title: Female 5ppm fish 2

description: collected at six weeks

source_name: female 5ppm

extract_protocol: Total RNA from individual fish was isolated using Trizol reagent (Invitrogen). One ml of Trizol was used for individual fish, which was homogenized by Power Gen 500 (Fisher), and 0.2 ml of chloroform was added for dissociation of nucleoprotein by shaking the tubes by hand for 15 seconds. The samples were centrifuged at 12000g for 15 minutes at 8℃. Upper aqueous phase was moved to a clean 1.5 ml Eppendorf tube, and 0.5 ml of isopropyl alcohol was added for precipitation of the RNA by incubating the samples at room temperature for 10 minutes. The samples were centrifuged at 12000g for 15 minutes at 8℃. Then the supernatant was removed and 1 ml of 75% ethanol was added for washing the pellet, and the samples were centrifuged at 12000g for 5 minutes at 8℃. The samples were air-dried then dissolved in RNase-free water. The concentration of RNA was determined by ND-1000 NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Further RNA-purification was performed using the RNeasy MiniElute cleanup kit (Qiagen) following the manufacturer’s protocol. Quality of zebrafish RNA was determined by Experion RNA StdSens chip (Bio-Rad).

value: 5ppm MeHg


title: RD-CONT-72H

status: Public on Dec 12 2012

type: RNA

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

country: Israel

institute: Sheba Medical Center at Tel HaShomer

hyb_protocol: Biotin-labeled cRNA (15 µg) was hybridized to a GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays (HG-U133, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Analysis was conducted with a GeneChip Scanner 3000.

data_processing: Differential gene expression was evaluated with the Microarray Suite 5.0 software (Affymetrix).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: prostate carcinoma cell lines

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: The P69 and M12 prostate cancer-derived cell lines were cultured in RPMI-1640 medium containing 10 ng/ml EGF, 0.1 nM dexamethasone, 5 µg/ml insulin, 5 µg/ml transferrin, and 5 ng/ml selenium.

extract_protocol: Total RNA was prepared from 5-Aza-treated and untreated P69 and M12 cells using the Trizol reagent (InVitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with the demethylating agent 5'-Aza-2'-deoxycytidine (5-Aza) for 72 h, with daily medium changes. At the end of the incubation period the cells were harvested and total RNA was prepared for cDNA microarray analysis.

tag: cell line

value: RD

tag: treatment

value: control

tag: time


title: M12-5AZA-72H


title: M12-5AZA-96H


title: Primary neonatal keratinocytes_control_rep1

status: Public on Nov 30 2012

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

country: USA

institute: Stanford

description: replicate 1

hyb_protocol: Affymetrix GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA normalization using justRMA package in R 2.11.1

source_name: Primary neonatal keratinocytes

label_protocol: Affymetrix 3' IVT Express Kit

growth_protocol: Keratinocytes were grown in subconfluent condition with the medium composed of 50% complete Keratinocyte-SFM (Life Technologies) and 50% Medium 154 (Life Technologies).

extract_protocol: Qiagen RNeasy Plus kits were used to isolate total RNA.

treatment_protocol: shRNA knock down

tag: cell type

value: Primary neonatal keratinocytes

tag: genotype/variation


title: P69-5AZA-72H


title: M12-CONT-96H


title: Primary neonatal keratinocytes_ACTL6a_i_rep1

description: replicate 1

value: ACTL6a knock down


title: M12-CONT-72H


title: control of 5 fish vs. common reference of 10

status: Public on Jun 01 2013

city: Clemson

first: Qing

last: Liu

state: SC

address: Jordan Hall

department: Biological Sciences

institute: Clemson University

description: collected at six weeks

hyb_protocol: Labeled DNAs were hybridized to prewarmed microarrays at 50°C for 16 hours. Following the first hybridization, arrays were washed in 2X SSC, 0.2% SDS solution at 50 ℃ 1 x 15 min, 2X SSC 1 x 15 min at room temperature, then 0.2X SSC for 1 x 15 min at room temperature. The fluorescent labeling hybridization (50 ℃ for 4hr) utilized the Genisphere 3DNA Cy3 and Cy5 capture reagents in formamide hybridization buffer. The slides were washed as described above, and the arrays were dried by centrifugation.

scan_protocol: Microarrays were scanned using the ScanArray Express (PerkinElmer) at 10 um resolution. The TIFF images of arrays were generated with ScanArray Express software and the intensities of raw data of two-channel arrays were collected by the ImaGene 6.0 (BioDiscovery).

data_processing: Statistical analysis of microarray data was performed using scripts written in R language. These scripts included functions of background correction and array normalization. Background correction was done using background subtraction by the function “backgroundCorrect” and normalization was done by the function  “normalizeBetweenArrays” with “lowess” method, which was implemented in the package LIMMA (version 2.18.3) from the Bioconductor project (version 2.4). Bayesian analysis generated p-values using the eBayes function.

organism: Oncorhynchus mykiss

source_name: common reference

label_protocol: RNA of ten fish from control group was pooled as a common reference, and total RNA of five individual fish from control and MeHg-treated groups were randomly selected for comparison to the common reference.  cDNA was synthesized from 1 μg pooled RNA using SuperScript II Reverse Transcriptase (Invitrogen) according to the manufacturer’s protocol . The common reference cDNA targets were labeled with Cy3 and cDNA of individual fish from each group was labeled with Cy5 using the Array 900 Expression Array Detection kit (Genisphere) according to the manufacturer’s protocol. Briefly, cDNA was denatured at 80 ℃ for 5 min in the presence of oligo (dT) primers with 3’ unique capture sequences (used in the Cy3 or Cy5 labeling reactions, respectively), then reverse transcribed at 42 ℃ (2.5 hours). The capture sequence-labeled cDNAs for each comparison were combined and incubated at 50 ℃ until applied to microarray hybridization.

growth_protocol: All rainbow trout were handled following Animal Care and Use Committee (ACUC) protocols of University of Wisconsin–Milwaukee. Eyed trout eggs were ordered from Fish and Wildlife Service of Ennis National Fish Hatchery (MT), reared in 10 ℃ dechlorinated, filtered municipal water (DFMW) in the NIEHS Children's Environmental Health Sciences Core Center (CEHSC) animal facility.  , and 45 days after hatching MeHg dietary exposures were initiated.

extract_protocol: Total RNA from individual fish was isolated using Trizol reagent (Invitrogen). One ml of Trizol was used for individual fish, which was homogenized by Power Gen 500 (Fisher), and 0.2 ml of chloroform was added for dissociation of nucleoprotein by shaking the tubes by hand for 15 seconds. The samples were centrifuged at 12000g for 15 minutes at 8℃. Upper aqueous phase was moved to a clean 1.5 ml Eppendorf tube, and 0.5 ml of isopropyl alcohol was added for precipitation of the RNA by incubating the samples at room temperature for 10 minutes. The samples were centrifuged at 12000g for 15 minutes at 8℃. Then the supernatant was removed and 1 ml of 75% ethanol was added for washing the pellet, and the samples were centrifuged at 12000g for 5 minutes at 8℃. The samples were air-dried then dissolved in RNase-free water. The concentration of RNA was determined by ND-1000 NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Further RNA-purification was performed using the RNeasy MiniElute cleanup kit (Qiagen) following the manufacturer’s protocol.

treatment_protocol: Fish were fed Biodiet starter (Bio-Oregon) (4% body weight per day) with MeHg added at 0ppm, 0.5ppm, 5ppm and 50ppm (with ethanol as vehicle) for six weeks.

tag: sample type

value: pooled RNA of 10 fish from control group

tag: tissue

value: whole fish

tag: developmental stage

value: juevenile

source_name: 5 fish from control group

value: RNA of 5 fish from control group

value: jeuvenile


title: P69-CONT-72H


title: P69-CONT-96H


title: RD-5AZA-72H


title: P69-5AZA-96H


title: Rh30-5AZA-72H


title: Airwayepithelial_Injured_WT_replicate1

status: Public on Nov 01 2012

city: Seattle

first: Sina

last: Gharib

state: WA

address: 850 Republican St.

department: Medicine

institute: University of Washington

hyb_protocol: Standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner, and the GeneChip Operating Software (GCOS) was used for image analysis.

data_processing: Background adjustment and quantile normalization using the Robust Multichip Average algorithm (http://www.bioconductor.org) using Log2 transformed intensities.

