title: Day: 7. Dose : 0ug. Replicate 2

value: male

tag: vendor

value: Statagene

value: reference


title: 3 μM SAR Mouse 1

status: Public on Jun 26 2012

type: RNA

city: Bilthoven

first: Mirjam

middle: M

last: Schaap

address: Antonie van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description: quality control: approved

hyb_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit  According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

scan_protocol: According to Affymetrix protocols, using a GeneChip HT Array Plate Scanner (Affymetrix)

data_processing: The raw data were subjected to a set of quality control checks. After passing array quality control, the arrays were annotated according to de Leeuw et al. (2008) and expression values were calculated using the robust multi-array average (RMA) algorithm (Affy package, version 1.22.0; Irizarry et al. 2003) available from the Bioconductor project (http://www.bioconductor.org) for the R statistical language (http://cran.r-project.org)). The normalized data was statistically analyzed for differential gene expression using a mixed linear model with coefficients for block (random) and each experimental group (fixed) (Smyth 2004; Wolfinger et al. 2001). A contrast analysis was applied to compare each exposure with the corresponding vehicle control. For hypothesis testing, a permutation-based Fs test was used (Cui et al. 2005). False discovery rate (FDR) correction was performed globally across all contrasts according to Storey and Tibshirani (2003). Only the annotated genes were used for further analysis.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Primary mouse hepatocytes Mouse #1

label_protocol: Biotins labeled cRNA samples were prepared as described in the Affymetrix GeneChip HT 3” IVT Express Technical Manual (Affymetrix) using 200 ng of purified total RNA as template for the reaction.

growth_protocol: Primary mouse hepatocytes were isolated from 8-10 weeks old male C57BL/6 mice by a modified two-step collagenase perfusion technique. Cells were cultured in a sandwich configuration in 6-wells  at 1.3 x 106 cells per well.

extract_protocol: RNA was extracted using QIAzol and purified using the miRNeasy mini kit and the QIAcube (Qiagen), according to the manufacturer’s protocol.

treatment_protocol: Hepatocytes were exposed for 24 hours to the 16 non-genotoxic carcinogens. Control cells were vehicle-treated (DMSO or PBS, 0.5%). After 24 hours of exposure, cells were collected in 1 ml RNAprotect (QIAgen) and stored at -80˚C for RNA isolation.

tag: strain

tag: gender

value: Male

tag: age

value: 8-9 weeks

tag: exposure

value: 3 μM SAR


title: Day: 1. Dose : 40ug. Replicate 6

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

country: USA

institute: Marshall University School of Medicine

hyb_protocol: Hybridized in the presence of 2X Hi-RPM hybrideizationbuffer (Agilent) at 65 C for a7 hours

scan_protocol: Scanned on Agilent scanner model G2505C

data_processing: Agilent Feature Extraction v10 was used for background subtraction and lowess normalization.

source_name: lung, aspirated with 40µg MWCNT, sacrificed after 1 day

label_protocol: 200 ng of total RNA labeled with QuickAmp labeling kit (Agilent) in the presence of cyadine-3 dCTP or cyadine-5 dCTP (Perkin Elmer)

growth_protocol: Male C57BL/6J mice (7 weeks old) were obtained from Jackson Laboratories, housed one per cage and and carred  for according to AAALAC-accredited, specific pathogen-free environmentally controlled facility. The animals were allowed to aclimate for 5 days before experimental use.

extract_protocol: Mice were euthanized with pentobarbital (100 mg/kg body weight, i.p.) and exsanguinaized by transection of abdominal aorta.  Lungs were removed and immediately placed in tubes containing RNAlater and stored at -80°C until RNA extraction.  Total RNA was extracted using RNeasy Midi kit according to manufacturer's protocol (Qaigen, CA).  RNA quality was determined using OD 260/280 ratio, and RNA with a ratio of >1.9 was used for further analysis.  Also, RNA integrity was analyzed using Agilent 2100 Bioanalyzer according to manufacturer's protocol (Agilent Technologies, CA)

treatment_protocol: MWCNT were obtained form Mitsui & Company, and prepared as previously described (Porter et al. 2010).  Mice were treated with vehicle (control) or MWCNT 10, 20, 40, 80 µg by pharyngeal aspiration.

tag: dose (ug)

tag: time (days)

source_name: Universal Mouse Reference RNA

tag: catalog#


title: Day: 1. Dose : 40ug. Replicate 2


title: DMSO Mouse 1

description: quality control: approved

value: 0.5 % DMSO


title: Day: 1. Dose : 40ug. Replicate 3


title: Day: 1. Dose : 20ug. Replicate 8

source_name: lung, aspirated with 20µg MWCNT, sacrificed after 1 day


title: Day: 1. Dose : 40ug. Replicate 1


title: Day: 1. Dose : 40ug. Replicate 7


title: Day: 1. Dose : 20ug. Replicate 7


title: 1 nM CA Mouse 1

description: quality control: approved

value: 1 nM CA


title: MMA-transformed human urothelial cells, URO-MSC52, slide 1

type: genomic

city: Tucson

first: Paul

last: Severson

state: AZ

address: 1515 N Campbell Ave

department: Pharmacology and Toxicology

institute: University of Arizona

hyb_protocol: Labeled MeDIPs (n=2) and labeled inputs (n=2) were all combined. This pool of the 4 labeling reactions was divided into two equal parts and each was vacuum concentrated to volume of 187.5 µl. 12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 50 µl of Agilent blocking agent (10x) and 250 µl of Agilent hybridization buffer (2x) were added to each half. Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then one of the halves was used for microarray hybridization (1 slide of a 2 slide array) for 28h at 65 oC. After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm).

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package. Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy. The RG object was transformed to an MA object and M values were again loess normalized between arrays.

molecule: genomic DNA

organism: Homo sapiens

source_name: Toxicant-transformed human urothelial cells, immunoprecipitated DNA

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction. Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled in duplicate using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes, respectively. For each reaction, DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE Healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C. Labeled targets were purified using the QIAquick PCR purification kit (Qiagen). The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).

growth_protocol: HUC cells were cultured in Urothelial Cell Medium. UROtsa cells and each of their toxicant-transformed descendants were cultured in DMEM supplemented with 5% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. BFTC cell lines were cultured in DMEM supplemented with 10% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. Nucleic acids from bladder tumor specimens were purchased from Origene Technologies. PrEC cells were cultured in PrEBM with added BulletKit. RWPE-1 and its toxicant-transformed descendent cell lines were cultured in K-SFM with 50 µg/mL BPE, 5 ng/mL EGF, and 1% vol/vol antibiotic-antimycotic solution. The prostate cancer cell lines PC3, LNCaP and DU145 were cultured in IMDM, RMPI-1640 and IMDM, respectively, with 10% FBS and 1% vol/vol antibiotic-antimycotic solution.

extract_protocol:
Extraction: Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase-treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl). Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts. Make sure that most of the DNA is between 300-600 bp long. Set aside 50 μl of sample in a new microfuge tube - Input DNA.
Immunoprecipitation: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice. When cold, add 2 μl of anti-methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr. Transfer samples and beads to a Handee spin cup column with paper filter (Pierce). Spin samples for ~10 seconds in a picofuge to remove the buffer. Wash beads for 5 min at 4 C with 400 ul each of the following buffers: low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 ul of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT. Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube. Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

treatment_protocol: Toxicant exposures are described in the characteristics section. The monomethylarsonous acid, sodium arsenite and cadmium chloride exposures were continuous. The MNU exposure was for 1 hour at a time, after which cells were given fresh media and grown to confluence. This exposure, wash and growth cycle was repeated three more times.

