol


title: X756

value: Grade I

source_name: Promega Female Reference genomic DNA G1547

tag: source


title: EpiSC line_ 129C1_rep1

source_name: EpiSC, 129C1, replicate 1

tag: cell type


title: X116LN

tag: er

source_name: Promega Female Reference genomic DNA G1550


title: Low Ca, treatment 2, 12h

description: Gene expression after 12 h in 7.68 mM LL37 treatment of low calcium condition

source_name: keratinocyte, Low Ca, 12 h, LL37-7.68 mM


title: SK-MEL-28 Agilent-014707 2 of 2 G4489A

city: Copenhagen

first: Christina

last: Dahl

address: Strandboulevarden 49

institute: Danish Cancer Society

hyb_protocol: Equal amounts of labeled DNA from the enriched and the reference samples were combined (2.5-4 µg each) and hybridized to the Human Promoter Array 244K (Agilent Technologies).

scan_protocol: Array scanning with Agilent G2565BA Microarray Scanner

data_processing: Data extraction and normalization were performed using the Feature extraction 9.5.3.1 software (Agilent technologies). DNA methylation levels were evaluated using the DNA analytics program (Agilent technologies), the UCSC database (http://genome.ucsc.edu) and the Galaxy tool (http://galaxy.psu.edu).

source_name: Melanoma Cell line

label_protocol: Reference and immunoprecipitated DNA were primed with 5µl Random Primers (supplied with Agilent Genomic DNA labeling kit PLUS) and incubated with 19µl Labeling Master Mix (Agilent) at 37°C for 2h. Immunoprecipitated methylated DNA was labeled with Cy5 fluorophore and the input genomic DNA was labeled with Cy3 fluorophore (Agilent Technologies).

growth_protocol: Melanoma cells were routinely cultured as monolayers in RPMI 1640 medium containing 10% fetal bovine serum and antibiotics at 37°C and 5% CO2. Primary human melanocytes (Invitrogen) were maintained in Medium 254 containing Human Melanocyte Growth Supplement 2 (Invitrogen) at 37°C and 5% CO2

extract_protocol: Genomic DNA was isolated using the Qiagen Mini Prep kit (Qiagen) and sonicated using a Bioruptor (Diagenode) to generate 200 to 600 bp fragments. Fragmented DNA (1.6 µg) was used as reference sample, while the remaining was subjected to immunoprecipitation. DNA was denatured for 5 min at 95°C and immunoprecipitated for 4 h at 4°C with 10 µg of monoclonal mouse antibody against 5-methylcytosine (Clone 33D3; 1 mg/mL; Eurogentec) bound to pan-mouse IgG Dynal magnetic beads (Invitrogen).

treatment_protocol: No treatment

tag: sample type

value: genomic DNA Input

value: MeDIP-DNA


title: FM79 Agilent-014707 2 of 2 G4489A


title: X421

source_name: Promega Female Reference genomic DNA G1544


title: S. aureus-fakAKO-rep2

city: Memphis

first: Matthew

middle: Wilmer

last: Frank

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St Jude Children's Research Hospital

description: Gene expression data for S. aureus fakAKO grown to OD600nm 0.45

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

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

source_name: S. aureus (in AH1263) fakAKO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: S. aureus WT (USA300) and fakAKO were grown to an OD600nm = 0.45

extract_protocol: Total RNA was isolated using Ambion RNAqueous purification kit according to the manufacturer's instructions and the purified RNA sample was treated with Turbo Dnase (Ambion).

tag: genotype

value: fakAKO

tag: genetic background

value: AH1263 is USA300 CA-MRSA strain LAC without p03


title: X487

tag: pr

source_name: Promega Female Reference genomic DNA G1545


title: S. aureus-fakAKO-rep3

treatment_protocol: S. aureus WT (USA300) and fakAKO were grown to an OD600nm = 0.45


title: Low Ca, control, 12h

description: Gene expression after 12 h in control of low calcium condition

source_name: keratinocyte, Low Ca, 12 h, control


title: HEMn Agilent-014707 2 of 2 G4489A

source_name: Human Epidermal Melanocytes, neonatal

tag: cell line

value: HEMn


title: Rat1 cells 105 min PE Treatment

city: Loma Linda

first: Daniel

middle: P

last: Morris

address: Loma LInda University

department: Center for Perinatal Biology

institute: Loma LInda University

description: 90 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

hyb_protocol: Cy5-labeled time point samples and an equimolar amount of rat reference RNA labeled with Cy3 were hybridized to a DNA chip containing the version 3 rat microarray (Operon Biotechnologies).  After hybridization, slides were washed sequentially. Details of hybridization and washing protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

scan_protocol: Scanned on a Gene Pix 5000 scanner in the Duke University Microarray Core facility.