label: Biotin labeled cRNA

organism: Mus musculus

source_name: Airway epithelial cell injured

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Affymetrix Mouse Genome 430A 2.0 oligonucleotide microarrays at University of Washington’s Center for Array Technology according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated using the Trizol protocol (Invitrogen; Carlsbad, CA). RNA quality was confirmed by a Bioanalyzer 2100 (Agilent; Santa Clara, CA).

treatment_protocol: Cells were cultured for 24 hours in serum-free medium before RNA isolation. Injury was created by 3 parallel scratches with a sterile p-200 pipet tip.

tag: strain

value: C57BL/6 mice

tag: genotype

value: WT

value: Airway epithelium

tag: culture

value: Air-liquid interface


title: Airwayepithelial_Injured_WT_replicate2


title: Airwayepithelial_Baseline_WT_replicate3

source_name: Airway epithelial cell uninjured

treatment_protocol: Cells were cultured for 24 hours in serum-free medium before RNA isolation.


title: Airwayepithelial_Baseline_WT_replicate2


title: Airwayepithelial_Baseline_WT_replicate4


title: Airwayepithelial_Injured_MMP7ko_replicate2

treatment_protocol: Cells were cultured for 24 hours in serum-free medium before RNA isolation. Injury was created by 3 parallel scratches with a sterile p-200 pipet tip


title: Airwayepithelial_Injured_MMP7ko_replicate3


title: Airwayepithelial_Injured_MMP7ko_replicate4


title: pwrn antisense RNA

status: Public on Oct 10 2012

description: Value is intensity fold over background

hyb_protocol: For hybridization ProtoArray Human Protein Microarray v5.0 (Invitrogen, cat# PAH052520) was used. Prior to hybridization, each microarray was equilibrated first to 40C overnight and then to 250C at least for 15 minutes. The microarray slide was assembled in Gentel SIMplex 16 Multi-Array System device (Gentel biosciences, cat# 4-1007) with custom modifications including modified bottom gasket and the top spacers (Additional file 1). The bottom gasket was cut out from silicone slab as a rectangular seal with the following dimensions in mm: outer 65L x 25W x 4H, inner 59L x 20W x 4H. Top spacers were cut out from polycarbonate piece as a rectangular shape with the following dimensions in mm: Upper spacer 5L x 22W x 1H, lower spacer 12L x 22W x 1H. First, microarray slide was placed inside Gentel SIMplex 16 Multi-Array device bottom holder piece, next the silicone gasket was carefully placed on the top of the slide and the device top piece held in place with tightening screws. The slide surface was blocked in 0.7 mL blocking buffer BL: 40 mM Tris-HCl (pH 8.0), 1% BSA (w/v) (globulin free, Sigma, cat# A7638), 100 μg/ml Yeast tRNA, 20 μg/mL heparin and 1 mM DTT for 1 hour at room T0C with gentle agitation. After completion of the blocking step, 10 pmol Cy5 labeled RNA was added to 0.7 mL binding buffer BB: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, 0.01% Igepal CA-630, 5% glycerol, 0.2 units/μl RNAseOUT. The blocking buffer was replaced with binding buffer containing labeled RNA and microarray slides incubated in the dark at 250C for 1 hour with gentle agitation. Following RNA hybridization binding buffer was removed and washing steps were implemented using 3 times exchange of 0.75 mL WB buffer: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, 0.01% Igipal 40, 5% Glycerol, 0.2 units/μl RNAseOUT for at least 5 minutes each. Finally, the microarray slide was washed in 0.75 mL washing buffer WBF: 40 mM Tris-HCl (pH 8.0), 150 mM sodium chloride, 0.5 mM Magnesium acetate, 10 μg/ml Yeast tRNA, 10 μg/mL heparin, 1 mM DTT, at least 3 times for 5 minutes each. After the last wash, the WBF buffer was removed partially in order to prevent the slide from drying prematurely and slide holder device disassembled immediately. The hybridized microarray slide was placed in ArrayIt microarray high-speed centrifuge and the residual WBF buffer removed via a 30 seconds. Dry slide was scanned at 635 nm (Cy5) using GenePix 4000B Microarray scanner (Molecular Devices) immediately after or at least within 2 hours of the completion of the hybridization.

scan_protocol: Dry slide was scanned at 635 nm (Cy5) using GenePix 4000B Microarray scanner (Molecular Devices) immediately after or at least within 2 hours of the completion of the hybridization. The intensity of the 635 nm wavelength signal at each spotted protein location was determined with GenePix Pro 6.1 software (Molecular Devices)

data_processing:
To quantify RNA-protein interactions, the intensity of 635 nm signal (F635) was divided by the local background intensity (B635) at each of the duplicate spots for a given protein
The sense and antisense IVT RNAs for each target were both labeled with Cy5 and hybridized to the same array.  Therefore, there are only 10 gpr files for the 20 Samples.  To avoid duplication, the gpr files are provided as supplementary files on the Series record.

source_name: In vitro transcribed RNA

label_protocol: RNA labeling for microarray hybridizations was performed using Label IT μArray Cy5 labeling kit (Mirus). We first carefully optimized the labeling procedure in order to achieve between 1 to 3 Cy5 dyes covalently attached to RNAs used. This was accomplished via the following modifications from the original manufacturers protocol: the total reaction volume was kept at 25 μl, the ratio of RNA:Label IT Cy5 reagent at 10:1 (w:v) and reaction time not more then 30 minutes at 370C. Briefly, 5 μg RNA in water was mixed with 5 μl Label IT Cy5, diluted 1 to 10 in water to obtain a final volume of 25 μl and incubated 30 minutes at 370C. The reaction was stopped by addition 2.5 μl of 10x STOP buffer (Mirus). The volume was increased to 100 μl with water, supplemented with glycogen (Invitrogen) to final concentration of 0.2 μg/μl, mixed and RNA ethanol precipitated in the presence of 0.5 M NaCl at -20oC for at least 1 hour. The labeled RNA was extensively washed in 70% ethanol, dried and resuspended in 16 μl water. RNA labeling density was evaluated using NanoDrop 1000 spectrophotometer (Thermo Scientific) and visualized using denaturing agarose gel-electrophoreses

extract_protocol: N/A.  RNA used was in vitro transcribed

tag: sequence

value: pwrn

tag: sense/antisense

value: antisense


title: Airwayepithelial_Baseline_MMP7ko_replicate1

treatment_protocol: Cells were cultured for 24 hours in serum-free medium before RNA isolation


title: Airwayepithelial_Baseline_MMP7ko_replicate4


title: Airwayepithelial_Baseline_WT_replicate1


title: Airwayepithelial_Baseline_MMP7ko_replicate2


title: myc sense RNA

description: Value is intensity fold over background

value: myc

value: sense


title: pwrn sense RNA

description: Value is intensity fold over background


title: p53 antisense RNA

description: Value is intensity fold over background


title: Airwayepithelial_Injured_MMP7ko_replicate1


title: myc antisense RNA

description: Value is intensity fold over background


title: p53 sense RNA

description: Value is intensity fold over background


title: lncrbm26 antisense RNA

description: Value is intensity fold over background


title: lncrbm26 sense RNA

description: Value is intensity fold over background


title: hras antisense RNA

description: Value is intensity fold over background

value: hras


title: dleu1 antisense RNA

description: Value is intensity fold over background


title: hras sense RNA

description: Value is intensity fold over background


title: sox2ot sense RNA

description: Value is intensity fold over background


title: sox2ot antisense RNA

description: Value is intensity fold over background


title: dleu1 sense RNA

description: Value is intensity fold over background


title: bcl2 sense RNA

description: Value is intensity fold over background


title: igf2rnc antisense RNA

description: Value is intensity fold over background


title: bcl2 antisense RNA

description: Value is intensity fold over background


title: igf2rnc sense RNA

description: Value is intensity fold over background


title: occ1 antisense RNA

description: Value is intensity fold over background


title: occ1 sense RNA

description: Value is intensity fold over background


title: TINCR RIAseq even pool

type: SRA

description: RNA sequencing

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to NCBI build 36.1/hg18 using TopHat (Trapnell et al. 2009, Langmead et al. 2010) with default options.
Search for enriched peaks in the even and odd samples compare to the input control was performed by scanning each gene using 100 nucleotides sliding windows. Number of reads that overlap with each 100 nucleotides sliding window was calculated using coverageBed function in BEDTools for even, odd, and input samples (Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842).
Signal in even, odd and input samples was defined as normalized reads counts to the total number of aligned read in each sample. Only sliding windows that have at least 1 read in every sample were included for downstream analysis. Enrichment score of each sliding window was defined as the minimun of even and odd signal divided by the signal in input
An average log2(EScore) and standard deviation of log2(EScore) were also calculated, noted here as mean and SD, and a sliding window was defined as enriched if its log2(EScore) > mean + 1.5SD
Genome_build: hg18

source_name: Differentiated keratinocytes

extract_protocol: cDNA was generated using the Ovation-v2 kit (Nugen) per manufacturer's protocol, and was further sheared into ~130bp fragments using a Covaris sonicator. Short cDNA fragments were then end-repaired, filled in with dA, and ligated to illumina-compatible adaptors. Successfully ligated cDNA were enriched with 15 rounds of PCR amplification, and final product of 200-400bp in size were gel purified and submitted for sequencing on a GAIIx

tag: differentiation

value: Day 5 differentiated

tag: crosslinking

value: 1% glutaraldehyde 10min r.t.

