title: Tunicamycin wt 2

value: wild type

value: Pooled BYxRM wt segregant grown on YPD+Tunicamycin biological replicate2


title: Neomycin wt 1

status: Public on Dec 01 2011

type: genomic

city: Princeton

first: Noorossadat

last: Torabi

state: NJ

address: 110 Carl Icahn Lab

department: Molecular Biology

country: USA

institute: Princeton University

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: BYxRM diploid hybrid

label_protocol: DNA was labeled using the BioPrime Array CGH Genomic Labeling Module (Invitrogen; 18095-012) with the sample being labeled with Cy3 dUTP and the reference being labeled with Cy5 dUTP. We used a BY/RM diploid as the reference for all hybridizations.

growth_protocol: Pooled Mata segregants from either wt or sup35 BYxRM cross were plated on YPD alone(control) or YPD+drug (selection) plates and were incubated at 30C for two days.

extract_protocol: DNA was extracted from the grown cells using Genomic-tip 100/G columns (Qiagen; 10243)

tag: genetic background

value: BYxRM diploid hybrid

tag: selection

tag: genotype

source_name: BYxRM wt selected segregant on Neomycin

tag: sample type

value: Pooled BYxRM wt segregant grown on YPD+Neomycin biological replicate1

value: BYxRM

value: BYxRM wt segregant


title: C_24h_4

type: RNA

city: Leipzig

first: Wibke

last: Busch

address: Permoser Str. 15

department: Bioanalytical Ecotoxicology

country: Germany

institute: UFZ Helmholtz Centre for Environmental Research

description: Gene expression of control embryos after 50 hpf - treated parallel to the 24 h exposed embryos

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit following manufacturer's instructions.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.1.1).

data_processing: Feature extraction files (processed signals) were used for statistics, quantile normalisation of all processed signals before significance testing.

molecule: total RNA

organism: Danio rerio

label_protocol: Synthesis of cDNA, cRNA and cRNA-labeling was performed with the Agilent Low RNA Input Linear Amplification Kit according to the manufacturer’s instructions. cRNA was labelled with Cy3.

growth_protocol: Zebrafish embryos were collected directly after fertilisation and treated starting 2 hpf in exposure medium.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: 50 embryos per treatment, treatments: control, 5,83 µM azinphos-methyl (APM), 509 µM 1,4-dimethoxybenzene (DMB), 14,2 µM 2,4-dinitrophenol (DNP), 24 h and 48 h (26-50 and 2-50 hpf), respectively; all in 4 independent replicates

tag: developmental stage

value: embryo

tag: exposure time

tag: treatment

value: control


title: DMB_24h_1

description: Gene expression of embryos treated with DMB for 24 h (26-50 hpf)

value: DMB 509 µM


title: 3MeK27.T [Agilent-027811]

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

description: 3MeK27H3 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)

organism: Homo sapiens

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

tag: fraction

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: C_24h_1

source_name: control embryos after 50 hpf - treated parallel to the 24 h exposed embryos


title: C_24h_3


title: 3MeK4.T [Agilent-027811]

description: 3MeK4H3 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: Neomycin sup35 2

source_name: BYxRM sup35 selected segregant on Neomycin

value: Pooled BYxRM sup35 segregant grown on YPD+Neomycin biological replicate2

value: BYxRM sup35 segregant


title: 3MeK4.U [Agilent-027811]

description: 3MeK4H3 ChIP for untreated SW480 cells

source_name: SW480 cells


title: H2O2 wt MRE11

source_name: BYxRM(MRE11BY) wt selected segregant on H2O2

value: BYxRM(MRE11BY) wt seleceted segregant on YPD+H2O2

value: BYxRM(MRE11BY) wt seleceted segregant


title: H2O2 wt SKY1

source_name: BYxRM(SKY1BY) wt selected segregant on H2O2

value: BYxRM(SKY1BY) wt seleceted segregant on YPD+H2O2

value: BYxRM(SKY1BY) wt seleceted segregant


title: 3MeK27.U [Agilent-027811]

description: 3MeK27H3 ChIP for untreated SW480 cells


title: H3.U [Agilent-027811]

description: H3 ChIP for untreated SW480 cells


title: H2O2 wt 1

value: wild type

source_name: BYxRM wt selected segregant on H2O2

value: Pooled BYxRM wt segregant grown on YPD+H2O2 biological replicate1


title: H2O2 wt 2

value: BYxRM diploid hybrid

value: Pooled BYxRM wt segregant grown on YPD+H2O2 biological replicate2


title: H3.T [Agilent-027811]

description: H3 ChIP for SW480 cells treated with 2mM H2O2 for 30min at 37°C


title: Neomycin sup35 1

value: Pooled BYxRM sup35 segregant grown on YPD+Neomycin biological replicate1

value: BYxRM


title: AcK16.U [Agilent-027811]

description: AcK16H4 ChIP for untreated SW480 cells


title: H2O2 sup35 SKY1

source_name: BYxRM(SKY1BY) sup35 selected segregant on H2O2

value: Pooled BYxRM(SKY1BY) sup35 segregant grown on YPD+H2O2

value: BYxRM(SKY1BY) sup35 segregant


title: Ethanol wt 2

source_name: BYxRM wt selected segregant on Ethanol

value: Pooled BYxRM wt segregant grown on YPD+Ethanol biological replicate2

value: BYxRM wt segregant


title: H2O2 sup35 2

source_name: BYxRM sup35 selected segregant on H2O2

value: Pooled BYxRM sup35 segregant grown on YPD+H2O2 biological replicate2


title: Ethanol sup35 1

source_name: BYxRM sup35 selected segregant on Ethanol

value: Pooled BYxRM sup35 segregant grown on YPD+Ethanol biological replicate1


title: Diamide wt SKY1

source_name: BYxRM(SKY1BY) wt selected segregant on Diamide

value: BYxRM(SKY1BY) wt seleceted segregant on YPD+Diamide


title: E6berbamine sup35 2

source_name: BYxRM wt selected segregant on E6berbamine

value: Pooled BYxRM wt segregant grown on YPD+E6berbamine biological replicate1


title: H2O2 sup35 1

value: Pooled BYxRM sup35 segregant grown on YPD+H2O2 biological replicate1

value: BYxRM sup35 segregant


title: H2O2 sup35 MRE11

source_name: BYxRM(MRE11BY) sup35 selected segregant on H2O2

value: Pooled BYxRM(MRE11BY) sup35 segregant grown on YPD+ H2O2

value: BYxRM(MRE11BY) sup35 segregant


title: E6berbamine sup35 1

value: wild type

source_name: BYxRM sup35 selected segregant on E6berbamine

value: Pooled BYxRM sup35 segregant grown on YPD+E6berbaminel biological replicate2


title: Ethanol sup35 2

source_name: BYxRM diploid hybrid

value: BYxRM diploid hybrid

value: Pooled BYxRM sup35 segregant grown on YPD+Ethanol biological replicate2


title: Ethanol wt 1

value: Pooled BYxRM wt segregant grown on YPD+Ethanol biological replicate1

value: BYxRM


title: E6berbamine wt 1

value: Pooled BYxRM wt segregant grown on YPD+E6berbamine biological replicate2


title: Diamide wt 1

source_name: BYxRM wt selected segregant on Diamide

value: Pooled BYxRM wt segregant grown on YPD+Diamide biological replicate1


title: E6berbaimine wt 2

value: Pooled BYxRM sup35 segregant grown on YPD+E6berbamine biological replicate1


title: Diamide sup35 1

source_name: BYxRM sup35 selected segregant on Diamide

value: Pooled BYxRM sup35 segregant grown on YPD+Diamide biological replicate1


title: Diamide wt MRE11

source_name: BYxRM(MRE11BY) wt selected segregant on Diamide

value: BYxRM(MRE11BY) wt seleceted segregant on YPD+Diamide

value: BYxRM(MRE11BY) wt seleceted segregant


title: Diamide sup35 SKY1

source_name: BYxRM(SKY1BY) sup35 selected segregant on Diamide

value: Pooled BYxRM(SKY1BY) sup35 segregant grown on YPD+Diamide

value: BYxRM(SKY1BY) sup35 segregant


title: Diamide sup35 MRE11

source_name: BYxRM(MRE11BY) sup35 selected segregant on Diamide

value: Pooled BYxRM(MRE11BY) sup35 segregant grown on YPD+Diamide


title: CoCl2 wt 2

source_name: BYxRM wt selected segregant on CoCl2

value: Pooled BYxRM wt segregant grown on YPD+CoCl2 biological replicate2

value: BYxRM wt segregant


title: Diamide sup35 2

value: wild type

value: Pooled BYxRM sup35 segregant grown on YPD+Diamide biological replicate2

value: BYxRM sup35 segregant


title: CoCl2 sup35 1

value: BYxRM diploid hybrid

source_name: BYxRM sup35 selected segregant on CoCl2

value: Pooled BYxRM sup35 segregant grown on YPD+CoCl2 biological replicate1


title: Cycloheximide sup35 1

source_name: BYxRM sup35 selected segregant on Cycloheximide

value: Pooled BYxRM sup35 segregant grown on YPD+Cycloheximide biological replicate1

value: BYxRM


title: Clorpromazine wt 2

source_name: BYxRM wt selected segregant on Chlorpromazine

value: Pooled BYxRM wt segregant grown on YPD+Chlorpromazine biological replicate2


title: Clorpromazine wt 1

value: Pooled BYxRM wt segregant grown on YPD+Chlorpromazine biological replicate1


title: Cycloheximide wt 1

source_name: BYxRM wt selected segregant on Cycloheximide

value: Pooled BYxRM wt segregant grown on YPD+Cycloheximide biological replicate1


title: Cycloheximide wt 2

value: Pooled BYxRM wt segregant grown on YPD+Cycloheximide biological replicate2


title: Clorpromazine sup35 1

source_name: BYxRM sup35 selected segregant on Chlorpromazine

value: Pooled BYxRM sup35 segregant grown on YPD+Chlorpromazine biological replicate1


title: CoCl2 sup35 2

value: Pooled BYxRM sup35 segregant grown on YPD+CoCl2 biological replicate2


title: CoCl2 wt 1

value: Pooled BYxRM wt segregant grown on YPD+CoCl2 biological replicate1


title: Clorpromazine sup35 2

value: Pooled BYxRM sup35 segregant grown on YPD+Chlorpromazine biological replicate2


title: Cycloheximide sup35 2

value: Pooled BYxRM sup35 segregant grown on YPD+Cycloheximide biological replicate2


title: mouse_CD4+CD8+CD69-_thymocytes_purified_mutA238L

city: Oeiras

first: Sílvia

middle: Cristina Paiva

last: Almeida

address: Rua da Quinta Grande, n 6

department: Infection and Immunity

country: Portugal

institute: Instituto Gulbenkian de Ciência

description: Gene expression data from a CD4+CD8+CD69- thymocyte population from male mice that were 14-16 weeks old

hyb_protocol: 10 µg of fragmented cRNA was used in a 200-µl hybridization containing added hybridization controls. 130 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (Midi_euk2v3_450) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with Affymetrix GCOS 1.4 software to obtain Absent/Present calls and for subsequent analysis with DNA-Chip Analyzer (dChip) Version Release 2006 (http://www.dchip.org, Wong Lab, Harvard). The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model (Li and Hung Wong, 2001). Only genes called Present in at least one of the three arrays were kept for downstream analysis (14963 genes). All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 3.

