title: Bovine corpus luteum_ Day-4 vs Day-10_reps1-3

city: MORGANTOWN

first: MADHUSUDHAN

middle: P

last: GORAVANAHALLY

state: WV

address: LIFE SCIENCES BUILDING

department: DEPARTMENT OF BIOLOGY

institute: WEST VIRGINIA UNIVERSITY

description: The current array data is compiled after normalization

hyb_protocol: The cDNAs from two experimental groups were randomly labeled with N-hydroxysuccinate-derived Cy3 or Cy5 dyes (GEHealthcare, Piscataway, NJ) to limit the effect of differential dye incorporation. The unincorporated dyes were removed from cDNA product using PCR purification kit (Quiagen) followed by mixing the Cy3 and Cy5-labeled cDNAs. The labeled cDNAs were concentrated to 20 microliter using Microcon YM-30 (Millipore, Billerica, MA) and mixed with 130 microliter of Slidehyb 3 solution (Ambion, Austin, Texas). Tecan HS400 automated microarray hybridization station (Tecan US, Durham, NC) was used for cDNA hybridization. The steps in the hybridization were as follows: 1) the slides were subjected to 60 °C for 2 min and prehybridized at 55°C for 30 m using prehybridization solution (5 SSC, 1% SDS, 1% BSA) with medium agitation, 2) brief washing was carried out at 60°C for 1 min and 140microliter of labeled cDNA mixture was loaded on to hybridization chamber, 3) hybridization was performed at 60 °C for 3 h followed by 55°C for a 13 h,4) washing was carried out twice with in 2X SSC, 0.1% SDS and twice with in  0.1X  SSC, 0.1% SDS at room temperature, 5) two more washes were given with 0.1X  SSC  followed by rinsing the slides with water and finally dried by centrifugation.

scan_protocol: The gene array after hybridization was scanned for spots using ScanArray Lite microarray scanner. The spots were aligned, integrated with original GAL files and signal intensities were quantified using ScanArray Express software (Perkin Elmer, Wellesley, MA).

data_processing: The micro array raw data was converted to GPR files and processed using GenePix Auto Processor (GPAP) software. Briefly, GPAP utilizes R-statistical language, Bioconductor and LIMMA package to preprocess the raw data by signal filtering, background correction and normalization. The data points with signal intensity values in both channels less than baseline value of 200 were filtered-out and the spots with log-transformed (base 2) ratio outside of 2 standard deviations from the mean were removed as outliers and average of log-transformed (base 2) ratio of each spot was calculated within and between array. Raw data was manually quality controlled by flaging and removing any spurious spots from analysis. The preprocessed expression data was normalized by the Loess-global intensity-dependent normalization. The GPAP output value consisted of M value [log2 (cy5/cy3)], t-statistic, P value (probability), and B-statistics for each spot. Two-fold change or more in the expressions of genes is indicated by M value ≥1.0 (up-regulated) or ≤-1.0 (down-regulated). The genes with two-fold changes or more in expression with P<0.05 were considered significantly different and selected for further analysis.

organism: Bos taurus

source_name: Corpus luteum (CL) tissue

label_protocol: Total RNA was reverse transcribed using Supertscript II reverse-trancriptase (Invitrogen) to generate cDNA containing minoallyl-dUTP. The cDNAs was randomly labeled with N-hydroxysuccinate-derived Cy3 or Cy5 dyes (GEHealthcare, Piscataway, NJ) to limit the effect of differential dye incorporation.

extract_protocol: Total RNA isolated using TRI reagent

tag: Bos taurus, beef cattle, female, age 4-7 years

value: CL tissue from Day 4 stage of estrous cycle

source_name: Corpus luteum

value: CL tissue from Day 10 stage of estrous cycle


title: AD4-DK4

status: Public on Feb 23 2009

type: RNA

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

country: France

institute: INSERM U675

description: Murine neuroblastoma cell line N18 infected with an adenovirus containing coding sequence of Dyrk1a gene (pAd-Dyrk1a vector) or with an adenovirus control vector (pAd-Track-CMV vector).

hyb_protocol: After checking the labeling efficiency and the product integrity, 750 ng Cy3- and 750 ng Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven, using an Agilent in situ hybridization kit. The slides were washed and then any traces of water were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels (less than 0.005%) for generating gray scale 16-bit TIFF image files.

data_processing:
The resulting images were processed using the GenePix Pro (v6.0.1.26) image analysis software. This included defining the spots, measuring the intensities, flagging the spots having inadequate quality control parameters and evaluating local background
The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block.

label: Cy5-CTP Agilent

molecule: total RNA

organism: Mus musculus

source_name: control vector

label_protocol: Briefly, 1-μg aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies).

extract_protocol: Trizol (InVitrogen)

tag: Murine neuroblastoma cell line N18 infected with an adenovirus control vector (pAd-Track-CMV vector)

label: Cy3-CTP Agilent


title: AD5-DK5

tag: Murine neuroblastoma cell line N18 infected with an adenovirus containing coding sequence of Dyrk1a gene (pAd-Dyrk1a vector)


title: P.falciparum timepoint sample 3 (42 hours post-invasion) versus 3D7 pool

city: Singapore

first: Bernardo

middle: J

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

description: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

organism: Plasmodium falciparum

source_name: Synchronized P. falciparum parasites, 42 hours post-invasion

extract_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

tag: Laboratory strain, sorbitol synchronized, harvested as an aliquot from a 6 liter biofermenter culture at 42 hours post-invasion

source_name: P. falciparum RNA reference pool

tag: Strain 3D7, mix of several samples collected across the 48-hour intraerythrocytic life cycle


title: Apoptotic A

type: protein

city: La Jolla

first: Gregg

last: Silverman

state: CA

address: 9500 Gilman Dr

department: Medicine

country: USA

institute: UC San Diego School of Medicine

description: Serum from a mouse immunized with apoptotic cells

hyb_protocol: On each slide were two nitrocellulose pads, with most antigens printed at 200 mg/ml on each pad in six replicates at known positions that alternated with printing of buffer alone to eliminate carry-over. Slides were then blocked (Whatman blocking buffer) and incubated for 2 h with 400 ml of serum diluted at 1 : 200 in phosphate-buffered saline (PBS), pH 7·4.

scan_protocol: Slides were washed with PBS, water-rinsed and then scanned (Genepix 4000B; Molecular Devices, Sunnyvale, CA, USA) using Genepix Pro version 6·0 software at 532 and 635 nm to detect IgG and IgM reactivity, respectively, with images saved as tiff files.