value: "even" probes which is one of two orthogonal sets of biotinylated oligos that were tiled across the RNA named TINCR

value: TINCR RIAseq even pool

value: differentiated keratinocytes


title: TINCR RIAseq odd pool

description: RNA sequencing

value: "odd" probes which is one of two two orthogonal sets of biotinylated oligos that were tiled across the RNA named TINCR

value: TINCR RIAseq odd pool


title: Input RNA

description: RNA sequencing

value: Input RNA


title: Hepatocellular carcinoma HCC15

status: Public on Sep 30 2012

city: Suwon, Korea

first: Jung Woo

last: Eun

state: Korea

address: Department of Gastroenterology

country: South Korea

institute: Ajou University of Korea

hyb_protocol: This protocol uses directly isolated RNA without RNA target amplification, and ultimately reflects the cellular microRNA molar ratio, thus providing for the reliability of hybridization signals. The streptavidin conjugated dye stain (SA-S Dye) and the staining buffer (Buffer S) reagents are also included in this kit. Their preparation and use in the post-hybridization staining procedure is described below in the hybridization assay section.

scan_protocol: The SA-S dye stain signal can be detected using the GenePix 4000B scanner’s 635 nm wavelength (Cy5) channel.

data_processing: he arrays with hybridized targets were scanned using an Axon scanner and the scanned images were analyzed using GenePix® Pro 5.0 software (Axon Instruments) and spots of poor quality determined by visual inspection were also removed from further analysis. The resulting data, the average of 3 mean fluorescence signal intensities for each probe, collected from each array was submitted to the GenePlex 3.0 (Istech Inc. Seoul, Korea) database. Data were normalized using the method of quantile normalization and class-specific filtering.

source_name: Hepatocellular carcinoma HCC

label_protocol: This procedure is used to attach a biotin label to the 5’ ends of RNA molecules.Total 10ug amount of RNA used.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen). RNA quality control was performed with Bio-Rad Experion.

value: Hepatocellular carcinoma HCC tissue


title: Hepatocellular carcinoma HCC16


title: Hepatocellular carcinoma HCC9


title: Hepatocellular carcinoma HCC11


title: Hepatocellular carcinoma HCC13


title: Hepatocellular carcinoma HCC5


title: Hepatocellular carcinoma HCC12


title: Hepatocellular carcinoma HCC10


title: siSTAU rep2

description: replicate 2

source_name: Organotypic human epidermis

growth_protocol: Keratinocytes were grown in Gibco SFM medium and nucleofected with a Lonza normal human keratinocyte kit according to manufacturer's protocol. After nucleofection, cells recovered in cell culture for 12-24 hours and then were seeded onto devitalized human dermis.

extract_protocol: Qiagen RNeasy kits were used to isolate total RNA.

treatment_protocol: Nucleofection with siRNA targeting the gene of interest or a non-targeting control

value: STAU Knock down 2

value: Organotypic human epidermis


title: Hepatocellular carcinoma HCC8


title: Hepatocellular carcinoma HCC6


title: Hepatocellular carcinoma HCC7


title: Hepatocellular carcinoma HCC14


title: Hepatocellular carcinoma HCC4


title: Control TINCR repB

description: replicate 2

value: Control TINCR B


title: siTINCR repA

description: replicate 2

value: TINCR Knock down A


title: siSTAU rep1

description: replicate 1

value: STAU Knock down 1


title: Airwayepithelial_Baseline_MMP7ko_replicate3

value: C57BL/6 mice

value: Airway epithelium

value: Air-liquid interface


title: Hepatocellular carcinoma HCC1


title: Normal liver N8

source_name: Normal liver

value: Normal liver tissue


title: Hepatocellular carcinoma HCC2


title: Normal liver N7


title: Normal liver N5


title: Normal liver N6


title: siTINCR repB

description: replicate 2

value: TINCR Knock down B


title: Control TINCR repA

description: replicate 1

value: Control TINCR A


title: Control STAU rep1

description: replicate 1

value: Control STAU 1


title: Control STAU rep2

description: replicate 2

value: Control STAU 2


title: Normal liver N4


title: Hepatocellular carcinoma HCC3


title: Normal liver N3


title: Normal liver N2


title: Normal liver N1


title: Visceral fat_OSA_10

status: Public on Sep 01 2012

hyb_protocol: Standard hybridization protocol was used as recommended by Affymterix

data_processing: Background adjustment and quantile normalization using the Robust Multichip Average algorithm  using Log2 transformed intensities.

source_name: Visceral adipose tissue

label_protocol: 100 ng of total RNA was labeled using Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer's protocols.

extract_protocol: Total RNA was obtained using RNeasy Lipid Tissue Mini Kit with DNase treatment (Qiagen, Valencia, CA) according to the manufacturer's protocol. The integrity of purified total RNA samples was assessed qualitatively on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Visceral fat biopsies were obtained intra-operatively from the omentum.  Samples were rinsed with PBS to remove excess blood, minced, immediately frozen in liquid nitrogen and stored at −80°C.

tag: subject

value: OSA


title: Visceral fat_OSA_5


title: Visceral fat_Control_1

value: Control


title: Visceral fat_OSA_4


title: Visceral fat_Control_6


title: Visceral fat_OSA_6


title: Visceral fat_Control_7


title: Visceral fat_Control_4


title: Visceral fat_OSA_7


title: Visceral fat_OSA_2


title: Visceral fat_OSA_3


title: Visceral fat_OSA_1


title: Visceral fat_OSA_8


title: Visceral fat_Control_5


title: Visceral fat_OSA_9


title: Visceral fat_Control_3


title: Visceral fat_Control_8


title: Visceral fat_Control_2


title: Keratinocytes_ΔNp63α WT_rep2

status: Public on Jun 18 2012

description:
replicate 2
WT_rep2.CEL

growth_protocol: Keratinocytes were grown in Gibco SFM medium till 100% confluent with addition of 1.2 mM Ca2+ for 3 Days to induce differentiation.

treatment_protocol: siRNA knock down

value: primary neonatal keratinocytes

value: ΔNp63α Overexpression


title: ADAR1 Control [miRNA]

status: Public on Aug 31 2012

description:
microRNA expression data from ADAR1 manipulated cell system
ADAR1 Control__mirs
C360_Control_(miRNA-1_0).CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix protocol.

data_processing: CEL file imported by Partek,  ,Pre-background Ajustment: Adjust for GC Content,Background Correction: RMA Background Correction,QuantileNormalization: Quantile Normalization,Log Probes using Base: 2Probeset Summarization: Mean

source_name: 624mel cells with non-manipulated ADAR1 expression

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 600 ng total RNA (Affymetrix wt_sensetarget_label_manual)

growth_protocol: The 624mel cel line was maintained in RPMI 1640 medium supplemented with 10% fetal calf serum and antibiotics

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Sigma). The extracted RNA was additionaly purified using PLG column according to the manufacturer's instructions.techique

treatment_protocol: 624mel cells were transduced with shRNA or control plasmids according to the manufacturer's instructions (Fermentas) and maintained in the apropriate selection medium containing puromycine. Selected stable transfectants that presented reduced ADAR1 expression, as compared to the control cells, were further grown and their total RNA was isolated.