label: biotin

organism: Mus musculus

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Mouse Genome 430A 2.0 Arrays, according to the manufacturer’s One-Cycle Target Labeling Assay. Briefly, 2.8 µg of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (One-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Animals were kept at the Instituto Gulbenkian de Ciência and animals of the same age and gender were used, that is, male mice between 14-16 weeks of age.

extract_protocol: Total RNA was extracted with QIAGEN Rneasy columns. Concentration and purity was determined by spectrophotometry and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Thymocyte cell suspensions were labelled with antibodies directly coupled to the fluorochrome and directed against the following mouse proteins, namely CD4-PE, CD8-APC and CD69-FITC.  The cells were purified in a FACSAria cytometer, selecting the population that was CD4+CD8+CD69-, that is the thymocytes that expressed CD4 and CD8 but that lacked CD69 expression.

tag: gender

value: male

tag: age

tag: organ

value: thymus

tag: cell population


title: prostate_DLP_low_fat_rep3

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 Dorsal Lateral Prostate of mouse fed with a low fat and no cholesterol diet

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.

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: In total, 18 SCID male mice were used in the study, one group of mice was fed a high fat and high cholesterol (HFHC) diet, and another group of 9 mice were fed a low fat and no cholesterol diet (LFNC).

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

treatment_protocol: After 6 weeks, the prostates of the mice were separately extracted as Ventral Prostate(VP), Dorsal Lateral Prostate (DLP), and Anterior Prostate (AP).

tag: strain

value: SCID

tag: tissue

value: prostate

tag: prostate region

value: DLP

tag: diet

value: low fat and no cholesterol


title: mouse_CD4+CD8+CD69-_thymocytes_purified_A238L


title: prostate_AP_low_fat_rep3

description: Gene expression data from Anterior Prostate of mouse fed with a low fat and no cholesterol diet

value: AP


title: prostate_VP_low_fat_rep2

description: Gene expression data from Ventral Prostate of mouse fed with a low fat and no cholesterol diet

value: VP


title: prostate_VP_low_fat_rep3

source_name: Ventral Prostate of mouse fed with a low fat and no cholesterol diet


title: prostate_AP_low_fat_rep2

source_name: Anterior Prostate of mouse fed with a low fat and no cholesterol diet


title: prostate_VP_low_fat_rep1


title: prostate_AP_high_fat_rep3

description: Gene expression data from Anterior Prostate of mouse fed with a high fat and high cholesterol diet

value: high fat and high cholesterol


title: prostate_DLP_low_fat_rep2

source_name: Dorsal Lateral Prostate of mouse fed with a low fat and no cholesterol diet


title: mouse_thymocytes_purified_Wt


title: prostate_DLP_low_fat_rep1


title: prostate_AP_low_fat_rep1


title: prostate_VP_high_fat_rep3

description: Gene expression data from Ventral Prostate of mouse fed with a high fat and high cholesterol diet


title: prostate_DLP_high_fat_rep3

description: Gene expression data from Dorsal Lateral Prostate of mouse fed with a high fat and high cholesterol diet


title: Diamide wt 2

tag: genetic background

value: BYxRM diploid hybrid

tag: selection

value: wild type

value: Pooled BYxRM wt segregant grown on YPD+Diamide biological replicate2

value: BYxRM

value: BYxRM wt segregant


title: prostate_DLP_high_fat_rep2

source_name: Dorsal Lateral Prostate of mouse fed with a high fat and high cholesterol diet


title: prostate_VP_high_fat_rep2

source_name: Ventral Prostate of mouse fed with a high fat and high cholesterol diet


title: prostate_DLP_high_fat_rep1


title: prostate_VP_high_fat_rep1


title: prostate_AP_high_fat_rep1

source_name: Anterior Prostate of mouse fed with a high fat and high cholesterol diet


title: prostate_AP_high_fat_rep2


title: DNMT1.T [Agilent-014707]

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

source_name: SW480 cells, 2mM H2O2, 30min

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

value: Chromatin immunoprecipitated genomic DNA (ChIP)

value: Whole cell extract genomic DNA (WCE)


title: Ash2l KD, replicate B

city: Worcester

first: Thomas

middle: G.

last: Fazzio

state: MA

address: LRB 519, 364 Plantation Street

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

description: gene expression in indicated KD

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent scanner immediately after washing.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1 (Agilent) using default parameters. We used quantile normalization.

source_name: embryonic stem cells, KD replicate B

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Feeder-free growth on gelatin coated dishes in standatd ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol.

extract_protocol: Trizol, followed by Invitrogen RNA micro columns.

treatment_protocol: In one well of a 24-well dish, 7X10^4 cells were transfected with 100 ng esiRNA using Lipofectamine 2000. After 12-15 hours, the media was replaced and cells were cultured until 48 hours post-transfection.

tag: cell type

value: embryonic stem cell

tag: genotype/variation


title: Suz12Ash2l KD, replicate A

description: gene expression in indicated KD

source_name: embryonic stem cells, KD replicate A

tag: developmental stage


title: Ash2l KD, replicate A

description: gene expression in indicated KD


title: Suz12 KD, replicate B

description: gene expression in indicated KD


title: EZH2.U [Agilent-014707]

description: EZH2 ChIP for untreated SW480 cells

source_name: SW480 cells

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


title: DNMT3B.T [Agilent-014707]

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

value: DNMT3B:Custom-made Antibody


title: gamma.H2AX.T [Agilent-014707]

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


title: DNMT3B.U [Agilent-014707]

description: DNMT3B ChIP for untreated SW480 cells


title: Suz12Ash2l KD, replicate B

description: gene expression in indicated KD


title: SIRT1.T [Agilent-014707]

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


title: Renal Clear Cell Carcinoma_TB4366

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

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: Mbd3Ash2l KD, replicate B

description: gene expression in indicated KD


title: Suz12 KD, replicate A

description: gene expression in indicated KD


title: Mbd3Suz12 KD, replicate A

description: gene expression in indicated KD


title: gamma.H2AX.U [Agilent-014707]

description: gamma-HA2X ChIP for untreated SW480 cells

tag: cell line


title: Mbd3 KD, replicate B

description: gene expression in indicated KD


title: SIRT1.U [Agilent-014707]

description: SIRT1 ChIP for untreated SW480 cells

tag: antibody


title: Brg1Ash2l KD, replicate A

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4360


title: Brg1 KD, replicate B

description: gene expression in indicated KD


title: Brg1 KD, replicate A

description: gene expression in indicated KD


title: Brg1Suz12 KD, replicate B

description: gene expression in indicated KD


title: Brg1Ash2l KD, replicate B

description: gene expression in indicated KD


title: Mbd3Suz12 KD, replicate B

description: gene expression in indicated KD


title: Brg1Suz12 KD, replicate A

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4347


title: EZH2.T [Agilent-014707]

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

tag: fraction


title: Brg1Mbd3 KD, replicate B

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_32742


title: Renal Clear Cell Carcinoma_TB4405


title: DNMT1.U [Agilent-014707]

description: DNMT1 ChIP for untreated SW480 cells


title: Tip60Brg1 KD, replicate A

description: gene expression in indicated KD


title: Brg1Mbd3 KD, replicate A

description: gene expression in indicated KD


title: Tip60Brg1 KD, replicate B

description: gene expression in indicated KD


title: Mbd3Ash2l KD, replicate A

description: gene expression in indicated KD


title: Tip60Ash2l KD, replicate A

description: gene expression in indicated KD


title: Tip60Suz12 KD, replicate A

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4362


title: Renal Clear Cell Carcinoma_TB4370


title: Renal Clear Cell Carcinoma_Z3094


title: p400Brg1 KD, replicate A

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4354


title: p400Brg1 KD, replicate B

description: gene expression in indicated KD


title: Tip60Mbd3 KD, replicate B

description: gene expression in indicated KD


title: Tip60Suz12 KD, replicate B

description: gene expression in indicated KD


title: p400Tip60 KD, replicate A

description: gene expression in indicated KD


title: Tip60 KD, replicate B

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4409


title: Tip60Ash2l KD, replicate B

description: gene expression in indicated KD


title: Tip60 KD, replicate A

description: gene expression in indicated KD


title: Tip60Mbd3 KD, replicate A

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4375


title: Renal Clear Cell Carcinoma_TB4349


title: p400 KD, replicate B

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_TB4346


title: Renal Clear Cell Carcinoma_TB4372


title: p400Tip60 KD, replicate B

description: gene expression in indicated KD


title: Renal Clear Cell Carcinoma_45619


title: p400 KD, replicate A

description: gene expression in indicated KD


title: p400Ash2l KD, replicate A

description: gene expression in indicated KD


title: Mbd3 KD, replicate A

description: gene expression in indicated KD


title: p400Suz12 KD, replicate B

description: gene expression in indicated KD


title: p400Mbd3 KD, replicate A

description: gene expression in indicated KD


title: EGFP KD, replicate B

description: gene expression in indicated KD

value: EGFP


title: Rabies, Fix, Spinalcord, 7dpi(mock), 06

city: Shinjuku-ku

first: Naoko

last: Sugiura

state: Tokyo

address: Toyama 1-23-1

country: Japan

institute: National Institute of Infectious Diseases

description: Gene expression in mock Spinalcord at 7dpi

hyb_protocol: After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60°C for 30 min.  These samples were hybridized onto the Whole Mouse Genome Microarray 44k probes × 4 arrays/ slide (Agilent) at 65°C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM).  Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing:
The image files were analyzed by using of Feature Extraction software (Agilent) and automatically exported with flag information.
The text file exported by Feature Extraction data was imported to GeneSpring. The raw data were normalized with per chip normalization (75th percentile) and per gene normalization (baseline to mean of mock samples).