tag: cell line

value: UROtsa

tag: cell type

value: ureter

tag: treatment

value: 52 weeks 50nM monomethylarsonous acid

tag: phenotype

value: malignant

tag: medip antibody

value: anti-methylcytosine

tag: antibody vendor

value: Diagenode

tag: antibody catalog #

tag: antibody lot#

source_name: Toxicant-transformed human urothelial cells, input DNA


title: 10 μM TCPOBOP Mouse 1

description: quality control: approved

value: 10 μM TCPOBOP


title: Day: 1. Dose : 20ug. Replicate 5


title: Day: 1. Dose : 20ug. Replicate 6


title: MMA-transformed human urothelial cells, URO-MSC12+24(-), slide 1

value: 12 weeks 50nM monomethylarsonous acid


title: Day: 1. Dose : 20ug. Replicate 4


title: Arsenite-transformed human urothelial cells, URO-ASSC, slide 1

description: URO-ASSC

value: 52 weeks 1µM sodium arsenite


title: Immortalized human urothelial cells, UROtsa_p95, slide 1

source_name: Immortalized human urothelial cells, immunoprecipitated DNA

value: immortal

source_name: Immortalized human urothelial cells, input DNA


title: 100 μM WY Mouse 1

description: quality control: approved

value: 100 μM WY


title: Day: 1. Dose : 20ug. Replicate 3

value: male

value: Statagene

value: reference


title: Day: 1. Dose : 20ug. Replicate 2


title: Day: 1. Dose : 10ug. Replicate 4

source_name: lung, aspirated with 10µg MWCNT, sacrificed after 1 day


title: Day: 1. Dose : 20ug. Replicate 1


title: Day: 1. Dose : 10ug. Replicate 5


title: Immortalized human urothelial cells, UROtsa_p41, slide 1


title: 300 μM CT Mouse 1

description: quality control: approved

value: Male

value: 8-9 weeks

value: 300 μM CT


title: 10 μM LAC Mouse 1

description: quality control: approved

value: 10 μM LAC


title: Immortalized human urothelial cells, UROtsa_p27, slide 1

value: UROtsa

value: ureter


title: 1 mM PB Mouse 1

description: quality control: approved

value: 1 mM PB


title: Day: 1. Dose : 10ug. Replicate 7


title: Day: 1. Dose : 10ug. Replicate 8


title: Day: 1. Dose : 10ug. Replicate 6


title: Normal human urothelial cells, HUC_p5, slide 1

source_name: Human urothelial cells, immunoprecipitated DNA

value: HUC

value: urinary bladder

value: normal

value: anti-methylcytosine

source_name: Human urothelial cells, input DNA


title: Normal human urothelial cells, HUC_p3, slide 1

value: Diagenode


title: Day: 1. Dose : 10ug. Replicate 3


title: Day: 1. Dose : 10ug. Replicate 2


title: Day: 1. Dose : 0ug. Replicate 6

source_name: lung, control treated, sacrificed after 1 day


title: 30 μM FK506 Mouse 4

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #4


title: Prostate adenocarcinoma cell line, PC3, slide 2

source_name: Prostate adenocarcinoma cell line, immunoprecipitated DNA

value: prostate

value: malignant

source_name: Prostate adenocarcinoma cell line, input DNA


title: Day: 1. Dose : 0ug. Replicate 8

value: male


title: Day: 1. Dose : 10ug. Replicate 1

value: Statagene


title: Day: 1. Dose : 0ug. Replicate 4

value: reference


title: Prostate carcinoma cell line, DU145, slide 2

source_name: Prostate carcinoma cell line, immunoprecipitated DNA

source_name: Prostate carcinoma cell line, input DNA


title: 10 nM TCDD Mouse 4

description: quality control: approved

value: Male

value: 10 nM TCDD


title: 30 μM HCE Mouse 4

description: quality control: approved

value: 8-9 weeks

value: 30 μM HCE


title: Day: 1. Dose : 0ug. Replicate 3


title: 1 mM CF Mouse 4

description: quality control: approved

value: 1 mM CF


title: Day: 1. Dose : 0ug. Replicate 7


title: Day: 1. Dose : 0ug. Replicate 5


title: Day: 1. Dose : 0ug. Replicate 2


title: Day: 1. Dose : 0ug. Replicate 1


title: Prostate carcinoma cell line, LNCaP, slide 2

description: LNCaP

value: LNCaP


title: 1 mM PB Mouse 4

description: quality control: approved

value: 1 mM PB


title: 1 μM CSA Mouse 4

description: quality control: approved

value: 1 μM CSA


title: 1 μM CSA Mouse 4.2

description: quality control: approved


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_30wk, slide 2

source_name: Toxicant-transformed human prostate epithelial cells, immunoprecipitated DNA

value: 30 weeks 5µM sodium arsenite

source_name: Toxicant-transformed human prostate epithelial cells, input DNA


title: MNU-transformed human prostate epithelial cells, WPE1-NB26, slide 2

value: 4 cycles of 1 hour 100µg/mL N-methyl-N-nitrosourea


title: Arsenite-transformed human prostate epithelial cells, CAsE-PE_33wk, slide 2

value: 33 weeks 5µM sodium arsenite

value: anti-methylcytosine


title: Control mtB6 Cell Replicate 3 vs. Mutant mtBALB Cell Replicate 3

first: Jaroslav

last: Janda

department: Dept. of Medicine

description: Biological replicate 3 of 4 Control wild type mtB6 cybrid cell line VERSUS biological replicate 3 of 4 Mutant mtBALB cybrid cell line.

hyb_protocol: Standard Agilent protocol was used - (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf). Water bath was equilibrated at 60 C. In a 1.5 mL nuclease-free microfuge tube, the following components were added - 300 ng cyanine 3-labelted linearly amplified cRNA, 10X blocking agent, nuclease free water and 25X fragmentation buffer. The mixture was incubated at 60 C for exactly 30 minutes to fragment RNA. 2x GEx Hybridization Buffer HI-RPM was added to 8x15K array formats at the appropriate volume to stop the fragmentation reaction. It was spinned for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. Sample was added on the array.

scan_protocol: After washing, arrays were scanned using a GenePix 4000B with laser excitation at 532 and 635 nm, and saved as 16-bit grayscale TIFF images.

data_processing: Raw data were extracted using Gene Pix Pro 6.0 program; then saved as "gpr" and "txt" files for each block individually (total 4 blocks on the chip what results in 4 hybridizations). Within arrays, loess normalization was done using the Limma package in R (version R2.5.1) (Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30(4):e15). Between arrays, normalization was also done with the Limma package so that the scale the log-ratios to have the same median-absolute-deviation (MAD) across arrays (Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. In: METHODS: Selecting Candidate Genes from DNA Array Screens: Application to Neuroscience, D. Carter (ed.). Methods Volume 31, Issue 4, December 2003, pages 265-273).

source_name: Control mtB6 Cell Replicate 3

label_protocol:
Standard Agilent protocol was used - (http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf).
1. Add 50 to 5000 ng of total or polyA RNA to a 1.5-mL microcentrifuge tube in an appropriate volume of 8.3 μL or less. Samples should be diluted such that at least 2 μL of sample is pipetted into the tube.
2. Prepare tubes for both Spike A Mix/cyanine 3-CTP and Spike B Mix/cyanine 5-CTP dyes.
3. Add 1.2 μL of T7 Promoter Primer (from the Agilent Quick Amp Kit, Two-Color).
4. Add 2 μL of diluted Spike-Mix (A or B).
5. Use nuclease-free water to bring the total reaction volume to 11.5 μL.
6. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.
7. Place the reactions on ice and incubate for 5 minutes.
8. Immediately prior to use, gently mix the components listed in Table 3 of Agilent document for the cDNA Master Mix by adding in the order indicated, and put on ice. 9. Prewarm the 5X first strand buffer at 80°C for 3 to 4 minutes to ensure adequate resuspensions of the buffer components. For optimal resuspension, briefly mix on a vortex mixer and spin the tube in a microcentrifuge to drive down the contents from the tube walls. Keep at room temperature until needed. MMLV-RT and RNaseOUT are enzymes, which need to be kept on ice and are to be added to the cDNA Master Mix just before starting the reactions. Be sure to use the 10 mM dNTP mix tube from the kit.
10. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.
11. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.
12. Incubate samples at 40°C in a circulating water bath for 2 hours.
13. Move samples to a 65°C circulating water bath and incubate for 15 minutes.
14. Move samples to ice. Incubate for 5 minutes.
15. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.
16. Immediately prior to use, gently mix the components listed in Table 4 in the order indicated for the Transcription Master Mix by pipetting at room temperature.
17. Prewarm the 50% PEG solution at 40°C for 1 minute. For optimal resuspension, briefly mix on a vortex mixer and spin the tube in a microcentrifuge to drive down the contents from the tube walls. Careful pipetting is required to ensure accurate volume. Keep at room temperature until needed. RNaseOUT, inorganic pyrophosphatase, and T7 RNA polymerase are enzymes, which need to be kept on ice and should be added to the Transcription Master Mix just before starting the reactions.
18. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.
19. Incubate samples in a circulating water bath at 40°C for 2 hours.

growth_protocol: mtB6 and mtBALB cybrid cells were kept in high glucose (4.5 g/L) Dulbecco's modified Eagle's medium (DMEM. GibcoBRL) supplemented with 10% fetal bovine serum (FBS, GibcoBRL)

extract_protocol: Total RNA extracted using QIAGEN RNeasy Mini Kit (Cat. No. 74104) following manufacturer's instructions

tag: cell passage

value: passage 3

value: fibroblasts

source_name: Mutant mtBALB Cell Replicate 3

value: BALB/cJ (BALB)


title: Control mtB6 Cell Replicate 4 vs. Mutant mtBALB Cell Replicate 4

description: Biological replicate 4 of 4 Control wild type mtB6 cybrid cell line VERSUS biological replicate 4 of 4 Mutant mtBALB cybrid cell line.

source_name: Mutant mtBALB Cell Replicate 4

source_name: Control mtB6 Cell Replicate 4


title: Immortalized human prostate epithelial cells, RWPE-1_p17, slide 2

source_name: Immortalized human prostate epithelial cells, immunoprecipitated DNA

value: prostate

value: immortal

value: Diagenode

source_name: Immortalized human prostate epithelial cells, input DNA


title: 100 μM WY Mouse 4

description: quality control: approved

value: Male

value: 100 μM WY


title: Control mtB6 Cell Replicate 2 vs. Mutant mtBALB Cell Replicate 2

description: Biological replicate 2 of 4 Control wild type mtB6 cybrid cell line VERSUS biological replicate 2 of 4 Mutant mtBALB cybrid cell line.

source_name: Mutant mtBALB Cell Replicate 2

source_name: Control mtB6 Cell Replicate 2


title: Immortalized human prostate epithelial cells, RWPE-1_p29, slide 2


title: MKO_rep_4

city: New York

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

description:
C5MKOS2020

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

hyb_protocol: 10 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm (version 2.16) as implemented in Bioconductor (version 2.40) / R (version 2.16).

source_name: Myd88 null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

label_protocol: RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix). Yield of fragmented samples was tested by Nanodrop and RNA size was assessed by Bioanalyzer using the Agilent RNA 6000 Pico kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated from ~1000 isolated glomeruli per mouse using the RNaqueous kit (Ambion, Austin, TX) including a DNase step. Total RNA concentration was assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and quality was assessed on a 2100 Bioanalyzer system (Agilent Technologies) using the Agilent RNA 6000 Nano kit. All of our samples had an RNA integrity score >8, and there was no indication of RNA degradation or contamination with DNA.

treatment_protocol: Mice underwent 85% liver resection and were sacrificed 2 hours later.

tag: genotype

value: Myd88 null

value: male

value: 10-12 weeks

tag: tissue

value: liver

value: 2 hours


title: Cadmium-transformed human prostate epithelial cells, CTPE, slide 2

description: CTPE

value: 10 weeks 10µM cadmium chloride

value: malignant


title: MRKO_rep_3

description:
D3RMKOS1118

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

source_name: Ager/Rage null/Myd88 null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

tag: strain

value: Ager null, Myd88 null

tag: gender


title: 100 μM HCH Mouse 4

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #4

tag: age

value: 8-9 weeks

tag: exposure

value: 100 μM HCH


title: 30 μM ARO Mouse 4

description: quality control: approved

value: 30 μM ARO


title: PBS Mouse 4

description: quality control: approved


title: Control mtB6 Cell Replicate 1 vs. Mutant mtBALB Cell Replicate 1

description: Biological replicate 1 of 4 Control wild type mtB6 cybrid cell line VERSUS biological replicate 1 of 4 Mutant mtBALB cybrid cell line.