tag: disease phenotype

value: stage IV melanoma,  metastatic lesion


title: ADAR1 KD [miRNA]

description:
microRNA expression data from ADAR1 manipulated cell system
ADAR1 KD__mirs
C359_ADAR1_kd_(miRNA-1_0).CEL

source_name: 624mel cells with reduced ADAR1 expression

value: stage IV melanoma,  metastatic lesion (enhanced aggressive phenotype)


title: Keratinocytes_p63i_rep2

description:
replicate 2
d3_p63i_rep2.CEL

value: TP63 knock down


title: Keratinocytes_ΔNp63α WT_rep1

description:
replicate 1
WT_rep1.CEL


title: Keratinocytes_R500P_rep2

description:
replicate 2
R500P_rep2.CEL

value: ΔNp63α(R500P) Overexpression


title: Keratinocytes_R500P_rep1

description:
replicate 1
R500P_rep1.CEL


title: ADAR1 Control [mRNA]

description:
Gene expression data from ADAR1 manipulated cell system
ADAR1 Control_expression
B634_Scr_(HuGene-1_0-st-v1).CEL


title: Keratinocytes_I482ti_rep1

description:
replicate 1
I482T_rep1.CEL

value: ΔNp63α(I482T) Overexpression


title: MC_RFP

status: Public on Apr 28 2012

description: RNA-seq from primary human melanocytes infected with RFP lentivirus (control)

data_processing:
Fragment length average = 350bp +/- 50bp
Briefly, Raw reads mapped to hg18 using Tophat. De novo assembly was performed using Scripture. Assembly to Refseq/Gencode was performed using Cufflinks and differential expression was calculated using Cuffdiff.

source_name: Melanocytes + RFP (Control)

growth_protocol: Melanocytes cultured in melanocyte medium 154 (Invitrogen).

extract_protocol: RNA extracted using RNeasy kit (Qiagen). Poly-A mRNA was selected for and processed using the Illumina RNA sequencing kit.

treatment_protocol: Melanocytes were infected with lentivirus transmitting either red fluorescent protein (RFP) control or BRAFv600e. Samples were harvested 3 days after infection for RNA extraction.

value: Melanocytes over-expressing red fluorescent protein (RFP) - control sample


title: mm4

description: RNA-seq from primary human melanoma sample

source_name: primary melanoma #2

value: Primary melanoma


title: Keratinocytes_p63i_rep1

description:
replicate 1
d3_p63i_rep1.CEL


title: Input

description: input

library_source: genomic

data_processing: Reads in each samples were aligned using "Bowtie"(version 0.12.6). Peaking calling was performed by "MACS" (version 1.4.0rc2). For complete methods please refer to the paper.

molecule: genomic DNA

source_name: keratinocytes

extract_protocol: Cells are crosslinked in 1% formaldehyde and lysates clarified by sonication. p63 DNA comlplexes were isolated using Santa Cruz anti-p63 4A4 antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody lot#

tag: chip antibody catalog#

value: neonatal keratinocytes

tag: differentiation stage


title: p63 Progenitor

description: p63 ChIP

value: anti-p63 4A4

value: Santa Cruz

tag: cell type

value: progenitor


title: ADAR1 KD [mRNA]

description:
Gene expression data from ADAR1 manipulated cell system
ADAR1 KD_expression
B635_KD1_(HuGene-1_0-st-v1).CEL


title: p63 Differentiated

description: p63 ChIP

value: differentiated


title: mm2

source_name: primary melanoma #1


title: Keratinocytes_siRNA control_rep2

description:
replicate 2
d3_CTRi_rep2.CEL

source_name: Primary neonatal keratinocytes

tag: genotype/variation

value: control


title: d3_kc_diff_1

status: Public on Feb 02 2012

description:
Paired end RNAseq
d3_kc_diff_1: Day 3 differentiated keratinocytes RNA sequencing paired end 1
d3_kc_diff_2: Day 3 differentiated keratinocytes RNA sequencing paired end 2
Day 3 differentiated keratinocytes BigWig file aligned to hg18

data_processing:
Reads in each sample were aligned to hg18 using TopHat and reference annotation based transcriptome assembly was performed with Cufflinks.  Differential expression analysis was performed with the Cuffdiff module of Cufflinks.
Genome Build:
d3_kc_diff.bw: hg18

molecule: polyA RNA

source_name: Primary human keratinocytes

growth_protocol: Keratinocytes were grown in Gibco SFM medium in sub-confluent conditions for the d0, progenitor state, and induced to differentiate by plating the cells at confluency and treating the cells with SFM medium + 1.2 mM Ca2+ for 3 or 6 days to induce differentiation.

extract_protocol: Illumina PE RNA seq library prep protocol

treatment_protocol: See above for differentiation induction cell culture conditions

value: primary keratinocytes

tag: day of differentiation


title: MC_BRAF

description: RNA-seq from primary human melanocytes infected with BRAFV600E lentivirus

source_name: Melanocytes + BRAFv600e

value: Melanocytes over-expressing BRAFv600e


title: Keratinocytes_siRNA control_rep1

description:
replicate 1
d3_CTRi_rep1.CEL

value: primary neonatal keratinocytes


title: Hep3B-Mock

status: Public on Mar 01 2012

description: RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenPlex 3.0

source_name: human HCC cell line

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

growth_protocol: Cell line was grown in RPMI1640 or DMEM medium supplemented with 10 % fetal bovine serum (FBS; Sigma, St Louis, MO), 100 units/ml of penicillin and streptomycin. Cultures were incubated at 37℃ in a humidified incubator at 5% CO2.

extract_protocol: For each the experimental conditions, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. RNA quality control was performed with Bio-Rad Experion.

treatment_protocol: The cells were harvested by Trypsin/EDTA, replated at 1.5 × 105 cells in a 60 mm dish, and allowed to grow overnight at 37℃ in a humidified incubator at 5% CO2. After 16~18 h of plating, the cells were transfected with empty mock and pcDNA_HDAC6 in Opti-MEM (Invitrogen). Transfection was carried out using 6μl of lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s specifications. After 4~6 h of transfection, the medium was replaced by new fresh RPMI 1640 medium supplemented with 10% FBS.

tag: cell line

tag: transfected

value: Mock


title: d6_kc_diff_1

description:
Paired end RNAseq
d6_kc_diff_1: Day 6 differentiated keratinocytes RNA sequencing paired end 1
d6_kc_diff_2: Day 6 differentiated keratinocytes RNA sequencing paired end 2
Day 6 differentiated keratinocytes BigWig file aligned to hg18

data_processing:
Reads in each sample were aligned to hg18 using TopHat and reference annotation based transcriptome assembly was performed with Cufflinks.  Differential expression analysis was performed with the Cuffdiff module of Cufflinks.
Genome Build:
d6_kc_diff.bw: hg18


title: d0_kc_diff_1

description:
Paired end RNAseq
d0_kc_diff_1: Progenitor keratinocytes RNA sequencing paired end 1
d0_kc_diff_2: Progenitor keratinocytes RNA sequencing paired end 2
Progenitor keratinocytes BigWig file aligned to hg18

data_processing:
Reads in each sample were aligned to hg18 using TopHat and reference annotation based transcriptome assembly was performed with Cufflinks.  Differential expression analysis was performed with the Cuffdiff module of Cufflinks.
Genome Build:
d0_kc_diff.bw: hg18


title: si-SIRT1

source_name: human hepatocellular carcinoma cell line

growth_protocol: Cell line was grown in RPMI1640 medium supplemented with 10 % fetal bovine serum (FBS; Sigma, St Louis, MO), 100 units/ml of penicillin and streptomycin. Cultures were incubated at 37℃ in a humidified incubator at 5% CO2.

extract_protocol: For each experimental condition, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. RNA quality control was performed with Bio-Rad Experion.