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 06

label_protocol: Three hundred nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 300 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter.  cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.

extract_protocol: Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.

treatment_protocol: Mouse spinal cords were treated with RNAlater (ABI) were stored at -80°C until use.

tag: Sex

value: female

value: 6 weeks old

tag: treatment group

value: mock


title: Rabies, Fix, Spinalcord, 7dpi(mock), 03

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 03

tag: age


title: Rabies, Fix, Spinalcord, 7dpi(inf), 06

description: Gene expression in infection Spinalcord at 7dpi

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 06

value: infection


title: p400Mbd3 KD, replicate B

description: gene expression in indicated KD


title: p400Ash2l KD, replicate B

description: gene expression in indicated KD


title: Rabies, Fix, Spinalcord, 7dpi(mock), 02

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 02


title: EGFP KD, replicate A

description: gene expression in indicated KD


title: Rabies, Fix, Spinalcord, 7dpi(mock), 04

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 04


title: Rabies, Fix, Spinalcord, 7dpi(mock), 05

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 05


title: Rabies, Fix, Spinalcord, 7dpi(inf), 03

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 03


title: Rabies, Fix, Spinalcord, 7dpi(inf), 05

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 05


title: SA_51

city: Stockholm

first: Christina

last: Orsmark Pietras

address: Hälsovägen 7-9

country: Sweden

institute: Karolinska Institutet

description: Patient with severe, therapy resistent asthma

hyb_protocol: Acccording to affymetrix standard proceedures

data_processing: affy package, justRMA, limma (Bioconductor)

source_name: Severe asthma

extract_protocol: Ambion RiboPure blood extraction kit including DNAse treatment

value: white blood cells

value: male


title: SA_62

scan_protocol: Acccording to affymetrix standard proceedures


title: Rabies, Fix, Spinalcord, 7dpi(mock), 01

source_name: Rabies, Fix, Spinalcord, 7dpi(mock), 01


title: Rabies, Fix, Spinalcord, 7dpi(inf), 02

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 02


title: Rabies, Fix, Spinalcord, 7dpi(inf), 04

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 04


title: SA_71

label_protocol: Acccording to affymetrix standard proceedures


title: SA_61


title: SA_291


title: Rabies, Fix, Brain, 7dpi(mock), 05

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 05

treatment_protocol: Mouse brains treated with RNAlater (ABI) were stored at -80°C until use.

tag: infection

value: brain


title: Rabies, Fix, Brain, 7dpi(mock), 06

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 06

tag: strain


title: SA_292

tag: tissue


title: Rabies, Fix, Brain, 7dpi(mock), 03

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 03


title: Rabies, Fix, Brain, 7dpi(mock), 04

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 04


title: SA_260


title: Rabies, Fix, Brain, 7dpi(mock), 02

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 02


title: Rabies, Fix, Brain, 7dpi(mock), 01

description: Gene expression in mock brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(mock), 01


title: SA_259


title: Rabies, Fix, Brain, 7dpi(inf), 06

description: Gene expression in infection brain at 7dpi

source_name: Rabies, Fix, Brain, 7dpi(inf), 06

value: Rabies virus (strain CVS-11)


title: SA_257


title: Rabies, Fix, Brain, 7dpi(inf), 05

source_name: Rabies, Fix, Brain, 7dpi(inf), 05


title: SA_253


title: SA_258


title: Rabies, Fix, Brain, 7dpi(inf), 04

source_name: Rabies, Fix, Brain, 7dpi(inf), 04


title: SA_271


title: SA_252


title: SA_12


title: Rabies, Fix, Brain, 7dpi(inf), 02

source_name: Rabies, Fix, Brain, 7dpi(inf), 02


title: SA_101


title: MA_63

description: Patient with well controlled asthma

source_name: Mild asthma


title: SA_114


title: SA_201


title: MA_94

description: Patient with well controlled asthma


title: Rabies, Fix, Brain, 7dpi(inf), 03

source_name: Rabies, Fix, Brain, 7dpi(inf), 03


title: MA_307

description: Patient with well controlled asthma


title: Rabies, Fix, Brain, 7dpi(inf), 01

source_name: Rabies, Fix, Brain, 7dpi(inf), 01


title: MA_306

description: Patient with well controlled asthma


title: MA_305

description: Patient with well controlled asthma


title: MA_303

description: Patient with well controlled asthma


title: MA_302

description: Patient with well controlled asthma


title: TrpR_glucose

city: La Jolla

first: Bernhard

last: Palsson

state: CA

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

hyb_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

data_processing: The raw data (.pair file) was subjected to per channel quantile normalization (Bolstad et al. Bioinformatics 19(2):185), IP/mock-IP ratio computation and enriched region identification as implemented in the NimbleScan software package, version 2.4.27 (www.nimblegen.com).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. Coli TrpR ChIP DNA glucose

growth_protocol: E. coli strains harboring TrpR-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 20 mg/L tryptophan.

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min. The cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. 6 uL of mouse antibody (NT63, Neoclone) was used to immunoprecipitate the chromatin complex of RNA polymerase subunit (rpoB) and DNA. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) then amplified PCR.

treatment_protocol: Cross-linked and sonicated chromatin complex of TrpR-8myc and DNA was immunoprecipitated by 9E10 myc antibody.

tag: genotype

value: 9E10 Myc tag antibody

tag: treatment

treatment_protocol: Cross-linked and sonicated chromatin complex of TrpR-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control.

value: normal mouse IgG

tag: antibody manufacturer

value: Upstate


title: MA_309

description: Patient with well controlled asthma


title: MA_67

description: Patient with well controlled asthma


title: MA_294

description: Patient with well controlled asthma


title: TrpR_Trp

scan_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

source_name: E. Coli TrpR ChIP DNA Tryptophan

growth_protocol: E. coli strains harboring TrpR-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented with 20 mg/L tryptophan.


title: p400Suz12 KD, replicate A

description: gene expression in indicated KD

source_name: embryonic stem cells, KD replicate A

value: embryonic stem cell


title: MA_237

description: Patient with well controlled asthma


title: Lrp_NH4Cl_3

source_name: E. Coli Lrp ChIP DNA NH4Cl 3

label_protocol: Performed by Nimblegen following their standard operating protocol (www.nimblegen.com)

growth_protocol: E. coli strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine.

treatment_protocol: Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by 9E10 myc antibody.

treatment_protocol: Cross-linked and sonicated chromatin complex of Lrp-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control.


title: MA_282

description: Patient with well controlled asthma


title: MA_301

description: Patient with well controlled asthma


title: MA_19

description: Patient with well controlled asthma


title: Lrp_NH4Cl_2

source_name: E. Coli Lrp ChIP DNA NH4Cl 2

value: glucose (2 g/L) minimal M9 medium supplemented without 10 mM leucine.


title: MA_290

description: Patient with well controlled asthma


title: MA_16

description: Patient with well controlled asthma


title: Lrp_Leu_3

source_name: E. Coli Lrp ChIP DNA Leucine 3

growth_protocol: E. coli strains harboring Lrp-8myc were grown in glucose (2 g/L) minimal M9 medium supplemented with 10 mM leucine.


title: Lrp_NH4Cl_1

source_name: E. Coli Lrp ChIP DNA NH4Cl 1


title: Lrp_Leu_1

source_name: E. Coli Lrp ChIP DNA Leucine 1

value: glucose (2 g/L) minimal M9 medium supplemented with 10 mM leucine.


title: MA_15

description: Patient with well controlled asthma


title: Lrp_Leu_2

source_name: E. Coli Lrp ChIP DNA Leucine 2


title: ArgR_NH4Cl_1

source_name: E. Coli ArgR ChIP DNA NH4Cl 1

growth_protocol: E. coli strains harboring ArgR-8myc were grown in glucose (2 g/L) minimal W2 medium supplemented with 2g/L glutamine.

treatment_protocol: Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by 9E10 myc antibody.

treatment_protocol: Cross-linked and sonicated chromatin complex of ArgR-8myc and DNA was immunoprecipitated by using normal mouse IgG for the control.


title: MA_14

description: Patient with well controlled asthma


title: ctrl_519

description: Healthy controls

source_name: Healthy control


title: ArgR_Arginine_2

source_name: E. Coli ArgR ChIP DNA Arginine 2

growth_protocol: E. coli strains harboring ArgR-8myc were grown in glucose (2 g/L) minimal W2 medium supplemented with 1g/L arginine.


title: MA_13

description: Patient with well controlled asthma


title: ArgR_NH4Cl_2

source_name: E. Coli ArgR ChIP DNA NH4Cl 2

value: glucose (2 g/L) minimal W2 medium supplemented with 2g/L glutamine.


title: Patient 82

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 GenomeStudio v2009.2 software (Illumina). Two-hundred and forty three probes, 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: melanoma

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

growth_protocol: Melanoma metastases were collected from 82 patients attending the Newcastle Melanoma Unit. The melanomas were cleaned of surrounding tissue, cut into 2-3 mm fragments and stored in vials in liquid nitrogen. Written consent was given by the patients for collection of their samples. Melanocytes were  cultured in Medium 154 (Cascade Biologics) and maintained in exponential growth at 37oC and 5% CO2.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, VIC, Australia) and the RNeasy Kit (Qiagen, VIC, Australia) according to the manufacturers’ instructions.

