title: Xenograft 930, biological rep 3

source_name: GBM Subcutaneous Xenograft

value: Subcutaneous Xenograft

tag: xenograft line


title: Xenograft 2322, biological rep 2

status: Public on Dec 01 2011

type: RNA

city: Durham

first: Jason

middle: W

last: Reeves

state: North Carolina

address: 101 Science Dr

country: USA

institute: Duke University

hyb_protocol: Following fragmentation, 10ug of biotinylated cRNA was hybridized for 16hr at 45C onto the Affymetrix Human Genome U133A Plus 2.0 Array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 according to standard protocols.

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

data_processing: data normalized using Bioconductor in R using either RMA or MAS5.0 normalization protocols (RMA provided, see website for MAS5).  Batch corrected expression values calculated by factor regression across Affymetrix doping and housekeeping controls

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug of Total RNA (ExpressionAnalysis Techinical Manual, 2005, Affymetrix).

growth_protocol: Xenograft lines grown SC or IC until 200 mm^3, cell lines cultured to 70% confluence in either serum free or serum containing media

extract_protocol: Total RNA extracted using Qiagen midi (xenograft), or mini (cell lines) kits.  Xenograft tissue pulverized in liquid nitrogen and homogenized using a rotor-stator homogenizer

tag: batch

tag: date of array

tag: line number

tag: line type


title: ttg mutant, biological rep2 at Mich

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

institute: University of Michigan

description: m-TTG_89, Analysis conducted at the University of Michigan

hyb_protocol: The cRNA was fragmented in the presence of heat and Mg2+, followed by hybridization to the Affymetrix ATH1 Arabidopsis genechip for 16 hr at 45C.  The arrays were then washed and stained using the Affymetrix Fluidics Station 400.

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

data_processing: The data were preprocessed in R using RMA with custom CDF files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp)

organism: Arabidopsis thaliana

source_name: ttg mutant

label_protocol: Biotin-labeled cRNA was synthesized according to the standard Affymetrix protocol from poly(A) RNA present in the total RNA prep.

growth_protocol: Seedlings were grown for 5 days in continuous light at 23C on vertically-oriented dishes containing MS media + 1% sucrose.

extract_protocol: WER::GFP-expressing cells were collected by FACS.  Total RNA was extracted from GFP-positive cells using the Rneasy kit (Qiagen, Inc).

treatment_protocol: Root were cut approximately 2 mm from the tip, including the entire developmental region.

tag: genotype

value: ttg1-13 WER::GFP

tag: cell type

value: root epidermal cells


title: Xenograft 645, biological rep 3


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep6

city: Dublin

first: David

middle: E

last: MacHugh

address: University College Dublin, Belfield

department: College of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

hyb_protocol: Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines for hybridisation onto Affymetrix GeneChip® arrays. Following the hybridisation for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script, before being inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000.

scan_protocol: All Affymetrix Bovine Genome Array microarrays were scanned using an Affymetrix GeneChip® Scanner 3000.

data_processing: Affymetrix® GeneChip® Bovine Genome Array data were analysed using Bioconductor [http://www.bioconductor.org] contained within the R statistical package (http://www.r-project.org). Normalisation of raw data was performed using the Factor Analysis for Robust Microarray Summarization (FARMS) algorithm. The FARMS algorithm uses only perfect match probes and a quantile normalization procedure, which provides the signal intensities.

organism: Bos taurus

label_protocol: Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The single stranded cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2. The enzymatically and chemically fragmented product (50-100 nt) was labelled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

extract_protocol: All RNA extractions were performed within two hours of blood collection. Briefly, 7.5 ml of whole heparinised blood was mixed with 42.5 ml of erythrocyte blood lysis buffer (10 mM KHCO3, 150 mM NH4Cl, 1 mM EDTA pH 8.0), and incubated for 5 min at room temperature with gentle agitation. Following centrifugation (750g for 10 min) the pelleted cells were washed once with 1× phosphate buffered saline (Invitrogen Ltd., Paisley, UK). The cell pellet was then fully resuspended in 2 ml Trizol® reagent (Invitrogen Ltd., Paisley, UK) and RNA was extracted as per the manufacturer’s instructions. The RNA was further purified using an RNeasy® kit with on-column DNase treatment (Qiagen Ltd., Crawley, UK) according to the manufacturer’s instructions. RNA quantity and quality was assessed using both the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the Agilent 2100 Bioanalyzer using an RNA 6000 Nano LabChip kit (Agilent Technologies, Cork, Ireland). All samples displayed a 260/280 ratio greater than 1.8 and RNA integrity numbers (RIN) greater than 8.0.

treatment_protocol: Sixteen animals were used for this study. Eight infected animals were selected from a panel of naturally M. bovis infected animals maintained for on-going disease surveillance at the Department of Agriculture, Fisheries and Food, Backweston Laboratory Campus (Celbridge, Co. Kildare, Ireland). These animals had a positive single intradermal comparative tuberculin test (SICTT) result and were also positive in the whole blood IFN-γ-based BoviGAM® assay [Prionics AG, Switzerland] (data not shown). Cattle were confirmed for BTB following detailed post-mortem pathological examination. Non-infected controls animals were sex matched and age-matched to the infected animals and were selected from a herd with no recent history of M. bovis infection. The control animals were shown to be negative for both the SICTT and IFN-γ tests (data not shown).

tag: tissue

value: Peripheral blood leukocyte

tag: cattle breed

value: Holstein-Friesian

tag: Sex

value: Female

tag: infection status

value: Control

tag: agent


title: ttg mutant, biological rep1 at Mich

description: m-TTG_111, Analysis conducted at the University of Michigan


title: Xenograft 320, biological rep 3


title: bhlh66 mutant, biological rep3 at Mich

description: m-S006430_70, Analysis conducted at the University of Michigan

source_name: bhlh66 mutant

value: bhlh66-1 WER::GFP


title: bhlh66 mutant, biological rep2 at Mich

description: m-S006430_62, Analysis conducted at the University of Michigan


title: Xenograft 317, biological rep 4


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep4


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep5


title: bhlh66 mutant, biological rep1 at Mich

description: m-S006430_105, Analysis conducted at the University of Michigan


title: Xenograft 270, biological rep 4


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep2


title: EndothelialCells_StaticControl_24hrs_rep3

city: Buffalo

first: Jennifer

last: Dolan

state: NY

address: 3435 Main Street

department: Neuroscience

institute: University at Buffalo

description:
Static4
PMS4_1_(Bovine).CEL

hyb_protocol: Standard protocol described in Affymetrix GeneChip 3' IVT Express Kit.

scan_protocol: Affymetrix GeneChip Scanner and software.

data_processing: All analyses were performed in R/Bioconductor. Affymetrix bovine CEL files were preprocessed and normalized using RMA. Informative, valid probe sets were determined using FARMS (Tolloen et al., 2007, Bioinformatics 23:2897-2902). FARMS represents an unbiased approach to remove non-informative probe sets based on their intra-probe set correlation. Sample to sample data exploration was performed using unsupervised hierarchial clustering and principle component analysis. Differential gene expression analysis was performed using a linear model approach and employing an empirical Bayes method for calculation of statistical significance (Bioconductor,limma package). We identified those probe sets whose expression were significantly enriched or depleted by at least two fold change and statistically significant following 1% FDR adjustment of p-values.

source_name: endothelial cells exposed to 0Pa of shear stress for 24 hrs

label_protocol: Conducted using Affymetrix standard protocols.

growth_protocol: Bovine Aortic Endothelial Cells were seeded on glass coverslips and allowed to grow to confluence for 5 days. Cells were maintained in DMEM with 10% FBS and 1% penicilin/streptomycin.

extract_protocol: Total RNA was extracted following Qiagen RNeasy Mini Kit protocol using spin column technology. Purity and integrity were confirmed.

treatment_protocol: 24 hrs before the flow experiments started culture media was changed and cells were allowed to equilibrate in flow media containing DMEM, 5% FBS, 1% pen/strep, and 8% Dextran 70. For treatment, cells were placed subjected to either 0,2 or 10Pa of shear stress by placement in a flow loop system in which media was circulated over the cells to produce the mentioned shear stress values. After 24 hours the experiment was ended and coverslips of cells removed from the chamber.

value: aorta

value: endothelial cells (Ecs)

tag: passage

tag: stress

value: 0Pa of shear stress


title: rhd6 mutant, biological rep3 at Mich

description: m-RHD6_xT3, Analysis conducted at the University of Michigan

source_name: rhd6 mutant

value: rhd6-1 WER::GFP


title: Xenograft 2339, biological rep 3


title: Xenograft 212, biological rep 3


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep1


title: rhd6 mutant, biological rep2 at Mich

description: m-RHD6_S8, Analysis conducted at the University of Michigan


title: Xenograft 08-714, biological rep 2


title: rhd6 mutant, biological rep1 at Mich

description: m-RHD6_S1, Analysis conducted at the University of Michigan


title: Renal Clear Cell Carcinoma_TB3874

type: genomic

city: Philadelphia

first: Vijay

middle: R

last: Dondeti

state: PA

address: 421 Curie Boulevard, 456 BRB II/III

institute: University of Pennsylvania School of Medicine

description: Genomic DNA extracted from renal tumors was genotyped using Illumina Infinium Genotyping BeadChips.

hyb_protocol: Hybridization was done according to Illumina's standard protocol

scan_protocol: The chips were scanned using Illuminaa's standard scanner.

data_processing: Genomic DNA extracted from renal tumors was genotyped using Infinium HumanHap550-v3 and Human610-Quadv1 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: clear cell renal cell carcinoma

label_protocol: 1 microgram of DNA was labelled according to Illumina's standard protocol

extract_protocol: The Wizard Genomic DNA Purification Kit from Promega was used to extract genomic DNA from the tumors

value: Renal tumor

tag: disease state

value: carcinoma


title: Peripheral blood leukocytes taken from non-infected, control cattle. Rep3


title: EndothelialCells_StaticControl_24hrs_rep1

description:
Static1
PMS1.CEL


title: EndothelialCells_StaticControl_24hrs_rep2

description:
Static3
PMS3.CEL


title: rhd6 mutant + MS, biological rep2 at Mich

description: m-RHD6MS_133, Analysis conducted at the University of Michigan

source_name: rhd6 mutant + MS


title: Renal Clear Cell Carcinoma_TB1149


title: Xenograft 08-430, biological rep 3


title: EZH2.T [Agilent-014706]

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

description: EZH2 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

hyb_protocol: 5 ug labeled material was mixed with blocking agent and hybridization buffer (Agilent Technologies) followed by denaturing at 95°C for 3 min and incubating at 37°C for 30 min. The mixtures were applied to microarrays in Agilent microarray hybridization chambers, and hybridizations were carried out for 40 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA) at 10 rpm.  Hybridized microarrays were washed and dried according to the Agilent CGH microarray wash protocol.