treatment_protocol: The SNU-182 cell lines were transfected each siRNA with Lipofectamine 2000 reagent (Invitrogen, Carlsbad, CA, USA)

tag: transfection

value: SIRT1 siRNA


title: Colo829 infected with BANCR shRNA 2

description: shRNA 2

source_name: Colo829 melanoma cells

growth_protocol: Colo829 cells were grown in RPMI 1640 medium supplemented with 10% FCS and antibiotics

treatment_protocol: Cells were lentivirally infected with either SCR control shRNA or independent shRNAs targeting BANCR

value: Colo829 melanoma cells

value: BANCR knockdown


title: si-Cont

value: Control siRNA


title: Colo829 infected with BANCR shRNA 1

description: shRNA 1


title: Colo829 infected with SCR control shRNA

description: Scrambled control

treatment_protocol: Cells were lentivirally infected with either SCR control shRNA or independent shRNAs targeting BLNCR1


title: Keratinocytes_ZNF750i_rep1

status: Public on Feb 15 2012

description: replicate 1

tag: treatment

value: ZNF750 knock down


title: Keratinocytes_I482T_rep2

description:
replicate 2
I482T_rep2.CEL

value: ΔNp63α(I482T) Overexpression


title: Keratinocytes_control_rep1

description: replicate 1


title: Keratinocytes_ZNF750i_rep2

description: replicate 2


title: Keratinocytes_control_rep2

description: replicate 2


title: Hep3B-pcDNA_HDAC6


title: Keratinocytes_siANCR_rep2

status: Public on Jan 01 2012

description: replicate 2

source_name: ANCR knockdown

growth_protocol: Keratinocytes were grown in Gibco SFM medium in subconfluent conditions to maintain the progenitor state

treatment_protocol: siRNA knock down (1nmol)

value: Primary neonatal keratinocytes


title: Keratinocytes_Klf4i_rep2

description: replicate 2

value: KLF4 knock down


title: Keratinocytes_siANCR_rep1

description: replicate 1


title: Keratinocytes_siRNA control_rep2

description: replicate 2

source_name: control


title: Keratinocytes_siRNA control_rep1

description: replicate 1


title: Keratinocytes_Klf4i_rep1

description: replicate 1


title: Ctr (C043)

status: Public on Dec 31 2011

description: RKO colon cancer cells transfected with empty Flag vector (Ctr).

scan_protocol: Affymetrix protocol

data_processing: CEL file imported by Partek, Pre-background Ajustment: Adjust for GC Content,Background Correction: RMA Background Correction, QuantileNormalization: Quantile Normalization, Log Probes using Base: 2 Probeset Summarization: Mean

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

treatment_protocol: Cell were harvested 24 h after transfection for mRNA extraction

value: empty Flag vector (Ctr)

value: RKO colon cancer cells


title: HIPK2 (C092)

description: RKO colon cancer cells transfected with HIPK2-Flag vector (HIPK2).

value: HIPK2-Flag vector (HIPK2)


title: Hep3B-shHDAC2

source_name: human liver cancer cell line

growth_protocol: Cell line was grown in RPMI-1640 medium supplemented with 10 % fetal bovine serum, 100 units/ml of penicillin and streptomycin. Cultures were incubated at 37℃ in a humidified incubator at 5% CO2.

treatment_protocol: HDAC2 gene silencing was performed by transfecting Hep3B cells with  HDAC2 shRNA expression plasmids for 48 hours.


title: keratinocyte_differentiated

hyb_protocol: All hybridizations were performed according to the manufacturer's instructions for the MAUI 12-bay hybridization system

scan_protocol: All arrays were scanned with the Axon Scanner and processed with GenePix software

data_processing: Array data was RMA normalized with the Nimblegen Nimblescan software. Probe-level data within each channel was mapped to the annotated non-coding RNAs and novel intergenic RNAs derived from the reference based assembly. The signal over each transcript was averaged to provide a measure of expression for each transcript. The change in expression was calculated as a fold change in the average intensity of each transcript between the two channels on the array.

source_name: keratinocyte differentiated RNA

label_protocol: Ambion Message Amp II

growth_protocol: Keratinocytes were grown in Gibco SFM medium in sub-confluent conditions for progenitor state, and induced to differentiate by plating the cells at confluency and treating the cells with SFM medium + 1.2 mM Ca2+ for 5 days to induce differentiation.

value: keratinocyte differentiated


title: MPC conditions, low self-renewal

status: Public on Dec 29 2011

description: MPC conditions, low self-renewal

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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

source_name: Melanoma primary tumor

growth_protocol: Cells were cultured in RPMI supplemented with FBS 10%, HEPES 2.5%, Na Pyruvate 1%, pen-strep 1%, L-Glutamate 2mM. Trypsine was used to dissociate cells from flask.

treatment_protocol: MPC conditions: cells were plated in MCDB 153 medium (Sigma-Aldrich Corp. St. Louis, MO, USA) containing 10% chelated FBS, 2% FBS, 2 mM glutamine, 10 ng/ml stem cell factor (SCF), 2.5 ng/ml basic fibroblast growth factor (bFGF) (both from R&D Systems Inc., Minneapolis MN, USA), and 100 nM endothelin 3 (EDN3) (American Peptide, Sunnyvale, CA, USA) for 14 days including one passage

tag: cell clone

value: MPC conditions, low self-renewal


title: RPMI low self-renewal

description: RPMI low self-renewal

value: RPMI low self-renewal


title: Hep3B-shSIRT7

growth_protocol: Cell line was grown in RPMI1640 medium supplemented with 10 % fetal bovine serum (FBS; Sigma, St Louis, MO), 100 units/ml of penicillin and streptomycin. Cultures were incubated at 37℃ in a humidified incubator at 5% CO2

extract_protocol: For each the experimental conditions, total RNA was extracted from three independent sets of the corresponding cell lines using TRIzol Reagent (Invitrogen), followed by clean up on Ambion columns (Illumina Total-Prep RNA Amplification Kit, Ambion). For each experimental condition, an RNA pool was then obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions. RNA quality control was performed with Bio-Rad Experion

treatment_protocol: The cells were harvested by Trypsin/EDTA, replated at 1 × 106 cells in a 100 mm dish, and allowed to grow overnight at 37℃ in a humidified incubator at 5% CO2. After 16~18 h of plating, the cells were transfected with mock vector and pSilencer-shSIRT7 in Opti-MEM (Invitrogen). Transfection was carried out using 10 μl of lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s specifications. After 4~6 h of transfection, the medium was replaced by new fresh RPMI 1640 medium supplemented with 10% FBS


title: Ctr (C084)

source_name: colon cancer cells transfected with empty Flag vector (Ctr).


title: MPC conditions, high self-renewal

description: MPC conditions, high self-renewal

value: MPC conditions, high self-renewal


title: Human adult kidney (AK63) spheroids

description:
Gene expression from human adult renal cells cultured in suspention in low attachment conditions
Sph AK2

hyb_protocol: Affymetrix wt labeling protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

scan_protocol: Affymetrix wt scanning protocol  as described in  https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

data_processing: RMA

source_name: Spheroid AK63 cells

label_protocol: Affymetrix biotin labeling_ wt kit  (Affymetrix)

growth_protocol: Normal human kidney samples were subjected to adherent and low attachment conditions, that promoted spheroid formation.

extract_protocol: RNA extraction was perfomed using TRIZOL (Invitrogen) protocol

treatment_protocol: Adherent renal cultures were subjected to low attachment conditions (PolyHEMA coated plates) in serum free medium.

value: adult renal cells

tag: culture condition


title: sorted AML (CD34+CD38-) rep5

status: Public on Dec 01 2011

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: affymetrix

source_name: sorted AML (CD34+CD38-)

treatment_protocol: Leukemic peripheral blood (PB) samples from five AML patients  were collected after obtaining informed consent.Mononuclear  cells (MNC) were purified from the samples by Ficoll–  Hypaque density gradient centrifugation, resulting in approximately  1–3 108 cells per sample. To determine the CD34 and  CD38 content, cells were labeled with anti-human CD34-  fluorescein isothiocyanate (FITC) anti-CD38-phycoerythrin (PE)  and IgG isotype control monoclonal antibodies (Miltenyi Biotec,  Auburn, CA, USA) and the CD34 and CD38 expression levels  were determined for each sample using FACS-Calibur (Becton  Dickinson, Franklin Lakes, NJ, USA).