value: metastatic melanoma tumor


title: Patient 81


title: Patient 76


title: Patient 77


title: Patient 79


title: ArgR_Arginine_1

source_name: E. Coli ArgR ChIP DNA Arginine 1

value: glucose (2 g/L) minimal W2 medium supplemented with 1g/L arginine.


title: Patient 78


title: Rabies, Fix, Spinalcord, 7dpi(inf), 01

source_name: Rabies, Fix, Spinalcord, 7dpi(inf), 01

value: female


title: Patient 75


title: ctrl_518

description: Healthy controls


title: Patient 80


title: Patient 73


title: ctrl_515

description: Healthy controls


title: Patient 74


title: Patient 67


title: ctrl_517

description: Healthy controls


title: Patient 68


title: Patient 71


title: Patient 72


title: ctrl_516

description: Healthy controls


title: Patient 70


title: ctrl_514

description: Healthy controls


title: ctrl_513

description: Healthy controls


title: Patient 66


title: Patient 65


title: Patient 69


title: new pediatric hepatocellular carcinoma cell line passaged from human tumor

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description:
AFW-1 P14
Standard Processing of genomic DNA of tumor sample

hyb_protocol: Standard Affymetrix protocol of SNP 6.0

scan_protocol: Standard Affymetrix protocol of SNP 6.0

data_processing:
Genotyping (CN5) and copy number analysis  (Birdseed) with the Affymetrix Genotyping Console
Standard export of copy number results (from .CNCHP file)

label: Standard Affy

source_name: Liver tumor

label_protocol: Standard Affymetrix protocol of SNP 6.0

growth_protocol: Cells were expanded from tissue samples in DMEM media with 10% FCS and antibiotics Pen/Strep. Passage was done with Accutase as protease and culture in DMEM complete media.

extract_protocol: Qiagen DNA extraction kit

tag: passage


title: Patient 64


title: Patient 63


title: Patient 61


title: new pediatric hepatocellular carcinoma cell line passaged from xenotransplant 2

description:
AFW-1 2P2
Standard Processing of genomic DNA of tumor sample


title: ctrl_512

description: Healthy controls


title: Patient 59


title: Patient 62


title: Patient 57


title: jmj24-1_pollen_replicate2

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14h at 42°C.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G

data_processing: Standard QC analysis, background normalization and quantile normalization were performed using R with AffyTiling and preprocessCore packages. We updated genomic location of each probe to arabidopsis genome TAIR9.

organism: Arabidopsis thaliana

label_protocol: 7.5 µg double-stranded DNA was fragmented and labeled using the Affymetrix GeneChip WT Double-Stranded DNA Terminal Labeling Kit.

growth_protocol: Plants were grown on sterile half-strength Murashige-Skoog (MS) medium for 18 days before being transferred to a greenhouse under similar conditions (22°C, 16/8h photoperiod cycles)

extract_protocol: Flower heads were agitated three times in 500 mL of buffer containing (10 mM CaCl2, 1 mM KCl, 2 mM MES, and 5% [w/v] Sucrose, pH 6.5). Pollen was collected by filtering through a 0.45μm filter paper and collected pollen was immediately frozen in liquid nitrogen. Total RNA was extracted by using Plant RNeasy mini kit (Qiagen) and treated with DNAse I

tag: ecotype

value: mature pollen


title: ctrl_508

description: Healthy controls


title: ctrl_509

description: Healthy controls


title: Patient 60


title: jmj24-1_pollen_replicate1

tag: genotype/variation


title: ctrl_511

description: Healthy controls


title: Patient 58


title: Patient 55


title: Patient 56


title: Patient 53


title: ctrl_507

description: Healthy controls


title: Patient 54


title: Patient 52


title: ctrl_506

description: Healthy controls


title: WT_pollen_replicate1

value: wild type


title: Patient 51


title: ctrl_505

description: Healthy controls


title: ASPIRIN INTOLERANT #1

city: PAMPLONA

first: Marien

last: Pascual

state: NAVARRA

address: AVDA. PIO XII, 55, LAB 1.04

department: Hemato-Oncology

country: Spain

institute: CIMA, Universidad de Nacarra

description: Patient diagnosed with aspirin intolerance, asthma and nasal polyps

hyb_protocol: See Roche NimbleGen website and R.R. Selzer et al., PMID: 16075461, for details.

scan_protocol: Scanned using a GenePix 4000B scanner (Axon Instruments) (See R.R. Selzer et al., PMID: 16075461).

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (See R.F. Thompson et al., PMID: 18353789, for more details). Robust multichip average (RMA) was then applied to each group independently (See R.A. Irizarry et al., PMID: 12925520).

source_name: B Lymphocytes CD19+

label_protocol: Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively.

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619)

treatment_protocol: PBMCs were isolated using Ficoll-Paque PLUS (GE Healthcare Bio-Sciences, Sweden) and CD19+ B lymphocytes were extracted from the buffy coat using a positive immuno-magnetic separation kit (Invitrogen)

tag: patient type

value: ASPIRIN INTOLERANT

tag: cell type

value: B Lymphocytes CD19+

tag: digested

value: MspI

value: HpaII


title: Patient 50


title: ctrl_504

description: Healthy controls

value: white blood cells

value: male


title: Patient 47


title: Patient 43


title: Patient 45


title: Patient 40


title: Patient 46


title: Patient 41


title: WT_pollen_replicate2


title: Patient 42


title: ASPIRIN INTOLERANT #2


title: ctrl_501

description: Healthy controls


title: Patient 44


title: ctrl_502

description: Healthy controls


title: Patient 48


title: Patient 39


title: ASPIRIN INTOLERANT #3


title: Patient 38


title: CONTROL#2

description:
Subject with no symptoms or history of asthma or other pulmonary diseases; no symptoms or history of allergy; negative skin prick tests to a battery of common aeroallergens and absence of familiar history of asthma or allergic diseases
CONTROL#2

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the revised HELP protocol (See M. Oda, et al., PMID:19386619

value: CONTROL


title: Patient 49


title: Patient 37


title: ctrl_503

description: Healthy controls


title: Patient 36


title: Patient 31


title: Patient 30


title: Patient 32


title: Patient 35


title: Patient 34


title: CONTROL#3

description:
Subject with no symptoms or history of asthma or other pulmonary diseases; no symptoms or history of allergy; negative skin prick tests to a battery of common aeroallergens and absence of familiar history of asthma or allergic diseases
CONTROL#3


title: ALLERGY#1

description:
Patient diagnosed of allergic asthma with positive skin prick tests and specific IgE only to Dermatophagoides pteronyssinus
ALLERGY#1

value: ALLERGY


title: CONTROL#1

description:
Subject with no symptoms or history of asthma or other pulmonary diseases; no symptoms or history of allergy; negative skin prick tests to a battery of common aeroallergens and absence of familiar history of asthma or allergic diseases
CONTROL#1


title: ALLERGY#3

description:
Patient diagnosed of allergic asthma with positive skin prick tests and specific IgE only to Dermatophagoides pteronyssinus.
ALLERGY#3


title: Patient 24


title: Patient 20


title: Patient 17


title: Patient 22


title: Patient 18


title: Patient 19


title: Patient 25


title: Patient 21


title: Patient 26


title: Patient 16


title: Patient 15


title: ABA JA 3h-2

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

hyb_protocol: 30 ug cRNA was hybridized to ATH1 GeneChip arrays.

scan_protocol: Arrays were scanned using a GSC3000 scanner according to the manufacturer's recommendations.

data_processing: RMA normalized using Cel file with affllmGUI.

source_name: T87 cultured cell, ABA+SA, 3hr

label_protocol: First-strand of cDNA was synthesized using 16 ug of total RNA and SuperScript Double-stranded cDNA Synthesis kit (Invitrogen). The labeled cRNA was synthesized using BioArray RNA Transcripts Labeling Kit (T7) (ENZO Life Sciences inc.). After labeling, the cRNA was digested partially by incubating in 40 mM Tris-acetate, pH8.0, 100 mM KOAc, 30 mM MgOAc, at 94C for 35 min.

growth_protocol: The cells were incubated and subcultured every seven days in 20 mL of a liquid modified JPL medium (Axelos et al., 1992) in a 100 mL baffled Erlenmeyer flask at 100 rpm on a rotary shake at 24C at a 16 h light and 8 h dark cycle.

extract_protocol: Total RNA was extracted from frozen tissue using TRIzol reagent (Invitrogen) and purified using a RNase MinElute Cleanup Kit (Qiagen).

treatment_protocol: Growing T87 cells were exposed to 25uM ABA and 300 uM SA for 3hr.

tag: cell line

value: ABA+SA

tag: treatment duration


title: Patient 14


title: Patient 10


title: Patient 9


title: Patient 7


title: Patient 13


title: Patient 5


title: Patient 11


title: Patient 28


title: Patient 4


title: Patient 3


title: Patient 27


title: ABA 3h-1

source_name: T87 cultured cell, ABA, 3hr

treatment_protocol: Growing T87 cells were exposed to 25 uM ABA for 3hr.

value: ABA


title: Patient 8


title: Patient 23


title: Patient 6


title: Melanocyte 7

source_name: melanocyte

value: primary melanocyte


title: Patient 2


title: Melanocyte 8


title: Patient 12


title: Melanocyte 2


title: Patient 29


title: Melanocyte 4


title: Melanocyte 5


title: Melanocyte 6


title: ALLERGY#2

description:
Patient diagnosed of allergic asthma with positive skin prick tests and specific IgE only to Dermatophagoides pteronyssinus.
ALLERGY#1


title: Patient 1


title: IPMN_Invasive Grade_Patient T569

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from Invasive IPMN

hyb_protocol: Target preparation for Affymetrix Human Exon 1.0 ST Arrays was performed using 5μg of amplified cDNA and the Encore Biotin Module following the manufacturer’s recommendations. Hybridization, washing and staining performed with the Affymetrix GeneChip® Fluidics Station 450.