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner and data were extracted using Feature Extraction Software (Agilent Technologies) with recommended data extraction protocol for array CGH.

data_processing:
Bioconductor packages limma and Ringo were used for data processing. The median signals of non-control probes were selected and normalized using Tukey-biweight scaling procedure.
Normalized log2 ratio (Cy5/Cy3) representing ChIP/WCE (do not include control probes)

source_name: SW480 cells, 2mM H2O2, 30min

label_protocol: 2 ug of ligation-mediated PCR fragments was mixed with 2.5x random primer solution (Agilent Technologies) and incubated at 95°C for 5 minutes. Labeling reactions were performed using a BioPrime Array CGH Genomic Labeling Module (Invitrogen) and Cydine-5 or Cydine-3 dUTP (Perkin Elmer) at 37°C for 3 hours.  The labeled sample was purified, concentrated with affinity columns and buffers provided in the kit. Both nucleic acid and dye concentrations of purified material were determined by NanoDrop ND-1000

growth_protocol: SW480 cells were obtained from American Type Culture Collection and maintained at 37°C and 5% CO2 in McCoy's 5a, supplemented with 10% fetal bovine serum.

extract_protocol: ChIP-on-chip was performed as previously described (McGarvey et al., Cancer Res. 2008 Jul 15;68(14):5753-9.), following Agilent's instructions.

treatment_protocol: Cells were either untreated or treated with 2mM H2O2 for 30min at 37°C

tag: cell line

value: Human colorectal adenocarcinoma cell line SW480 (CCL-228)

tag: antibody

value: EZH:Cell Signaling, #4905, Lot2 05/2009

tag: fraction

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: rhd6 mutant + MS, biological rep3 at Mich

description: m-RHD6MS_136, Analysis conducted at the University of Michigan


title: Renal Clear Cell Carcinoma_TB3827


title: Renal Clear Cell Carcinoma_TB3895


title: Xenograft 08-537, biological rep 3

tag: batch

value: Subcutaneous Xenograft

tag: xenograft line


title: EndothelialCells_Normal WSS_24hrs_rep3

description:
Normal4
PMN4_1_(Bovine).CEL

source_name: endothelial cells exposed to 2Pa of shear stress for 24 hrs

value: 2Pa of shear stress


title: rhd6 mutant + MS, biological rep1 at Mich

description: m-RHD6MS_130, Analysis conducted at the University of Michigan

value: root epidermal cells


title: EndothelialCells_Normal WSS_24hrs_rep2

description:
Normal3
PMN3.CEL


title: rhd6 mutant + IAA, biological rep3 at Mich

description: m-RHD6IAA_155, Analysis conducted at the University of Michigan

source_name: rhd6 mutant + IAA


title: DNMT3B.T [Agilent-014706]

description: DNMT3B ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

value: DNMT3B:Custom-made Antibody


title: EZH2.U [Agilent-014706]

description: EZH2 ChIP for untreated SW480 cells

source_name: SW480 cells


title: EndothelialCells_Normal WSS_24hrs_rep1

description:
Normal1
PMN1.CEL


title: Renal Clear Cell Carcinoma_GOG0256


title: Cell Line H80OTR, biological rep 1

source_name: GBM Serum Cell Line

tag: date of array

tag: line number

value: Serum Cell Line


title: DNMT3B.U [Agilent-014706]

description: DNMT3B ChIP for untreated SW480 cells


title: Renal Clear Cell Carcinoma_TB4097


title: EndothelialCells_High WSS_24hrs_rep3

description:
High4
PMH4_1_(Bovine).CEL

source_name: endothelial cells exposed to 10Pa of shear stress for 24 hrs

value: 10Pa of shear stress


title: Cell Line D54TR, biological rep 2

tag: line type


title: EndothelialCells_High WSS_24hrs_rep2

description:
High3
PMH3.CEL

tag: cell type


title: rhd6 mutant + IAA, biological rep2 at Mich

description: m-RHD6IAA_134, Analysis conducted at the University of Michigan

tag: genotype


title: rhd6 mutant + IAA, biological rep1 at Mich

description: m-RHD6IAA_131, Analysis conducted at the University of Michigan


title: Renal Clear Cell Carcinoma_TB4123

tag: tissue


title: Renal Clear Cell Carcinoma_TB4124


title: rhd6 mutant + ACC, biological rep3 at Mich

description: m-RHD6ACC_138, Analysis conducted at the University of Michigan

source_name: rhd6 mutant + ACC


title: Xenograft 717, biological rep 2


title: DNMT1.U [Agilent-014706]

description: DNMT1 ChIP for untreated SW480 cells


title: Xenograft 456, biological rep 2


title: Xenograft 645, biological rep 2


title: Renal Clear Cell Carcinoma_TB3858


title: Renal Clear Cell Carcinoma_TB4027


title: dHA3

city: Göteborg

first: Keith

middle: EJ

last: Tyo

address: Kemivägen 10

department: Chemical and Biological Engineering

institute: Chalmers University of Technology

hyb_protocol: 45 degree C for 16 hours

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA, USA)

data_processing: RMA

organism: Saccharomyces cerevisiae

source_name: Cells from recombinant yeast

label_protocol: 250 ng of the total RNA was used to synthesize cDNA using Affymetrix 3’ IVT Express kit and successively aRNA was synthesized (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: total RNA was extracted from cells through mechanical disruption with glass beads, purified using the RNeasy kit (Qiagen, Hilden, Germany)

tag: strain

value: CEN-PK 113-5D hac1::kanMX (p426-YapAmy)


title: Renal Clear Cell Carcinoma_TB3945


title: gamma.H2AX.U [Agilent-014706]

description: gamma-HA2X ChIP for untreated SW480 cells


title: Xenograft 317, biological rep 2


title: Xenograft 263, biological rep 3


title: rhd6 mutant + ACC, biological rep1 at Mich

description: m-RHD6ACC_132, Analysis conducted at the University of Michigan


title: rhd6 mutant + ACC, biological rep2 at Mich

description: m-RHD6ACC_135, Analysis conducted at the University of Michigan


title: Renal Clear Cell Carcinoma_TB3960


title: dHA2


title: SIRT1.T [Agilent-014706]

description: SIRT1 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: DNMT1.T [Agilent-014706]

description: DNMT1 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: rhd2 mutant, biological rep3 at Mich

description: m-RHD2_77, Analysis conducted at the University of Michigan

source_name: rhd2 mutant

value: rhd2-1 WER::GFP


title: Renal Clear Cell Carcinoma_TB4030


title: dHA1


title: EndothelialCells_High WSS_24hrs_rep1

description:
High1
PMH1.CEL

value: aorta

value: endothelial cells (Ecs)


title: Stem Cell Line 08-714, biological rep 1

source_name: GBM Stem Cell Line

value: Stem Cell Line


title: Melanocytes p53shRNA shRNA replicate 2

city: New Lambton Heights

first: Kelly

last: Kiejda

state: NSW

address: HMRI

country: Australia

institute: University of Newcastle

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All samples were cubic spline normalised and background subtracted using BeadStudio version 3.2.7 software (Illumina). Two-hundred and ninety probes, representing 247 unique transcripts and 181 unique target genes, identified through literature and database searches to either be regulated by p53 or known to regulate p53 activity, were used for further analysis.

label: Biotin

source_name: melanocyte

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

growth_protocol: All melanoma cell lines were cultured in DMEM containing 5% FCS (Commonwealth Serum Laboratories, VIC, Australia) and maintained in exponential growth at 37oC and 5% CO2. Melanocytes were  cultured in Medium 154 (Cascade Biologics). FLOW2000 and HDF1314 fibroblasts were cultured in DMEM containing 10% FCS (Commonwealth Serum Laboratories).

extract_protocol: Total RNA was extracted using the SV Total RNA Isolation System Kit according to the manufacturers’ instructions (Promega, NSW, Australia)

treatment_protocol: To generate p53 silenced stable cell lines, Mel-RM, IgR3 and melanocytes were transduced at an MOI of 10 with either a virus encoding p53 shRNA or control shRNA. Cells were transduced twice with three days in between each transduction.

value: primary melanocyte

tag: transfection

value: p53shRNA shRNA


title: dHI2

value: CEN-PK 113-5D hac1::kanMX (p426-YapIns)


title: gamma.H2AX.T [Agilent-014706]

description: gamma-HA2X ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C

value: Human colorectal adenocarcinoma cell line SW480 (CCL-228)


title: dHI3


title: Xenograft 08-445, biological rep 2

source_name: GBM Subcutaneous Xenograft


title: rhd2 mutant, biological rep2 at Mich

description: m-RHD2_50, Analysis conducted at the University of Michigan


title: Melanocytes Control shRNA replicate 2

value: Control shRNA


title: Xenograft 08-624, biological rep 3


title: dHI1


title: Renal Clear Cell Carcinoma_TB4101

description: Genomic DNA extracted from renal tumors was genotyped using Illumina Infinium Genotyping BeadChips.

value: Renal tumor

value: carcinoma


title: Renal Clear Cell Carcinoma_TB4020


title: Melanocytes Control shRNA replicate 1


title: Renal Clear Cell Carcinoma_TB3856


title: Xenograft 2339, biological rep 2

value: Subcutaneous Xenograft


title: SIRT1.U [Agilent-014706]

description: SIRT1 ChIP for untreated SW480 cells

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: Met2

city: Gaithersburg

first: Peter

last: Johansson

state: Maryland

address: 8717 Grovemont Circle

department: Pediatric Oncology Branch

institute: National Cancer Institute

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina standard protocol

data_processing: Illumina data were processed by Illumina BeadStudo V2010.3. Log R ratios were calculated as the sum of the two intensities (corresponding to alleles A and B) divided by the average intensity across samples in our larger batch of samples.

source_name: Metastatic Neuroblastoma Tumor

label_protocol: Illumina standard protocol

extract_protocol: QIAamp DNA Mini Kit

tag: gender

value: Female

tag: age

value: Liver Metastasis

tag: Stage


title: Mel-RM p53shRNA shRNA replicate 2

source_name: melanoma

value: Mel-RM


title: myc1 mutant, biological rep3 at Mich

description: m-MYC1_67, Analysis conducted at the University of Michigan

source_name: myc1 mutant

value: myc1-1 WER::GFP

value: root epidermal cells


title: myc1 mutant, biological rep1 at Mich

description: m-MYC1_106, Analysis conducted at the University of Michigan


title: Xenograft 08-430, biological rep 2


title: myc1 mutant, biological rep2 at Mich

description: m-MYC1_46, Analysis conducted at the University of Michigan


title: dHN3

value: CEN-PK 113-5D hac1::kanMX (p426GPD)


title: dHN2


title: Mel-RM p53shRNA shRNA replicate 1


title: Xenograft 2322, biological rep 1


title: Melanocytes p53shRNA shRNA replicate 1


title: dHN


title: mrh3 mutant, biological rep3 at Mich

description: m-MRH3_73, Analysis conducted at the University of Michigan

source_name: mrh3 mutant

value: mrh3-3 WER::GFP


title: Renal Clear Cell Carcinoma_44073A1

source_name: clear cell renal cell carcinoma

tag: disease state


title: Mel-RM Control shRNA replicate 2

tag: cell line


title: Cell Line U138P, biological rep 1

value: Serum Cell Line


title: WTA3

value: CEN-PK 113-5D (p426-Yap-Amy)


title: Mel-RM Control shRNA replicate 1


title: mrh3 mutant, biological rep2 at Mich

description: m-MRH3_57, Analysis conducted at the University of Michigan


title: Cell Line D54P, biological rep 2


title: Cell Line H80TR, biological rep 1


title: IgR3 p53shRNA shRNA replicate 2

value: p53shRNA shRNA


title: WTA1


title: IgR3 p53shRNA shRNA replicate 1


title: Renal Clear Cell Carcinoma_TB4045


title: Xenograft 475, biological rep 2


title: Xenograft 456, biological rep 3


title: mrh2 mutant, biological rep2 at Mich

description: m-MRH2_56, Analysis conducted at the University of Michigan

source_name: mrh2 mutant

value: mrh2-1 WER::GFP


title: WTI3

value: CEN-PK 113-5D (p426-YapIns)