title: Human adult kidney (AK62) spheroids

description:
Gene expression from human adult renal cells cultured in suspention in low attachment conditions
Sph AK1

source_name: Spheroid AK62 cells


title: sorted AML (CD34+CD38+) rep2

source_name: sorted AML (CD34+CD38+)


title: sorted AML (CD34+CD38-) rep4


title: Human adult kidney (AK64) monolayer cultured cells

description:
Gene expression from human adult renal cells cultured as monolayer
Mono AK3

source_name: Monolayer AK64 cells

value: monolayer


title: RPMI high self-renewal

description: RPMI high self-renewal

value: RPMI high self-renewal


title: osteoblast_progenitor

source_name: osteoblast progenitor RNA

growth_protocol: See Cell Applications website for protocols for tissue-specific growth and differentiation protocols

value: osteoblast progenitor


title: sorted AML (CD34+CD38+) rep3


title: adipocyte_progenitor

source_name: adipocyte progenitor RNA

value: adipocyte progenitor


title: Human adult kidney (AK63) monolayer cultured cells

description:
Gene expression from human adult renal cells cultured as monolayer
Mono AK2

source_name: Monolayer AK63 cells


title: osteoblast_differentiated

source_name: osteoblast differentiated RNA

value: osteoblast differentiated


title: Human adult kidney (AK62) monolayer cultured cells

description:
Gene expression from human adult renal cells cultured as monolayer
Mono AK1

source_name: Monolayer AK62 cells


title: keratinocyte_progenitor

source_name: keratinocyte progenitor RNA

value: keratinocyte progenitor


title: adipocyte_differentiated

source_name: adipocyte differentiated RNA

value: adipocyte differentiated


title: Human adult kidney (AK64) spheroids

description:
Gene expression from human adult renal cells cultured in suspention in low attachment conditions
Sph AK3

source_name: Spheroid AK64 cells


title: sorted AML (CD34+CD38-) rep2


title: sorted AML (CD34+CD38-) rep3


title: sorted AML (CD34+CD38-) rep1


title: liver with CCl4+Ebs_noT

description:
A884
Mouse liver injected with CCl4 and transplanted with late Ebs, tumor was not observed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix standard protocol

data_processing: CEL file imported by Partek,  Pre-background Ajustment: Adjust for GC Content, Background Correction: RMA Background Correction, Normalization : QuantileNormalization, Log Probes using Base: 2Probeset Summarization

source_name: liver with CCl4+Ebs

growth_protocol: The mice were housed in temperature and humidity controlled environment with a 12-hr light-dark cycle, and maintained on standard mouse chow and water ad libitum. The mice were sacrificed 4 weeks post transplantation.

treatment_protocol: The livers were harvested and immediately frozen in liquid nitrogen for RNA isolation.

tag: strain/model

value: scid beige mouse

tag: gender

value: female

tag: tissue

value: liver


title: liver with CCl4+Ebs_T1

description:
A885
Mouse liver injected with CCl4 and transplanted with late Ebs, tumor was observed.


title: liver w/o treatment

description:
A883
negative control

source_name: liver w/o treatment


title: liver with CCl4+Ebs_T2

description:
A886
Mouse liver injected with CCl4 and transplanted with late Ebs, tumor was observed.


title: sorted AML (CD34+CD38+) rep1


title: Hep3B mock

status: Public on Aug 17 2011

source_name: human HCC cell line

growth_protocol: Cell line were maintained in RPMI 1640 medium supplemented with 10% FBS, penicillin (100 U/mL) and streptomycin (100 µg/mL)

treatment_protocol: The HDAC1 shRNA template oligos were synthesized by Cosmo4 Company (Korea) and then cloned into pSilencer 3.1-H1 neo (Ambion). The target sequences for shRNAs were as follows: HDAC1 shRNA, 5′-GGCAAGTATTATGCTGTTA-3′; HDAC1 scrambled shRNA, 5′-GTATGTTCCGGTAAGATAT-3′.

value: mock


title: Hep3B shHDAC1

value: shHDAC1 transfection


title: EP-AR T/ERG 1

status: Public on Dec 30 2010

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 1.0 st array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000

data_processing: The data were analyzed with RMA using Partek software (rma-gene-default)

source_name: EP-AR T/ERG

label_protocol: Biotinylated cRNA were prepared according to the Whole Genome Affymetrix protocol from 600 ng total RNA

growth_protocol: Human PrECs were obtained from BioWhittaker (Rockland, ME) and propagated in defined medium (PrEGM) as recommended.

treatment_protocol: PrECs were infected with different combinations of amphotropic retroviruses encoding AR or T/ERG with or without dihydrotestostrone |(DHT) for 96 hrs.

value: immortalized prostate epithelial cells

value: EP-AR T/ERG


title: EP-AR+DHT 3

source_name: EP-AR+DHT

value: EP-AR


title: normal mucosa N1

status: Public on Sep 28 2010

description: Patient 1 : normal mucosa

hyb_protocol: Cy5-labeled cDNA targets were hybridized with Cy3-labeled reference in 40ul of hybridization solution [50% DIG EasyHyb (ROCHE, Basel, Switzerland) and 30ug of herring sperm DNA] for 18h at 42°C in a humidified conventional hybridization chamber.

scan_protocol: Washed slides were scanned using a GenePix 4000B scanner (Axon Instruments, Union City, CA), and Cy3/Cy5-signals were measured using GenePix Pro 3.0 microarray analysis software (Axon Instruments, Union City, CA)

data_processing: Spot intensities were corrected for background intensities and normalized for dye bias using LOWESS regression with the print-tip group correction. The data were then normalized for the distribution of ratios of test RNA to reference RNA in each dataset. Genes expressed in 80% or more of the samples were selected for further analyses.

source_name: normal mucosa

label_protocol: The reference RNA was labeled with Cyanine-3 (Cy-3), and test samples were labeled with Cyanine-5 (Cy-5)

extract_protocol: Total RNA was extracted from the snap-frozen samples using TRIzol reagent according to the manufacturer's protocol (Life Technology, Rockville, MD).

value: normal mucosa

tag: patient id

source_name: UHR

value: Universe Human Reference cell line


title: normal mucosa N3

description: Patient 3 : normal mucosa


title: EP-AR T/ERG+DHT 4

source_name: EP-AR T/ERG+DHT


title: EP-AR T/ERG+DHT 2


title: EP-AR T/ERG+DHT 3


title: normal mucosa N2

description: Patient 2 : normal mucosa


title: normal mucosa N8

description: Patient 8 : normal mucosa


title: EP-AR 1

source_name: EP-AR


title: normal mucosa N7

description: Patient 7 : normal mucosa


title: EP-AR T/ERG 2


title: EP-AR 2


title: normal mucosa N10

description: Patient 10 : normal mucosa


title: EP-AR+DHT 1


title: EP-AR+DHT 4


title: EP-AR T/ERG+DHT 1


title: MKN-1 shHDAC2

source_name: human gastric cancer cell line

treatment_protocol: The HDAC2 deficient cell lines HDAC2 KD (Knockdown)1 and KD2 were each created by transfecting MKN-1 cells with 2 µg of HDAC2 shRNA expression plasmids. Stable clones were selected by growing each transfected cell in medium containing 0.5 mg/mL of G418 (Geneticin, Invitrogen, Carlsbad, CA).

value: shHDAC2 transfection


title: normal mucosa N5

description: Patient 5 : normal mucosa


title: MKN-1 mock


title: EP-AR+DHT 2


title: gastric carcinoma C10

description: Patient 10 : gastric carcinoma

source_name: gastric carcinoma

value: gastric carcinoma


title: normal mucosa N4

description: Patient 4 : normal mucosa


title: gastric carcinoma C9

description: Patient 9 : gastric carcinoma


title: gastric carcinoma C8

description: Patient 8 : gastric carcinoma


title: gastric carcinoma C6

description: Patient 6 : gastric carcinoma


title: gastric carcinoma C7

description: Patient 7 : gastric carcinoma


title: HIPK2 (C051)

source_name: RKO colon cancer cells transfected with HIPK2-Flag vector (HIPK2).

value: HIPK2-Flag vector (HIPK2)

value: RKO colon cancer cells


title: gastric carcinoma C3

description: Patient 3 : gastric carcinoma


title: gastric carcinoma C1

description: Patient 1 : gastric carcinoma


title: gastric carcinoma C2

description: Patient 2 : gastric carcinoma


title: gastric carcinoma C4

description: Patient 4 : gastric carcinoma


title: gastric carcinoma C5

description: Patient 5 : gastric carcinoma


title: gastric adenoma A10

description: Patient 10 : gastric adenoma

source_name: gastric adenoma

value: gastric adenoma


title: gastric adenoma A8

description: Patient 8 : gastric adenoma


title: Parkinson's disease, A39

status: Public on Mar 10 2010

description: Gene expression data from substantia nigra

hyb_protocol: Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

scan_protocol: Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

data_processing: MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.