source_name: Control mtB6 Cell Replicate 1

value: passage 3

value: fibroblasts

source_name: Mutant mtBALB Cell Replicate 1

value: BALB/cJ (BALB)


title: MRKO_rep_4

description:
D4RMKOS1219

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: MKO_rep_1

description:
C1MKOS312

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: MKO_rep_3

description:
C4MKOS1015

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: Normal human prostate epithelial cells, PrEC_p4, slide 2

source_name: Human prostate epithelial cells, immunoprecipitated DNA

value: PrEC

value: prostate

value: normal

value: anti-methylcytosine

value: Diagenode

source_name: Human prostate epithelial cells, input DNA


title: MRKO_rep_1

description:
D1RMKOS516

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: male

value: 10-12 weeks


title: 10 μM TCPOBOP Mouse 4

description: quality control: approved

value: Male

value: 10 μM TCPOBOP


title: MKO_rep_2

description:
C2MKOS413

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: Myd88 null

value: liver

value: 2 hours


title: MRKO_rep_2

description:
D2RMKOS617

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: Ager null, Myd88 null


title: 30 μM FK506 Mouse 3

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #3

value: 8-9 weeks


title: 300 μM CT Mouse 4

description: quality control: approved

value: 300 μM CT


title: RKO_rep_6

description:
B6RKOS1911

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

source_name: Ager/Rage null C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

value: Ager null


title: RKO_rep_5

description:
B5RKOS1710

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: RKO_rep_3

description:
B3RKOS1508

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: Bladder tumor specimen CD564409, slide 2

source_name: Bladder tumor specimen, immunoprecipitated DNA

value: bladder tumor

value: urinary bladder

value: malignant

source_name: Bladder tumor specimen, input DNA


title: WT_rep_4

description:
A4WTS804

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

source_name: WT C57BL/6 mice, liver, 10-12 weeks old, sacrificed 2 hours after 85% liver resection

value: WT


title: WT_rep_5

description:
A5WTS1805

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: PBS Mouse 3

description: quality control: approved


title: RKO_rep_1

description:
B1RKOS1306

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: Bladder tumor specimen CD563428, slide 2

value: anti-methylcytosine


title: Bladder tumor specimen CD564293, slide 2

value: Diagenode


title: 3 μM SAR Mouse 3

description: quality control: approved

value: 3 μM SAR


title: 10 μM LAC Mouse 3

description: quality control: approved

value: 10 μM LAC


title: WT_rep_3

description:
A3WTS703

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: male

value: 10-12 weeks


title: WT_rep_1

description:
A1WTS101

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.


title: Normal human prostate epithelial cells, PrEC_p3, slide 2

value: PrEC

value: prostate

value: normal


title: Bladder tumor specimen CD565196, slide 2


title: 1 nM CA Mouse 3

description: quality control: approved

value: Male

value: 1 nM CA


title: 10 μM TCPOBOP Mouse 3

description: quality control: approved

value: 8-9 weeks

value: 10 μM TCPOBOP


title: Bladder tumor specimen CD564450, slide 2

value: bladder tumor


title: Bladder tumor specimen CD565095, slide 2

value: urinary bladder


title: RKO_rep_2

description:
B2RKOS1407

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: Ager null

value: liver

value: 2 hours


title: 1 μM CSA Mouse 3

description: quality control: approved

value: 1 μM CSA


title: Blackfoot urothelial carcinoma cell line 905, slide 2

source_name: Urothelial carcinoma cell line, immunoprecipitated DNA

value: malignant

value: anti-methylcytosine

value: Diagenode

source_name: Urothelial carcinoma cell line, input DNA


title: Arsenite-transformed human urothelial cells, URO-ASSC, slide 2

description: URO-ASSC

source_name: Toxicant-transformed human urothelial cells, immunoprecipitated DNA

value: UROtsa

value: ureter

value: 52 weeks 1µM sodium arsenite

source_name: Toxicant-transformed human urothelial cells, input DNA


title: WT_rep_2

description:
A2WTS202

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: WT

value: male

value: 10-12 weeks


title: mammary tumor _FVB-WT

city: Washington

first: Robert

middle: I

last: Glazer

state: DC

address: 3970 Reservoir Rd, NW

department: Oncology

institute: Georgetown University

description: Gene expression data from progestin/DMBA induced mammary tumor in WT mice

hyb_protocol: Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.

scan_protocol: The GeneChip® was scanned using an Agilent Gene Array scanner.

data_processing: Raw data generation was performed with the Affymetrix GeneChip® Operating software 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal <300 in all experimental groups were excluded from analysis.

source_name: Wild-type mice treated with progestin/DMBA and maintained on standard rodent chow .

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

growth_protocol: All animal studies were conducted under GUACUC protocol 09-061. Female FVB/wild-type littermates were used in this study.

extract_protocol: Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).

treatment_protocol: Mice were maintained on standard rodent chow and injected s.c. with  15 mg MP suspension (Depo-Provera™), followed by four weekly doses of 1 mg DMBA/0.1 ml cottonseed oil  administered by gavage. GW9662 were administered one day after the last dose of DMBA

value: mammary tumor

value: FVB

tag: genotype/variation

value: progestin/DMBA


title: 300 μM CT Mouse 3

description: quality control: approved

value: Male

value: 8-9 weeks

value: 300 μM CT


title: DMSO Mouse 3

description: quality control: approved

value: 0.5 % DMSO


title: 100 μM WY Mouse 3

description: quality control: approved

value: 100 μM WY


title: 100 μM HCH Mouse 3

description: quality control: approved

value: 100 μM HCH


title: 30 μM ARO Mouse 3

description: quality control: approved

value: 30 μM ARO


title: Blackfoot urothelial carcinoma cell line 909, slide 2

value: urinary bladder

value: malignant

value: anti-methylcytosine

value: Diagenode


title: 1 mM CF Mouse 3

description: quality control: approved

value: 1 mM CF


title: MMA-transformed human urothelial cells, URO-MSC12+24(-), slide 2

value: UROtsa

value: ureter

value: 12 weeks 50nM monomethylarsonous acid


title: mammary tumor _FVB-WT-GW9662

description: Gene expression data from progestin/DMBA induced mammary tumor in WT mice treated with 0.1% GW9662

source_name: Wild-type mice treated with progestin/DMBA and maintained on a diet supplemented with 0.1% GW9662 .

value: mammary tumor

value: FVB

value: WT


title: 1 mM TCE Mouse 3

description: quality control: approved

value: Male

value: 8-9 weeks

value: 1 mM TCE


title: MMA-transformed human urothelial cells, URO-MSC52, slide 2

value: 52 weeks 50nM monomethylarsonous acid


title: 1 mM PB Mouse 3

description: quality control: approved

value: 1 mM PB


title: Tumor MEF-Atg5 (-/-) rep1

city: Hsinchu

first: Yen-Ju

last: Lin

address: 195, Sec. 4, Chung Hsing Rd., Chutung

country: Taiwan

institute: Industrial Technology Research Institute

hyb_protocol: After purification, 2 microgram labeled RNA was hybridized onto microarray at 55℃ for 21 h.

scan_protocol: Arrays were scanned using Agilent DNA Microarray Scanner G2565B (Agilent Technologies, Inc. CA, USA) at settings of 100 PMT (for Cy3) and of 5 micron, and the resulting images was analyzed with Agilent Feature Extraction software version 9.5.

data_processing: Data normalization was performed with CyclicLoess in R program downloaded from BioConductors (http://www.bioconductor.org/). After normalization, we import data into GeneSpringGX (V10.0.1) software to perform statistical analysis for significant genes finding.

source_name: tumor

label_protocol: For miRNA expression profiling, in brief, total 3.27 microgram of small RNA was dephosphorylated with calf intestine alkaline phosphatase (CIAP) at 37℃ for one hour, and then ligated to pCp-cy3 with T4 RNA ligase at 16℃ for overnight.

growth_protocol: MEF-Atg5 (+/+)-Ras and MEF-Atg5(-/-)-Ras which harbor an inducible H-rasVal12 oncogene were derived from mouse MEF-Atg5 (+/+) and MEF-Atg5(-/-) fibroblast. These cell lines were maintained in Dulbecco's modified Eagle's medium (GIBCO, 12100-061) with 10 % fetal bovine serum (Biological Industries, 04-001-1A).

extract_protocol: Small RNA was enriched from total RNA by using mirVana miRNA isolation kit (Ambion, Inc.). The quality and quantity of RNA was estimated with NanoDrop and Agilent 2100 bioanalyzer.

treatment_protocol: MEF-Atg5 (+/+)-Ras and MEF-Atg5(-/-)-Ras were treated with IPTG for 48 hr. In addition, MEF-Atg5(+/+)-Ras and MEF-Atg5(-/-)-Ras cell lines were injected s.c. into NOD/SCID mice. These mice were divided into IPTG drinking water (12.5 mM) and normal water groups, then tumor volume was measured over 14 days.

value: tumor


title: Tumor MEF-Atg5 (+/+) rep2


title: Cell MEF-Atg5 (-/-) rep2

source_name: Cell line


title: Cell MEF-Atg5 (-/-) rep1


title: Immortalized human urothelial cells, UROtsa_p95, slide 2

source_name: Immortalized human urothelial cells, immunoprecipitated DNA

value: immortal

source_name: Immortalized human urothelial cells, input DNA


title: Cadmium-transformed human urothelial cells, URO-CDSC, slide 2

description: URO-CDSC

value: 52 weeks 1µM cadmium chloride

value: malignant


title: RKO_rep_4

description:
B4RKOS1609

Gene expression of livers from 10-12 week-old mice, sacrificed 2 hours after liver resection.