title: mrh2 mutant, biological rep1 at Mich

description: m-MRH2_127, Analysis conducted at the University of Michigan


title: WTA2


title: WTI2


title: mrh1 mutant, biological rep3 at Mich

description: m-MRH1_91, Analysis conducted at the University of Michigan

source_name: mrh1 mutant

value: mrh1-1 WER::GFP


title: HDF1314 replicate 2

source_name: fibroblast


title: mrh3 mutant, biological rep1 at Mich

description: m-MRH3_41, Analysis conducted at the University of Michigan


title: WTI1


title: Xenograft 245, biological rep 3


title: Xenograft 270, biological rep 3


title: IgR3 Control shRNA replicate 1

value: Control shRNA


title: FLOW2000 replicate 2


title: WTN2


title: Xenograft 2159, biological rep 4

value: Subcutaneous Xenograft


title: HDF1314 replicate 1


title: mrh2 mutant, biological rep3 at Mich

description: m-MRH2_72, Analysis conducted at the University of Michigan


title: Xenograft 08-624, biological rep 2


title: rhd2 mutant, biological rep1 at Mich

description: m-RHD2_38, Analysis conducted at the University of Michigan

value: rhd2-1 WER::GFP


title: WTN3


title: mrh1 mutant, biological rep2 at Mich

description: m-MRH1_71, Analysis conducted at the University of Michigan


title: IgR3 Control shRNA replicate 2


title: lrx1 mutant, biological rep3 at Mich

description: m-LRX_85, Analysis conducted at the University of Michigan

source_name: lrx1 mutant

value: lrx1-4 WER::GFP


title: WTN1

extract_protocol: RNA was isolated using the RNeasy Minikit (Qiagen, Valencia, CA, USA).  Cells were lysed in RNeasy RLT buffer using Lysing Matrix C (MP Biomedicals Solon, OH, USA) in a Fast Prep 24 (MP Biomedicals Solon, OH, USA) as follows: 20 s at speed 6, 1 min at 4oC, 20 s at speed 6.


title: Xenograft 08-446, biological rep 3


title: Melanocytes replicate 2

value: primary melanocyte


title: mrh1 mutant, biological rep1 at Mich

description: m-MRH1_66, Analysis conducted at the University of Michigan


title: FLOW2000 replicate 1


title: lrx1 mutant, biological rep2 at Mich

description: m-LRX_74, Analysis conducted at the University of Michigan


title: Xenograft 08-500, biological rep 2


title: lrx1 mutant, biological rep1 at Mich

description: m-LRX_52, Analysis conducted at the University of Michigan


title: Xenograft 2360, biological rep 2


title: Cell Line H80P, biological rep 1

source_name: GBM Serum Cell Line


title: wild type rep-2

city: Sevilla

first: Cristina

last: González-Aguilera

email: cgonagu@upo.es, aguilo@us.es

address: Avda Américo Vespucio s/n

department: Molecular Biology

country: Spain

institute: Universidad de Sevilla-CSIC/CABIMER

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix GCOS software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (affylmGUI interface) of R/Bioconductor project.

source_name: wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Cell were cultured in YPD rich medium at 30ºC up to exponential phase

extract_protocol: Rneasy mini Kit (Qiagen) of total RNA was performed according to the manufacturer's instruction.

tag: genotype/variation

value: wild type


title: Melanocytes replicate 1


title: wild type rep-3


title: ire mutant, biological rep3 at Mich

description: m-IRE_75, Analysis conducted at the University of Michigan

source_name: ire mutant

value: ire1-2 WER::GFP


title: Sk-Mel-28 replicate 2


title: nab2-1 rep-3

source_name: nab2-1 mutant

value: W303-1A  nab2∆HIS3 nab2-1 (CEN LEU2)

value: nab2-1 mutant


title: Sk-Mel-28 replicate 1


title: nab2-1 rep-1


title: Xenograft 645, biological rep 1


title: Me1007 replicate 2


title: gl3 egl3 mutant, biological rep2 at Mich

description: m-GL3EGL3_6, Analysis conducted at the University of Michigan

source_name: gl3 egl3 mutant

value: gl3-1 egl3-1 WER::GFP

value: root epidermal cells


title: ire mutant, biological rep2 at Mich

description: m-IRE_69, Analysis conducted at the University of Michigan


title: Xenograft 717, biological rep 3


title: Xenograft 317, biological rep 3


title: gl3 egl3 mutant, biological rep3 at Mich

description: m-GL3EGL3_98, Analysis conducted at the University of Michigan


title: Xenograft 263, biological rep 2


title: Me4405 replicate 1


title: wild type rep-1


title: Me4405 replicate 2


title: gl3 egl3 mutant, biological rep1 at Mich

description: m-GL3EGL3_119, Analysis conducted at the University of Michigan


title: Xenograft 2159, biological rep 2


title: Xenograft 270, biological rep 2


title: MM200 replicate 1


title: ire mutant, biological rep1 at Mich

description: m-IRE_32, Analysis conducted at the University of Michigan


title: nab2-1 rep-2


title: gl2 mutant, biological rep3 at Mich

description: m-GL2_xT2, Analysis conducted at the University of Michigan

source_name: gl2 mutant

value: gl2-1 WER::GFP


title: nab2-td 30 min rep-3

description: C Glez44.CEL

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G.

source_name: nab2-td after 30 min of the induction of the degron

growth_protocol: Cells were cultured in YPD rich medium supplied with 0.1mM CuSO4 at 26ºC up to OD600 0.6 and then transferred to YPGal without CuSO4 at 26ºC during 30 min to allow the expression of Ubr1 (T=0). Next the temperature was shifted at 37ºC to induce the degron and cells were collected after 30 min (T30) and 75 min (T75).

extract_protocol: RNeasy mini kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Nab2-td is expressed under the control of the CUP1 promoter and tagged with an HA epitope and a DHFR domain in the N-terminal region of the protein. The DHFR domain has an ubiquitination motif recognized by the ubiquitin ligase Ubr1 expressed under the GAL1 promoter. The DHFR domain is only exposed at 37ºC.  Permissive conditions (Glucose and CuSO4 at 26ºC). Restrictive conditions (Galactose without CuSO4 at 37ºC).

value: W303-1A ubr1∆::GAL-UBR1 (HIS3) nab2-td (URA3)

tag: genome/variation


title: Xenograft 08-714, biological rep 3

source_name: GBM Subcutaneous Xenograft

tag: batch


title: nab2-td 75 min rep-2

description: C Glez46_2.CEL

source_name: nab2-td after 75 min of the induction of the degron


title: nab2-td 75 min rep-1

description: C Glez45.CEL

value: nab2-td after 75 min of the induction of the degron


title: MM200 replicate 2

source_name: melanoma


title: nab2-td 30 min rep-1

description: C Glez42.CEL

value: nab2-td after 30 min of the induction of the degron


title: gl2 mutant, biological rep2 at Mich

description: m-GL2_S9, Analysis conducted at the University of Michigan


title: IgR3 replicate 2


title: csld3 mutant, biological rep2 at Mich

description: m-CSLD3_64, Analysis conducted at the University of Michigan

source_name: csld3 mutant

value: csld3-1 WER::GFP


title: Xenograft 08-500, biological rep 1

tag: xenograft line


title: nab2-td 0 min rep-3

description: C Glez41.CEL

source_name: nab2-td without inducing the degron

value: nab2-td without inducing the degron


title: csld3 mutant, biological rep3 at Mich

description: m-CSLD3_x45, Analysis conducted at the University of Michigan


title: Xenograft 08-624, biological rep 1

tag: date of array


title: Xenograft 2360, biological rep 1

tag: line number


title: nab2-td 0 min rep-2

description: C Glez40.CEL


title: csld3 mutant, biological rep1 at Mich

description: m-CSLD3_55, Analysis conducted at the University of Michigan


title: IgR3 replicate 1


title: nab2-td 0 min rep-1

description: C Glez39.CEL


title: Xenograft 08-537, biological rep 2

tag: line type


title: Cell Line D54OTR, biological rep 2

value: Serum Cell Line


title: Mel-RM replicate 2

value: Mel-RM


title: RSG_12h_rep5

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

description: replicate 5

data_processing: The data were normalised using average normalisation with BeadsStudio 3.1.3.0 (Illumina)

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

growth_protocol: THP-1 cells (ATCC TIB-202) were maintained in RPMI-1640 medium supplemented with 10% FBS at 37C and 5% CO2.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit following the standard protocol provided with the extraction kit.

treatment_protocol: THP-1 cells were differentiated with PMA (10ng/ml) over the course of 40h. Cells were washed and incubated with medium w/o PMA for 2 hours prior to stimulation.

tag: differentiation

value: PMA-differentiated THP-1 cells

tag: treatment

value: RSG (1microM)

tag: time (hrs)


title: wild type 75 min rep-2

description: C Glez38.CEL

source_name: wild type after  75 min of induction of the degron

tag: strain

value: W303-1A ubr1∆::GAL-UBR1 (HIS3)


title: Stem Cell Line 08-698, biological rep 1

source_name: GBM Stem Cell Line

value: Stem Cell Line


title: Xenograft 930, biological rep 2

value: Subcutaneous Xenograft


title: cpc try mutant, biological rep3 at Mich

description: m-CPCTRY_118, Analysis conducted at the University of Michigan

source_name: cpc try mutant

tag: genotype

value: cpc-1 try-82 WER::GFP

tag: cell type


title: nab2-td 75 min rep-3

description: C Glez47.CEL


title: cpc try mutant, biological rep2 at Mich

description: m-CPCTRY_112, Analysis conducted at the University of Michigan


title: nab2-td 30 min rep-2

description: C Glez43.CEL


title: Mel-RM replicate 1


title: cpc try mutant, biological rep1 at Mich

description: m-CPCTRY_109, Analysis conducted at the University of Michigan


title: gl2 mutant, biological rep1 at Mich

description: m-GL2_100, Analysis conducted at the University of Michigan


title: wild type 75 min rep-1

description: C Glez37.CEL

value: wild type


title: RSG_12h_rep4

description: replicate 4


title: RSG_12h_rep3

description: replicate 3


title: RSG_12h_rep6

description: replicate 6


title: Xenograft 475, biological rep 3


title: wild type 30 min rep-2

description: C Glez36rep.CEL

source_name: wild type after  30 min of induction of the degron


title: wild type 30 min rep-1

description: C Glez35.CEL


title: Xenograft 320, biological rep 2


title: cow1 mutant, biological rep1 at Mich

description: m-COW_113, Analysis conducted at the University of Michigan

source_name: cow1 mutant

value: cow1-3 WER::GFP


title: cow1 mutant, biological rep2 at Mich

description: m-COW_116, Analysis conducted at the University of Michigan

value: root epidermal cells


title: wild type 0 min rep-2

description: C Glez34.CEL

source_name: wild type without inducing the degron


title: Xenograft 212, biological rep 2


title: wild type 0 min rep-1

description: C Glez33_2.CEL


title: cobl9 mutant, biological rep3 at Mich

description: m-COBL9_51, Analysis conducted at the University of Michigan

source_name: cobl9 mutant

value: cobl9-1 WER::GFP


title: RSG_12h_rep1

description: replicate 1


title: RSG_12h_rep2

description: replicate 2


title: RSG_8h_rep6

description: replicate 6


title: cobl9 mutant, biological rep2 at Mich

description: m-COBL9_25, Analysis conducted at the University of Michigan


title: cobl9 mutant, biological rep1 at Mich

description: m-COBL9_18, Analysis conducted at the University of Michigan


title: Me1007 replicate 1


title: Xenograft 2159, biological rep 3


title: AC2

city: Bangalore

first: soumya

last: gupta

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

description: Gene expression in stimulated (activated) T-cells

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65C, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) witht he following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software.