label: Biotin

source_name: Substantia nigra

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

tag: age

value: F


title: gastric adenoma A4

description: Patient 4 : gastric adenoma


title: gastric adenoma A7

description: Patient 7 : gastric adenoma


title: gastric adenoma A3

description: Patient 3 : gastric adenoma


title: Control, A12


title: Parkinson's disease, A41

value: M


title: Parkinson's disease, A9


title: Parkinson's disease, A10


title: Control, A48


title: Human ES (H9.2)_control

status: Public on Jun 28 2010

description:
B44_C
Gene expression of  human embryonic stem cells (H9.2) that were transfected with negative control siRNA

source_name: Human embryonic stem cells (H9.2)_negative control siRNA

growth_protocol: Human embryonic stem cells (H9.2)  were grown under feeder-free conditions on matrigel and in conditioned medium that was deived from mitotically inactivated mouse embryonic fibroblasts

extract_protocol: RNA extraction was perfomed using Trizol reagent (Invitrogen) according to the manufacturer protocol

treatment_protocol: The embryonic stem cells were transfected with ADAR1 specific siRNA or with negative control siRNA (Applied Biosystems)  using Lipofectamine 2000 (Invitrogen). 44 hours after siRNA transfections, the cells were harvested for RNA extraction

value: Embryonic stem cells

value: control siRNA


title: gastric adenoma A5

description: Patient 5 : gastric adenoma


title: Parkinson's disease, A42


title: Control, A49


title: gastric adenoma A1

description: Patient 1 : gastric adenoma


title: Control, A11


title: Parkinson's disease, A43


title: Control, A46


title: Control, A44


title: Human ES (H9.2)_ADAR1-siRNA

description:
B46_KD
Gene expression of human embryonic stem cells (H9.2) of which ADAR1 was silenced by ADAR1-siRNA transfection

source_name: Human embryonic stem cells(H9.2)_ADAR1 specific siRNA


title: gastric adenoma A2

description: Patient 2 : gastric adenoma


title: F1M20CX-7

status: Public on Jan 16 2010

hyb_protocol: Fifteen microgram of DIG labeled fragmented cRNA was used for microarray hybridization and performed according to the Applied Biosystems protocols

scan_protocol: Chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems 1700 Chemiluminescent Microarray Analyzer, according to the manufacturer's instructions. Images were auto-gridded and chemiluminescent signals were quantified, corrected for background, and spatially normalized.

data_processing: For primary data filtering, spots with a SNR (Signal to Noise Ratio) <1.5 were excluded, and the remaining filtered data were used for further analysis. Quantile normalization was used to normalize data. All process performed using GenPlex software (Istech Inc., Korea)

label: Digoxigenin-UTP

source_name: male, 20mg/kg MDMA

label_protocol: 1 microgram of total RNA was used to transcribe DIG labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT kit v2.0

growth_protocol: Male and female C57BL/6N mice (6 weeks), purchased from the Orient Co. Ltd., were kept under SPF-conditions. All mice were acclimatized in the laboratory according to the ‘Guide for the Care and Use of Laboratory Animals’ (US NIH publication No. 86-23, 1985 Ed.)

extract_protocol: Brain regions were then dissected free, frozen on dry ice, and stored in a LN2 tank until further analysis. Total RNA was isolated from the brain tissue using the TRI reagent (Molecular Research Center, Cincinnati, OH.,USA), according to the manufacturer's instructions (Life Technology, Rockville, MD, USA). Briefly, the tissues were frozen in liquid nitrogen, pulverized, homogenized in 1 ml of TRI reagent, and incubated for 5 min at room temperature; 200 µl if chloroform was added, vigorously mixed, and incubated for 3 min at room temperature. The samples were centrifuged at 14000 rpm for 20 min, aqueous phases were transferred to fresh tubes with an equal volume of isopropanol, and incubated on ice for 30 min. After centrifugation at 14000 rpm for 15 min, RNA pellets were washed in 75% ethanol and dissolved in RNase-free water. RNA qualities were assessed using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA), and concentrations were determined using a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Samples with a minimum 28S/18S ratio of > 1.6 were selected for further study.

treatment_protocol: MDMA ((±)-3, 4-methylenedioxymethamphetamine hydrochloride, CAS # 92279-84-0, purity ≥99.9%) was obtained from the Reproductive and  Development Toxicology Division of the Toxicological Research Department, The National Institute of Toxicological Research, Seoul, Korea. MDMA was dissolved in isotonic saline at doses of 20 mg/kg at volumes corresponding to 3ml/kg, and was administered orally (p.o.).

tag: strain

value: cerebral cortex

tag: sex

value: male

tag: chemical

value: 20mg/kg MDMA


title: F1MCCX-3

source_name: male, non-treated

value: non-treated


title: F1F20CX-4

source_name: female, 20mg/kg MDMA

value: female


title: F1MCCX-4


title: F1M20CX-4


title: F1M20CX-8


title: F1MCCX-7


title: F1F20CX-5


title: F1MCCX-10


title: F1F20CX-6


title: F1MCCX-5


title: F1MCCX-2


title: F1M20CX-2


title: F1M20CX-9


title: F1M20CX-3


title: F1MCCX-1


title: F1M20CX-5


title: F1MCCX-8


title: F1F20CX-3


title: F1F20CX-7


title: F1FCCX-6

source_name: female, non-treated


title: F1FCCX-7


title: F1M20CX-6


title: F1M20CX-1


title: F1MCCX-6


title: F1F20CX-2


title: F1MCCX-9


title: F1F20CX-1


title: F1F20CX-8


title: F1FCCX-5


title: F1FCCX-4


title: F1FCCX-1


title: F1FCCX-2


title: Balb/c day 6, biological rep 4, tech rep 1

status: Public on Oct 01 2007

description: Gene expression data from whole brain infected mouse, day 6

hyb_protocol: Following fragmentation, cRNA was hybridized to GeneChip MOE 430A 2.0 Array per Affymetrix protocols.

scan_protocol: Microarrays were scanned using Affymetrix GeneChip Scanner and GeneChip Operating Software (GCOS) was used for image analysis.

data_processing: Background adjustment and quantile normalization across all microarrays was performed using the Robust Multichip Average algorithm (RMAExpress).

source_name: Whole brain day 6

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

growth_protocol: All adult male mice were housed in the same SPF facility.

extract_protocol: Brains were homogenized in Trizol Reagent and total RNA was isolated according to the manufacturers' instructions. RNA was further purified of gDNA contamination and concentrated using a RNeasyPlus Mini Kit.

treatment_protocol: Cryopreserved P. berghei ANKA was thawed and passaged through naïve B6 donor mice until parasitemia in the passage animals reached approximately 10%. On day 0, mice were infected by intraperitoneal injection with 500,000 freshly isolated PbA parasitized erythrocytes. Parasitemia was monitored daily after Day 3 using thin blood smears