data_processing: Genepix Pro version 6·0 software was used to analyse the intensity of each spot with foreground and background fluorescence intensities determined for each spot on the slide, with output as a gpr file. Data were extracted from the gpr files with r software (http://www.r-project.org). Background correction used a Matlab script, and the mean values for replicate spots determined with jmp version 7·0 software (http://www.jmp.com). Comparisons of array data for subjects and controls were performed and visual depictions generated with Cluster version 3·0 (Stanford University)  and Java TreeView (http://rana.lbl.gov/EisenSoftware.htm). Background levels were therefore determined based on replicate slides developed without antibodies, and with sera from healthy adult controls (not shown). In these studies, a level of 600 digital fluorescence intensity units was set as a threshold for significant reactivity, which was greater than the mean background plus 2 standard deviations (s.d.).

molecule: protein

label_protocol: After washing with Tris-buffered saline/0·1% Tween 20, the slides were reacted with Cy-5 labelled anti-human IgG and Cy-3- labelled anti-human IgM (Jackson Immunoresearch, West Grove, PA, USA) for 1 h incubation, then washed with PBS/0·05% Tween20.

growth_protocol: The mice were from a 14-week old C57BL/6 strain. The monoclonal antibodies were derived from hybridoma supernatant

extract_protocol: At the end of the injection courses, the mice were bled for their serum. Monoclonal antibodies were purified using standard protocols for IgM purifications.

treatment_protocol: The mouse serum was either naive, injected with saline (PBS) or injected with 25 million apoptotic thymocytes at three weekly timepoints.

tag: strain

tag: concentration

value: 1:200 Dilution

tag: sample

value: Serum


title: P.falciparum timepoint sample 4 (46 hours post-invasion) versus 3D7 pool

hyb_protocol: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

source_name: Synchronized P. falciparum parasites, 46 hours post-invasion

tag: Laboratory strain, sorbitol synchronized, harvested as an aliquot from a 6 liter biofermenter culture at 46 hours post-invasion


title: PBMC_BCG_009

status: Public on Feb 24 2009

city: London

first: Helen

middle: Alison

last: Fletcher

address: Keppel Street

department: IID

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

description: healthy HIV negative infant vaccinated with BCG within 48hrs of birth

hyb_protocol: Amplified RNA (1000ng per array) was hybridized to the Illumina HumanRefSeq-8 BeadChip according to the manufacturer's instructions (Illumina, San Diego, CA, USA).

scan_protocol: Arrays were scanned with an Illumina bead array reader confocal scanner, according to the manufacturer's instructions.  Hardware BeadStation systeIllumina Inc. Software BeadStudio version 1.5.1.3

data_processing: Data was background subtracted using the BeadStudio version 1.5.1.3 software by subtracting the AVG-Signal-negative value for each array from each transcript value. The data was normalized using the VSN2 software: Variance stabilization and calibration for microarray data, which is available as part of the BioConductor project.

label: biotin

organism: Homo sapiens

source_name: PBMC, BCG stimulated 12 hours

label_protocol: A median 124ng (range 63-174ng) extracted RNA was amplified using the Illumina RNA Amplification Kit (Ambion, Austin, TX, USA), based on the Eberwine protocol [13]. A Biotin-16-UTP label was incorporated into amplified RNA during the in vitro transcription process (Perkin Elmer Life and Analytical Sciences, Woodbridge, Ontario, Canada).

growth_protocol: PBMC were thawed, washed in RPMI 1640 (Biowhittaker, Walkersville, MD, USA), and “rested” for 6 hours at 1 X 106 cells in 1ml 10% pooled human AB serum in RPMI 1640 supplemented with L-glutamine at 2mM (Biowhittaker), at 37°C and in 5% CO2.

extract_protocol: PBMC were harvested and processed with the QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany), according to the manufacturers instructions. to isolate RNA.  RNA was DNAse treated using the on-column DNAse digestion kit (Qiagen, Hilden, Germany).

treatment_protocol: PPD (20µg/ml) or BCG, reconstituted from the vaccine vial as previously described [12], at an MOI of 0.18, was then added to the cells.  PBMC incubated with medium alone served as negative (unstimulated) control. Incubation was continued for 12 hours at 37°C and in 5% CO2.

tag: 10 week old infant


title: PBMC_UNS_011

source_name: PBMC, unstimulated 12 hours


title: P.falciparum timepoint sample 2 (38 hours post-invasion) versus 3D7 pool

source_name: Synchronized P. falciparum parasites, 38 hours post-invasion

label_protocol: RNA extraction, cDNA synthesis and labeling as well as microarray hybridizations of the four samples representing time points 1, 2, 3, and 4 against a reference RNA pool were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

tag: Laboratory strain, sorbitol synchronized, harvested as an aliquot from a 6 liter biofermenter culture at 38 hours post-invasion


title: PBMC_BCG_027


title: DK2-AD2


title: WTB.1-152F7A.1

description: Technical replicate E12.5 mouse telencephalon from 152F7 or wild type mouse both in FVB Background

label: Cy5-CTP Perkin.Elmer

source_name: Wild Type

extract_protocol: Trizol Protocol (InVitrogen)

tag: FVB embryonic telencephalon

label: Cy3-CTP Perkin.Elmer


title: PBMC_PPD_009

source_name: PBMC, PPD stimulated 12 hours


title: P.falciparum timepoint sample 1 (34 hours post-invasion) versus 3D7 pool

source_name: Synchronized P. falciparum parasites, 34 hours post-invasion

tag: Laboratory strain, sorbitol synchronized, harvested as an aliquot from a 6 liter biofermenter culture at 34 hours post-invasion


title: DK3-AD3


title: PBS  B

description: Serum from a second mouse immunized with saline solution


title: 152F7B.2-WTA.2


title: DK1-AD1


title: telencephalon 12.5

city: Szeged

first: Agnes

last: Zvara

address: Temesvari krt 62

country: Hungary

institute: Biological Research Center

description: genepix

hyb_protocol: ventana, 42C, 6 hours

scan_protocol: Scanarray Lite, Laser 100,100, PTM 80,80

data_processing: Each spot was defined by automatic positioning of a grid of circles over the image. The average and median pixel intensity ratios calculated from both channels and the local background of each spot were determined. Local background corrected intensity ratios was determined for each spot. The background-corrected expression data were filtered for flagged spots and weak signal. Normalization was performed by the global Lowess method. Students t-test was applied to determine the p value.