data_processing: The gprocessed signal was calculated for its mean in each sample. The data set was normalized with that mean value, and the resulting values were used for further analysis to find differentially expressing genes.

organism: Mus musculus

source_name: stimulated (activated) T-cells

label_protocol: RNA was labeled using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: Freshly isolated spleen from 7 week old C57/Bl6 mice was used to isolate CD4 naïve T-cells (resting/naïve) using R&D magcellect kit.

extract_protocol: Total RNA was isolated from the cells using Qiagen RNA extraction kit, using the protocol suggested by manufacturer

treatment_protocol: CD4 naïve T-cells were stimulated with aCD3-aCD28 coated beads for 48 hours for activation (Activated/ stimulated cells)

tag: tissue

value: Spleen

value: CD4 T-cells

tag: gender

value: 1 male+ 1 female mouse

tag: age

value: 7 weeks


title: Xenograft 245, biological rep 2


title: RSG_8h_rep4

description: replicate 4

tag: cell line


title: Xenograft 08-446, biological rep 1


title: RSG_8h_rep5

description: replicate 5


title: Xenograft 08-537, biological rep 4


title: Xenograft 08-500, biological rep 3


title: AC1


title: wer myb23 mutant, biological rep2 at Duke

description: d-WERMYB_D2, Analysis conducted at Duke University

source_name: wer myb23 mutant

value: wer-1 myb23-1 WER::GFP


title: cow1 mutant, biological rep3 at Mich

description: m-COW_122, Analysis conducted at the University of Michigan


title: wer myb23 mutant, biological rep1 at Duke

description: d-WERMYB_D1, Analysis conducted at Duke University


title: RSG_8h_rep3

description: replicate 3


title: NC2

description: Gene expression in resting (naïve) CD4 T-cells

source_name: resting (naïve) CD4 T-cells


title: RSG_8h_rep2

description: replicate 2


title: Xenograft 320, biological rep 1


title: NC1


title: RSG_8h_rep1

description: replicate 1


title: wer myb23 mutant, biological rep3 at Duke

description: d-WERMYB_D3, Analysis conducted at Duke University


title: Cdx2 vs control 7/8 somites tech1 dyeswap

city: Utrecht

first: Cesca

last: van de Ven

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved using Feature Extraction Software (V.9.5.3, Agilent Technologies).

source_name: Posterior part of 7/8 somite embryos

label_protocol: 300 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Embryos were isolated from uterus at 4/5 somite and 7/8 somites stages. dissected at the same axial levels by using the last somite boundary and the base of the allantois as landmarks.

extract_protocol: Rna was isolated using RiboPure Kit (Ambion)

treatment_protocol: Tissue was stored in RNAlater (Ambion)

tag: Stage

value: 7/8 somite

value: Cdx2 null mutant


title: Xenograft 475, biological rep 1


title: Xenograft 08-430, biological rep 1


title: Xenograft 2159, biological rep 1


title: ttg mutant, biological rep2 at Duke

description: d-TTG_D2, Analysis conducted at Duke University

source_name: ttg mutant

value: ttg1-13 WER::GFP


title: ttg mutant, biological rep3 at Duke

description: d-TTG_D3, Analysis conducted at Duke University


title: RSG_3h_rep4

description: replicate 4

value: PMA-differentiated THP-1 cells

value: RSG (1microM)


title: Cdx2 vs control 7/8 somites tech1


title: ttg mutant, biological rep1 at Duke

description: d-TTG_D1, Analysis conducted at Duke University


title: Xenograft 08-308, biological rep 3

source_name: GBM Subcutaneous Xenograft


title: RSG_3h_rep3

description: replicate 3


title: RSG_3h_rep5

description: replicate 5


title: gl3 egl3 mutant, biological rep3 at Duke

description: d-GL3EGL3_D3, Analysis conducted at Duke University

source_name: gl3 egl3 mutant

value: gl3-1 egl3-1 WER::GFP


title: RSG_3h_rep6

description: replicate 6


title: Cdx2 vs control 4/5 somites tech1 dyeswap

source_name: Posterior part of 4/5 somite embryos

value: 4/5 somite


title: gl3 egl3 mutant, biological rep2 at Duke

description: d-GL3EGL3_D2, Analysis conducted at Duke University


title: Cdx2 vs control 4/5 somites tech1


title: RSG_3h_rep2

description: replicate 2


title: RSG_3h_rep1

description: replicate 1


title: gl3 egl3 mutant, biological rep1 at Duke

description: d-GL3EGL3_D1, Analysis conducted at Duke University


title: Cdx2 vs control 7/8 somites bio1 dyeswap


title: cpc try mutant, biological rep3 at Duke

description: d-CPCTRY_D3, Analysis conducted at Duke University

value: cpc-1 try-82 WER::GFP


title: Xenograft 2339, biological rep 1

value: Subcutaneous Xenograft


title: Cdx2 vs control 7/8 somites bio1

value: wild type


title: Xenograft 717, biological rep 1


title: RSG_1.5h_rep4

description: replicate 4


title: RSG_1.5h_rep5

description: replicate 5


title: Cdx2 vs control 4/5 somites bio1


title: Cdx2 vs control 4/5 somites bio1 dyeswap


title: Xenograft 08-308L, biological rep 2


title: Cell Line D54P, biological rep 1

source_name: GBM Serum Cell Line

value: Serum Cell Line


title: RSG_1.5h_rep3

description: replicate 3


title: Cell Line UW15P, biological rep 1


title: cpc try mutant, biological rep2 at Duke

description: d-CPCTRY_D2, Analysis conducted at Duke University

value: root epidermal cells


title: pDC_sample_11

city: Melbourne

first: Christopher

last: Bye

state: Victoria

address: University of Melbourne

institute: The Florey Institute of Neuroscience and Mental Health

description:
09.01.04 7(Cy5)vs14(Cy3).gpr
CD123+ blood plasmacytoid DCs

hyb_protocol: Standard Invitrogen hybridisation protocol

scan_protocol: Scanned using an Axon GenePix 4000B scanner and images were processed using GenePix 5.0 software with standard protocol and morphological opening background estimation

data_processing: A weighted normalization was applied using the robust splines technique (limma package)

source_name: mature model MDDCs

label_protocol: mRNA was amplified using the messageAMP kit (Ambion) before the SuperScript Indirect cDNA Labeling Core kit (Invitrogen LifeTechnologies) was used to reverse transcribe the amplified RNA in the presence of aminoallyl and aminohexyl modified dNTPs followed by incorporation of Cy3 or Cy5 (Amersham Biosciences) fluorochromes into the cDNA.

extract_protocol: Total RNA was extracted from frozen cell pellets using the RNAqueous-Midi kit (Ambion).

treatment_protocol:
Dendritic cells and monocytes from human blood and skin using magnetic bead and flow cytometry based cell sorting. Isolation of blood mononuclear cell populations and DC was described in (1). Isolation of skin dendritic cells was done as described in (2). Preparation of MDDCS was done as described in (3-5).
References
1. Cameron, P. U., Handley, A. J., Baylis, D. C., Solomon, A. E., Bernard, N., Purcell, D. F., and Lewin, S. R. (2007) Preferential infection of dendritic cells during human immunodeficiency virus type 1 infection of blood leukocytes, J Virol 81, 2297-2306.  2. McLellan, A. D., Heiser, A., Sorg, R. V., Fearnley, D. B., and Hart, D. N. (1998) Dermal dendritic cells associated with T lymphocytes in normal human skin display an activated phenotype, J Invest Dermatol 111, 841-849.  3. Harman, A. N., Wilkinson, J., Bye, C. R., Bosnjak, L., Stern, J. L., Nicholle, M., Lai, J., and Cunningham, A. L. (2006) HIV induces maturation of monocyte-derived dendritic cells and Langerhans cells, J Immunol 177, 7103-7113.  4. Harman, A. N., Kraus, M., Bye, C. R., Byth, K., Turville, S. G., Tang, O., Mercier, S. K., Nasr, N., Stern, J. L., Slobedman, B., Driessen, C., and Cunningham, A. L. (2009) HIV-1-infected dendritic cells show 2 phases of gene expression changes, with lysosomal enzyme activity decreased during the second phase, Blood 114, 85-94.  5. Harman, A. N., Lai, J., Turville, S., Samarajiwa, S., Gray, L., Marsden, V., Mercier, S., Jones, K., Nasr, N., Cumming, H., Donaghy, H., Mak, J., Churchill, M., Hertzog, P., and Cunningham, A. L. (2011) HIV infection of dendritic cells subverts the interferon induction pathway via IRF1 and inhibits type 1 interferon production, Blood.

value: mMDDC

value: pDC


title: IC Xenograft 645, biological rep 2

source_name: GBM Subcutaneous Xenograft, Grown Intracranially


title: pDC_sample_9

description:
07.01.04 7(Cy5)vs12(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: pDC_sample_10

description:
09.01.04 7(Cy5)vs13(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: RSG_1.5h_rep1

description: replicate 1


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep7

value: Peripheral blood leukocyte

tag: cattle breed

value: Holstein-Friesian

tag: Sex

value: Female

tag: infection status

value: Infected

tag: agent

value: Mycobacterium bovis


title: pDC_sample_8

description:
07.01.04 7(Cy5)vs11(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: Stem Cell Line ALPS 1514, biological rep 1

source_name: GBM Stem Cell Line

tag: batch

tag: date of array

tag: line number

value: Stem Cell Line

value: ALPS 1514


title: cpc try mutant, biological rep1 at Duke

description: d-CPCTRY_D1, Analysis conducted at Duke University

source_name: cpc try mutant


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep8


title: RSG_0.5h_rep6

description: replicate 6

tag: differentiation

value: PMA-differentiated THP-1 cells

tag: treatment

value: RSG (1microM)


title: pDC_sample_7

description:
07.01.04 7(Cy5)vs10(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: Cell Line MGRI-P, biological rep 1

tag: line type

value: MGRI-P


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep5


title: pDC_sample_6

description:
30.12.03 7(Cy5)vs8(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: RSG_0.5h_rep5

description: replicate 5

tag: time (hrs)


title: Xenograft 456, biological rep 1

tag: xenograft line


title: Xenograft 212, biological rep 1


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep6

tag: tissue


title: RSG_0.5h_rep4

description: replicate 4


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep3


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep2


title: RSG_0.5h_rep3

description: replicate 3


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep4


title: pDC_sample_5

description:
30.12.03 7(Cy5)vs5(Cy3).gpr
CD123+ blood plasmacytoid DCs

tag: cell type


title: RSG_0.5h_rep2

description: replicate 2


title: pDC_sample_4

description:
30.12.03 7(Cy5)vs4(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: pDC_sample_3

description:
23.12.03 7(Cy5)vs3(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: Peripheral blood leukocytes taken from Mycobacterium bovis infected cattle. Rep1


title: pDC_sample_2

description:
30.12.03 7(Cy5)vs2(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: pDC_sample_1

description:
30.01.04 7(Cy5)vs1(Cy3).gpr
CD123+ blood plasmacytoid DCs


title: MPpnrsv-MPpnrsv∆HR replicate 4

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

hyb_protocol: 150 pmol of labeled-aRNA were dried and resuspended in hybridization buffer containing 3×SSC, 0.1% SDS, 0.1% salmon sperm DNA and 50% formamide. Microarray hybridization was performed manually using Telechem Hybridization Chambers, following Corning instructions.

scan_protocol: Slides were scanned using a GenePix 4000B scanner and analysed using GenePix 6.0 software (Molecular Devices).