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

data_processing: The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite (version 6.5, build 6.10.0312) and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization. Exons were then summarized to genes using the average of the probesets.

source_name: Human Intraductal Papillary Mucinous Neoplasm

label_protocol: RNA was amplified and labeled using the WT-Ovation™ FFPE System V2, WT-Ovation™ Exon Module, and the Encore™ Biotin Module (NuGEN), which enables amplification and target preparation of the low quality RNA from FFPE, LCM samples.

extract_protocol: RNA was isolated from the LCM tissues using the PureLink™ FFPE RNA Isolation Kit (Invitrogen) according to manufacturer's protocols.

tag: patient

tag: disease state

value: Intraductal Papillary Mucinous Neoplasm (IPMN)

tag: tumor grade

value: Invasive


title: Melanocyte 3


title: IPMN_High Grade_Patient T573

description: Gene expression data from High grade IPMN

value: High grade


title: IPMN_Low Grade_Patient T569

description: Gene expression data from Low grade IPMN

value: Low grade


title: IPMN_Invasive Grade_Patient T573

description: Gene expression data from Invasive IPMN


title: IPMN_High Grade_Patient R574


title: IPMN_High Grade_Patient T569


title: Melanocyte 1


title: IPMN_Moderate Grade_Patient G579

description: Gene expression data from Moderate grade IPMN

value: Moderate grade


title: IPMN_Moderate Grade_Patient R581


title: IPMN_Moderate Grade_Patient F572


title: irradiated MEFs exposed to nilotinib, biological replicate 3

city: Monrovia

first: Nora

last: Heisterkamp

address: 1218 S Fifth Avenue

department: Department of Systems Biology

institute: Beckman Research Institute City of Hope

description:
MEFs-nilotinib-3
Gene expression data for irradiated MEFs exposed to 16 nM nilotinib for 9 days

hyb_protocol: Automatically washed and stained with streptavidin-phycoerythrin using a fluidics system.

scan_protocol: Scanned uisng a Hewlett-Packard GeneArray Scanner.

data_processing: Results were analyzed using Partek and Ingenuity Systems (version 7.1) software

source_name: irradiated MEFs exposed to nilotinib

label_protocol: Converted to biotinylated cRNA with an Enzo High Yield RNA transcript labeling kit.

growth_protocol: MEFs were grown to 80% confluency, then harvested by trypsinisation. After irradiation (Gammacelll 1000; 1000 rad, 15 minutes),  cells were plated at 2.5x10e6/10-cm dish in McCoy's 5A Modified Medium with 15%  heat-inactivated FBS, 110 mg/ml sodium pyruvate, 2 mM L-glutamine, 100 U/ml penicilllin/streptomycin, 50 uM b-mercaptethanol and 10 ng/ml murine IL-3. d0 was 24 hours after plating.

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

treatment_protocol: MEFs were separated from ALL cells (if present) using a 0.4 uM Transwell filter. MEFs or MEFs/ALL cells were treated with DMSO or with 16 nM nilotinib for 9 days. ALL cells (if present) were removed, membranes were carefully removed, MEFs were examined to ensure no contaminating ALL cells were present and RNA was isolated from the MEFs.

value: wild type

value: fibroblast


title: IPMN_Low Grade_Patient R574


title: irradiated MEFs exposed to nilotinib, biological replicate 2

description:
MEFs-nilotinib-2
Gene expression data for irradiated MEFs exposed to 16 nM nilotinib for 9 days


title: IPMN_Invasive Grade_Patient J847

description: Gene expression data from Invasive IPMN


title: IPMN_Low Grade_Patient R581


title: IPMN_Low Grade_Patient E582


title: IPMN_High Grade_Patient J847


title: IPMN_Low Grade_Patient F572


title: IPMN_Invasive Grade_Patient R574

description: Gene expression data from Invasive IPMN


title: IPMN_Low Grade_Patient G579


title: irradiated MEFs exposed to DMSO, biologcal replicate 3

description:
MEFs-DMSO-3
Gene expression data for irradiated MEFs exposed to DMSO for 9 days

source_name: irradiated MEFs exposed to DMSO


title: irradiated MEFs exposed to DMSO, biologcal replicate 2

description:
MEFs-DMSO-2
Gene expression data for irradiated MEFs exposed to DMSO for 9 days


title: irradiated MEFs exposed to nilotinib, biological replicate 1

description:
MEFs-nilotinib-1
Gene expression data for irradiated MEFs exposed to 16 nM nilotinib for 9 days


title: IPMN_Invasive Grade_Patient E582

description: Gene expression data from Invasive IPMN


title: IPMN_Low Grade_Patient D570


title: IPMN_High Grade_Patient D566


title: POST_06

first: Louise

middle: C

last: Showe

address: 3601 Spruce St

institute: The Wistar Institute

description: post- surgery sample

hyb_protocol: Samples were hybridized to the human Illumina MicroRNA v2 (Universal 12 Beadchip 1536 bead type) Sentrix Beadchip Array (http://www.illumina.com/pages.ilmn?ID=240) according to standard Illumina protocol.

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina BeadStudio v.3.0 software was used to export expression levels and detection p-values for each probe of each sample. Arrays were quantile normalized and filtered to remove non-informative miRNA probes. A probe was called non-informative if it had expression signals with detection p-value>0.05 in all samples or if it had expression signals less than 2 average background levels in all samples.

source_name: Peripheral Blood Mononuclear Cells (PBMC) from Non-small Cell Lung Cancer (NSCLC) patients taken before and after surgery.

label_protocol: Illumina Label Protocol

extract_protocol: RNA purification was carried out at Wistar using TriReagent Molecular Research) as recommended and controlled for quality using the Bioanalyzer. Only samples with 28S/16S ratios >0.75 were used for further studies. A constant amount (500ng) of total RNA was amplified as recommended by Illumina.

value: Non-small Cell Lung Cancer (NSCLC)

tag: surgery

value: POST

tag: smoking

value: Q

tag: race

value: W

tag: Sex

value: F

tag: age

tag: copd

value: N

tag: dx

value: LSCC

tag: Stage

tag: days between sample collection


title: IPMN_Low Grade_Patient B845


title: PRE_17

description: pre- surgery sample

value: Peripheral Blood Mononuclear Cells (PBMC)

value: PRE

value: M

value: Y

value: AC


title: PRE_14

description: pre- surgery sample


title: POST_15

description: post- surgery sample

value: NSCLC


title: IPMN_Invasive Grade_Patient B845

description: Gene expression data from Invasive IPMN

value: Intraductal Papillary Mucinous Neoplasm (IPMN)

value: Invasive


title: Patient 33

tag: tissue

value: metastatic melanoma tumor


title: IPMN_Invasive Grade_Patient D566

description: Gene expression data from Invasive IPMN


title: irradiated MEFs exposed to DMSO, biologcal replicate 1

description:
MEFs-DMSO-1
Gene expression data for irradiated MEFs exposed to DMSO for 9 days

tag: genotype

value: wild type

tag: cell type

value: fibroblast


title: PRE_12

description: pre- surgery sample

value: Non-small Cell Lung Cancer (NSCLC)


title: IPMN_Moderate Grade_Patient B571

value: Moderate grade


title: irradiated MEFs exposed to nilotinib-treated ALL cells, biological replicate 3

description:
MEFs-nilotinib ALL-3
Gene expression data for irradiated MEFs exposed to nilotinib-treated 8093 Bcr/Abl transgenic preB acute lymphoblastic leukemia cells for 9 days

source_name: irradiated MEFs exposed to nilotinib-treated 8093 Bcr/Abl transgenic preB ALL cells


title: IPMN_Low Grade_Patient C583

value: Low grade


title: irradiated MEFs exposed to nilotinib-treated ALL cells, biological replicate 1

description:
MEFs-nilotinib ALL-1
Gene expression data for irradiated MEFs exposed to nilotinib-treated 8093 Bcr/Abl transgenic preB acute lymphoblastic leukemia cells for 9 days


title: IPMN_High Grade_Patient B845

value: High grade


title: IPMN_Low Grade_Patient B571


title: irradiated MEFs exposed to DMSO-treated ALL cells

description:
MEFs -DMSO ALL
Gene expression data for irradiated MEFs exposed to DMSO-treated 8093 Bcr/Abl transgenic preB acute lymphoblastic leukemia cells for 9 days

source_name: irradiated MEFs exposed to DMSO-treated 8093 Bcr/Abl transgenic preB ALL cells


title: plusF4

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description:
One allele with functional RB/one allele RB floxed plus Cre (heterozygous RB), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 3_+F4_8-31-10.CEL

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

source_name: frozen liver tissue

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: Mice were raised and bred according to NIH guidelines with the highest regard for animal care and safety.

extract_protocol: RNA was harvested from frozen liver tissue using RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight.

tag: treatment

value: TX

tag: rb genotype/variation

value: LOH


title: pool 3-319

city: Hannover

first: Sya

last: Ukena

address: Carl-Neuberg-Strasse 1

institute: Hannover Medical School

description: Healthy donor matched GvHD d120

hyb_protocol: according to manufacturers instruction (febit biomed)

scan_protocol: Wizard software on standard Microsoft Windows Workstation PC

data_processing: summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1

source_name: RNA from sorted CD4+CD25high Tregs

label_protocol: MPEA, microfluidic primer extension assay Biotin labeling

extract_protocol: Blood from SCT patients were isolated by Ficoll gradient and subsequently CD4+CD25high Tregs were separated by FACS cell sorting. Cells were resuspended 700µl Qiazol ( Qiagen GmbH, Hilden) reagent and stored at -70°C. Total RNA was isolated using miRNeasy kit (Qiagen GmbH, Hilden) and the resulting RNA pellets were stored in 70% Ethanol at -70°C until delivery to febit biomed.