source_name: Tg telencephalon 12.5 day

label_protocol: Standard protocol by Genisphere

extract_protocol: trizol

tag: Tg telencephalon embryonic 12.5 day

source_name: WT telencephalon 12.5 day

tag: WT telencephalon embryonic 12.5 day


title: mesencephalon-diencephalon 12.5 day

description: genepix

source_name: Tg mesencephalon-diencephalon 12.5

tag: Tg mesencephalon-diencephalon embrionic 12.5 day

source_name: WT mesencephalon-diencephalon 12.5

tag: WT mesencephalon-diencephalon embrionic 12.5 day


title: mesencephalon-diencephalon 11.5

description: genepix

source_name: Tg mesencephalon-diencephalon 11.5 day

tag: Tg mesencephalon-diencephalon embrionic 11.5 day

source_name: WT mesencephalon-diencephalon 11.5 day

tag: WT mesencephalon-diencephalon embrionic 11.5 day


title: WTB.2-152F7A.2


title: 152F7B.1-WTA.1


title: telencephalon 13.5

description: genepix

source_name: Tg telencephalon 13.5

tag: Tg telencephalon embrionic 13.5 day

source_name: WT telencephalon 13.5 day

tag: WT telencephalon embrionic 13.5 day


title: T15 IgM (125 ng/ml)

description: T15 Monoclonal IgM Antibody at a concentration of 125 ng/ml

source_name: Hybridoma

value: 125 ng/ml

value: IgM


title: NC17D8 control T15 Isotype IgM (2000 ng/ml)

description: NC17D8 Isotype Monoclonal IgM Antibody at a concentration of 2000 ng/ml


title: telencephalon 11.5

description: genepix

hyb_protocol: vnetana, 42C, 6 hours

source_name: Tg telencephalon 11.5 day

tag: embrionic day 11.5

source_name: wt telencephalon 11.5 day

tag: embrionic day 11.5 wild type


title: Naïve B

description: Serum from a second Naïve Mouse

tag: strain

tag: concentration


title: Naïve A

description: Serum from a Naïve mouse

tag: sample


title: T15 IgM (500 ng/ml)

description: T15 Monoclonal IgM Antibody at a concentration of 500 ng/ml

value: 500 ng/ml


title: T15 IgM (31 ng/ml)

description: T15 Monoclonal IgM Antibody at a concentration of 31 ng/ml

value: 31 ng/ml


title: Male_CAST14D_D66

status: Public on Feb 21 2009

city: Novato

first: Simon

last: Melov

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

hyb_protocol: Standard Affy hybridization protocol.

scan_protocol: Standard Affy scan protocol.

data_processing: Global changes in gene expression were examined using the HG U133 plus gene micro-array (Affymetrix, Santa Clara, CA) which contains 54,675 human probe sequences. The background correction, normalization and derivation of expression measure were based on the Affymetrix signal (MAS 5.0 algorithm).

source_name: vastus lateralis, 14 days

label_protocol: Standard Affy labeling protocol.

growth_protocol: Recreationally active, non-smoking, healthy men (N=12) and women (N=12) participated in the trial.  Demographics included:  age (men = 20.5 ± 1.7; women = 21.1 ± 2.7 y), height (men = 178.4 ± 5.4; women = 164.3 ± 5.5 cm), and body mass index (men = 24.3 ± 3.5; women = 22.8 ± 2.2) (Table 1).  All of the women were eumenorrheic and ~ 50 % were tested in each phase of the menstrual cycle.

extract_protocol: Total RNA was extracted from muscle using a commercially available TRIzol® Reagent (Invitrogen Canada) following the manufacturer’s instructions. The concentration and purity of the RNA was spectrophotometrically determined by measuring the absorbance at 260 (OD260) and 280 (OD280) with an OD260/OD280 ratio of ~1.8 indicative of good quality RNA. The integrity of RNA samples were assessed by RNA agarose-formaldehyde gel electrophoresis and evaluating the ratio of 28S to 18S rRNA bands.

tag: gender

value: male

tag: condition

value: cast

tag: time

value: 14 days


title: Female_CAST02D_D26

source_name: vastus lateralis, 2 days

value: female

value: 2 days


title: Female_CAST14D_D24


title: Female_CAST14D_D26


title: Female_PRECAST_D26

source_name: vastus lateralis, time 0

value: precast


title: Female_CAST02D_D23


title: Male_CAST02D_D66


title: Female_CAST14D_D23


title: Female_CAST02D_D20


title: Female_CAST14D_D21


title: Female_CAST02D_D21


title: PBS  A

description: Serum from a mouse immunized with saline solution


title: Female_PRECAST_D24


title: Female_CAST02D_D24


title: Female_PRECAST_D21


title: Female_CAST14D_D20


title: Female_CAST14D_D17


title: Female_CAST02D_D19


title: Female_CAST14D_D19


title: Female_PRECAST_D23


title: Male_PRECAST_D66


title: Female_PRECAST_D20


title: HepG2-plate-exp1-plate1-rep1

city: Setagaya

first: Seiichi

last: Ishida

state: Tokyo

address: 1-18-1, Kamiyoga

department: Pharmacology

country: Japan

institute: National Institute of Health Sciences

description: Data from 1st plate culture (five days). plate; 1, GeneChip measurement; 1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix Microarray Suite Version 5.0

source_name: HepG2 cells cultured in tissue culture plate, five days

label_protocol: Standard Affymetrix protocol with 10.0 ug of total RNA

growth_protocol: Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum was used as medium. Cells were cultured in the radial flow bioreactor cell culture system (ABLE Corporation, Tokyo) of 5ml capacity or in the tissue culture plate  (60 mm diameter; BD Falcon, Franklin Lakes, NJ).  Hydroxyapatite with a dimmer of 0.6 - 1.0 mm was used as the scaffold of cells in the radial flow bioreactor cell culture system.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: Cells were washed twice with phosphate buffered saline (PBS ; SIGMA, St. Louis, MO)

tag: HepG2 human hepatocellular carcinoma cell line

tag: human liver cancer


title: Female_PRECAST_D19


title: Female_PRECAST_D18


title: Female_PRECAST_D17


title: Female_PRECAST_D15


title: Female_PRECAST_D14


title: Female_CAST14D_D16


title: Female_CAST14D_D18


title: Female_CAST14D_D15


title: Female_CAST14D_D14


title: Female_CAST14D_D13


title: Male_CAST14D_D11


title: Male_PRECAST_D12


title: Female_PRECAST_D16


title: Female_CAST02D_D16


title: Female_PRECAST_D13


title: Male_CAST02D_D11


title: Female_CAST02D_D15


title: Female_CAST02D_D14


title: Female_CAST02D_D13


title: Female_CAST02D_D17


title: Male_CAST02D_D12


title: Female_CAST02D_D18


title: Male_CAST14D_D09


title: Male_CAST14D_D10


title: Male_CAST14D_D12


title: Male_CAST02D_D09


title: Male_PRECAST_D09


title: Male_PRECAST_D11


title: Male_PRECAST_D08


title: Male_CAST02D_D07


title: Male_PRECAST_D07


title: Male_CAST02D_D08


title: Male_PRECAST_D06


title: Male_CAST14D_D06


title: Male_CAST14D_D07


title: Male_CAST02D_D05


title: Male_CAST14D_D05


title: Male_CAST14D_D08


title: Male_PRECAST_D10


title: Male_PRECAST_D05


title: Male_CAST02D_D06


title: C. albicans TOR1-1/TOR1 cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R4).