tag: Balb/C

tag: Adult, male


title: Balb/c day 6, biological rep 3, tech rep 1


title: Balb/c day 3, biological rep 2, tech rep 2

description: Gene expression data from whole brain infected mouse, day 3

source_name: Whole brain day 3


title: Balb/c day 6, biological rep 4, tech rep 2


title: Balb/c day 6, biological rep 1, tech rep 2


title: F1FCCX-3


title: Balb/c day 3, biological rep 1, tech rep 2


title: Balb/c day 1, biological rep 4, tech rep 2

description: Gene expression data from whole brain infected mouse, day 1

source_name: Whole brain day 1


title: Balb/c day 6, biological rep 3, tech rep 2


title: Balb/c day 3, biological rep 2, tech rep 1


title: Balb/c day 3, biological rep 3, tech rep 2


title: Balb/c day 6, biological rep 2, tech rep 2


title: Balb/c day 6, biological rep 1, tech rep 1


title: Balb/c day 1, biological rep 2, tech rep 2


title: Balb/c day 3, biological rep 4, tech rep 1


title: Balb/c day 3, biological rep 1, tech rep 1


title: Balb/c day 1, biological rep 1, tech rep 1


title: Balb/c day 1, biological rep 4, tech rep 1


title: Balb/c day 1, biological rep 3, tech rep 1


title: Balb/c day 3, biological rep 3, tech rep 1


title: Balb/c day 1, biological rep 1, tech rep 2


title: Balb/c day 6, biological rep 2, tech rep 1


title: Balb/c day 1, biological rep 3, tech rep 2


title: Balb/c day 0, biological rep 4, tech rep 2

description: Gene expression data from whole brain of uninfected mouse

source_name: Whole brain day 0, uninfected


title: Balb/c day 0, biological rep 3, tech rep 2


title: Balb/c day 0, biological rep 2, tech rep 2


title: Balb/c day 0, biological rep 4, tech rep 1


title: Balb/c day 3, biological rep 4, tech rep 2


title: B6 day 6, biological rep 3, tech rep 2


title: Balb/c day 0, biological rep 1, tech rep 2


title: B6 day 6, biological rep 3, tech rep 1


title: B6 day 6, biological rep 4, tech rep 2


title: Balb/c day 0, biological rep 3, tech rep 1


title: Balb/c day 0, biological rep 2, tech rep 1


title: B6 day 6, biological rep 1, tech rep 1


title: Balb/c day 0, biological rep 1, tech rep 1


title: B6 day 3, biological rep 4, tech rep 2


title: B6 day 6, biological rep 4, tech rep 1


title: Balb/c day 1, biological rep 2, tech rep 1


title: B6 day 3, biological rep 3, tech rep 2


title: B6 day 6, biological rep 2, tech rep 2


title: B6 day 3, biological rep 2, tech rep 2


title: B6 day 1, biological rep 3, tech rep 1


title: B6 day 3, biological rep 4, tech rep 1


title: B6 day 6, biological rep 1, tech rep 2


title: B6 day 1, biological rep 2, tech rep 2


title: B6 day 3, biological rep 2, tech rep 1


title: B6 day 3, biological rep 1, tech rep 1


title: B6 day 3, biological rep 1, tech rep 2


title: B6 day 3, biological rep 3, tech rep 1


title: B6 day 1, biological rep 3, tech rep 2


title: B6 day 0, biological rep 2, tech rep 1


title: B6 day 1, biological rep 4, tech rep 2


title: B6 day 1, biological rep 4, tech rep 1


title: B6 day 0, biological rep 3, tech rep 2


title: B6 day 0, biological rep 4, tech rep 1


title: B6 day 0, biological rep 1, tech rep 2


title: B6 day 0, biological rep 1, tech rep 1


title: B6 day 1, biological rep 1, tech rep 1


title: B6 day 0, biological rep 4, tech rep 2


title: B6 day 1, biological rep 1, tech rep 2


title: B6 day 6, biological rep 2, tech rep 1


title: B6 day 0, biological rep 2, tech rep 2


title: MV+LPS 4

status: Public on Aug 01 2005

description: MV+LPS mice received 2 microliter/gm LPS (2.5 ng/microliter) in the oropharynx with a pipette, 30 minutes later they were anesthetized, intubated and ventilated at a tidal volume of 10 microliter/gm body wt, PEEP = 0 and FiO2 = 0.21  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.

source_name: whole mouse lung homogenate


title: MV+LPS 6


title: MV+LPS 2


title: B6 day 0, biological rep 3, tech rep 1


title: MV+LPS 3


title: MV+LPS 5

source_name: whole mouse homogenate


title: MV+LPS 1


title: LPS 2

description: LPS mice were spontaneously breathing room air and received 2 microliter/gm LPS (2.5 ng/microliter) in the oropharynx with a pipette.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.


title: B6 day 1, biological rep 2, tech rep 1


title: MV 1

description: MV mice received 2microliter/gm PBS in the oropharynx with a pipette, 30 minutes later they were anesthetized, intubated and ventilated at a tidal volume of 10 microliter/gm body wt, PEEP = 0 and FiO2 = 0.21.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.


title: LPS 6


title: MV 4


title: LPS 3


title: LPS 1


title: Control 5

description: Control mice were spontaneously breathing room air and received 2microliter/gm PBS in the oropharynx with a pipette.  They were sacrificed 4 hrs later, whole lung removed, homogenized and total RNA isolated.  Labeled cRNA was prepared and hybridized to an Affymetrix GeneChip 430A microarray using Affymetrix protocol.  Microarray was scanned with the GeneChip Scanner and image analysis was performed with Affymetrix MAS 5.0 software.  Background adjustment and quantile normalization of microarray data was performed using RMAExpress.


title: Control 3


title: Control 6


title: Control 4


title: MV 3


title: Control 2


title: MV 5


title: LPS 4


title: MV 2


title: MV 6


title: Control 1


title: Hypoxia day 28, replicate 2

status: Public on Mar 16 2005

description:
Whole lungs of BALB/c (n=5) exposed to 21 days of 0.5 atm hypoxia then returned to sea level pressure for 7 days and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 28

source_name: control lungs day 28


title: Hypoxia day 35, replicate 3

description:
Whole lungs of BALB/c (n=5) exposed to 21 days of 0.5 atm hypoxia then returned to sea level pressure for 14 days and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 35

source_name: control lungs day 35


title: Hypoxia day 28, replicate 1


title: Hypoxia day 28, replicate 3


title: Hypoxia day 35, replicate 4


title: Hypoxia day 24, replicate 4

description:
Whole lungs of BALB/c (n=5) exposed to 21 days of 0.5 atm hypoxia then returned to sea level pressure for 3 days and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 24

source_name: control lungs day 24


title: Hypoxia day 35, replicate 2


title: Hypoxia day 28, replicate 4


title: Hypoxia day 24, replicate 2


title: Hypoxia day 35, replicate 1


title: LPS 5


title: Hypoxia day 24, replicate 3


title: Hypoxia day 22, replicate 4

description:
Whole lungs of BALB/c (n=5) exposed to 21 days of 0.5 atm hypoxia then returned to sea level pressure for 1 day and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 22

source_name: control lungs day 22


title: Hypoxia day 22, replicate 1


title: Hypoxia day 21, replicate 1

description:
Whole lungs of BALB/c (n=5) exposed to 21 days of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 21

source_name: control lungs day 21


title: Hypoxia day 21, replicate 4


title: Hypoxia day 7, replicate 1

description:
Whole lungs of BALB/c (n=5) exposed to 7 days of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 7

source_name: control lungs day 7


title: Hypoxia day 3, replicate 4

description:
Whole lungs of BALB/c (n=5) exposed to 3 days of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 3

source_name: control lungs day 3


title: Hypoxia day 7, replicate 3


title: Hypoxia day 14, replicate 3

description:
Whole lungs of BALB/c (n=5) exposed to 14 days of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 14

source_name: control lungs day 14


title: Hypoxia day 22, replicate 2


title: Hypoxia day 7, replicate 4


title: Hypoxia day 14, replicate 1


title: Hypoxia day 21, replicate 2


title: Hypoxia day 22, replicate 3


title: Hypoxia day 14, replicate 4


title: Hypoxia day 7, replicate 2


title: Hypoxia day 21, replicate 3


title: Hypoxia day 3, replicate 3


title: Hypoxia day 14, replicate 2


title: Hypoxia day 3, replicate 2


title: Hypoxia day 24, replicate 1


title: Hypoxia day 1, replicate 4

description:
Whole lungs of BALB/c (n=5) exposed to 1 day of 0.5 atm hypoxia and time-matched control mice (n=5) were pooled separately.
Total RNA isolation was accomplished with Qiagen RNeasy Midi Kit reagents. Total RNA (50 µg) was annealed with 5 µg oligo dT12-18, and reverse-transcribed into cDNA with Superscript II reverse transcriptase for 2h at 42¡C in the presence of 0.5 mM dGTP, 0.5 mM dCTP, 0.5 mM dATP, 0.3 mM dTTP, 0.2 mM amino-allyl dUTP. After hydrolysis of RNA in 0.2 M NaOH, Tris was removed from the reaction with a Microcon-30 concentrator.
The cDNA from Hypoxic and Control groups was covalently coupled separately with Cy5 and Cy3 monoreactive fluors in 50 mM sodium bicarbonate, pH 9.0, followed by quenching with 2.7 M hydroxylamine. The Cy5 and Cy3 labeled cDNAs were combined and purified with a QIAquick PCR purification kit and suspended in 36 µl of 3X SSC and 0.8 mg/ml of poly-A for hybridization to the microarray.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, log base 2 expression ratios of median intensities were normalized using lowess method.
Keywords = hypoxia, pulmonary hypertension, vascular remodeling

source_name: hypoxic lungs day 1

source_name: control lungs day 1


title: Hypoxia day 3, replicate 1


title: Hypoxia day 1, replicate 1


title: Hypoxia day 1, replicate 3


title: Hypoxia day 1, replicate 2