treatment_protocol: stored at -20 degree

tag: gender

value: patient pool

value: CD4+CD25high Tregs

tag: sample type

value: healthy donor

tag: gvhd

value: matched d120


title: irradiated MEFs exposed to nilotinib-treated ALL cells, biological replicate 2

description:
MEFs-nilotinib ALL-2
Gene expression data for irradiated MEFs exposed to nilotinib-treated 8093 Bcr/Abl transgenic preB acute lymphoblastic leukemia cells for 9 days


title: PRE_15

description: pre- surgery sample

tag: disease state

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: surgery

value: PRE

value: Q

value: W

value: M

value: Y


title: FF4

description:
RB floxed without Cre (Wild-Type), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 4_FF4_8-31-10.CEL

value: WT


title: FFC2

description:
RB floxed with Cre (RB knockout), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 13_19_FFC2_4_27_2010.CEL

value: KO


title: NF4

description:
RB-N750F mutant, treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 1_NF4_8-31-10.CEL


title: NF5

description:
RB-N750F mutant, treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 2_NF5_8-31-10.CEL


title: NIH3T3 quiescent p27.1

city: Barcelona

first: oriol

last: bachs

email: obachs@ub.edu, raffaellapippa@ub.edu

address: Casanova 143

department: Cell Biology, Immunology and Neurosciences

institute: University of Barcelona

hyb_protocol: 4 ug of each labeled DNA was hybridized onto each of the two slides of the Agilent Mouse Promotor 244K microarray set according to the manufacturer's protocol for mammalian CHIP on chip (v9.1, November 2006) with mouse Cot DNA and Agilent blocking reagent in 1X Agilent hybridizations buffer 40 hours at 65ºC in a rotating chamber at 10 rpm. Slides chambers were disamembled in Oligo aCGH/ChIP-on-chip Wash Buffer 1 and washed with agitation 5 minutes in the same buffer at room temperature followed by 5 minutes in Oligo aCGH/ChIP-on-chip Wash Buffer 2 at 31 ºC, and two steps without agitation to recue background and remove water componen t 1 minute in acetonitrile and 30 seconds at room temperature, and 30 seconds Agilent Stabilization and Washing solution at room temperature after which slides came out dry and protected from photobleaching. Two separate comparisons were performed (IP versus input and IgG versus input) on two slide sets, for a total of four slides.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT and 5 um resolution.

data_processing: Raw data was extracted using Feature Extraction (Agilent). The data analysis was performed using LIMMA package from R of Bioconductor while the intrachip normalization was obtained with LOESS method.

source_name: p27 IP

label_protocol: DNA was amplified and labelled according to the manufacturer's protocol for mammalian CHIP on chip (v9.1, November 2006) modified by adding microcentrifugation column purification steps instead of ethanol precipitations between different enzymatic reactions. Estimated nanogram amounts of p27  (IP) or control (IgG) immunoprecipitated DNA (below the detection limit of the nanodrop spectrophotometer) or 200 ng of input DNA were polished by blunt ending with T4 DNA polymerase (NEB) followed by purification with Qiaquick (Qiagen) columns. Double stranded DNA linkers (generated by annealing primers JW102 5’-GCGGTGACCCGGGAGATCTGAATTC-3‘ and JW103 5’-GAATTCAGATC-3‘) were ligated to the ends of blunt ended DNA fragments with T4 DNA ligase (NEB), followed by purification with Qiaquick (Qiagen) columns. Amplification was performed by two or three rounds of ligation mediated PCR using Taq polymerase (Applied Biosystems) with Thermopol buffer (NEB) with primer JW102, with at least 4 technical repetitions in the second round to obtain at least 10 ug of DNA. Amplified template was labelled by random priming with the Bioprime CGH labelling kit (Invitrogen) with Cy5-dUTP (2 reactions each for IP and IgG samples), and Cy3-dUTP (4 reactions for input)  using 2 ug of template per reaction. Unincorporated deoxynucleotides were removed by microcentrifugation columns afrom the Invitrogen kit and quantified by Nanodrop spectrophotometry to verify yield specific activity according to specifications.

growth_protocol: NIH3T3 cells were cultured in Dulbecco's modified Eagle Medium (DMEM) supplemented with 10% donor bovine serum (DBS) and maintained at 37ºC and 5% CO2

extract_protocol: NIH3T3 cells were maintained without serum during 24 h at 37ºC and 5% CO2. Cells were fixed with formaldehyde at room temperature for 10 min. Fixation was blocked with glycine, and cells were washed twice in cold 1x PBS before lysation. Chromatin was sheared to an average of 800 bp as verified on a 1% agarose gel. Clarified lysates were agitated overnight at 4ºC with anti-IgG polyclonal  antibody (SIGMA). Following this incubation Protein G/A agarose was added and allowed to bind for 2hours at 4ºC. Immunoprecipitates were washed three times in 1x RIPA, three times with RIPA-NaCl, two times with LiCl buffer and two times with 1x TE before eluition. Crosslinks were reversed overnight at 65ºC. DNA was purified by incubation with Proteinase K (Roche) for 2 h at 55ºC, and using the Illustra GFX PCR DNA Purification kit (GE healthcare). DNA was sonicated prior to processing and fragments of 500-800bp were analyzed.

treatment_protocol: For serum starvation, cells were maintained without serum during 24 h.

value: quiescent NIH3T3

tag: antibody

value: p27 test immunoprecipitation

source_name: input

value: N/A (input DNA reference)


title: NIH3T3 quiescent IgG.1

source_name: IgG IP

value: IgG control immunopreciptation


title: pool 2-319

description: Healthy donor matched no GvHD d60

value: matched no d60


title: PRE_18

description: pre- surgery sample

value: Non-small Cell Lung Cancer (NSCLC)

tag: smoking

tag: race

value: B

tag: Sex

value: N

value: AC


title: pool 6

description: GvHD > d100

value: patient pool

value: CD4+CD25high Tregs

value: SCT

value: late


title: PRE_07

description: pre- surgery sample

value: Peripheral Blood Mononuclear Cells (PBMC)

value: PRE

value: Q

value: W

value: M

tag: age

tag: copd

tag: dx

value: BAC


title: PRE_05

description: pre- surgery sample

tag: Stage

tag: days between sample collection


title: PRE_04

description: pre- surgery sample

tag: cell type

value: F

value: Y


title: pool 3

description: no GvHD > d100

value: no late


title: PRE_06

description: human: total RNA

value: Non-small Cell Lung Cancer (NSCLC)

value: LSCC


title: PRE_02

description: pre- surgery sample


title: PRE_03

description: pre- surgery sample

value: S

value: N

value: NSCLC


title: pool 1-319

description: Healthy donor matched no GvHD d60

value: patient pool

value: CD4+CD25high Tregs

value: healthy donor

value: matched no d60


title: pool 1

description: no GvHD < d100

value: SCT

value: no early


title: POST_17

description: post- surgery sample

value: Peripheral Blood Mononuclear Cells (PBMC)

value: POST

value: Q

value: W

value: AC


title: POST_18

description: post- surgery sample

value: B

value: M


title: FFC1

description:
RB floxed with Cre (RB knockout), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 12_18_FFC1_4_27_2010.CEL

tag: treatment

value: TX

value: KO


title: pool 4

description: GvHD < d100

value: early


title: POST_14

description: post- surgery sample

value: Non-small Cell Lung Cancer (NSCLC)

value: N


title: FF3

description:
RB floxed without Cre (Wild-Type), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 11_17_FF3_4_27_2010.CEL

tag: rb genotype/variation

value: WT


title: UF2

description:
RB floxed without Cre (Wild-Type), untreated
Raw data file: 08_14_UF2_4_27_2010.CEL

value: NT (non-treated)


title: UF1

description:
RB floxed without Cre (Wild-Type), untreated
Raw data file: 07_13_UF1_4_27_2010.CEL


title: NF3

description:
RB-N750F mutant, treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 03_9_NF3_4_27_2010.CEL


title: plusF3

description:
One allele with functional RB/one allele RB floxed plus Cre (heterozygous RB), treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 06_12_+F3_4_27_2010.CEL

value: LOH


title: POST_07

description: post- surgery sample

value: Y

value: BAC


title: POST_12

description: post- surgery sample

value: Peripheral Blood Mononuclear Cells (PBMC)

value: F

value: LSCC


title: NF2

description:
RB-N750F mutant, treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 02_8_NF2_4_27_2010.CEL


title: Split KCl roots - 2hours - repeat 2

city: NYC

first: Sandrine

last: Ruffel

state: NY

address: 100 Washington Square East. 1009 Main Building

department: Biology

institute: New York University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 10 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is EukGE-WS2v4_450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using MAS5.0v

source_name: Split KCl roots - 2hours - repeat 2

label_protocol: Samples were enzymatically fragmented and biotinylated using the IVT - labeling kit (Affymetrix)

growth_protocol: Plants are grown on a custom-made basal Murashige and Skoog solid medium (no nitrogen, no sucrose), supplemented with 0.5 mM NH4-succinate, 0.1mM KNO3 and 3mM sucrose. After 8-10 days, the primary root was cut below the first two lateral roots and roots still grown on these plates for 4 more days. Then, each plant with two main roots was transferred on individual 10x10 cm plates containing the same 40 ml solid medium supplemented with 0.5mM NH4+-succinate as the nitrogen source. The solid medium was divided in two compartments by a trench to allow the physical separation of the two roots.

extract_protocol: RNA extractions were carried out on roots collected at 2 hours, 8 hours and 2 days after the beginning of the split-root treatment with TRIzol (Invitrogen)

treatment_protocol: We selected the 12-14 days old plants with balanced roots on both sides and they were transferred on 12x12cm segmented agar plates containing either 5mM KNO3 or 5mM KCl on both sides for the controls or 5mM KNO3 on one side and 5mM KCl on the other side for the split. These plates contained 60 ml of solid basal MS medium supplemented with 0.3mM sucrose. The KNO3 or KCl compartments were obtained by spreading concentrated KNO3 and KCl solution on the solid medium 24 hr before the experiments to allow diffusion of the solutions

tag: tissue

value: roots

tag: ecotype

value: Columbia

value: 5mM KCl on both sides for 2 hours


title: POST_05

description: post- surgery sample

value: POST

value: W

value: M

value: AC


title: quorum-sensing conditions, 4 hours, replicate 3

city: Bremen

first: Barbara

last: Reinhold-Hurek

department: Microbe-Plant-Interactions

institute: University Bremen

description:
301721
Biological replicate 3 of 3. Early exponential growth conditions versus quorum-sensing conditions for four hours.