city: Durham

first: Robert

last: Bastidas

address: 322 CARL, Research Drive Box 3546

department: Molecular Genetics and Microbiology

institute: Duke University

description: Data was extracted using GenePix Pro 4 software (Molecular Devices).

hyb_protocol: Labeled cDNA were hybridized overnight at 42°C to a 70-mer C. albicans AROS V1.2 oligo microarray set (OPERON technologies) printed at Duke University microarray facility.

scan_protocol: Hybridized arrays were scanned with an Axon GenePix scanner (GenePix 400B, Molecular Devices).

data_processing: Value corresponds to Normalized log2 Cy5(635 nm)/Cy3(532 nm) ratio of medians extracted by GenePix Pro 4 software and normalized by Lowess (per spot/per chip) using GeneSpring software.

organism: Candida albicans

source_name: Candida albicans TOR1-1/TOR1 cells, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #4

label_protocol: cDNA from 15 ug of total RNA was synthesized using an AffinityScriptTM-Multiple Temperature Reverse Transcriptase kit (Stratagene).  cDNA generated from drug vehicle treated cells were used as reference and labeled with Cy3 (Amersham) and cDNA synthesized from rapamycin treated cells were labeled with Cy5 (Amersham) and used as the experimental sample.

growth_protocol: Cell cultures were grown in YPD liquid medium at 30°C to an O.D600=0.5, and treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 60 minutes at 30°C.

extract_protocol: Total RNA was extracted using a RiboPureTM-Yeast RNA extraction kit (Ambion Inc).

treatment_protocol: Cell cultures were treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 60 minutes at 30°C.

value: TOR1-1/TOR1 cells

source_name: Candida albicans drug vehicle (90% EtOH 10% Tween-20)


title: C. albicans TOR1-1/TOR1 cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R2).

source_name: Candida albicans TOR1-1/TOR1 cells, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #2

value: TOR1-1/TOR1 cells.


title: Male_CAST14D_D04


title: Male_CAST02D_D04


title: Male_PRECAST_D04


title: Male_CAST14D_D02


title: C. albicans TOR1-1/TOR1 cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R1).

source_name: Candida albicans TOR1-1/TOR1 cells, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #1


title: Male_CAST02D_D02


title: C. albicans TOR1-1/TOR1 cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R3).

source_name: Candida albicans TOR1-1/TOR1 cells, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #3


title: Candida albicans cells in Spider medium upon treatment with the Tor1 inhibitor rapamycin (R1).

data_processing: Value corresponds to Cy5(635 nm)/Cy3(532 nm) ratio of medians extracted by GenePix Pro 4 software and normalized by Lowess (per spot/per chip) using GeneSpring software.

source_name: Candida albicans, Spider liquid medium 37°C, 20 nM rapamycin 90 minutes

growth_protocol: Cell cultures were grown in YPD liquid medium at 30°C to an O.D600=0.5.  Cells were washed twice and resuspended in Spider liquid medium.  Cultures were treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 90 minutes at 37°C.

treatment_protocol: Cell cultures were treated with either 20 nM rapamycin or drug vehicle (90% EtOH 10% Tween-20) and shaken for 90 minutes at 37°C.

value: wild type cells (SC5314)


title: Male_PRECAST_D02


title: Male_CAST14D_D01


title: Male_CAST02D_D01


title: Candida albicans cells in Spider medium upon treatment with the Tor1 inhibitor rapamycin (R2).

source_name: Candida albicans, Spider liquid medium 37°C, 20 nM rapamycin 90 minutes. Biological replicate #2


title: Candida albicans cells in Spider medium upon treatment with the Tor1 inhibitor rapamycin (R3).

source_name: Candida albicans, Spider liquid medium 37°C, 20 nM rapamycin 90 minutes. Biological replicate #3


title: Candida albicans cells in Spider medium upon treatment with the Tor1 inhibitor rapamycin (R4).

source_name: Candida albicans, Spider liquid medium 37°C, 20 nM rapamycin 90 minutes. Biological replicate #4


title: Male_PRECAST_D01


title: Candida albicans cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R2).

source_name: Candida albicans, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #2


title: VUMC_LGCIN6_b251495015494_s129_3

status: Public on Feb 20 2009

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: CIN1 lesion, patient age 36 years, contains high risk Human Papilloma Virus

hyb_protocol: hybridisations were performed according to the manufacturer's instructions (Agilent Technologies)

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spots were quantified in Feature Extraction software version 9.5.1 (Agilent Technologies) using default settings.

molecule: genomic DNA

source_name: uterine cervix

label_protocol: as described by Snijders et al, Nat Genetics, volume 29, p 263-4

extract_protocol: as described in Van zeeburg et al, Cancer Res, volume 65, p 1271-76, 2005

tag: cervical intraepithelial neoplasia (CIN) lesion, grade 1

source_name: Reference DNA

label_protocol: as ch1, Cy5 in stead of Cy3

extract_protocol: as described in Wilting et al, J Pathol, volume 209, p 220-30

tag: Pooled DNA from the blood of 10 normal male individuals


title: Candida albicans cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R1).

source_name: Candida albicans, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #1


title: S2 cells CTCF RNAi versus control RNAi treatment replicate 4

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: An Analysis of the effects of reduction of CTCF protein levels in S2 cells treated with CTCF-specific RNAi as compared to S2 cells treated with control RNAi directed against the firefly luciferase gene.

hyb_protocol: Genomics Solution GeneTAC hybridisation station with Ocimum hybridisation buffer. Hybridisation and washing described in detail at http://www.flychip.org.uk/protocols/hybridisation/hyb_oligoMWG.php

scan_protocol: Axon 4000B scanner using standard protocols (http://www.flychip.org.uk/protocols/imaging/scanning2.php)

data_processing:
Spot finding and quantitation via the Dapple package.
Normalisation accross the 4 biological replicates for both conditions (specific and control RNAi) using VSN. Normalised ratio 'M' (asinh transform functionally equivalent to the log[2] ratio) is given in the VALUE column. See http://www.flychip.org.uk/services/analysis/ for details and references

organism: Drosophila melanogaster

source_name: S2 cells CTCF-specific RNAi

label_protocol: Standard direct incorporation of Cy dyes during 1st strand cDNA synthesis (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.php) using 50 µg of total RNA.

growth_protocol: S2 cells were grown in Drosophila's Schneider Medium (GIBCO) supplemented with 10% FCS and 1% Penicillin/Streptomycin at 25°C.