value: Ager null

value: male

value: 10-12 weeks

value: liver

value: 2 hours


title: 10 nM TCDD Mouse 3

description: quality control: approved

value: 10 nM TCDD


title: 10 μM LAC Mouse 5

description: quality control: approved

source_name: Primary mouse hepatocytes Mouse #5

value: 10 μM LAC


title: Tumor MEF-Atg5 (+/+) rep1


title: Immortalized human urothelial cells, UROtsa_p27, slide 2

value: UROtsa

value: ureter

value: anti-methylcytosine

value: Diagenode


title: DMSO Mouse 5

description: quality control: approved

value: Male

value: 8-9 weeks

value: 0.5 % DMSO


title: 30 μM HCE Mouse 3

description: quality control: approved

value: 30 μM HCE


title: 1 nM OA Mouse 3

description: quality control: approved

value: 1 nM OA


title: Tumor MEF-Atg5 (-/-) rep2

value: tumor


title: Normal human urothelial cells, HUC_p5, slide 2

source_name: Human urothelial cells, immunoprecipitated DNA

value: HUC

value: urinary bladder

value: normal

source_name: Human urothelial cells, input DNA


title: 1 nM CA Mouse 5

description: quality control: approved

value: 1 nM CA


title: Cell MEF-Atg5 (+/+) rep2

value: MR


title: Immortalized human urothelial cells, UROtsa_p41, slide 2

value: immortal


title: 1 nM OA Mouse 5

description: quality control: approved


title: Normal human urothelial cells, HUC_p3, slide 2


title: Cell MEF-Atg5 (+/+) rep1


title: V010015_I_B

status: Public on Jun 25 2012

city: South San Francisco

last: Diggans

state: CA

address: 7000 Shoreline Ct

institute: Veracyte Inc.

hyb_protocol: GeneChip Fluidics 450 (Affymetrix).

scan_protocol: Gene Chip DX v2 (Afffymetrix).

data_processing:
RMA normalization using Affymetrix Power Tools (APT) software. Affymetrix control probes were filtered out.
probe group file: AfirmaT.pgf
meta-probeset file: N/A
For exon data, analysis was conducted using only core probesets and annotation/transcript assignments were based upon genome build hg18.

source_name: Thyroid FNA, cytology I, histology B

label_protocol: Encore Biotin module (NuGEN).

extract_protocol: Total RNA extracted via the AllPrep Micro kit from Qiagen, quantitated via Quant-IT (Invitrogen) and quality determined via Bioanalyzer Picochip (Agilent Technologies). Amplified via WT Ovation FFPEv2, WT Ovation Exon module (NuGEN).

value: thyroid nodule

tag: cytology

value: indeterminate

tag: histology

value: benign

value: female

tag: patient age (yrs)


title: V010013_I_B


title: V010014_I_B


title: V010007_B_B

source_name: Thyroid FNA, cytology B, histology B

value: male


title: V010019_I_M

source_name: Thyroid FNA, cytology I, histology M

value: malignant


title: V010006_I_B


title: 1 mM TCE Mouse 5

description: quality control: approved

value: Male

value: 8-9 weeks

value: 1 mM TCE


title: V010020_M_M

source_name: Thyroid FNA, cytology M, histology M


title: V010017_M_M


title: V010008_I_M


title: V010009_I_M


title: V010012_M_M


title: V010016_I_M


title: V010010_M_M


title: V010003_M_M


title: V010005_I_B


title: V010004_I_B


title: acell_pheromone_control

city: San Francisco

first: Trevor

last: Sorrells

department: Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing: Lowess normalization. See Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133

organism: Kluyveromyces lactis

source_name: control ChIP of WT a cells responding to pheromone

growth_protocol: P04 starvation 10h

treatment_protocol: pheromone induction 4h

tag: cell type

value: a cell

value: WT

source_name: input DNA from WT a cells responding to pheromone


title: acell_pheromone_a2myc

hyb_protocol: Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133

source_name: ChIP of a2-myc in a cells responding to pheromone

source_name: input DNA from a2-myc a cells responding to pheromone


title: V010018_I_B


title: alphacell_control

scan_protocol: Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133

source_name: control ChIP of WT alpha cells

value: alpha cell

source_name: input DNA from WT alpha cells


title: acell_a2myc

source_name: ChIP of a2-myc in a cells

label_protocol: Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133

source_name: input DNA from a2-myc a cells


title: V010001_I_B


title: alphacell_alpha2myc

source_name: ChIP of alpha2-myc in alpha cells

extract_protocol: Nobile CJ, Nett JE, Hernday AD, Homann OR, Deneault J-S, et al. (2009) Biofilm Matrix Regulation by Candida albicans Zap1. PLoS Biol 7(6): e1000133. doi:10.1371/journal.pbio.1000133

source_name: input DNA from alpha2-myc alpha cells


title: acell_control

source_name: control ChIP of WT a cells

source_name: input DNA from WT a cells


title: V010011_M_M


title: V010317_I_B


title: V010318_I_B


title: V010319_B_B


title: V010314_I_B


title: V010315_I_B


title: V010316_M_M


title: V010313_B_B


title: V010312_I_M


title: V010311_I_B


title: V010302_M_M


title: V010308_I_M


title: V010309_B_B


title: V010303_I_B


title: V010307_I_B


title: V010304_I_M


title: V010002_I_B


title: V010310_I_M


title: V010299_I_B


title: V010298_I_B


title: V010300_I_B


title: V010301_I_M


title: V010296_I_B


title: V010297_I_M


title: V010295_I_B


title: V010294_I_M


title: V010293_M_M


title: V010292_B_B


title: V010291_I_B


title: V010305_I_B


title: V010290_I_B


title: V010306_I_B


title: V010287_M_M


title: V010288_I_M


title: V010286_I_M


title: V010289_B_B


title: V010285_I_M


title: V010283_I_B


title: V010284_I_B


title: V010281_I_B


title: V010274_I_M


title: V010277_I_B


title: V010270_I_M


title: V010276_M_M


title: V010272_I_B


title: V010267_I_M


title: V010271_B_B


title: V010279_I_B


title: V010269_I_B


title: V010268_I_B


title: V010275_M_M


title: V010266_M_M


title: V010273_I_B


title: V010265_M_M


title: V010264_I_B


title: V010263_B_B


title: V010262_M_M


title: V010282_I_B


title: V010278_B_M

source_name: Thyroid FNA, cytology B, histology M


title: V010259_I_M


title: V010260_B_B


title: V010257_I_B

source_name: Thyroid FNA, cytology I, histology B


title: V010254_I_M


title: V010256_I_B


title: V010258_I_B


title: V010280_I_M


title: V010255_I_B


title: V010253_I_B


title: V010251_I_B


title: V010261_I_B


title: V010246_I_B


title: V010244_I_B


title: V010245_M_M


title: V010247_I_B


title: V010249_B_B

source_name: Thyroid FNA, cytology B, histology B


title: V010250_I_B


title: V010248_I_B


title: V010252_I_B


title: V010242_I_B


title: V010241_I_B


title: V010234_I_B


title: V010240_M_M


title: V010238_I_M

source_name: Thyroid FNA, cytology I, histology M


title: V010232_I_B


title: V010230_I_B


title: V010236_I_M


title: V010237_I_B


title: V010235_I_B


title: V010228_I_B


title: V010239_I_B


title: V010233_M_M

source_name: Thyroid FNA, cytology M, histology M


title: V010231_M_M


title: V010229_B_B


title: V010226_I_B


title: V010225_I_B


title: V010227_I_B


title: V010243_I_B


title: V010224_B_B


title: V010218_I_M


title: V010219_I_M


title: V010220_I_B


title: V010217_I_B


title: V010221_I_B


title: V010222_I_B


title: V010216_B_B


title: V010215_I_B


title: V010214_I_M


title: V010213_B_M


title: V010211_I_B


title: V010212_I_B


title: V010205_I_B


title: V010208_I_B


title: V010209_I_M


title: V010204_I_M


title: V010201_I_B


title: V010210_I_B


title: V010200_M_M


title: V010206_I_B


title: V010199_B_M


title: V010203_B_B


title: V010223_I_B


title: V010198_I_B


title: V010196_I_B


title: V010207_I_B


title: V010195_I_B


title: V010197_I_M


title: V010194_I_B


title: V010193_I_B


title: V010202_I_B


title: V010192_I_M


title: V010186_I_B


title: V010189_M_M


title: V010187_I_B


title: V010191_I_B


title: V010183_B_B


title: V010188_I_B


title: V010185_M_M


title: V010184_I_M


title: V010182_I_B


title: V010177_I_B


title: V010178_I_B


title: V010176_I_B


title: V010179_I_B


title: V010175_B_B


title: V010174_I_M


title: V010172_I_M


title: V010171_I_M


title: V010173_M_M


title: V010170_I_B


title: V010169_I_B


title: V010168_I_M


title: V010167_I_M


title: V010190_M_M


title: V010181_I_M


title: V010166_I_M


title: V010180_I_M


title: V010163_B_B


title: V010164_I_B


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title: V010154_I_B


title: V010150_B_B


title: V010151_M_M


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title: V010146_I_B


title: V010145_B_B


title: V010142_I_B


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title: V010139_I_M


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title: V010131_I_M


title: V010116_I_M


title: V010114_M_M


title: V010119_I_B


title: V010117_I_B


title: V010120_I_B


title: V010118_I_B


title: V010125_B_B


title: V010123_I_M


title: V010115_I_M


title: V010121_I_M


title: V010110_I_B


title: V010113_M_M


title: V010111_I_B


title: V010112_I_M


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title: V010106_I_B


title: V010109_B_B


title: V010103_I_M


title: V010105_B_B


title: V010101_I_B


title: V010102_I_B


title: V010100_I_B


title: V010098_I_B


title: V010099_I_B


title: V010107_B_B


title: V010096_B_B


title: V010097_B_B


title: V010094_I_M


title: V010093_M_M


title: V010104_I_B


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title: V010086_I_M


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title: V010069_I_M


title: V010091_I_B


title: V010077_I_M


title: V010067_M_M


title: V010064_I_B


title: V010066_M_M


title: V010065_I_B


title: V010076_M_M


title: V010057_I_B


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title: V010061_I_B


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title: V010052_M_M


title: V010059_B_B


title: V010050_M_M


title: V010053_I_B


title: V010068_B_B


title: V010048_B_B


title: V010047_I_B


title: V010049_I_M


title: V010063_I_B


title: V010045_I_B


title: V010046_I_B


title: V010055_I_B


title: V010044_I_B


title: V010054_I_B


title: V010043_I_M


title: V010042_I_B


title: V010041_M_M


title: V010040_I_B


title: V010037_B_B


title: V010035_I_B


title: V010032_I_B


title: V010038_I_M


title: V010033_I_B


title: V010031_I_B


title: V010030_I_B


title: V010034_I_B


title: V010029_I_M


title: V010028_M_M


title: V010027_I_M


title: V010025_I_B


title: V010023_I_M


title: V010022_B_B


title: V010021_I_B


title: V010039_I_B


title: V010036_I_B


title: V010026_I_B


title: RQ6687-6hr-50uM PGE2 - mAdbID:106253

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 106253

hyb_protocol: Sample Hybridization Protocol Other: Hybridization: Combine Cy3 and Cy5 labeled target (adjust the color to purple) and complete dry the sample by speed vacuum . Add 37ul of the following mixture to the dried target (for 20x40mm slide): 1ul 50x Denhardt’s blocking solution (Sigma Cat# 2532) 1ul poly dA (8mg/ml Pharmacia Cat# 27-7988-01) 1ul yeast tRNA (4mg/ml Sigma Cat# R8759) 10ul Human Cot I DNA (1mg/ml Gibco BRL Cat# 15279-011) 3ul 20X SSC 1ul 10% SDS 20ul of DEPC H2O Heat for 2 min at 99oC and Cool to RT. Apply target mixture to array slide, add coverslip, place in humidified hyb chamber, and hybridize at 65oC over night.