data_processing:
Data was analyzed using GeneSpring.  Two color data was subject to Lowess normalization and background subtraction.   Ratio of sample/reference (Cy5/Cy3) signal for each time point was then divided by the averaged sample/reference (Cy5/Cy3) signal observed for the three untreated replicates in order to normalize the data series to zero time RNA levels. All time point sample values were retained to ensure that elimination of very low mRNA levels in untreated samples did not remove higher activated expression levels.
Following Lowess normalization and background subtraction, the ratio of sample/reference (Cy5/Cy3) signal for each time point was divided by the average sample/reference (Cy5/Cy3) signal observed for the three untreated replicates in order to normalize the data series to zero-time, untreated RNA levels. This normalized ratio, representing the fold-change in poly-A mRNA relative to untreated cells, was subject to Log 10 transformation to generate the reported values.
Non-numeric values indicate signal is absent in this point but present at other time points.
Log 10 transformation of the normalized poly-A mRNA levels at each time point relative to the average of the triplet untreated zero points.    Non-numeric values indicate signal is absent in this point but present at other time points.
Cy3 Reference counts following lowess normalization and background subtraction.  Non-numeric values indicate signal is absent in this point but present at other time points.
Cy5 Sample counts following lowess normalization and background subtraction.  Non-numeric values indicate signal is absent in this point but present at other time points.

organism: Rattus rattus

source_name: Rat-1 Fibroblast Serum PE 105 min

label_protocol: Total RNA was reverse transcribed using Super script II and Oligo dT primers.  RNA from individual time points was labeled with Cy5 while reference RNA was labeled with Cy3.  In order to ensure all upregulated points were captured by the reference RNA, it was created by combining an equal amounts of RNA from untreated cells with a mix form across the time series (30 min, 1h, 2h, 8h and 24h). Details of labeling protocols can be found at http://www.genome.duke.edu/cores/microarray/services/spotted-arrays/protocols/

growth_protocol: A characterized rat-1 fibroblast cell line stably expressing HA-tagged human alpha-1a Adrenergic Receptor at 1.77±0.24 pmole/mg total protein was grown under 5% CO2 at  37°C in growth medium containing Dulbecco's Eagle Modified Medium supplemented with 10% fetal bovine serum (Hyclone, SH30071.03HI), penicillin (100 U/ml), streptomycin (100 µg/ml) and 0.5 mg/ml G418 to maintain selection.  Two days prior to use (42-50h), cells at 75% confluence were trypsinized and plated at 2 to 2.5 million cells per 15 cm dish in growth medium without G418 and grown to about 75% confluence in growth medium under 5% CO2 at 37°C until treatment.

extract_protocol: Following treatment, media was removed first by pouring then by aspiration for 5 secs followed by immediate addition of 10 ml of Trizol for total RNA extraction. Cells were then incubated in Trizol with rotation for 20 to 40 minutes at room temperature prior to storage at -80°C.  Later, 5 ml of these Trizol preparations in 15 ml tubes were thawed and the total RNA extracted as recommended by the manufacturer employing the tabletop centrifuge modification. Total RNA was resuspended to 1ug/ul in water.

treatment_protocol: Cells grown as described were stimulated by addition of filter sterilized phenylephrine (PE) stock in water to a final concentration of 10 uM, followed by gentle circular rotation to ensure mixing with minimal agitation.  At the appropriate time the media was removed quickly followed by immediate addition of Trizol for total RNA extraction.

value: derived embyonic fibroblast from Fisher 2408 Rat

value: fibroblast

value: phenylephrine

value: 105 min

source_name: Rat-1 Fibroblast Combined Reference


title: S. aureus-WT-rep2

description: Gene expression data for S. aureus WT (USA300) grown to OD600nm 0.45

source_name: S. aureus (AH1263) WT

value: wild type


title: S. aureus-WT-rep3


title: EpiSC line_ 129C1_treated with IWP2_rep2

source_name: EpiSC, 129C1_treated with IWP2, replicate 2


title: EpiSC line_ Wt1_rep1

source_name: EpiSC, Wt1, replicate 1


title: S. aureus-fakAKO-rep1


title: Rat1 cells 75 min PE Treatment

description: 60 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 75 min

value: 75 min


title: Rat1 cells 120 min PE Treatment

description: 120 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 120 min

value: 120 min


title: FM55M2 Agilent-014707 2 of 2 G4489A


title: EpiSC line_ Wt1_rep2

description: Gene expression of undifferentiated EpiSCs.

source_name: EpiSC, Wt1, replicate 2


title: X704

source_name: Breast Cancer aCGH

value: breast cancer

value: luminal

value: Grade II

source_name: Promega Female Reference genomic DNA G1542

value: pooled Female Reference DNA


title: Rat1 cells 90 min PE Treatment

description: 75 min PE (10 uM) treated Rat-1 fibroblasts, growth conditions, harvested at 75% confluence.

source_name: Rat-1 Fibroblast Serum PE 90 min

value: 90 min


title: X350

value: Grade I

source_name: Promega Female Reference genomic DNA G1540


title: Rat1 cells 240 min PE Treatment

source_name: Rat-1 Fibroblast Serum PE 240 min

value: 240 min


title: S. aureus-WT-rep1


title: X412

value: Grade III

source_name: Promega Female Reference genomic DNA G1541


title: FM 6 Agilent-014707 2 of 2 G4489A

source_name: Melanoma Cell line

value: FM 6

value: genomic DNA Input

value: MeDIP-DNA


title: X613

source_name: Promega Female Reference genomic DNA G1539