extract_protocol: S2 cells were harvested after 6 days incubation with dsRNA by scraping. After quick centrifugation the supernatant was removerd and cells were resuspended and homogenized in 1ml TRIZOL. The material was frozen in liquid nitrogen and sent for processing to FlyChip (http://www.flychip.org.uk/).

treatment_protocol: 2x10^6 S2 cells were treated with 32µg dsRNA corresponding to the CTCF gene according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html).

tag: Drosophila melanogaster S2 cells

source_name: S2 cells control  RNAi

extract_protocol: S2 cells were harvested after 6 days incubation with dsRNA by scraping. After quick centrifugation the supernatant was removed and cells were resuspended and homogenized in 1ml TRIZOL. The material was frozen in liquid nitrogen and sent for processing to FlyChip (http://www.flychip.org.uk/).

treatment_protocol: 2x10^6 S2 cells were treated with 32µg dsRNA corresponding to the firefly luciferase gene according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html).


title: VUMC_LGCIN2_b251495015494_s129_2

description: CIN1 lesion, patient age 22 years, contains high risk Human Papilloma Virus


title: VUMC_LGCIN4_b251495015494_s129_2

description: CIN1 lesion, patient age 40 years, contains high risk Human Papilloma Virus


title: S2 cells CTCF RNAi versus control RNAi treatment replicate 3


title: Candida albicans cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R3).

source_name: Candida albicans, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #3


title: Candida albicans cells in YPD medium upon treatment with the Tor1 inhibitor rapamycin (R4).

source_name: Candida albicans, YPD liquid medium 30°C, 20 nM rapamycin 60 minutes. Biological replicate #4


title: Male_CAST02D_D10

source_name: vastus lateralis, 2 days


title: S2 cells CP190 RNAi vs control RNAi rep1

description: An Analysis of the effects of reduction of CP190 protein levels in S2 cells treated with CP190-specific RNAi as compared to S2 cells treated with control RNAi directed against the firefly luciferase gene.

source_name: S2 cells control RNAi

label_protocol: Standard direct incorporation of Cy dyes during 1st strand cDNA synthesis (http://www.flychip.org.uk/protocols/gene_expression/direct_labelling.php) using 50 microgrammes of total RNA.

growth_protocol: S2 cells were grown in Drosophila's Schneider Medium (GIBCO) supplemented with 10% FCS and 1% Penicilin/Streptomycin at 25°C.

treatment_protocol: 2x10 7 S2 cells were treated with 32µg dsRNA corresponding to the firefly luciferase gene according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html) . After 6 days of incubation at 25°C RNA was extracted with TRIZOL.

source_name: S2 cells CP190-specific RNAi

treatment_protocol: 2x10 7 S2 cells were treated with 32µg dsRNA corresponding to the CP190 gene according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html).


title: S2 cells CTCF RNAi versus control RNAi treatment replicate 1


title: S2 cells CP190 RNAi vs control RNAi rep3

treatment_protocol: 2x10 7 S2 cells were treated with 32µg dsRNA corresponding to the firefly luciferase gene according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html).


title: VUMC_LGCIN5_b251495015494_s129_3

description: CIN1 lesion, patient age 38 years, contains high risk Human Papilloma Virus


title: S2 cells CTCF RNAi versus control RNAi treatment replicate 2


title: VUMC_LGCIN1_b251495015494_s129_4

description: CIN1 lesion, patient age 26 years, contains high risk Human Papilloma Virus


title: S2 cells CP190 RNAi vs control RNAi rep4


title: CIN lesion grade 2/3 VUMC_HGCIN41_b45_s89

description: CIN3 lesion, patient age 26 years, contains high risk Human Papilloma Virus

hyb_protocol: Hybridisations were performed as described by Snijders et al, Nat Genetics, volume 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 – Perkin Elmer Life Sciences).

data_processing: Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalised by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.

tag: cervical intraepithelial neoplasia (CIN) lesion, grade 2/3


title: S2 cells CP190 RNAi vs control RNAi rep2


title: VUMC_LGCIN3_b251495015494_s129_1

description: CIN1 lesion, patient age 35 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN46_b45_s32

description: CIN3 lesion, patient age 35 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN43_b45_s69

description: CIN2 lesion, patient age 27 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN44_b45_s31


title: CIN lesion grade 2/3 VUMC_HGCIN45_b45_s91

description: CIN3 lesion, patient age 29 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN40_b45_s29

description: CIN3 lesion, patient age 30 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN42_b45_s90

description: CIN2 lesion, patient age 31 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN39_b45_s64

description: CIN3 lesion, patient age 34 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN38_b45_s63


title: CIN lesion grade 2/3 VUMC_HGCIN37_b45_s62

description: CIN3 lesion, patient age 47 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN36_b45_s28

description: CIN3 lesion, patient age 31 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN34_b45_s61


title: CIN lesion grade 2/3 VUMC_HGCIN30_b45_s57

description: CIN3 lesion, patient age 37 years, contains high risk Human Papilloma Virus


title: WT Footpad Adult-2

city: Baltimore

first: Chang-Yi

last: Cui

state: MD

address: 251 Bayview Blvd Suite 100, 10C222

department: NIA

institute: NIH

description: WT Footpad Adult-2

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 4 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: WT

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: RNAs were isolated by Trizol by standard protocol (Invitorogen). RNA samples were then subjected to LiCl precipitation to eliminate genomic DNA contamination.

tag: cell type

value: Footpads

tag: age

value: Adult (9w)

tag: development stage

value: adult

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

tag: Universal Mouse Reference


title: Tabby Footpad Adult-2

description: Tabby Footpad Adult-2

source_name: Ta

tag: strain

tag: genetic modification

value: gene knock out


title: CIN lesion grade 2/3 VUMC_HGCIN32_b45_s59


title: Tabby Footpad Adult-1

description: Tabby Footpad Adult-1


title: CIN lesion grade 2/3 VUMC_HGCIN33_b45_s60


title: CIN lesion grade 2/3 VUMC_HGCIN31_b45_s58

description: CIN2 lesion, patient age 25 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN28_b45_s55

description: CIN3 lesion, patient age 25 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN35_b45_s27

description: CIN3 lesion, patient age 22 years, contains high risk Human Papilloma Virus


title: Tabby Footpad P5-1

description: Tabby Footpad P5-1

value: mixed sex


title: Tabby Footpad P5-2

description: Tabby Footpad P5-2


title: WT Footpad P5-1

description: WT Footpad P5-1


title: WT Footpad P5-2

description: WT Footpad P5-2


title: CIN lesion grade 2/3 VUMC_HGCIN29_b45_s56


title: WT Footpad Adult-1

description: WT Footpad Adult-1


title: CIN lesion grade 2/3 VUMC_HGCIN27_b45_s54

description: CIN2 lesion, patient age 38 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN26_b45_s53