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.74

data_processing:
BRB ArrayTool Data Processing
Calculation Method: Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 300, and spot size less than 25um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes.

source_name: Pooled Normal Donor PBMC

label_protocol:
Cy3 Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy3) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

extract_protocol:
RNA extraction with TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: BLOOD

value: PBMC

tag: sample pooling protocol

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

organism: Macaca mulatta

source_name: Rhesus macaques 6hr 50uM PGE2

label_protocol:
Cy5 Labeling Protocol
Other: Target labeling by reverse transcription: 4ul First strand buffer 1ul dN6 primer (8ug/ul; Boehringer Mannheim Cat# 1034731 resuspended in 250ul DEPC H2O) 2ul 10X low T - dNTP (5mM A, C and GTP, 2mM dTTP) 2ul Cy-dUTP (1mM Cy5) 2ul 0.1 M DTT 1ul RNasin 3-6ug amplified mRNA in 7 ul DEPC H2O Mix well and heat to 65C for 5min then cool down to 42C. Add 1.5ul SSII and Incubate for 90 min at 42C. Add 2.5ul 500mM EDTA and heat to 65C for 1min. Add 5ul 1M NaOH and incubate at 65C for 15min to hydrolyze RNA. Add 12.5ul 1M Tris immediately to neutralize the pH. Add 35ul of 1xTE. Target clean up: Prepare Bio-6 column and run target solution through it. Collect flow through and add 200ul 1xTE. Concentrate target to ~20ul using a microcon YM-30 column (Millipore Cat# 42410).

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 50 uM
Treatment time: 6 hours

value: CD34+ mobilized peripheral blood stem cells (MPBSC)

tag: treatment type

value: small molecule

tag: agent

tag: treatment dose

value: 50 uM

tag: treatment time

value: 6 hours


title: RQ6848-6hr-Untreated - mAdbID:106254

description: mAdb experiment ID: 106254

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.8

source_name: Rhesus macaques 6hr Untreated

treatment_protocol:
Treatment time: 6 hours
In-vitro treatment: Dimethyl sulfoxide (DMSO) vehicle solution

tag: in-vitro treatment


title: V010024_M_M

value: thyroid nodule


title: RQ6873-6hr-Untreated - repeat 1 - mAdbID:106246

description: mAdb experiment ID: 106246

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.03 Temperature: 33.83

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: RQ6709-6hr-10uM PGE2 - mAdbID:106244

description: mAdb experiment ID: 106244

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.02 Temperature: 33.65

source_name: Rhesus macaques 6hr 10uM PGE2

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 10 uM
Treatment time: 6 hours

value: 10 uM


title: RQ6687-6hr-10uM PGE2 - mAdbID:106252

description: mAdb experiment ID: 106252

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.02 Temperature: 33.71


title: RQ6848-6hr-50uM PGE2 - mAdbID:106256

description: mAdb experiment ID: 106256

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.97 Temperature: 33.93


title: RQ6848-6hr-10uM PGE2 - mAdbID:106255

description: mAdb experiment ID: 106255

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.98 Temperature: 33.9


title: RQ6873-6hr-10uM PGE2 - repeat 2 - mAdbID:106249

description: mAdb experiment ID: 106249

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 4.31 Temperature: 27.82


title: RQ6873-6hr-50uM PGE2 - mAdbID:106250

description: mAdb experiment ID: 106250

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.77


title: RQ6873-6hr-10uM PGE2 - repeat 1 - mAdbID:106248

description: mAdb experiment ID: 106248

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.83


title: RQ6709-6hr-Untreated - mAdbID:106243

description: mAdb experiment ID: 106243

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.04 Temperature: 33.59


title: RQ6709-6hr-50uM PGE2 - mAdbID:106245

description: mAdb experiment ID: 106245

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.71


title: Human D3-12hr-50uM PGE2 - mAdbID:106237

description: mAdb experiment ID: 106237

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.04 Temperature: 33.41

source_name: Hs 12hr 50uM PGE2

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 50 uM
Treatment time: 12 hours

value: 12 hours


title: RQ6687-6hr-Untreated - mAdbID:106251

description: mAdb experiment ID: 106251


title: RQ6783-6hr-50uM PGE2 - mAdbID:106242

description: mAdb experiment ID: 106242

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.09 Temperature: 33.56


title: RQ6783-6hr-Untreated - repeat 1 - mAdbID:106240

description: mAdb experiment ID: 106240

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.03 Temperature: 33.44

source_name: Rhesus macaques 2hr Untreated

treatment_protocol:
Treatment time: 2 hours
In-vitro treatment: Dimethyl sulfoxide (DMSO) vehicle solution

value: 2 hours


title: V010366_I_B

scan_protocol: Scanner 3000 7G (Affymetrix).

data_processing:
RMA normalization using Affymetrix Power Tools (APT) software.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.full.mps
For exon data, analysis was conducted using only core probesets and annotation/transcript assignments were based upon genome build hg18.

value: indeterminate

value: benign

value: female


title: RQ6783-0hr-Untreated - mAdbID:106238

description: mAdb experiment ID: 106238

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.03 Temperature: 33.41

source_name: Rhesus macaques 0hr Untreated

treatment_protocol:
Treatment time: 0 hours
In-vitro treatment: Dimethyl sulfoxide (DMSO) vehicle solution

value: 0 hours


title: V010367_M_M

value: malignant

value: male


title: Human D3-12hr-Untreated - mAdbID:106235

description: mAdb experiment ID: 106235

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.05 Temperature: 33.22

value: BLOOD

value: PBMC

source_name: Hs 12hr Untreated

treatment_protocol:
Treatment time: 12 hours
In-vitro treatment: Dimethyl sulfoxide (DMSO) vehicle solution


title: V010070_I_M

scan_protocol: Gene Chip DX v2 (Afffymetrix).


title: V010368_I_B


title: RQ6873-6hr-Untreated - repeat 2 - mAdbID:106247

description: mAdb experiment ID: 106247

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 4.36 Temperature: 27.24

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

value: CD34+ mobilized peripheral blood stem cells (MPBSC)


title: V010365_B_B


title: RQ6783-6hr-Untreated - repeat 2 - mAdbID:106239

description: mAdb experiment ID: 106239

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.08;; 5.11 Temperature: 26.08


title: RQ6783-6hr-10uM PGE2 - mAdbID:106241

description: mAdb experiment ID: 106241

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.01 Temperature: 33.47

value: small molecule


title: Human D3-12hr-10uM PGE2 - mAdbID:106236

description: mAdb experiment ID: 106236

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.04 Temperature: 33.35

source_name: Hs 12hr 10uM PGE2

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 10 uM
Treatment time: 12 hours


title: Human D3-6hr-10uM PGE2 - mAdbID:106233

description: mAdb experiment ID: 106233

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.04 Temperature: 32.98

source_name: Hs 6hr 10uM PGE2

value: 6 hours


title: HL60 untreated

city: Bronx

first: Boris

last: Bartholdy

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on Human Genome 133 plus2 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station

scan_protocol: Standard Affymetrix Scanner protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; CEL files were generated. CEL files processed/normalized using DNA-Chip Analyzer (dChip) to generate probeset-level signal intensity data.  dChip-processed signal intensity  dChip-processed signal intensity  dChip-processed signal intensity

source_name: HL60 cells, untreated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from ~5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: Cells were cultured in RPMI + 10% FBS

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

treatment_protocol: HL60 cells were untreated, or treated with 3ug/ml of Eltrombopag for 36 hrs in RPMI with 10% FBS

tag: cell line

value: hematopoietic stem


title: Human D3-6hr-50uM PGE2 - mAdbID:106234

description: mAdb experiment ID: 106234

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 5.05 Temperature: 33.07

tag: tissue

source_name: Hs 6hr 50uM PGE2

value: 50 uM


title: HL60 EP 3ug/ml

source_name: HL60 cells, 3ug/ml Eltrombopag (EP)


title: V010364_I_M

value: thyroid nodule


title: V010363_I_B

source_name: Thyroid FNA, cytology I, histology B


title: V010362_I_B


title: V010361_M_M


title: Human D3-6hr-Untreated - mAdbID:106232

description: mAdb experiment ID: 106232

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.04 Temperature: 32.83

source_name: Hs 6hr Untreated

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: Human D3-2hr-50uM PGE2 - mAdbID:106231

description: mAdb experiment ID: 106231

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.07;; 5.21 Temperature: 25.44

source_name: Hs 2h 50uM PGE2

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 50 uM
Treatment time: 2 hours

value: 2 hours


title: V010358_I_M

source_name: Thyroid FNA, cytology I, histology M

value: indeterminate


title: V010357_B_B

source_name: Thyroid FNA, cytology B, histology B

value: benign


title: V010356_I_M

value: female


title: V010355_B_B


title: V010354_M_M

source_name: Thyroid FNA, cytology M, histology M


title: V010353_I_M


title: V010352_I_B


title: V010360_I_B


title: Human D3-0hr-Untreated - mAdbID:106228

description: mAdb experiment ID: 106228

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.03 Temperature: 32.28

source_name: Pooled Normal Donor PBMC

source_name: Hs 0hr Untreated

value: 0 hours


title: Human D2-12hr-Untreated - mAdbID:106225

description: mAdb experiment ID: 106225

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.97 Temperature: 31.73

value: 12 hours


title: V010351_M_M

value: malignant


title: Human D3-2hr-Untreated - mAdbID:106229

description: mAdb experiment ID: 106229

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.04 Temperature: 32.4

value: BLOOD

source_name: Hs 2hr Untreated


title: Human D2-6hr-Untreated - mAdbID:106222

description: mAdb experiment ID: 106222

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.93 Temperature: 31.39

value: PBMC


title: Human D2-6hr-10uM PGE2 - mAdbID:106223

description: mAdb experiment ID: 106223

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.93 Temperature: 31.48

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

value: 10 uM


title: V010349_M_M

scan_protocol: Scanner 3000 7G (Affymetrix).