data_processing: Data were normalized by mean global intensity and Lowess correction. Spots with a net intensity in both channels lower than twice the median signal background were removed as low-signal spots, and were not considered for further analysis. Significance analysis of microarrays (SAM; 41 Tusher et al., 2001) was performed on the pre-processed and normalized data sets to identify differentially expressed genes.

source_name: 6h-culture of MPpnrsv-expressing yeast

label_protocol: RNA samples were amplified using Message Amp II amplification kit (Ambion). 7.5 μg of UTP-aminoallyl-amplified RNA (aRNA) were labelled using Cy3or Cy5 dye (GE Healthcare), purified using Megaclear columns (Ambion), and quantified using Nanodrop spectrophotometer.

growth_protocol: Yeast cell cultures were grown 24h in minimal medium with doxycycline (100 mg/ml). These cultures were then pelleted and diluted to an OD600 nm of 0.1 into fresh minimal medium without doxycycline. At 6 h total RNA was extracted from yeast cells transformed with pCM:MPpnrsv and pCM:MPpnrsvΔHR.

extract_protocol: RNA was extracted usingTrizol method.

tag: strain

value: BY4741 background

tag: genotype/variation

value: MPpnrsv-expressing

source_name: 6h-culture of MPpnrsvΔHR-expressing yeast

value: MPpnrsvΔHR-expressing


title: mDC_sample_10

description:
16.03.04 7(Cy5)vs15(Cy3).gpr
CD11c+ blood myeloid

value: mDC


title: MPpnrsv-MPpnrsv∆HR replicate 3


title: MPpnrsv-MPpnrsv∆HR replicate 2


title: IC Xenograft 645, biological rep 1

extract_protocol: Total RNA extracted using Qiagen midi (xenograft), or mini (cell lines) kits.  Xenograft tissue pulverized in liquid nitrogen and homogenized using a rotor-stator homogenizer

value: Subcutaneous Xenograft, Grown Intracranially


title: Xenograft 08-714, biological rep 1

value: Subcutaneous Xenograft


title: MPpnrsv-WT replicate 4

growth_protocol: Yeast cell cultures were grown 24h in minimal medium with doxycycline (100 mg/ml). These cultures were then pelleted and diluted to an OD600 nm of 0.1 into fresh minimal medium without doxycycline. At 6 h total RNA was extracted from yeast cells transformed with the empty pCM262 vector (pCM construct), pCM:MPpnrsv and pCM:MPpnrsvΔHR

source_name: 6h-culture of wild-type yeast

value: wild type


title: RSG_0.5h_rep1

description: replicate 1

tag: cell line


title: mDC_sample_9

description:
12.03.04 7(Cy5)vs16(Cy3).gpr
CD11c+ blood myeloid

value: mMDDC


title: Xenograft 08-308L, biological rep 1


title: DMSO_12h_rep6

description: replicate 6

value: DMSO


title: DMSO_12h_rep3

description: replicate 3


title: DMSO_12h_rep4

description: replicate 4


title: Cell Line MGRI-OTR, biological rep 1

value: Serum Cell Line

value: MGRI-OTR


title: Xenograft 270, biological rep 1


title: DMSO_12h_rep5

description: replicate 5


title: Stem Cell Line 08-499, biological rep 1


title: MPpnrsv-MPpnrsv∆HR replicate 1


title: Cell Line D54TR, biological rep 1


title: mDC_sample_8

description:
PC3 Array 19 (New Array) - 26.05.06.gpr
CD11c+ blood myeloid


title: MPpnrsv-WT replicate 3


title: MPpnrsv-WT replicate 1


title: MPpnrsv-WT replicate 2


title: mDC_sample_7

description:
Array PC4 Sample 1 - 29.06.06.gpr
CD11c+ blood myeloid


title: mDC_sample_6

description:
Array PC4 Sample 13 - 04.07.06.gpr
CD11c+ blood myeloid


title: mDC_sample_5

description:
Array PC4 Sample 12 - 04.07.06.gpr
CD11c+ blood myeloid


title: DMSO_12h_rep1

description: replicate 1


title: DMSO_12h_rep2

description: replicate 2


title: mDC_sample_3

description:
Array PC4 Sample 10 - 04.07.06.gpr
CD11c+ blood myeloid


title: DMSO_8h_rep5

description: replicate 5


title: Xenograft 930, biological rep 1


title: Xenograft 317, biological rep 1


title: THB_Glioma_s8

city: Umeå

first: Jonas

last: Nilsson

address: NUS

country: Sweden

institute: Radiation Sciences, Oncology

description:
raw data file: Raw_8.txt
THB_glioma_8

hyb_protocol: cRNA was hybridized using the Agilent Gene Expression Hybridization Kit (5188-5242) according to the manufacturer´s protocol.

scan_protocol: Slides scanned using an Agilent Microarray Scanner (G2565BA), and analysis was preformed using feature extraction software version 9.5 (Agilent Technologies) and the Agilent GE2-v5_95 protocol with defult settings.

data_processing:
Array normalization was performed with R-package Limma within the Bioconductor software.
Two chanel raw data has been converted to normalized one chanel data. To avoid duplication, raw data files are therefore provided as a tar archive on the Series record. Please see 'description' field for raw data file matching each Sample.

label_protocol: RNA samples were labeled using the Agilent Low RNA Input Linear Amp Kit Plus (5188-5340) according to manufacturer´s protocol.

extract_protocol: RNA was prepared using the miRVana RNA Purification kit (Ambion) or miRNeasy (Qiagen) following the manufacturer's recommendations. RNA was quantified and quality checked with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: sample type

value: brain tumor


title: DMSO_8h_rep3

description: replicate 3


title: Xenograft 08-308, biological rep 1


title: DMSO_8h_rep4

description: replicate 4


title: Stem Cell Line ALPS 1462, biological rep 2

value: Stem Cell Line

value: ALPS 1462


title: IC Xenograft 645, biological rep 3


title: DMSO_8h_rep6

description: replicate 6

value: PMA-differentiated THP-1 cells


title: THB_Glioma_s7

description:
raw data file: Raw_7.txt
THB_glioma_7


title: Cell Line 08-499, biological rep 1


title: mDC_sample_4

description:
Array PC4 Sample 11b - 04.07.06.gpr
CD11c+ blood myeloid


title: THB_Glioma_s5

description:
raw data file: Raw_5.txt
THB_glioma_5


title: mDC_sample_2

description:
Array PC4 Sample 9 - 04.07.06.gpr
CD11c+ blood myeloid


title: THB_Glioma_s6

description:
raw data file: Raw_6.txt
THB_glioma_6


title: DMSO_8h_rep2

description: replicate 2


title: DMSO_8h_rep1

description: replicate 1


title: Xenograft 245, biological rep 1


title: THB_Glioma_s4

description:
raw data file: Raw_4.txt
THB_glioma_4


title: Xenograft 263, biological rep 1


title: DMSO_3h_rep6

description: replicate 6


title: CD14_mono_sample_9

description:
PC3 Array 18 (New Array) - 06.06.06.gpr
CD14+ monocytes

value: CD14 mono


title: CD16_mono_sample_11

description:
Array PC4 Sample 3 - 29.06.06.gpr
CD16/M-DC8+ monocytes/DCs

value: CD16 mono


title: mDC_sample_1

description:
Array PC4 Sample 4b - 29.06.06.gpr
CD11c+ blood myeloid


title: CD16_mono_sample_10

description:
Array PC4 Sample 2 - 29.06.06.gpr
CD16/M-DC8+ monocytes/DCs


title: THB_Glioma_s3

description:
raw data file: Raw_3.txt
THB_glioma_3


title: CD14_mono_sample_8

description:
PC3 Array 13 (New Array) - 06.06.06.gpr
CD14+ monocytes


title: DMSO_3h_rep5

description: replicate 5


title: THB_Glioma_s2

description:
raw data file: Raw_2.txt
THB_glioma_2


title: Xenograft 08-537, biological rep 1


title: Cell Line D54OTR, biological rep 1


title: DMSO_3h_rep3

description: replicate 3


title: Cell Line UW15OTR, biological rep 1


title: CD16_mono_sample_9

description:
PC3 Array 12 (New Array) - 06.06.06.gpr
CD16/M-DC8+ monocytes/DCs


title: DMSO_3h_rep4

description: replicate 4


title: RSG_1.5h_rep2

description: replicate 2

value: RSG (1microM)


title: THB_Glioma_s1

description:
raw data file: Raw_1.txt
THB_glioma_1


title: THB_Control_s11

description:
co-hybridized vs. THB_non-relev_s3, a non-relevant test sample
raw data file: Raw_11.txt
THB_control_11

value: healty control


title: DMSO_3h_rep2

description: replicate 2


title: Stem Cell Line ALPS 1462, biological rep 1


title: THB_Control_s10

description:
co-hybridized vs. THB_non-relev_s2, a non-relevant test sample
raw data file: Raw_10.txt
THB_control_10


title: DMSO_3h_rep1

description: replicate 1


title: THB_Control_s12

description:
co-hybridized vs. THB_non-relev_s4, a non-relevant test sample
raw data file: Raw_12.txt
THB_control_12


title: Xenograft 2224, biological rep 2


title: Stem Cell Line ALPS 1459, biological rep 1

value: ALPS 1459


title: Xenograft 2224, biological rep 1


title: DMSO_1.5h_rep5

description: replicate 5


title: THB_Control_s9

description:
co-hybridized vs. THB_non-relev_s1, a non-relevant test sample
raw data file: Raw_9.txt
THB_control_9


title: THB_Control_s7

description:
raw data file: Raw_7.txt
THB_glioma_7


title: CD16_mono_sample_6

description:
PC3 Array 01 (New Array) - 26.05.06.gpr
CD16/M-DC8+ monocytes/DCs


title: CD16_mono_sample_7

description:
PC3 Array 17 (New Array) - 26.05.06.gpr
CD16/M-DC8+ monocytes/DCs


title: CD14_mono_sample_6

description:
PC3 Array 05 (New Array) - 01.06.06.gpr
CD14+ monocytes


title: CD14_mono_sample_7

description:
PC3 Array 07 (New Array) - 01.06.06.gpr
CD14+ monocytes


title: DMSO_1.5h_rep6

description: replicate 6


title: CD16_mono_sample_5

description:
PC3 Array 03 - 17.05.06 (2nd scan).gpr
CD16/M-DC8+ monocytes/DCs


title: Xenograft 54, biological rep 1


title: THB_Control_s4

description:
raw data file: Raw_4.txt
THB_glioma_4


title: Xenograft 08-308, biological rep 2


title: THB_Control_s5

description:
raw data file: Raw_5.txt
THB_glioma_5


title: Xenograft 693, biological rep 2


title: CD14_mono_sample_5

description:
PC3 Array 16 - 23.05.06.gpr
CD14+ monocytes


title: DMSO_1.5h_rep3

description: replicate 3


title: Xenograft 54, biological rep 2


title: CD16_mono_sample_4

description:
PC3 Array 02 - 17.05.06.gpr
CD16/M-DC8+ monocytes/DCs


title: DMSO_1.5h_rep2

description: replicate 2


title: CD16_mono_sample_8

description:
PC3 Array 08 (New Array) - 01.06.06.gpr
CD16/M-DC8+ monocytes/DCs


title: THB_Control_s3

description:
raw data file: Raw_3.txt
THB_glioma_3


title: THB_Control_s6

description:
raw data file: Raw_6.txt
THB_glioma_6


title: Xenograft 693, biological rep 1


title: CD16_mono_sample_3

description:
PC3 Array 15 - 23.05.06.gpr
CD16/M-DC8+ monocytes/DCs


title: DMSO_1.5h_rep4

description: replicate 4


title: CD14_mono_sample_4

description:
PC3 Array 14 - 23.05.06.gpr
CD14+ monocytes


title: Xenograft 43, biological rep 3


title: DMSO_0.5h_rep5

description: replicate 5


title: DMSO_1.5h_rep1

description: replicate 1


title: THB_Control_s2

description:
raw data file: Raw_2.txt
THB_glioma_2


title: Xenograft 08-499, biological rep 3


title: Xenograft 08-695, biological rep 3


title: DMSO_0.5h_rep3

description: replicate 3


title: DMSO_0.5h_rep4

description: replicate 4


title: CD14_mono_sample_3

description:
PC3 Array 11 - 16.05.06.gpr
CD14+ monocytes


title: DMSO_0.5h_rep6

description: replicate 6


title: CD14_mono_sample_2

description:
PC3 Array 10 - 23.05.06.gpr
CD14+ monocytes


title: THB_Control_s1

description:
raw data file: Raw_1.txt
THB_glioma_1


title: Xenograft 245PR, biological rep 3


title: Hut78-SATB1 cell replicate 3

city: Vancouver

first: Youwen

last: Zhou

address: 835 W 10th Ave

country: Canada

institute: University of British Columbia

description: Biological replicate 1 of Hut78 cells transduced with empty MIG vector

hyb_protocol: Hybridizations were performed on Whole Human Genome Oligo microarrays (G4112F, Agilent Technologies, Canada), comprising 41,059 60-nt oligonucleotide probes, most represented as single spots.