title: Tabby Footpad P3-2

description: Tabby Footpad P3-2


title: CIN lesion grade 2/3 VUMC_HGCIN25_b45_s25


title: CIN lesion grade 2/3 VUMC_HGCIN23_b45_s88

description: CIN3 lesion, patient age 28 years, contains high risk Human Papilloma Virus


title: WT Footpad P3-1

description: WT Footpad P3-1


title: Tabby Footpad P1-1

description: Tabby Footpad P1-1


title: Tabby Footpad P1-2

description: Tabby Footpad P1-2


title: CIN lesion grade 2/3 VUMC_HGCIN19_b45_s87

description: CIN2 lesion, patient age 40 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN22_b45_s33


title: WT Footpad P3-2

description: WT Footpad P3-2


title: WT Footpad P1-2

description: WT Footpad P1-2


title: CIN lesion grade 2/3 VUMC_HGCIN18_b45_s52

description: CIN2 lesion, patient age 32 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN20_b45_s38

description: CIN3 lesion, patient age 42 years, contains high risk Human Papilloma Virus


title: Tabby Footpad P3-1

description: Tabby Footpad P3-1


title: CIN lesion grade 2/3 VUMC_HGCIN24_b45_s24

description: CIN3 lesion, patient age 26 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN17_b45_s51

description: CIN2/3 lesion, patient age 51 years, contains high risk Human Papilloma Virus


title: CTCF wt SL2 cell line replicate 2

description: WGA amplified DNA was labelled, hybridized and scanned by imaGenes (www.imagenes-bio.de)

hyb_protocol: performed by imaGenes (www.imagenes-bio.de)

data_processing: raw signals of all channels in all all replicate arrays were normalized and log2 transformed using the 'vsn' package in R/Bioconductor.

source_name: IP DNA; CTCF SL2 cell line

extract_protocol: ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 10 minutes at 18°C. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Branson-250 Sonicator (http.www.bransonultrasonics.com) 4 times 30 seconds using the microtip setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4¬∞C. 500 ¬µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 1ml RIPA buffer at 4¬∞C over night. After washing and crosslink reversal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). IP DNA was amplified using the WGA kit (Sigma).

tag: Drosophila melanogaster cell line SL2

source_name: Input DNA; SL2 cell line

extract_protocol: Input DNA;  cells were crosslinked in growth medium using 1% formaldehyde for 10 minutes at 18°C. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Branson-250 Sonicator (http.www.bransonultrasonics.com) 4 times 30 seconds using the microtip setting. Fragment size of the obtained chromatin was checked to be between 300 bp and 700 bp. After crosslink reversal, nucleic acids were purified on GFX columns (GE Healthcare). Input DNA was amplified using the WGA kit (Sigma).


title: CP190 wt SL2 cell line replicate 1

scan_protocol: performed by imaGenes (www.imagenes-bio.de)

source_name: IP DNA; CP190 SL2 cell line


title: CP190 wt SL2 cell line replicate 2

label_protocol: performed by imaGenes (www.imagenes-bio.de)


title: CTCF wt SL2 cell line replicate 2


title: WT Footpad E17.5-4

description: WT Footpad E17.5-4

tag: gender

value: embryo

source_name: Universal Mouse Reference Cell Line Pool

label_protocol: Total RNA was labeled using Agilents Fluorescent Linear Amplification kit, according to manufacturers instructions (Product Number G2554A or P/N G2556-66002, Version 3.0, June 2002).

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts


title: CIN lesion grade 2/3 VUMC_HGCIN13_b45_s23

description: CIN3 lesion, patient age 51 years, contains high risk Human Papilloma Virus

source_name: uterine cervix


title: Tabby Footpad E16.5-3

description: Tabby Footpad E16.5-3


title: WT Footpad E16.5-4

description: WT Footpad E16.5-4


title: WT Footpad P1-1

description: WT Footpad P1-1


title: CIN lesion grade 2/3 VUMC_HGCIN21_b45_s62

description: CIN3 lesion, patient age 30 years, contains high risk Human Papilloma Virus

source_name: Reference DNA


title: CIN lesion grade 2/3 VUMC_HGCIN14_b45_s48

description: CIN2/3 lesion, patient age 35 years, contains high risk Human Papilloma Virus


title: Tabby Footpad E16.5-4

description: Tabby Footpad E16.5-4


title: WT Footpad E17.5-3

description: WT Footpad E17.5-3


title: WT Footpad E16.5-3

description: WT Footpad E16.5-3


title: CTCF wt SL2 cell line replicate 1


title: CIN lesion grade 2/3 VUMC_HGCIN15_b45_s37

description: CIN3 lesion, patient age 35 years, contains high risk Human Papilloma Virus


title: Tabby Footpad E17.5-3

description: Tabby Footpad E17.5-3


title: CIN lesion grade 2/3 VUMC_HGCIN11_b45_s46

description: CIN3 lesion, patient age 36 years, contains high risk Human Papilloma Virus


title: Tabby Footpad E15.5-2

description: Tabby Footpad E15.5-2

value: Wild-type


title: CIN lesion grade 2/3 VUMC_HGCIN16_b45_s49

description: CIN2 lesion, patient age 34 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN10_b45_s45


title: CIN lesion grade 2/3 VUMC_HGCIN9_b45_s36

description: CIN2/3 lesion, patient age 31 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN12_b45_s47

description: CIN3/CIS lesion, patient age 40 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN8_b45_s86

description: CIN3 lesion, patient age 34 years, contains high risk Human Papilloma Virus


title: CP190 wt SL2 cell line replicate 1


title: Tabby Footpad E17.5-4

description: Tabby Footpad E17.5-4


title: CP190 wt SL2 cell line replicate 2


title: WT Footpad E15.5-1

description: WT Footpad E15.5-1


title: CIN lesion grade 2/3 VUMC_HGCIN7_b45_s44


title: WT Footpad E15.5-2

description: WT Footpad E15.5-2


title: CIN lesion grade 2/3 VUMC_HGCIN3_b45_s41


title: CIN lesion grade 2/3 VUMC_HGCIN6_b45_s43

description: CIN3 lesion, patient age 29 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN2_b45_s40

description: CIN2 lesion, patient age 27 years, contains high risk Human Papilloma Virus


title: CIN lesion grade 2/3 VUMC_HGCIN1_b45_s39

description: CIN3 lesion, patient age 54 years, contains high risk Human Papilloma Virus


title: 04-18-07_Ye_HG-U133A_2_0_J2_10

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Treated with EerI in 10 hours

hyb_protocol: Followed standard Affymetrix protocols

scan_protocol: Followed standard Affymetrix protocols

data_processing: Affymetrix Microarray Suite version 5.0

source_name: EerI, 10 hours

label_protocol: Followed standard Affymetrix protocols

extract_protocol: Qiagen:RNeasy Protect Mini, or Midi, or Maxi Kits

treatment_protocol: Treated with EerI for 10 hours

tag: Treated with EerI for 10 hours


title: CTCF wt SL2 cell line replicate 2


title: Sa_rep3

city: Legnaro

first: Luca

last: Bargelloni

state: PD

address: Viale dell'Università 16

department: Dept. Sanità Pubblica, Patologia Comparata ed Ig. Veterinaria

country: Italy

institute: Agripolis

description: Pool of gilthead seabream larvae collected at  24, 48, 72 and 94 hours post-hatching