title: V010350_M_M


title: V010079_I_B


title: Human D2-2hr-50uM PGE2 - mAdbID:106221

description: mAdb experiment ID: 106221

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5 Temperature: 31.33

value: CD34+ mobilized peripheral blood stem cells (MPBSC)

value: small molecule


title: V010359_I_M

value: male


title: Human D2-2hr-Untreated - mAdbID:106219

description: mAdb experiment ID: 106219

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.93 Temperature: 30.94


title: Human D2-2hr-10uM PGE2 - mAdbID:106220

description: mAdb experiment ID: 106220

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.97 Temperature: 31.15

source_name: Hs 2h 10uM PGE2


title: Human D3-2hr-10uM PGE2 - mAdbID:106230

description: mAdb experiment ID: 106230

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.05 Temperature: 32.61


title: Human D2-12hr-10uM PGE2 - mAdbID:106226

description: mAdb experiment ID: 106226

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5 Temperature: 31.97


title: Human D2-6hr-50uM PGE2 - mAdbID:106224

description: mAdb experiment ID: 106224

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.95 Temperature: 31.58

value: 50 uM

value: 6 hours


title: V010348_I_M

value: thyroid nodule


title: Human D2-12hr-50uM PGE2 - mAdbID:106227

description: mAdb experiment ID: 106227

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.02 Temperature: 32.13

source_name: Hs 12hr 50uM PGE2


title: Human D2-0hr-Untreated - mAdbID:106218

description: mAdb experiment ID: 106218

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.91 Temperature: 30.69

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: V010347_B_B


title: Human D4-24hr-50uM PGE2 - repeat 2 - mAdbID:106217

description: mAdb experiment ID: 106217

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.83 Temperature: 30.48

source_name: Hs 24hr 50uM PGE2

treatment_protocol:
Treatment type: small molecule
Agent: 16,16-dimethyl-prostaglandin E2 (dmPGE2)
Treatment dose: 50 uM
Treatment time: 24 hours

value: 24 hours


title: V010346_B_B

value: benign


title: Day 6 Post-Infection rep3

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio_2010.3

source_name: C57BL6/J mouse lung tissue

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol provided with the kit

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

tag: strain

tag: virus

tag: time post-infection

value: day 6

value: lung


title: Human D4-24hr-Untreated - mAdbID:106215

description: mAdb experiment ID: 106215

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.7 Temperature: 30.17

source_name: Hs 24hr Untreated

treatment_protocol:
Treatment time: 24 hours
In-vitro treatment: Dimethyl sulfoxide (DMSO) vehicle solution


title: V010344_I_M

value: indeterminate

tag: gender

value: female


title: V010345_I_B


title: Day 4 Post-Infection rep3

description: replicate 3

value: day 4


title: Human D4-12hr-Untreated - mAdbID:106213

description: mAdb experiment ID: 106213

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 4.59 Temperature: 29.44

value: BLOOD

value: PBMC

source_name: Hs 12hr Untreated

value: 12 hours


title: V010343_I_B


title: Human D4-6hr-50uM PGE2 - mAdbID:106212

description: mAdb experiment ID: 106212

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 4.56 Temperature: 29.29

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Hs 6hr 50uM PGE2

value: CD34+ mobilized peripheral blood stem cells (MPBSC)


title: V010341_M_M

value: malignant


title: V010340_I_B

value: male


title: Human D4-12hr-50uM PGE2 - mAdbID:106214

description: mAdb experiment ID: 106214

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.66 Temperature: 29.96

value: small molecule

value: 50 uM


title: V010342_I_B

value: thyroid nodule


title: Day 2 Post-Infection rep3

description: replicate 3

value: day 2


title: Day 3 Post-Infection rep3

description: replicate 3

value: day 3


title: Human D4-24hr-50uM PGE2 - repeat 1 - mAdbID:106216

description: mAdb experiment ID: 106216

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 4.44 Temperature: 28.28

value: 24 hours


title: Human D4-0hr-Untreated - mAdbID:106210

description: mAdb experiment ID: 106210

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 4.47 Temperature: 28.65

value: 0 hours

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: V010338_I_B

scan_protocol: Scanner 3000 7G (Affymetrix).

value: indeterminate

value: benign


title: Human D4-6hr-Untreated - mAdbID:106211

description: mAdb experiment ID: 106211

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.09;; 4.51 Temperature: 29.01

value: BLOOD

value: 6 hours


title: RQ6686-24hr-Untreated - mAdbID:104360

description: mAdb experiment ID: 104360

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.9 Temperature: 32.92

value: PBMC

source_name: Rhesus macaques 24hr Untreated


title: Day 6 Post-Infection rep2

description: replicate 2

value: day 6

value: lung


title: Day 5 Post-Infection rep2

description: replicate 2

value: day 5


title: Day 3 Post-Infection rep2

description: replicate 2


title: RQ6686-24hr-50uM PGE2 - mAdbID:104359

description: mAdb experiment ID: 104359

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.93 Temperature: 32.71

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Rhesus macaques 24hr 50uM PGE2

value: CD34+ mobilized peripheral blood stem cells (MPBSC)


title: RQ6686-12hr-Untreated - mAdbID:104358

description: mAdb experiment ID: 104358

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.15;; 4.98 Temperature: 32.55

source_name: Rhesus macaques 12hr Untreated

value: 12 hours


title: Day 1 Post-Infection rep3

description: replicate 3

value: day 1


title: Day 5 Post-Infection rep3

description: replicate 3


title: Day 2 Post-Infection rep2

description: replicate 2

value: day 2


title: Day 4 Post-Infection rep2

description: replicate 2

value: day 4


title: Day 1 Post-Infection rep2

description: replicate 2


title: V010337_I_B

source_name: Thyroid FNA, cytology I, histology B

value: thyroid nodule

value: female


title: V010336_I_M

source_name: Thyroid FNA, cytology I, histology M

value: malignant


title: V010335_I_B

value: indeterminate


title: V010333_M_M


title: V010334_I_B

value: benign


title: V010332_B_B

source_name: Thyroid FNA, cytology B, histology B


title: RQ6686-6hr-Untreated - mAdbID:104356

description: mAdb experiment ID: 104356

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.14;; 3.59 Temperature: 32.98

value: BLOOD

source_name: Rhesus macaques 6hr Untreated

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: RQ6686-12hr-50uM PGE2 - mAdbID:104357

description: mAdb experiment ID: 104357

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.03 Temperature: 32.13

source_name: Pooled Normal Donor PBMC

value: PBMC

source_name: Rhesus macaques 12hr 50uM PGE2

value: small molecule

value: 50 uM


title: V010331_M_M

source_name: Thyroid FNA, cytology M, histology M

value: male


title: RQ6686-0hr-Untreated - mAdbID:104352

description: mAdb experiment ID: 104352

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.08 Temperature: 31.45

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Rhesus macaques 0hr Untreated

value: 0 hours


title: Day 3 Post-Infection rep1

description: replicate 1

value: day 3

value: lung


title: V010330_I_M


title: RQ6686-2hr-Untreated - mAdbID:104354

description: mAdb experiment ID: 104354

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.06 Temperature: 31.7

source_name: Rhesus macaques 2hr Untreated

value: CD34+ mobilized peripheral blood stem cells (MPBSC)

value: 2 hours


title: Day 5 Post-Infection rep1

description: replicate 1

value: day 5


title: Day 1 Post-Infection rep1

description: replicate 1

value: day 1


title: RQ6686-2hr-50UM PGE2 - mAdbID:104353

description: mAdb experiment ID: 104353

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.14;; 5.08 Temperature: 31.61

source_name: Rhesus macaques 2h 50uM PGE2


title: Day 6 Post-Infection rep1

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

source_name: C57BL6/J mouse lung tissue

value: day 6


title: Human D1-24hr-Untreated - mAdbID:104350

description: mAdb experiment ID: 104350

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 4.76 Temperature: 29.47

source_name: Hs 24hr Untreated

value: 24 hours


title: Day 2 Post-Infection rep1

description: replicate 1

value: day 2


title: V010328_M_M

value: thyroid nodule

value: malignant


title: Human D1-24hr-50uM PGE2 - mAdbID:104349

description: mAdb experiment ID: 104349

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 5.06 Temperature: 31.18

value: BLOOD

value: PBMC

source_name: Hs 24hr 50uM PGE2


title: Human D1-12hr-Untreated - mAdbID:104347

description: mAdb experiment ID: 104347

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.97 Temperature: 31.03

source_name: Hs 12hr Untreated

value: 12 hours

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: Uninfected Control rep3

description: replicate 3

value: uninfected control


title: Human D1-12hr-50uM PGE2 - mAdbID:104345

description: mAdb experiment ID: 104345

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.96 Temperature: 30.78

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Hs 12hr 50uM PGE2

value: small molecule

value: 50 uM


title: V010327_I_B

value: indeterminate

value: benign

value: female


title: KOF fetal liver #3

city: Dresden

first: Björn

last: Hiller

address: Fiedlerstrasse 42

department: Institute for Immunology

country: Germany

institute: TU Dresden

hyb_protocol: Hybridization, staining and scanning of the GeneChip Mouse Genome 430 2.0microarrays were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3 (Affymetrix)

data_processing: Microarray data was analysed using the Genespring GX software

source_name: E14.5 Rnaseh2b KOF embryo

label_protocol: RNA was reverse transcribed, amplified and biotin-labeled using the Message Amp II-Biotin Enhanced Kit (Ambion)

extract_protocol: RNA extraction was performed by the acid guanidinium thiocyanate-phenol-chloroform method (Chomczynski, P. & Sacchi, N. The single-step method of RNA isolation by acid guanidiniumthiocyanate-phenol-chloroform extraction: twenty-something years on. Nat. Protoc. 1, 581-585(2006).)