scan_protocol: Agilent microarray slides will be scanned using the Agilent DNA Microarray Scanner and quantified using Agilent’s Feature Extraction software.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) and GeneSpring GX software was used for background subtraction and LOWESS normalization.

source_name: Hut78-SATB1 clone 28

label_protocol: 500ng RNA were reverse-transcribed into cDNA and linearly amplified by in vitro transcription in the presence of fluorescent-labeled CTP using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color from Agilent following the manufacturer’s instructions. Each microarray was hybridized with 825ng of each amplified cDNA labelled with Cy5 or Cy3 at a specific activity between 8 and 15 pmol/µg.

growth_protocol: Hut78 cell line was cultured in RPMI 1640 medium with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 10-4 M beta-mercaptoethanol in 37℃ with 5% CO2.

extract_protocol: Total RNA were extracted and purified by Trizol reagent then cleaned us using Qiagen RNAeasy kit.

treatment_protocol: SATB1 gene was stably transduced into Hut78 cells with retrovirus mediated gene transduction using MSCV-IRES-GFP vector (MIG). Individual cell clones of stably transduced cells were isolated and analyzed by FACS sorting.

value: CD4+ T lymphocyte

tag: disease

value: Sezary syndrom

tag: transducer

source_name: Hut78-MIG control replicate 3

value: MIG vector


title: CD16_mono_sample_2

description:
PC3 Array 09 (Selmir Array) - 19.05.06.gpr
CD16/M-DC8+ monocytes/DCs


title: CD16_mono_Cultured_sample_1

description:
MDDC vs MDDC 05.09.05.gpr
Cultured CD16/M-DC8+ monocytes/DCs

value: CD16 mono Cultured


title: DMSO_0.5h_rep2

description: replicate 2


title: Xenograft 2224, biological rep 3

city: Durham

first: Jason

last: Reeves

address: 101 Science Dr

institute: Duke University

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

data_processing: data normalized using Bioconductor in R using either RMA or MAS5.0 normalization protocols (RMA provided, see website for MAS5).  Batch corrected expression values calculated by factor regression across Affymetrix doping and housekeeping controls

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2ug of Total RNA (ExpressionAnalysis Techinical Manual, 2005, Affymetrix).

value: Subcutaneous Xenograft


title: CD16_mono_sample_1

description:
PC3 Array 06 (Selmir Array) - 18.05.06.gpr
CD16/M-DC8+ monocytes/DCs

value: mMDDC


title: Hut78-SATB1 cell replicate 2

source_name: Hut78-SATB1 clone 11

source_name: Hut78-MIG control replicate 2


title: Fra2/tg_14 wk_lung_rep7

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

hyb_protocol: Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution labeled with the second dye. This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization, slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying, slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2.  Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500. Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10.

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA).  Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500. Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10.

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation.

source_name: fra-2 transgenic, 14 weeks

label_protocol: For labeling, 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according to the TIGR protocol (Hegde P, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562).

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA, individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: background

value: C57BL6 x CBA

tag: genotype

value: fra-2 (Fosl-2 gene) transgenic

tag: gender

value: male

tag: age

value: 14 weeks

value: lung

tag: mouse id

source_name: wild type pool, 14 weeks

value: wild type


title: DMSO_0.5h_rep1

description: replicate 1

tag: differentiation

value: PMA-differentiated THP-1 cells

tag: treatment

value: DMSO


title: Fra2/tg_14 wk_lung_rep5


title: Xenograft 693, biological rep 3

hyb_protocol: Following fragmentation, 10ug of biotinylated cRNA was hybridized for 16hr at 45C onto the Affymetrix Human Genome U133A Plus 2.0 Array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 according to standard protocols.

source_name: GBM Subcutaneous Xenograft

tag: batch

tag: date of array

tag: line number

tag: line type


title: Xenograft 43, biological rep 1

tag: xenograft line


title: Fra2/tg_14 wk_lung_rep6

tag: tissue


title: Xenograft 43, biological rep 2


title: Fra2/tg_14 wk_lung_rep8


title: Hut78-SATB1 cell replicate 1

source_name: Hut78-SATB1 clone 2

tag: cell line

tag: cell type

source_name: Hut78-MIG control replicate 1


title: CD14_mono_Cultured_sample_1

description:
MDLA8 D65 vsMDDC (no sat) 24-06-05.gpr
Cultured CD14+ monocytes

value: CD14 mono Cultured


title: mDC_Cultured_sample_1

description:
CD1C+ D4 vsMDDC 06-07-05.gpr
Cultured CD11c+ blood myeloid

value: mDC Cultured


title: CD14 expressing DDCs 4

description: sample 4

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R, batch effects removed in PARTEK Genomics Suite

source_name: CD14 expressing DDCs

label_protocol: RNA amplified and labeled with biotin using Illumina total prep RNA Amp kit (Ambion)

treatment_protocol: Dendritic cells and monocytes from human blood and skin using magnetic bead and flow cytometry based cell sorting. Isolation of blood mononuclear cell populations and DC was described in (1). Isolation of skin dendritic cells was done as described in (2). Preparation of MDDCS was done as described in (3-5).     References  1. Cameron, P. U., Handley, A. J., Baylis, D. C., Solomon, A. E., Bernard, N., Purcell, D. F., and Lewin, S. R. (2007) Preferential infection of dendritic cells during human immunodeficiency virus type 1 infection of blood leukocytes, J Virol 81, 2297-2306.  2. McLellan, A. D., Heiser, A., Sorg, R. V., Fearnley, D. B., and Hart, D. N. (1998) Dermal dendritic cells associated with T lymphocytes in normal human skin display an activated phenotype, J Invest Dermatol 111, 841-849.  3. Harman, A. N., Wilkinson, J., Bye, C. R., Bosnjak, L., Stern, J. L., Nicholle, M., Lai, J., and Cunningham, A. L. (2006) HIV induces maturation of monocyte-derived dendritic cells and Langerhans cells, J Immunol 177, 7103-7113.  4. Harman, A. N., Kraus, M., Bye, C. R., Byth, K., Turville, S. G., Tang, O., Mercier, S. K., Nasr, N., Stern, J. L., Slobedman, B., Driessen, C., and Cunningham, A. L. (2009) HIV-1-infected dendritic cells show 2 phases of gene expression changes, with lysosomal enzyme activity decreased during the second phase, Blood 114, 85-94.  5. Harman, A. N., Lai, J., Turville, S., Samarajiwa, S., Gray, L., Marsden, V., Mercier, S., Jones, K., Nasr, N., Cumming, H., Donaghy, H., Mak, J., Churchill, M., Hertzog, P., and Cunningham, A. L. (2011) HIV infection of dendritic cells subverts the interferon induction pathway via IRF1 and inhibits type 1 interferon production, Blood.

tag: source tissue

value: Skin

value: CD14 DDC


title: CD1a expressing epidermal LCs 2

description: sample 2

source_name: CD1a expressing epidermal LCs

value: CD1a LC


title: CD14_DDC_Cultured_sample_2

description:
CD1C+ D1 vsMDDC 06-07-05.gpr
Cultured CD14 expressing DDCs

source_name: mature model MDDCs

value: CD14 DDC Cultured


title: Xenograft 245PR, biological rep 1


title: Xenograft 245PR, biological rep 2


title: Fra2/tg_14 wk_lung_rep4


title: CD14 expressing DDCs 3

description: sample 3


title: CD1a expressing epidermal LCs 1

description: sample 1


title: CD14_mono_sample_1

description:
CD1C+ D3 vsMDDC 06-07-05.gpr
CD14+ monocytes

value: CD14 mono


title: pDC_Cultured_sample_1

description:
CD1C+ D2 vsMDDC 06-07-05.gpr
Cultured CD123+ blood plasmacytoid DCs

value: pDC Cultured


title: Fra2/tg_14 wk_lung_rep3


title: CD14 expressing DDCs 1

description: sample 1


title: Xenograft 08-499, biological rep 2

value: Subcutaneous Xenograft


title: CD14_DDC_Cultured_sample_1

description:
CD14+ D04 vsMDDC 28-06-05.gpr
Cultured CD14 expressing DDCs

value: mMDDC


title: CD14 expressing DDCs 2

description: sample 2


title: CD1a_LC_sample_4

description:
CD14+ D30 vsMDDC 28-06-05.gpr
CD1a expressing epidermal LCs


title: Xenograft 08-695, biological rep 1


title: Xenograft 08-695, biological rep 2


title: Fra2/tg_14 wk_lung_rep2

value: C57BL6 x CBA

value: fra-2 (Fosl-2 gene) transgenic


title: Xenograft 54, biological rep 3


title: CD1a_LC_sample_3

description:
CD123+ D04 vsMDDC 29-06-05.gpr
CD1a expressing epidermal LCs


title: Xenograft 08-499, biological rep 1


title: Fra2/tg_14 wk_lung_rep1

value: male

value: 14 weeks


title: CD1a_LC_sample_2

description:
CD14+ D65 vsMDDC 28-06-05.gpr
CD1a expressing epidermal LCs


title: CD1a_LC_sample_1

description:
CD123+ D09 vsMDDC 29-06-05.gpr
CD1a expressing epidermal LCs


title: CD1a expressing DDCs 2

description: sample 2

source_name: CD1a expressing DDCs

value: CD1a DDC


title: CD1a expressing DDCs 3

description: sample 3


title: CD1a expressing DDCs 1

description: sample 1


title: ET166 vs. WT Replicate 2

city: Boston

first: Mark

last: Umbarger

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

hyb_protocol: Purified labeled cDNA was mixed with 19 ng yeast tRNA and the volume was increased to 55 uL via addition of buffer EB.  This mixture was then combined with 55 uL of Agilent hybridization buffer, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Arrays were scanned with an Agilent Technologies Scanner GS2505C with the CGH_105_Dec08 protocol

data_processing: Statistical analyses were performed using R, a system for statistical computation and graphics (Ihaka, 1996)(http://www.r-project.org). Background correction with Normal + Exp Model and loess normalization were applied using the limma package from Bioconductor (Gentleman et al., 2004; Wettenhall and Smyth, 2004).