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5, filtering and cyclic lowess normalization

label: Cyanine 3

organism: Sparus aurata

source_name: Larvae at four different larval developmental stage

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissues samples

tag: Pool of around 40 larvae snap frozen and stored at -80∞C


title: CIN lesion grade 2/3 VUMC_HGCIN5_b45_s34

description: CIN3 lesion, patient age 31 years, contains high risk Human Papilloma Virus


title: 04-18-07_Ye_HG-U133A_2_0_J2_0

description: Treated with EerI in 10 hours

source_name: EerI, 0 hours

treatment_protocol: Treated with EerI for 0 hours

tag: Treated with EerI for 0 hours


title: S. aureus_mvaK-IPTG-3

city: Cambridge

first: Carl

middle: J.

last: Balibar

state: MA

address: 500 Technology Sq.

department: Infectious Diseases

institute: Novartis Institutes for BioMedical Research

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, - IPTG, rep3

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 45C on GeneChip S. aureus Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Workstation 450.

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

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

organism: Staphylococcus aureus subsp. aureus RN4220

source_name: S. aureus mvaK regulated mutant grown without IPTG in NZYM broth harvested in exponential phase

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 15 ug total RNA

growth_protocol: S. aureus were grown overnight in NZYM Broth with 5 ug/mL erythromycin to maintain regulated mutants. Cells were then diluted 5000 fold in fresh NZYM without antibiotic and cultures were grown for 6-8 hours with vigorous shaking at 37 degrees C. In mid-exponential phase an equivalent of 15 mL of culture at OD600 = 1.0 were harvested by centrifugation.

extract_protocol: RNA was extracted from cell pellets using the Purescript RNA Isolation Kit (Gentra Systems, Minneapolis, MN) with an initial 0.3 µg/µL lysostaphin (Sigma, St. Louis, MO) treatment to achieve cell lysis. 100 µg of total RNA was treated with 7 units of RNase-free DNase I (QIAGEN, Valencia, CA) and then further purified using the RNeasy Plus Mini Kit (QIAGEN, Valencia, CA).

treatment_protocol: Cells were resuspended in 4 mL water and 8 mL of RNAProtect Bacteria Reagent (QIAGEN, Valencia, CA), reacted for at least 30 minutes, pelleted by centrifugation, then frozen at -80 degrees C until further use.

tag: RN4220 derivative requiring IPTG for growth


title: Axillary meristem from 10-day-old soybean seedlings repliacte 2

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

address: University of Melbourne

department: Land and Food

country: Australia

institute: University of Melbourne

description: Two independent biological replicates were used in the experiment

scan_protocol: Carried out by AGRF according to standard protocol at www.affymetrix.com

data_processing: Expression levels were estimated from Affymetrix hybridization intensity data using MicroArray Suite 5.0 (Affymetrix 2001). Raw numeric values representing the signal of each feature were imported into AffylmGUI (Affymetrix linear modeling Graphical User Interface [78] for linear modeling of the microarray data and for identifying differentially expressed genes in SAMs. The data was normalized using Robust Multiarray Averaging (RMA) method and a linear model was then used to average data between replicate arrays and to look for variability between them [78]. The list of transcripts that were detected to be differentially expressed at adjusted p-value of <0.05 was then filtered using a relatively conservative selection method. We applied a cut-off of a 1.5-fold ratio of expression and filtered out those genes with expression levels that were called as “Marginal” or “Absence” in all six arrays according to the Affymetrix Statistical Algorithms.

organism: Glycine max

source_name: vegetative axillary meristem

label_protocol: cDNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)

growth_protocol: Soybean plants [Glycine max. (L) Merr. Cv. Bragg] were grown in a greenhouse located at the University of Melbourne, Victoria, Australia.

extract_protocol: All RNA was extracted using using Qiagen RNeasy Mini Kit with on column DNAse digestion.

tag: axillary meristem dissected from 10-day-old soybean plants grown under greenhouse conditions


title: 06-19-07_Ye_HG-U133A_2_0_B2_10

description: Treated by Bzm with 10 hour

source_name: Bzm, 10 hours

treatment_protocol: Treated with Bzm for 10 hours

tag: Treated with Bzm for 10 hours


title: 04-18-07_Ye_HG-U133A_2_0_J1_10

description: Treated with EerI in 10 hours


title: 04-18-07_Ye_HG-U133A_2_0_J1_0

description: Treated with EerI in 0 hours


title: CIN lesion grade 2/3 VUMC_HGCIN4_b45_s42

tag: Pooled DNA from the blood of 10 normal male individuals


title: Sa_rep4


title: Sa_rep1


title: 06-19-07_Ye_HG-U133A_2_0_B1_10

description: Treated by Bzm with 10 hour


title: Tabby Footpad E15.5-1

description: Tabby Footpad E15.5-1


title: Axillary meristem from 10-day-old soybean seedlings

hyb_protocol: DNA labelling and Affymetrix Soybean GeneChip hybridization was carried out by AGRF (Australian Genome Research Facility, Melbourne, Australia)

tag: Axillary meristems dissected from soybean plants that have been grown for 10-days under greenhouse conditions.