hyb_protocol: The combined Cy3/Cy5-labelled targets were dried in a vacuum concentrator dissolved in 60 µl DIG Easy hybridization solution (Roche, Mannheim, Germany) and 1 µl of sonicated salmon sperm (5 µg/µl) was added. Prior to hybridization, the targets were denatured at 65°C for 10 min. The hybridization of fluorescently labelled cDNA targets to oligonucleotide microarrays was performed at 42°C in a hybridization chamber (ArrayIt, Sunnyvale, CA, USA) in a water bath for 14 to 18 hours. It was crucial to apply stringent conditions throughout all preparative steps. Therefore, the chamber, as well as the cover slip, had to be pre-heated to 42°C before the target was applied.

scan_protocol: The Cy3- and Cy5-fluorescence was scanned at 532 nm and 635 nm with the GenePix Scanner 4000A (Molecular Devices, Sunnyvale, CA, USA) with a pixel size of 10 µm. In this study, image analysis was performed with the GenePix 4.1 program and the subsequent analyses were carried out with the open-source software Microarray Data Analysis System (MIDAS v2.19) of TM4 (Saeed et al. 2003, http://www.tm4.org/). After scanning, raw data images of the slides that contain information about gene expression levels were obtained by the GenePix software. These images were analyzed by identifying each spot on the array (with the help of an array layout template) with measurements of its fluorescence intensity and the corresponding background intensity. With the file transformation tool Express Converter v.2.1 (http://www.tm4.org/utilities.html), data files generated from GenePix (.gpr) were converted to TM4 files (.mev) that could be uploaded to the MIDAS platform.

data_processing: Before the intensity values that were measured with GenePix could be compared, normalization with MIDAS was necessary. This critical step compensated for variability by appropriately adjusting the data. In this study, the LOWESS (locally weighted scattered plot smoothing) normalization was performed using the block mode as set-up parameter as this mode allowed correction of systematic spatial variation between the grids of the array. The normalized data for each spot were exported to Excel and aligned to the corresponding Azoarcus sp. BH72 gene name. The experiments were performed in triplicates and each gene was spotted in four replicates on every slide resulting in twelve intensity values per fluorescent dye. The expression ratios for each gene were calculated by dividing the corresponding intensity values from one condition by the intensity values from the other condition. To obtain an average expression fold, the mean of the replicate expression ratios was calculated. Moreover, a one-tailed paired t-test was performed and only genes that showed an expression fold of at least 1.8 and a P-value ≤ 0.05 were regarded as being differentially expressed.

organism: Azoarcus sp.

source_name: cells from a bacterial culture grown until the early exponential growth phase

label_protocol: For coupling of fluorescent dyes to the aminoallyl-labelled first strand cDNA, aliquots of Cy3 NHS or Cy5-NHS esters (GE Healthcare) were dissolved in 60 µl of first strand cDNA, mixed and incubated for 90 min at room temperature in the dark. Blocking of all remaining dyes (quenching) was necessary after labelling. This quenching was achieved by adding 4.5 µl hydroxylamine (4 M) to the sample solution, followed by an incubation for 15 min at room temperature. Subsequent cleaning up of labelled cDNA from remaining dyes was performed with the CyScribe GFX Purification Kit (GE Healthcare) according to manufacturer’s instructions. The Cy5- and Cy3-labelled cDNA that was used in one hybridization experiment were cleaned up together. The labelled cDNA (60 µl) was stored at  20°C until microarray hybridization.

growth_protocol: Azoarcus sp. BH72 was grown aerobically in VM-Ethanol medium (0.4 g/l KH2PO4, 0.6 g/l K2HPO4, 1.1 g/l NaCl, 0.5 g/l NH4Cl, 0.2 g/l MgSO4, 26 mg/l CaCl2, 10 mg/l MnSO4, 2 mg/l Na2MoO4, 0.66 mg/l Fe(III)-EDTA, 1 g/l yeast extract, 3 g/l bacto peptone, 6 ml/l ethanol, pH 6.8) at 37°C with constant shaking at 180 -200 rpm. For bacteria cultivation, the Erlenmeyer flasks were only 1/10 filled to assure sufficient oxygen aeration. For collection of conditioned culture supernatants, strain BH72 was grown in VM-Ethanol medium at 37°C. After 24 h, pre-cultures were diluted 1:6 with fresh medium and incubated for another 24 h. The optical density at 578 nm was measured and only supernatants from cultures that reached the stationary growth phase (OD578 > 1) were harvested by centrifugation with 12,857 g for 20 min at room temperature, the supernatants were supplemented with 3 ml/l ethanol and subjected to quorum sensing experiments. For the transcriptomic approach, pre-cultures of Azoarcus sp. BH72 were grown in VM-Ethanol medium until the early exponential growth phase (OD578nm of 0.3). Parts of this culture were harvested and served as control samples. The remaining culture was used for growth under quorum sensing conditions. Therefore, these cultures were further incubated for one and four hours with four volumes of conditioned culture supernatant from Azoarcus sp. BH72 wild type.

extract_protocol: The cell pellets were re-suspended in a 1:1 mixture of pre-warmed phenol-chloroform-isoamylalcohol (25:24:1, pH 4.7) and NAES solution (50 mM sodium acetate, 10 mM EDTA, 1 % SDS, pH 5.1). This suspension was incubated for 5 min at 65°C in a water bath, followed by 10 min incubation on ice. For phase separation, the mixture was centrifuged for 10 min at 12°C and 8000 x g. The upper phase was transferred and mixed with the same volume of phenol-chloroform-isoamylalcohol. This phenol extraction was repeated three times (centrifugation see above), followed by an extraction with equal volume of chloroform isoamylalcohol (24:1). RNA precipitation was performed with the same volume of isopropanol for 45 min on ice. The RNA was pelleted by centrifugation (12900 x g, 10 min at 4°C) and salts were removed with 1 ml of Ethanol (70 %). The dried RNA was dissolved in 100 µl 1 x RNAsecure (Applied Biosystems, Foster City, CA, USA), frozen in liquid nitrogen and kept at -80°C until further processing.

treatment_protocol: The cells from two independent cultures were harvested quickly by centrifugation (room temperature, 5 min, 6800 g), pellets were suspended in PBS, centrifuged again and stored at -80°C until RNA isolation.

tag: strain

tag: condition

value: early exponential growth

tag: sample type

value: control

source_name: cells from a bacterial culture grown in the presence of cell-free conditioned supernatant for four hours

value: cell-free conditioned supernatant

tag: time

value: 4 hrs

value: quorum sensing


title: quorum-sensing conditions, 4 hours, replicate 1

description:
301713
Biological replicate 1 of 3. Early exponential growth conditions versus quorum-sensing conditions for four hours.


title: NF1

description:
RB-N750F mutant, treated for 24 hours with diethylnitrosamine (DEN)
Raw data file: 01_7_NF1_4_27_2010.CEL

value: TX


title: quorum-sensing conditions, 4 hours, replicate 2

description:
301715
Biological replicate 2 of 3. Early exponential growth conditions versus quorum-sensing conditions for four hours.


title: quorum-sensing conditions, 1 hour, replicate 1

description:
302725
Biological replicate 1 of 3. Early exponential growth conditions versus quorum-sensing conditions for one hour.

source_name: cells from a bacterial culture grown in the presence of cell-free conditioned supernatant for one hour

value: 1 hr


title: quorum-sensing conditions, 1 hour, replicate 3

description:
302943
Biological replicate 3 of 3. Early exponential growth conditions versus quorum-sensing conditions for one hour.


title: POST_02

description: post- surgery sample

tag: disease state

value: Non-small Cell Lung Cancer (NSCLC)

value: Peripheral Blood Mononuclear Cells (PBMC)

tag: surgery

tag: smoking

value: Q

value: Y


title: POST_04

description: post- surgery sample

tag: race

tag: Sex

value: F

tag: age


title: POST_03

description: post- surgery sample

value: S

tag: copd

value: N

tag: dx

value: NSCLC

tag: Stage


title: IPMN_Moderate Grade_Patient H577

description: Gene expression data from Moderate grade IPMN

tag: patient

value: Intraductal Papillary Mucinous Neoplasm (IPMN)

tag: tumor grade

value: Moderate grade


title: quorum-sensing conditions, 1 hour, replicate 2

description:
302942
Biological replicate 2 of 3. Early exponential growth conditions versus quorum-sensing conditions for one hour.

value: early exponential growth


title: quiescent p27CK MEFs 3

description: Gene expression data from p27CK MEFs cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix 1.0 ST murine array. Chips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Scanner Axon 4000B

data_processing: The normalization of the arrays was done using the rma method as implemented in the Affy package of R Bioconductor. Quality control measurements were done using ArrayQualityMetrics package of R Bioconductor.

source_name: CK

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

growth_protocol: Wt, CK and p27KO MEFs were cultured in DMEM supplemented with 10% fetal bovin serum (FBS). All cultures were maintained at 37ºC and 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy Kit (QIagen). RNAs from quiescent MEFs from wt or delta51 mice were analyzed using a Bioanalyzer (Agilent). Only samples with RIN number greater than 9 and a ratio A260/280 over than 2 were further used in microarray analysis. Retrotranscription was made followed by labeling with biotin.

treatment_protocol: For serum starvation, cells were maintained without serum during 72 h.

tag: cell type

value: MEFs

tag: genotype/variation


title: quiescent p27KO MEFs 1

description: Gene expression data from p27KO MEFs cells

source_name: KO


title: quiescent p27KO MEFs 3


title: quiescent p27KO MEFs 2


title: 2690-TF

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

description: squamous cell lung carcinoma _Tumor Front_2690

hyb_protocol: Purified and dye-labeled sample and reference cDNA was combined for two-color hybridizations with 520 µl hybridization buffer (4x SSC, 50% formamide, 2% SDS), agitated for 30 min at 60 °C, heated for 10 min at 70 °C on a thermo mixer and subsequently applied to preheated (60 °C) gasket slides (Agilent Technologies, Santa Clara, USA). Microarrays were place onto loaded gasket slides, assembled in SureHyb hybridization chambers (Agilent) and incubated for 23 hours at 42 °C and a rotation speed of 4 rpm in an Agilent DNA Microarray Hybridization Oven. Hybridized arrays were washed at 35 °C with (i) 0.5x SSC, 0.1% SDS for 4 minutes; (ii) 0.05x SSC, 0.1% SDS for 4 minutes; (iii) 0.05x SSC for 2 minutes; (iv) 0.05x SSC, 0.05% Tween-20 for 30 seconds. Immediately thereafter, slides were dried by centrifugation in 50 ml Falcon tubes at 2500 rpm for 5 minutes. All hybridization experiments were repeated with inversely labeled sample and reference.