organism: Caulobacter vibrioides

source_name: ET166 swarmer cells

label_protocol: 15 µg of total RNA were primed with random hexamer primers (Invitrogen) at 65 C for 10 min.  RNA was then reverse transcribed at 42 C for 2 hrs in the presence of 400 units SuperScript II Reverse Transcriptase, dATP, dGTP, dTTP, and Cy 3/5 dCTP (GE-Health). Labeled cDNA was purified via QiaQuick column and was eluted in 50 uL.

growth_protocol: Cells were synchronized via the Percol method and were resuspended in M2G at a final OD600 of 0.4.  The resulting culture was allowed to grow for 15 min at 30 C and cells were subsequently pelleted via centrifugation.  The supernatant was removed via aspiration and cells were flash frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated using the Qiaquick system

tag: strain

organism: Caulobacter vibrioides CB15

source_name: WT swarmer cells


title: ET163 vs. WT Replicate 2

source_name: ET163 swarmer cells


title: CD14_DDC_sample_6

description:
CD123+ D30 vsMDDC 29-06-05.gpr
CD14 expressing DDCs


title: ET163 vs. WT Replicate 1


title: CD11c+ blood myeloid 2

description: sample 2

source_name: CD11c+ blood myeloid

value: Blood

value: CDC11c+ mDC


title: CD1a_DDC_sample_4

description:
CD123+ D65 vsMDDC 29-06-05.gpr
CD1a expressing DDCs


title: THB_Control_s8

description:
raw data file: Raw_8.txt
THB_glioma_8

tag: sample type

value: healty control


title: CLM_3h

city: Pohang

first: Taek-Kyun

last: Kim

state: Gyeongbuk

address: San 31, Hyoja-dong, Nam-gu

department: Interdisciplinary Bioscience and Bioengineering

country: South Korea

institute: POSTECH

description: Gene expression data from LNCaP human prostate tumor cells serum-startved for 3h followed by CLM medium

hyb_protocol: Microarray hybridization was performed by following general Affymetrix protocol at Dana-Farber Cancer Institute microarray core facility.

scan_protocol: Scanning of microarrays were performed by following general Affymetrix protocol at Dana-Farber Cancer Institute microarray core facility.

data_processing: Data normalization and summarization of expression values for each probe were calculated using gcRMA method. Quantile normalization of the data was performed with gcrma R/Bioconductor package v2.11.

source_name: LNCaP human prostate tumor cells

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

growth_protocol: LNCaP human prostate tumor cells were purchased from American Type Culture Collection (ATCC, Manassas, VA) and kept cultured in RPMI1640 media (Invitrogen, Carlsbad, CA) supplemented with 10% FBS and 1% Penicillin/Streptomycin at 37°C under 5% CO2.

extract_protocol: The RNAs were extracted using a Qiagen RNEasy tissue extraction kit (Qiagen Inc., Valencia, California).

treatment_protocol: LNCap human prostate tumor cells were serum-starved for 0h, 3h and 16h followed by CLM medium.

value: LNCaP

tag: treatment group

value: serum-starved for 3h followed by CLM medium


title: ET166 vs. WT Replicate 1


title: CLM_0h

description: Gene expression data from LNCaP human prostate tumor cells serum-startved for 0h followed by CLM medium

value: serum-starved for 0h followed by CLM medium


title: CD14_DDC_sample_5

description:
In vivo LC (3) vs MDDC (5).gpr
CD14 expressing DDCs

value: CD14 DDC


title: CD11c+ blood myeloid 1

description: sample 1


title: CLM_16h

description: Gene expression data from LNCaP human prostate tumor cells serum-startved for 16h followed by CLM medium

value: serum-starved for 16h followed by CLM medium


title: CD14_DDC_sample_4

description:
MDLA8 D09 vsMDDC 24-06-05.gpr
CD14 expressing DDCs


title: CD16/M-DC8+ monocytes/DCs 2

description: sample 2

source_name: CD16/M-DC8+ monocytes/DCs,

value: CD16 mono


title: CD11c+ blood myeloid 3

description: sample 3


title: CD16/M-DC8+ monocytes/DCs 3

description: sample 3


title: CD16/M-DC8+ monocytes/DCs 1

description: sample 1


title: CD14+ monocytes 2

description: sample 2

source_name: CD14+ monocytes

value: CD14 mono


title: C32 E318K 48h Induced

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v11.5.1 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: C32_E318K MITF_Induced for 48 hours

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

growth_protocol: Cells were cultured in 10% heat-inactivated fetal calf serum (Invitrogen, Melbourne, Australia) in RPMI-1640 medium supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 3 mM HEPES at 5% CO2, 99% humidity at 37C.

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Cells were treated with 1 ug/ml tetracycline for 48 hours, then harvested for RNA extraction.

tag: genotype/variation

value: tetracycline repressor lentiviral construct with E318K MITF under tet operator 2 lentiviral control

tag: mitf isoform

value: E318K Mutant

tag: expression

value: Induced 1 ug/ml Tetracycline 48 hours


title: C32 E318K Uninduced

scan_protocol: Labelled cRNA was hybridized to HumanHT-12 v4 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

source_name: C32_E318K MITF_Uninduced

value: Uninduced


title: C32 WT 48h Induced

source_name: C32_WT MITF_Induced for 48 hours

value: tetracycline repressor lentiviral construct with WT MITF under tet operator 2 lentiviral control

value: Wild-type


title: CD14_DDC_sample_3

description:
MDLA8 D30 vsMDDC 24-06-05.gpr
CD14 expressing DDCs

value: mMDDC


title: CD1a_DDC_sample_3

description:
Sample 1 23.11.06.gpr
CD1a expressing DDCs

value: CD1a DDC


title: MUTZ3 LCs

description: sample 1

source_name: MUTZ3 LCs

value: Blood

value: MUTZ3 LC


title: CD14_DDC_sample_2

description:
Sample 7 28.11.06.gpr
CD14 expressing DDCs


title: C32 WT Uninduced

source_name: C32_WT MITF_Uninduced


title: HT144 E318K 48h Induced

source_name: HT144_E318K MITF_Induced for 48 hours


title: CD14+ monocytes 1

description: sample 1


title: mature model MDDCs 3

description: sample 3


title: HT144 E318K Uninduced

source_name: HT144_E318K MITF_Uninduced


title: CD14_DDC_sample_1

description:
Sample 5 28.11.06.gpr
CD14 expressing DDCs


title: CD1a_DDC_sample_2

description:
Sample 3 23.11.06.gpr
CD1a expressing DDCs


title: HT144 WT 48h Induced

source_name: HT144_WT MITF_Induced for 48 hours


title: HT144 WT Uninduced

source_name: HT144 _WT MITF_Uninduced


title: CD1a_DDC_sample_1

description:
Sample 4 23.11.06.gpr
CD1a expressing DDCs

source_name: mature model MDDCs


title: mature model MDDCs 2

description: sample 2


title: mature model MDDCs 1

description: sample 1


title: MDDC_Reference_sample_1

description:
Sample 2 23.11.06.gpr
mature model MDDCs


title: immature model MDDCs 3

description: sample 3

source_name: immature model MDDCs

value: iMDDC


title: aCGH Tumor 1164

city: South San Francisco

first: Christiaan

middle: Nicolaas

last: Klijn

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

description: aCGH analysis of Trp53-/-;Cdh1-/- murine mammary tumor

hyb_protocol: Hybridizations were carried out for 18 hr at 428C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation.

scan_protocol: Arrays were scanned at 5-lm resolution using the GenePix4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA). Data were extracted from scanned images using NimbleScan 2.0 extraction software (NimbleGen Systems, Inc.), which allows for automated grid alignment, extraction, and generation of data files.

data_processing: Deletion and amplification breakpoints were determined by automated segmentation analysis of data sets as follows: each array data set was imported into R (www.r-project.org; Ihaka et al., 1996) for normalization. The normalize.qspline method from the affy Bioconductor package (www.bioconductor.org; Gentleman et al., 2004) was used to normalize the signal intensities of the test vs. reference.

source_name: DNA from Trp53-/-;Cdh1-/- murine mammary tumor

label_protocol: The labeling of genomic DNA samples for oligonucleotide microarray CGH analysis was performed using the method of Brennen et al., (2004) with modifications. Genomic DNA was randomly fragmented by sonication to a size range of 500–2,000 bp. For labeling, each DNA sample (1 lg) was denatured at 988C in the presence of 1 O.D. of 50-Cy3- or 50-Cy5-labeled random nonamer (TriLink Biotechnologies, SanDiego, CA) in 62.5 mM Tris-HCl, pH 7.5, 6.25 mM MgCl2, and 0.0875% b-mercaptoethanol. The denatured sample was chilled on ice, and then incubated with 100 units (exo-) Klenow fragment (NEB, Ipswich, MA) and dNTP mix (6 mM each in Tris, EDTA (TE), Invitrogen, Carlsbad, CA) for 2 hr at 378C. Reactions were terminated by addition of 0.5 M EDTA (pH 8.0); the end products were precipitated with isopropanol and resuspended in water. Fifty-fold amplification was typically achieved. The Cy-labeled test sample (Cy3) and reference sample (Cy5) were combined (15 lg each) and dried down by vacuum centrifugation. The reference sample was a pool of six male individuals (Promega, Madison, WI). The sample was rehydrated in 40 ll of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 958C for 5 min, and then cooled to 428C.

extract_protocol: Genomic DNA of tumor and spleen samples was extracted by the Qiagen Gentra Puregene Tissue kit according to the manufacturer’s specifications.

value: mixed background FVB/N and 129-OLA

tag: genotype

source_name: DNA from Trp53F/F;Cdh1F/F murine spleen


title: immature model MDDCs 2

description: sample 2


title: aCGH Tumor 1182


title: aCGH Tumor 555


title: aCGH Tumor 999


title: aCGH Tumor 1180


title: 03JOS029

city: Amsterdam

first: Rinske

last: Drost

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

description:
aCGH data of KP mouse mammary tumor
GFF file column header descriptions:
CHROMOSOME: The chromosome or parent sequence on which the probe is located. This column can be different from the chromosome indicated by SEQ_ID and/or PROBE_ID.
CHR_POSITION: The genomic position of the probe on the chromosome. This column can be different than the probe position indicated in the POSITION column.
RAW_DATAPOINTS: Total number of features in the window.
POSITION_COUNT: Total number of genomic positions in the window.
RATIO_CORRECTED: The normalized log2 ratio of the experimental and reference signals (EXP_NORM - REF_NORM). This signal will be normalized and spatially corrected if these options were used.
WINDOW_SIZE: The size of the averaging window in base pairs

hyb_protocol: Samples were hybridized and washed according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

scan_protocol: Arrays were scanned with the MS 200 Microarray Scanner and the MS 200 Data Collection Software according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

data_processing:
Background correction and normalization was performed in the NimbleScan program according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).
Probe annotation and corrected log2 ratios were imported into the R programming language from the NimbleScan output.

source_name: DNA derived from KP mouse mammary tumor

label_protocol: Tumor and spleen samples were labeled with Nimblegen dual-color DNA labeling kit according to manufacturer's protocol (http://www.nimblegen.com/products/lit/NG_CGHCNV_Guide_v8p0.pdf).

extract_protocol: Genomic DNA of tumor and spleen samples was extracted by proteinase K lysis and organic extraction with phenol-chloroform.