tag: age

tag: line

value: embryo

tag: genotype/variation

value: KOF


title: Uninfected Control rep2

description: replicate 2

value: lung


title: MEFs (Wildtype)

city: Wako

first: Yuen Yan

middle: Joanna

last: Ip

state: Saitama

address: 2-1 Hirosawa

department: Advanced Science Institute

country: Japan

institute: RIKEN

description: Gene expression data from MEFs

hyb_protocol: After fragmentation, the aRNA synthesized from total RNA harvested from MEFs were hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Hybridization was carried out in AFFYMETRIX GeneChip Hybridization Oven 640 at 45°C overnight.  All arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: AFFYMETRIX GeneChip Scanner 3000 was used to scan the GeneChips.

data_processing: The data were analyzed with Aligent GeneSpring GX.

source_name: MEFs from wildtype mouse

label_protocol: Biotin-labeled aRNA were prepared from 100 ng total RNA using GeneChip 3’IVT Express Kit (Affymetrix).

growth_protocol: MEFs were prepared from E13.5 mouse embryos and were maintained for 2 weeks before RNA extraction.

extract_protocol: Total RNA was extracted with Trizol reagent according to the manufacturer's protocol.

treatment_protocol: No treatment was performed.

value: Embryonic Fibroblast

tag: genotype

value: Wildtype

value: Embryonic Day 13.5


title: KOF fetal liver #2

scan_protocol: according to the Affymetrix GeneChip Expression Analysis Technical Manual P/N 702232 Rev. 3 (Affymetrix)


title: V010329_I_M

scan_protocol: Scanner 3000 7G (Affymetrix).

value: thyroid nodule

tag: cytology

tag: histology

value: malignant

tag: patient age (yrs)


title: V010326_I_M


title: V010325_I_M


title: Human D1-6hr-Untreated - mAdbID:104344

description: mAdb experiment ID: 104344

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.91 Temperature: 30.6

value: BLOOD

tag: cell type

value: PBMC

tag: sample pooling protocol

source_name: Hs 6hr Untreated

value: CD34+ mobilized peripheral blood stem cells (MPBSC)

value: 6 hours


title: MEFs (Malat1 Knock-out)

description: Gene expression data from MEFs

source_name: MEFs from Malat1 knock-out mouse

value: Malat1 Knock-out


title: V010324_I_M

source_name: Thyroid FNA, cytology I, histology M


title: Uninfected Control rep1

description: replicate 1

value: uninfected control


title: KOF fetal liver #1


title: wild type fetal liver #1

source_name: E14.5 Rnaseh2b wild type embryo

value: wild type


title: Human D1-6hr-50uM PGE2 - mAdbID:104342

description: mAdb experiment ID: 104342

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.13;; 4.87 Temperature: 30.29

source_name: Pooled Normal Donor PBMC

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Hs 6hr 50uM PGE2

tag: treatment type

value: small molecule

tag: agent

tag: treatment dose

value: 50 uM

tag: treatment time


title: Human D1-2hr-Untreated - mAdbID:104341

description: mAdb experiment ID: 104341

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.12;; 4.83 Temperature: 30.05

tag: tissue

source_name: Hs 2hr Untreated

value: 2 hours

tag: in-vitro treatment

value: Dimethyl sulfoxide (DMSO) vehicle solution


title: wild type fetal liver #3

value: embryo


title: V010322_I_B

source_name: Thyroid FNA, cytology I, histology B

value: indeterminate

value: benign

value: female


title: V010321_I_B

value: thyroid nodule


title: V010320_I_B


title: wild type fetal liver #2


title: Human D1-2hr-50uM PGE2 - mAdbID:104338

description: mAdb experiment ID: 104338

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.11;; 4.78 Temperature: 29.78

value: BLOOD

source_name: Hs 2h 50uM PGE2


title: Human D1-0hr-Untreated - mAdbID:104336

description: mAdb experiment ID: 104336

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 10;; 10 LaserPower: 3.1;; 4.46 Temperature: 28.98

value: PBMC

source_name: Hs 0hr Untreated

value: 0 hours


title: V010323_I_B

value: male


title: KLS TIF1γ wtwt

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

country: France

institute: IGBMC

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

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

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

source_name: bone marrow KLS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 25 ng total RNA (Expression Analysis Technical Manual:Two-cycle target labeling assay, 2001, Affymetrix).

growth_protocol: KLS cells purified from bone marrow of mice conditionally inactivated for TIF1γ gene and wildtype mice.

extract_protocol: total RNA was isolated using RNeasy micro kit (qiagen) according to the manufacturer's instructions

value: bone marrow lin-,c-kit+, Sca+ cell


title: HNSCC case PBL 173

status: Public on Jun 24 2012

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: HNSCC case

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted DNeasy blood and tissue kit according to standard instructions

value: Peripheral Blood

tag: disease

value: HNSCC case


title: control PBL 184

source_name: control

value: control


title: HNSCC case PBL 174


title: KLS TIF1γ Δ/Δ

value: TIF1γ Δ/Δ


title: control PBL 183


title: control PBL 179


title: HNSCC case PBL 177


title: Hippocampus (Malat1 Knock-out), Biological rep 1

description: Exon expression data from neurons

hyb_protocol: Following fragmentation, the aRNA synthesized from total RNA extracted from neurons were hybridized to Affymetrix Mouse Exon 1.0 ST Array overnight in AFFYMETRIX GeneChip Hybridization Oven 640 at 45°C. All arrays were washed and stained in the Affymetrix Fluidics Station 450.

data_processing:
Data were analyzed with Aligent GeneSpring GX.
Probe group was assigned using Aligent GeneSpring GX with the option Affymetrix Exon Expression and the technology file MoEx-1_0-st-v1_na30_mm9_2009-11-09.
Meta-probeset was assigned using Aligent GeneSpring GX with the full set of probes.

source_name: Hippocampus from Malat1 knock-out mouse

growth_protocol: Hippocampi were dissected from 3 month old male mice.

treatment_protocol: The mice were not treated before being sacrificed.

value: 3 months

value: Hippocampus

value: Malat1 Knock-out

tag: strain


title: HNSCC case PBL 168


title: control PBL 182


title: control PBL 180


title: HNSCC case PBL 172


title: control PBL 170


title: control PBL 175


title: control PBL 181


title: Hippocampus (Malat1 Knock-out), Biological rep 2

description: Exon expression data from neurons

tag: age


title: HNSCC case PBL 178


title: HNSCC case PBL 169


title: Hippocampus (Wildtype), Biological rep 1

description: Exon expression data from neurons

source_name: Hippocampus from wildtype mouse

value: Wildtype


title: control PBL 167


title: control PBL 176


title: control PBL 166


title: Hippocampus (Wildtype), Biological rep 2

description: Exon expression data from neurons


title: control PBL 164


title: control PBL 171


title: HNSCC case PBL 163


title: HNSCC case PBL 162


title: HNSCC case PBL 158


title: HNSCC case PBL 157


title: HNSCC case PBL 152


title: HNSCC case PBL 145


title: control PBL 151


title: HNSCC case PBL 147


title: HNSCC case PBL 149


title: HNSCC case PBL 143


title: HNSCC case PBL 160


title: Day 4 Post-Infection rep1

description: replicate 1

source_name: C57BL6/J mouse lung tissue

tag: virus

tag: time post-infection

value: day 4

value: lung


title: RQ6686-6hr-50uM PGE2 - mAdbID:104355

description: mAdb experiment ID: 104355

scan_protocol: Creator: GenePix Pro 4.0.1.17 Scanner: GenePix 4000B [84945] ScanPower: 33;; 33 LaserPower: 3.15;; 3.61 Temperature: 33.04

value: Pooled PBMC's from 6 donors aphereses. PBMC were separated using ficoll (LSM separation medium) before RNA extraction

source_name: Rhesus macaques 6hr 50uM PGE2

value: CD34+ mobilized peripheral blood stem cells (MPBSC)