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: Following image extraction, low quality spots were filtered and the background intensities were corrected by normexp with offset 50  (Ritchie, ME, Silver, J, et al., 2007) and within array robustspline normalization was applied. Quantile normalization was applied between arrays for further normalization. Annotation of oligonucleotide probes present on the gene expression array was retrieved by alignment to EnsEMBL database version 55_37.

source_name: tumor invasion front

label_protocol: For amplification and labeling 25 ng of total RNA from each area or reference mRNA (Universal Human Reference RNA, Agilent) were subjected to two rounds of linear amplification using the in-vitro transcription-based TAcKLE protocol (Schlingemann J, Thuerigen O, et al., 2005). Subsequent generation of cDNA yielded separately labeled Cy3 and Cy5 tumor- and reference samples, respectively. (21).

growth_protocol: Primary squamous cell lung carcinoma samples were obtained from the Thorax Clinic, University of Heidelberg, Germany.

extract_protocol: For RNA isolation, microdissected tissues from consecutive cryosections were pooled into a final volume of 350 μL QIAzol Lysis Reagent (Qiagen, Hilden, Germany). Total RNA extraction was carried out using a miRNEasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions and subsequently examined for integrity using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: RNA samples from each patient were distinguished according to  i) inner tumor, ii) tumor invasion front, iii) adjacent lung front, and iv) normal lung

tag: diagnosis

value: squamous cell lung carcinoma

tag: location

value: Tumor Front

source_name: Universal Human Reference RNA (Stratagene)

tag: tissue

value: pooled cell line derivations


title: quiescent p27CK MEFs 1


title: Control KNO3 roots - 2hours - repeat 1

source_name: Control KNO3 roots - 2hours - repeat 1

value: roots

tag: ecotype

value: Columbia

tag: treatment

value: 5mM KNO3 on both sides for 2 hours


title: 2690-LF

description: squamous cell lung carcinoma _Lung Front_2690

source_name: adjacent lung

value: Lung Front


title: quiescent p27CK MEFs 2


title: 2505-NL

description: squamous cell lung carcinoma _Normal Lung_2505

source_name: distant normal lung

value: Normal Lung


title: quiescent p27WT MEFs 3

description: Gene expression data from WT MEFs cells

source_name: WT

value: wild type


title: 2505-TF

description: squamous cell lung carcinoma _Tumor Front_2505


title: quiescent p27WT MEFs 1

description: Gene expression data from WT MEFs cells


title: 0.5uM ecdy 2hrs rep 3

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

hyb_protocol: See http://www.flyarrays.com/ under protocols. Modifications by Scott:-use 5uL 50mM EDTA-precipitate probe for at least 1 hour-use 20uL DIG EasyHyb per humidifying well-final hyb volume is 80uL

scan_protocol: Images of the hybridized microarrays were obtained using a ScanArray 4000 scanner (Perkin-Elmer) and were quantified using QuantArray 3.0 software (Perkin-Elmer)

data_processing: Data were normalized using lowest sub-grid normalization (Yang, 2002) and Genetraffic Duo (Stratagene /Agilent) analysis software.

organism: Drosophila melanogaster

source_name: Kc 167 cells, 0.5uM 20-hydroxy-ecdysone, 2hrs

label_protocol: CDMC Direct Labeling Protocol. See http://www.flyarrays.com/ under protocols.

extract_protocol:
Trizol Method
Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.  Trizol is used at a ratio of 1 mL per 10^7 cells.  Extraction procedure is as described by the manufacturer with centrifugation in a Sorvall SS-34 rotor.  Final pellets are air dried and then resuspended in Sigma 18 meg-ohm water to obtain a final RNA concentation of no less than 4ug per uL.

tag: agent

value: 0.5uM 20-hydroxy-ecdysone

tag: cell line

tag: cell extraction

value: The sample had an [RNA] of 3.83 ug per uL and an OD ratio of 2.01.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water

source_name: Kc 167 cells, Ethanol Control

value: Ethanol Control

value: The sample had an [RNA] of 2.95 ug per uL and an OD ratio of 2.00.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water


title: 0.5uM ecdy 2hrs rep 2

growth_protocol: Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.

tag: protocol

value: The sample had an [RNA] of 4.19 ug per uL and an OD ratio of 1.98.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 2.45 ug per uL and an OD ratio of 2.00.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water


title: 0.5uM ecdy 2hrs rep 1

value: The sample had an [RNA] of 3.16 ug per uL and an OD ratio of 1.98.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 3.99 ug per uL and an OD ratio of 1.99.Details:2.5mL Trizol500uL chloroform1.9mL isopropanol1.2mL 75 percent EtOH-brought up in 20uL Sigma 18 meg-ohm water


title: quiescent p27WT MEFs 2

description: Gene expression data from WT MEFs cells

value: MEFs


title: 2505-TC

description: squamous cell lung carcinoma _Tumor Center_2505

source_name: inner-tumor

value: squamous cell lung carcinoma

value: Tumor Center


title: 0.5uM ecdy 4hrs rep 3

description: 0.5uM ecdy 4hrs (12920690) July 19, 2004

hyb_protocol: See http://www.flyarrays.com/ under protocols.Modifications by Scott:-use 5uL 50mM EDTA-precipitate probe for at least 1 hour-use 20uL DIG EasyHyb per humidifying well-final hyb volume is 80uL

source_name: 0.5uM 20-hydroxy-ecdysone, 4hrs

growth_protocol: Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.  Trizol is used at a ratio of 1 mL per 10^7 cells.  Extraction procedure is as described by the manufacturer with centrifugation in a Sorvall SS-34 rotor.  Final pellets are air dried and then resuspended in Sigma 18 meg-ohm water to obtain a final RNA concentation of no less than 4ug per uL.

extract_protocol: Trizol Method

tag: rna sample

value: The sample had an [RNA] of 6.74 ug per uL and an OD ratio of 2.01. Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water

source_name: Ethanol Control

value: The sample had an [RNA] of 5.79 ug per uL and an OD ratio of 1.92. Details:5.0 mL Trizol1 mL chloroform3.5 mL isopropanol2.5 mL 75% EtOH-brought up in 50 uL Sigma 18 meg-ohm water


title: H3K9me2 ChIP in nitrogen-starved wild-type cells

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220). Immunoprecipitated DNA was recovered by incubation with protein G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C.

tag: condition

value: Nitrogen-starved

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog#

value: Nitrogen starved

tag: input

value: Whole-cell extract DNA


title: 2505-LF

description: squamous cell lung carcinoma _Lung Front_2505

value: Lung Front

value: pooled cell line derivations


title: 2502-NL

description: squamous cell lung carcinoma _Normal Lung_2502

value: Normal Lung


title: 0.5uM ecdy 4hrs rep 2

description: 0.5uM ecdy 4hrs (12920866) Jun 29, 2004

value: The sample had an [RNA] of 4.05 ug per uL and an OD ratio of 2.01. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water

value: The sample had an [RNA] of 4.85 ug per uL and an OD ratio of 2.02. Details:3.5 mL Trizol700uL chloroform2.5 mL isopropanol1.5 mL 75% EtOH-brought up in 40uL Sigma 18 meg-ohm water


title: H3K9me2 ChIP in ∆epe1 cells

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

value: ∆epe1 cells


title: 2502-TF

description: squamous cell lung carcinoma _Tumor Front_2502

value: Tumor Front


title: 2502-LF

description: squamous cell lung carcinoma _Lung Front_2502


title: After step-up, Time 6, replicate 4

city: Durham

first: Ji

last: Zhang

state: NC

address: Room 136 Hudson Hall

department: Department of Biomedical Engineering

institute: Duke University

hyb_protocol: • Make hybridization buffer fresh each time.  • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA.  • Add 1ul each poly dA and appropriate Cot-1 DNA.  • Heat at 95ºC for 2 minutes and put on ice to cool down.  • Mix well and load sample to the array slide with lifter cover slip.  • Hybridize overnight in 42ºC water bath.

scan_protocol: Scanned by GenePix 4000B and quantified using GenePix software

data_processing: LOWESS normalized. Agilent GeneSpring GX was used.

organism: Sus scrofa

source_name: Cultured endothelial cells

label_protocol: Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion), and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.

growth_protocol: Porcine aortic endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum. Passage 3 - 5 cells were used.

extract_protocol: Qiagen RNeasy  kit following manufacturer's protocol

tag: cell type

value: Cultured endothelial cells

tag: time point

value: 360 minutes

source_name: reference RNA

value: cultured porcine aortic endothelial cells (passage 3)


title: 10uM ecdy 4hrs rep1

source_name: Drosophila melanogaster, Kc 167 cells, 10uM 20-hydroxy-ecdysone, 4hrs

extract_protocol: Cultures are grown to a minimum density of 5x10^6 cells per mL prior to extraction.  Trizol is used at a ratio of 1 mL per 10^7 cells.  Extraction procedure is as described by the manufacturer with centrifugation in a Sorvall SS-34 rotor.  Final pellets are air dried and then resuspended in Sigma 18 meg-ohm water to obtain a final RNA concentation of no less than 4ug per uL.

value: embryo-derived

tag: developmental stage

value: late embryonic

value: 10uM 20-hydroxy-ecdysone

value: The sample had an [RNA] of 3.66 ug per uL and an OD ratio of 2.03. Details:3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water

source_name: Drosophila melanogaster, Kc 167 cells, Ethanol Control

value: Ethanol Control

value: Six tubes of control cells (3.0x10^7 cells per tube) were extracted separately.  Following verification of the quality of each sample by spec ratio they were pooled.  The final sample had an [RNA] of 3.37 ug per uL and an OD ratio of 1.99.Details (per tube):3mL Trizol600uL chloroform2.5mL isopropanol1.5mL 75 percent EtOH-brought up in 50uL Sigma 18 meg-ohm water