value: Mammary tumor

value: KP

source_name: DNA derived from KP mouse spleen

value: Spleen


title: NCI-H460-siRNA rep1

city: Delhi

first: Neeru

last: Saini

address: Mall Road

department: FGU

institute: IGIB

description: This  sample is hybridized to  4090082069_C array

hyb_protocol: Refer to the Illumina Gene Expression System Manual

data_processing: Average Normalization using Illumina Beadstudio

label: Streptavidin Cy3

source_name: NCI-H460 cell line

label_protocol: As described in the illumina Human-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

extract_protocol: The total RNA was extracted using TRIzol reagent (Invitrogen Corporation) according to the manufacturer's protocol.The RNA was resuspended in diethyl pyrocarbonate-treated water, quantified by UV absorbance at 260/280 nm and immediately used for RNA amplification and labeling by Illumina TotalPrep RNA amplification kit

value: Human lung cancer cell line NCI-H460

value: STAT6 knockdown


title: NCI-H460-siRNA rep2

description: This  sample is hybridized to 4090082069_D array

scan_protocol: Refer to the Illumina Gene Expression System Manual


title: NCI-H460-control rep1

description: This  sample is hybridized to  4090082069_E array

value: control


title: aCGH Tumor 1176


title: aCGH Tumor 1158


title: 01JOS169


title: aCGH Tumor 551


title: NCI-H460-control rep2

description: This  sample is hybridized to 4090082069_F array


title: GIST-T1 cells with siCONT

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: gene expression in GIST-T1 cells transfected with control siRNA

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

source_name: control siRNA

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: GIST-T1 cells were maintained in DMEM supplemented with 10% fatal bovine serum.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen).

treatment_protocol: GIST-T1 cells in 6-well plates were transfected with 100 pmol of Stealth siRNA (Invitrogen) or a Stealth RNAi Negative Control Medium GC (Invitrogen) using Lipofectamine2000 (Invitrogen).

value: gastrointestinal stromal tumor

tag: sirna

value: control siRNA


title: keratinocytes Gli1- CD34- rep2

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: primarily interfollicular epidermis and follicle infundibulum

hyb_protocol: according to manufacturer

scan_protocol: according to manufacturer

data_processing: The data were analyzed with GenomeStudio version 2010.3. The data are log2 transformed and no normalization is applied.

source_name: Dorsal skin

label_protocol: Nugen ovation-pico labeling

growth_protocol: Gli1-eGFP mice were housed and bred on an outcrossed Swiss Webster background in the animal facility at Memorial Sloan-Kettering Cancer Center (MSKCC) according to IACUC protocols.

extract_protocol: Trizol

treatment_protocol: Keratinocytes from dorsal trunk skin were isolated using published methods (Jensen et al., 2010, Nat Protoc 5, 898-911).

value: keratinocyte

value: Gli1- CD34-

tag: keratinocyte source

tag: stage of hair cycle

value: telogen


title: 01JOS165


title: 01JOS181


title: GIST-T1 cells with siHOTAIR

description: gene expression in GIST-T1 cells transfected with siRNA targeting HOTAIR

source_name: siRNA targeting HOTAIR

value: siRNA targeting HOTAIR


title: 04LIU028


title: aCGH Tumor 549


title: keratinocytes Gli1- CD34- rep3

value: primarily interfollicular epidermis and follicle infundibulum


title: 03JOS155


title: aCGH Tumor 1152


title: keratinocytes Gli1- CD34- rep1


title: immature model MDDCs 1

description: sample 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

value: Blood


title: aCGH Tumor 528


title: aCGH Tumor 232


title: keratinocytes Gli1- CD34+ rep3

description: hair follicle bulge without Hh responding cells

value: Gli1- CD34+


title: aCGH Tumor 546


title: 04LIU054


title: aCGH Tumor 223


title: keratinocytes Gli1- CD34+ rep2

value: hair follicle bulge without Hh responding cells


title: aCGH Tumor 230

value: mixed background FVB/N and 129-OLA


title: aCGH Tumor 342


title: 03JOS105

value: Mammary tumor


title: aCGH Tumor 587


title: 03JOS026

value: KP


title: Cerebellum 1 year after birth Nos2-/- 51

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

hyb_protocol: Purified dye-labelled sample and reference cDNA were combined for two-color hybridizations with 140 µl UltraHyb buffer (Ambion) pre-warmed to 70 °C and agitated for 30–60 min at 60°C. Subsequently, the sample hybridization mix was heated to 70 °C for 10 minutes and then applied to pre-heated (60°C) microarrays mounted in a GeneTAC Hybridization Station (Genomic Solutions, Ann Arbor). Hybridization conditions were set to 42 °C for 23 hours with gentle agitation. Thereafter, the arrays were automatically washed at 36°C with (i) 0.5× SSC, 0.1% (w/v) SDS for 5 min; (ii) 0.05× SSC, 0.1% (w/v) SDS for 3 min; and (iii) 0.05× SSC for 2 min. Flow time was set to 40 s. Immediately after the final washing step, the arrays were unmounted, immersed in 0.05× SSC, 0.1% (w/v) Tween 20 and dried by centrifugation.

scan_protocol: Microarray read out was accomplished in a two-color Agilent Scanner G25505B with 5 µm resolution and automatically adjusting PMT voltages according to manufacturer’s specification. Recorded images were analyzed using GenePix Pro 6.0 software (Axon).

data_processing: Processing of raw data included filter application based on i) mean-to-median ratio in both color channels (< 3.0), ii) minimal signal intensity in at least one color channel (> 250), iii) signal-to-background ratio in at least one color channel (> 1.5) and iv) manual user flag for each feature. Subsequently, variance stabilization normalization (vsn) was applied and the gene-wise average signal values of color switch experiments were calculated. Annotation of oligonucleotide probes present on the gene expression array was retrieved by alignment to EnsEMBL database version 54.

source_name: Cerebellum sample, Nos2-/-

label_protocol: For reverse transcription:  RNA/primer-mix: 2 µg total RNA, 500 ng (dT)-T7 primer, total volume 6 µl  * denature RNA/primer 4' at 70°C, chill on ice;  RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl  * add ice cold RT-mix, mix well  * incubate 1h at 50°C with heated lid, inactivate 15' at 65°C, chill on ice;  For second strand synthesis:  SSS-mix: 15 µl 5x 2nd strand buffer (Invitrogen), 1.5 µl 10 mM dNTP-mix, 2.22 µl DNA Pol. I (9 U/µl) (Promega), 0.1 µl RNase H (10 U/µl) (Epicentre), 0.5 µl DNA Ligase (10 U/µl) (USB), 45.68 µl RNase-free water, total volume 65 µl  * add ice cold SSS-mix to RT reaction, mix well  * incubate 2h at 14-16°C in thermal cycler  * add 3.33 µl T4 DNA-Pol. (3 U/µl) (NEB) , mix by flicking  * incubate 15' at 14-16°C in thermal cycler, heat inactivate 10' at 70°C  * add 75 µl phenol/chlorof./isoamylalc. (pH 8), mix vigorously by pipetting  * transfer to prespun (30'' at 16000xg) PLG Heavy 0.5 ml (Eppendorf)  * spin 5' at 16000xg  * transfer aq. phase to prepared (resuspend, drain by gravity, 2' at 1000g) P-6 MicroSpin column (BioRad)  * spin 4' at 1000xg, recover eluate  * transfer eluate to 0.5 ml PCR tube  * add LPA, 3.5 µl 5 M NaCl, 220 µl 100% Ethanol, mix well  * precipitate 60' at -80°C over night  * spin tube 30' at 16000xg, 4°C, remove supernatant  * wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000xg, remove supernatant  * resuspend dried cDNA-pellet in 10 µl water  For In Vitro transcription:  IVT-mix (Promega): 6 µl RNase free water, 8 µl 5x T7 Transcr. buffer, 3 µl each 100 mM ATP, GTP, CTP, UTP, 4 µl T7 Enzyme-mix, total volume 30 µl  * add IVT-mix to 10 µl cDNA, mix by pipetting  * incubate 12h at 37°C  For aRNA cleanup:  RLT / β-ME – mix: 3.5 µl β-mercapto-ethanol, 76.5 µl water, 350 µl RLT (Qiagen RNeasy), total volume 430 µl  * add RLT / β-ME-mix to IVT product (aRNA), mix well  * add 250 µl 100% ethanol, apply to RNeasy Mini column (Qiagen)  * spin 15 at 8000xg, discard flow-through, transfer column to new 2 ml tube  * wash with 500 µl RPE, spin 15 at 8000xg, discard flow-through  * add 30 µl RNase-free water onto membrane, spin 1' at 8000xg,repeat eluting step,  * precipitate aRNA with 1 µl LPA, 30 µl 7.5M ammonium-acetate and 227.5 µl 100% ethanol  * wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000xg, remove supernatant  * resuspend in RNase-free water ( 200 µg/µl)  For 2nd Round RT:  RNA/primer-mix: 5 µl aRNA (1 µg), 1 µg N6-random-primer, total volume 6 µl  * RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl  * denature RNA/primer-mix 5' at 70°C, snap cool on ice 2', hold 5' at room temperature, mix well  * incubate:  20' at 37°C  20' at 42°C  10' at 50°C  10' at 55°C  15' at 65°C  hold at 37°C  * add 1 µl RNase H-dilution (1:10 in 5x 2nd strand buffer, (Invitrogen))  * incubate 30' at 37°C, 2' at 95°C  For Klenow-labeling (per channel):  Klenow-mix (Invitrogen): 40 µl 2.5X Random Primer Solution, 10 µl 10X dNTP-(low dTTP)-mix*, 3 µl Cy-labeled dUTP (Cy3 or Cy5), 34 µl water, 2 µl Klenow fragment Exo- (40 U/µl), total volume 89 µl  * add to cDNA (11 µl), mix gently but thoroughly  * incubate 16h at 37°C  * add 450 µl TE to labeled cDNA, apply to Microcon YM-30 column (Millipore)  * spin 13’ at 16000xg, discard flow-through  * wash with 430 µl TE (measure dye incorporation on NanoDrop), add 18.75 µl blocking-mix (12.5 µl Cot-1 DNA (1 µg/µl), 2.5 µl poly-A RNA (5 µg/µl), 3.75 µl tRNA (10 µg/µl))  * spin 13’ at 16000xg, discard flow-through  * elute labeled cDNA by inverting column into new tube, spin 8’ at 16000xg  * 2 mM dATP, 2mM dCTP, 2mM dGTP, 0.5 mM dTTP

growth_protocol: Conservation breeding of the Nos2 knock-out mouse strains B6;129P2-Nos2tm1Lau/J and Ptch1 knockt-out mouse B6;129P2-Ptch1tm1Mps/J was conducted on wooden litter at 22±2 °C and 55±5 % relative humidity. Illumination was set to 320 Lux with a 12 hour day-night rhythm. Grain pellets (15 mm) and ozonized pH-adjusted (pH2.6-3.0) drinking water were available ad libitum. Accordingly, crossbreeding was performed under theses standard conditions.

extract_protocol: Total RNA of tissue samples was isolated by CsCl density gradient centrifugation

value: Cerebellum

tag: genetic background

value: C57BL/6 129P2 mixed

tag: age

value: 1 year of age

source_name: Universal Mouse Reference RNA (Stratagene)


title: keratinocytes Gli1- CD34+ rep1


title: Cerebellum 1 year after birth Nos2-/- 49

value: Universal Mouse Reference RNA (Stratagene)


title: keratinocytes Gli1+ rep3

description: Hh responding cells

value: Hh responding cells


title: keratinocytes Gli1+ rep2

description: Hh responding cells


title: aCGH Tumor 180


title: 02JOS023

value: Spleen


title: aCGH Tumor 178


title: aCGH Tumor 1634


title: Cerebellum 1 year after birth Nos2-/- 44


title: 03JOS014


title: 05LIU051


title: Cerebellum 6 weeks after birth Nos2-/- 7

value: 6 weeks after birth


title: aCGH Tumor 1178