value: small molecule

value: 50 uM

value: 6 hours


title: control PBL 161


title: HNSCC case PBL 146


title: HNSCC case PBL 155


title: control PBL 150


title: control PBL 144


title: HNSCC case PBL 156


title: HNSCC case PBL 141


title: HNSCC case PBL 142


title: HNSCC case PBL 159


title: HNSCC case PBL 137


title: control PBL 153


title: control PBL 140


title: control PBL 139


title: HNSCC case PBL 148


title: control PBL 154


title: HNSCC case PBL 134


title: HNSCC case PBL 127


title: control PBL 126


title: control PBL 135


title: HNSCC case PBL 131


title: control PBL 133


title: control PBL 121


title: control PBL 129


title: HNSCC case PBL 120


title: control PBL 115


title: HNSCC case PBL 128


title: HNSCC case PBL 136


title: control PBL 123


title: control PBL 125


title: HNSCC case PBL 122


title: HNSCC case PBL 130


title: control PBL 117


title: control PBL 119


title: control PBL 118


title: HNSCC case PBL 138


title: HNSCC case PBL 114


title: HNSCC case PBL 116


title: control PBL 111


title: HNSCC case PBL 110


title: control PBL 112


title: control PBL 124


title: control PBL 113


title: HNSCC case PBL 165


title: HNSCC case PBL 132


title: HNSCC case PBL 108


title: HNSCC case PBL 105


title: HNSCC case PBL 107


title: HNSCC case PBL 109


title: control PBL 106


title: control PBL 104


title: HNSCC case PBL 103


title: HNSCC case PBL 98


title: V010339_B_B

source_name: Thyroid FNA, cytology B, histology B

value: thyroid nodule

value: benign

tag: gender

value: female


title: HNSCC case PBL 99

value: Peripheral Blood

value: HNSCC case


title: HNSCC case PBL 100


title: control PBL 101

value: control


title: control PBL 94


title: control PBL 89


title: control PBL 88


title: control PBL 93


title: control PBL 102


title: HNSCC case PBL 96


title: control PBL 83


title: control PBL 84


title: control PBL 97


title: HNSCC case PBL 90


title: control PBL 91


title: control PBL 92


title: HNSCC case PBL 85


title: HNSCC case PBL 86


title: control PBL 95


title: HNSCC case PBL 87


title: control PBL 75


title: control PBL 81


title: control PBL 82


title: HNSCC case PBL 74


title: HNSCC case PBL 79


title: HNSCC case PBL 76


title: control PBL 77


title: HNSCC case PBL 78


title: control PBL 72


title: control PBL 73


title: control PBL 80


title: HNSCC case PBL 71


title: control PBL 69


title: HNSCC case PBL 70


title: HNSCC case PBL 68


title: HNSCC case PBL 66


title: HNSCC case PBL 61


title: control PBL 55


title: control PBL 47


title: control PBL 67


title: HNSCC case PBL 45


title: HNSCC case PBL 56


title: control PBL 63


title: HNSCC case PBL 58


title: control PBL 53


title: control PBL 60


title: control PBL 62


title: control PBL 48


title: control PBL 43


title: HNSCC case PBL 64


title: HNSCC case PBL 51


title: control PBL 57


title: control PBL 59


title: HNSCC case PBL 54


title: control PBL 50


title: control PBL 46


title: HNSCC case PBL 41


title: control PBL 44


title: HNSCC case PBL 42


title: HNSCC case PBL 52


title: HNSCC case PBL 49


title: HNSCC case PBL 65


title: HNSCC case PBL 40


title: control PBL 39


title: HNSCC case PBL 34


title: control PBL 31


title: HNSCC case PBL 29


title: control PBL 37


title: HNSCC case PBL 35


title: control PBL 22


title: control PBL 24


title: control PBL 30


title: HNSCC case PBL 32


title: HNSCC case PBL 38


title: HNSCC case PBL 27


title: control PBL 33


title: control PBL 26


title: control PBL 21


title: HNSCC case PBL 28


title: control PBL 16


title: HNSCC case PBL 25


title: control PBL 23


title: HNSCC case PBL 17


title: control PBL 11


title: HNSCC case PBL 12


title: control PBL 18


title: control PBL 19


title: control PBL 15


title: HNSCC case PBL 14


title: control PBL 10


title: HNSCC case PBL 13


title: HNSCC case PBL 20


title: control PBL 5


title: control PBL 4


title: HNSCC case PBL 8


title: absorptive enterocytes of jejunum (14_JE_PAT26) [LDM]

city: Berne

first: Pascale

last: Anderle

state: BE

address: Buehlstrasse 28

department: Institute of Biochemistry and Molecular Medicine

country: Switzerland

institute: University of Berne

hyb_protocol: cRNA was hybridized to Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, USA).

scan_protocol: Standard Affymetrix protocol

data_processing: Robust multi-array averaging and quantile normalization were used to quantify gene expression (R, Bioconductor, RMA package).

source_name: laser-dissected normal enterocytes

label_protocol: 100 ng of total RNA were amplified and labeled using Affymetrix protocols.

extract_protocol: Total RNA was extracted using the total RNA extraction Nucleospin II kit by Machery-Nagel (Oensingen, Switzerland).

treatment_protocol: Immediately after resection of human tissue, samples were put on ice and sections of one cm length of small intestine and colon (tumor regions and adjacent normal epithelium), respectively, were cut, washed in chilled PBS, embedded in OCT and frozen immediately. One section of the ileum und two of the jejunum were first stored in RNAlater at 4 C for shipping, then rinsed with chilled PBS and embedded in OCT and frozen immediately. 12 µm frozen sections were cut and mounted on Leica or Zeiss membranes for dissecting microscopy (Leica Microsystems, Germany and PALM Microbeam, Germany), fixed in 96 % ethanol for 30 s and colored for an equivalent time hematoxylin/eosin solution, respectively. Primary fibroblasts were cultured in DMEM Glutamax supplemented with 10% FCS, 5mL penicillin/streptomycin and 0.5 mL gentamycin.

value: jejunum

value: normal enterocytes

tag: laser-dissected

value: yes


title: Chronic active plaque 1 (CAP1)

city: Stanford

first: May

last: Han

address: 1201 Welch Road

institute: Stanford University

description:
Fresh-frozen autopsy brain samples
Gene expression data from active MS brain lesions -following demyelination with active inflammation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 2.0 array (Affymatrix). GeneChips were washed and stained in the GeneChip Hybridization Oven 640.

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

data_processing: The data were analyzed with Affymatrix Gene Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: MS brain lesion (following demyelination-active inflammation)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (3'IVT protocol from Affymatrix ).

growth_protocol: Fresh-frozen autopsy brain samples from MS and control subjects were studied

extract_protocol: Total RNA from MS and control brain samples were extracted utilizing RNAEasy kit from Qiagen.

treatment_protocol: MS brain lesions were characterized histologically according to disease activity as AP (active plaque), CAP (chronic active plaque), CP (chronic plaque). Control brain samples were analyzed to rule out neurological disorders.

tag: histology

value: chronice active plaque

tag: disease state

value: multiple sclerosis following demyelination-active inflammation

value: multiple sclerosis brain lesion


title: HNSCC case PBL 3

tag: cell type


title: absorptive enterocytes of ileum (11_IL_PAT31) [LDM]

growth_protocol: Primary fibroblasts were cultured in DMEM Glutamax supplemented with 10% FCS, 5mL penicillin/streptomycin and 0.5 mL gentamycin.

value: ileum


title: control PBL 6


title: HNSCC case PBL 1

value: Peripheral Blood Lymphocyte


title: HNSCC case PBL 9


title: cancer-associated fibroblasts (07_CAF8) [LDM]

source_name: primary cell cultures of cancer-associated fibroblasts

value: colon

value: no


title: absorptive enterocytes of ileum (12_IL_Spain) [LDM]


title: normal colonocytes (06_N14) [LDM]

source_name: laser-dissected normal colonocytes

value: normal colonocytes


title: absorptive enterocytes of ileum (10_IL_Biopredict) [LDM]


title: Chronic plaque 2 (CP2)

description:
Fresh-frozen autopsy brain samples
Gene expression data from chronic MS brain lesions - after inflammation has subsided and gliosis has set in

source_name: MS brain lesion (after inflammation has subsided -late stage)

value: chronic plaque

value: multiple sclerosis after inflammation has subsided-late stage


title: HNSCC case PBL 36


title: Chronic active plaque 2 (CAP2)


title: tumor cells (02_E8) [LDM]

source_name: laser-dissected tumor cells

value: tumor cells


title: Active plaque (AP)

description:
Fresh-frozen autopsy brain samples
Gene expresssion data from active MS brain lesions - early stage before demyelination

source_name: MS brain lesion (early stage-active inflammation)

value: active plaque

value: multiple sclerosis early stage-active inflammation


title: cancer-associated fibroblasts (09_CAF17) [LDM]

value: primary cell cultures of cancer-associated fibroblasts


title: normal colonocytes (04_N3) [LDM]


title: normal colonocytes (05_N8) [LDM]


title: Chronic plaque 1 (CP1)


title: control PBL 7

value: Peripheral Blood

value: control


title: cancer-associated fibroblasts (08_CAF14) [LDM]


title: absorptive enterocytes of jejunum (13_JE_PAT25) [LDM]

value: jejunum

value: normal enterocytes

value: yes


title: tumor cells (03_E9) [LDM]


title: tumor cells (01_E3) [LDM]


title: 3-week CDX2-knockdown Caco-2 cells, grown on filters (N02_CacoCDX2) [cell line]

source_name: colon carcinoma derived cell line

growth_protocol: SW480 were cultured in RPMI 1640 containing 10% fetal calf serum (FCS), Caco-2, HT29, LS174T in Dulbecco's modified Eagle essential medium (DMEM) Glutamax containing 10% FCS and T84 in RPMI 1640 containing 10% FCS and 2 mM glutamine. For the culture of Caco-2LD cells antibiotic mixture (100 U/ml penicillin, 100 µg/ml streptomycin) was added to the media. All cell lines were cultured in 37°C and 5% CO2. CacoReadyTM kit cells (Readycell, Barcelona, Spain) were cultured on 24-transwells filters for either 14 days in DMEM Low glucose containing 10% FCS, 1% L-Glutamine and 1% Penicillin/Streptomycin, then 4 days of culture in semi-solid shipping media and again 3 days in culture media (Readycell’s patented technology), or for 3 weeks in the absence of the semi-solid shipping media. Differentiated Caco-2LD cells were grown at low density and then differentiated on 0.4 µm PET filters as described by Natoli et al J Cell Physiol 226, 1531-1543 (2011).

tag: cell line

value: CDX2-knockdown Caco-2 cells

tag: growth protocol

value: 3-week , grown on filters


title: HNSCC case PBL 2

value: HNSCC case


title: 3-week CDX2-knockdown Caco-2 cells, grown on filters (N01_CacoCDX1) [cell line]

value: colon


title: Control 2

description:
Fresh-frozen autopsy brain samples
Gene expression data from healthy control brain samples

source_name: White matter from age-matched healthy controls

value: healthy control

value: brain white matter


title: CacoReady cells, exposed to shipping media, grown on filters (73_cacoR) [cell line]

value: CacoReady cells


title: Caco-2LD cells, grown on filters (63_cacoF) [cell line]

value: Caco-2LD cells

value: grown on filters


title: CacoReady cells, grown on filters (70_cacoB) [cell line]


title: CacoReady cells, grown on filters (68_cacoB) [cell line]


title: CacoReady cells, exposed to shipping media, grown on filters (72_cacoR) [cell line]


title: 3-week, negative control Caco-2 cells, grown on filters (N03_CacoGFP) [cell line]

value: negative control Caco-2 cells


title: LS174T cells (28_LS174T) [cell line]

value: LS174T cells


title: 3-week HT29 cells (20_HT29) [cell line]

value: HT29 cells


title: CacoReady cells, exposed to shipping media, grown on filters (71_cacoR) [cell line]


title: 3-week T84 cells (23_T84) [cell line]

value: colon, metastatic site lung

value: T84 cells


title: 3-week Caco-2 cells (67_caco_JD) [cell line]

value: Caco-2 cells


title: Caco-2LD cells, grown on filters (65_cacoF) [cell line]


title: 3-week HT29 cells (19_HT29) [cell line]