title: Sa_rep2


title: Sa_Stage4_I

description: Pool of gilthead sea bream larvae collected at 96 hours post-hatching

source_name: Larvae at 96 hours post-hatching


title: Sa_Stage4_H


title: S. aureus_mvaK-IPTG-2

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, - IPTG, rep2


title: 06-19-07_Ye_HG-U133A_2_0_B2_0

description: Treated by Bzm with 0 hour

source_name: Bzm, 0 hours

treatment_protocol: Treated with Bzm for 0 hours

tag: Treated with Bzm for 0 hours


title: S. aureus_mvaK+IPTG-3

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, + IPTG, rep3

source_name: S. aureus mvaK regulated mutant grown with 1 mM IPTG in NZYM broth harvested in exponential phase


title: Sa_Stage4_D


title: S. aureus_mvaA-IPTG-2

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, - IPTG, rep2

source_name: S. aureus mvaA regulated mutant grown without IPTG in NZYM broth harvested in exponential phase

tag: RN4220 derivative requiring IPTG or mevalonate for growth


title: Sa_Stage1_C

description: Pool of seabream larvae collected at 24 hours post-hatching

source_name: Larvae at 24 hours post-hatching

tag: Pool of around 50 larvae snap frozen and stored at -80∞C


title: S. aureus_mvaK+IPTG-1

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, + IPTG, rep1


title: S. aureus_mvaA-IPTG-3

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, - IPTG, rep3


title: Sa_Stage4_G


title: S. aureus_mvaK+IPTG-2

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, + IPTG, rep2


title: S. aureus_mvaA+IPTG-3

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, + IPTG, rep3

source_name: S. aureus mvaA regulated mutant grown with 1 mM IPTG in NZYM broth harvested in exponential phase


title: Sa_Stage4_C


title: S. aureus_mvaK-IPTG-1

description:
Gene expression data from exponentially growing cells
mvaK regulated mutant RN4220, - IPTG, rep1


title: S. aureus_mvaA-IPTG-1

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, - IPTG, rep1


title: 125 mg/kg/day OP-treated, rat 3, 35 day exposure

city: Laval

first: Patrick

last: Devine

state: QC

address: 531 boulevard des Prairies

department: INRS-Institut Armand-Frappier

country: Canada

institute: Institut national de la recherche scientifique

description: biological replicate, 3 of 4, OP-treated rat

hyb_protocol: Cy3- and Cy5-labelled total RNA was mixed and incubated at 60°C for 30 min. The mix was hybridized to rat 22K oligo microarray slides (Agilent, cat #G4130A) at 60°C for 17h. Slides were washed twice in 6x SSPE, 0.005% N-lauroylsarcosine followed by a single wash each in 0.6x SSPE, 0.005% N-lauroylsarcosine and stabilization and drying solution (Agilent).

scan_protocol: Slides were scanned in a ScanArray Express scanner (Perkin Elmer, Torrance, CA) using the ScanArray Express software (ver. 3.0).

data_processing: Microarray data were analyzed using GeneSpring (version 7.3.1, Agilent). Lowess normalization (per spot and per chip) was performed on results. Using the median spot intensity and backgrounds, genes showing consistent expression above baseline (p<0.05) were identified. From those, significant treatment-dependent differences in gene expression were determined by Student’s t-test for those genes with 2-fold or greater differential expression between OP and PG treatment groups using normalized log10 of the ratio.

organism: Rattus norvegicus

source_name: Pooled liver RNA, female Sprague-Dawley rat, 35 day exposure, combined OP- and solvent-treated samples (n=8 rats)

label_protocol: Low RNA Input Linear Amplification Kit (Agilent, cat # 5184-3523) was used according to the manufacturer’s instructions using 1µg RNA/sample (28s:18s ratio ≥1.8). Liver RNA from 8 individual animals was pooled before cDNA synthesis and labeling, labeled with Cy5; uterine RNA from individual rats labeled separately as biological replicates, labeled with Cy3.

extract_protocol: total RNA extraction was performed using the Tri Reagent method (Sigma Chemical Co) following the manufacturer's instructions.

treatment_protocol: tissue weighed then flash frozen in liquid nitrogen

tag: female Sprague-Dawley rat pooled liver RNA

source_name: Uterus RNA, female Sprague-Dawley rat, 35 day OP exposure

tag: female Sprague-Dawley rat uterine RNA


title: 03-62_BC

city: Charlottesville

first: Weibin

last: Shi

state: VA

address: 480 Ray C Hunt Drive

department: Radiology

institute: University of Virginia

description: Gene expression data from aorta of 6-week-old female C57BL/6 apoE-/- mice fed chow diet.

hyb_protocol: Following fragmentation, cRNA were hybridized to mouse arrays MOE430A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the the Affymetrix Scanner 3000

data_processing: The data were analyzed using the Gene Chip Operating System.

source_name: C57BL/6 apoE-/- mice on chow diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were weaned onto a chow diet at 3 weeks of age and switched onto a Western diet at 4 weeks of age and maintained on the diet for 2 weeks.

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

treatment_protocol: One group of mice was fed a chow diet and the other fed a western diet.

tag: strain

tag: condition

value: hyperlipidemia


title: Sa_Stage1_E


title: 03-62_BW

description: Gene expression data from aorta of 6-week-old female C57BL/6 apoE-/- mice fed Western diet for 2 weeks.

source_name: C57BL/6 apoE-/- mice on Western diet

value: extreme hyperlipidemia


title: Sa_Stage1_B


title: 03-62_CC

description: Gene expression data from aorta of 6-week-old female C3H apoE-/- mice fed chow diet.

source_name: C3H apoE-/- mice on chow diet


title: 03-62_CW

description: Gene expression data from aorta of 6-week-old female C3H apoE-/- mice fed Western diet for 2 weeks.

source_name: C3H apoE-/- mice on Western diet


title: 125 mg/kg/day OP-treated, rat 4, 35 day exposure

description: biological replicate, 4 of 4, OP-treated rat


title: 125 mg/kg/day OP-treated, rat 1, 35 day exposure

description: biological replicate, 1 of 4, OP-treated rat


title: CTCF wt SL2 cell line replicate 1

description: WGA amplified DNA was labelled, hybridized and scanned by imaGenes (www.imagenes-bio.de)

source_name: IP DNA; CTCF SL2 cell line

tag: Drosophila melanogaster cell line SL2

source_name: Input DNA; SL2 cell line


title: Sa_Stage1_A


title: 06-19-07_Ye_HG-U133A_2_0_B1_0

description: Treated by Bzm with 0 hour


title: 125 mg/kg/day OP-treated, rat 2, 35 day exposure

description: biological replicate, 2 of 4, OP-treated rat


title: S. aureus_mvaS-IPTG-3

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, - IPTG, rep3

source_name: S. aureus mvaS regulated mutant grown without IPTG in NZYM broth harvested in exponential phase


title: S. aureus_mvaA+IPTG-1

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, + IPTG, rep1


title: S. aureus_mvaA+IPTG-2

description:
Gene expression data from exponentially growing cells
mvaA regulated mutant RN4220, + IPTG, rep2


title: Vehicle, rat 2, 35 day exposure

description: biological replicate, 2 of 4, vehicle-treated rat

source_name: Uterus RNA, female Sprague-Dawley rat, 35 day vehicle exposure


title: S. aureus_mvaS+IPTG-2

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, + IPTG, rep2

source_name: S. aureus mvaS regulated mutant grown with 1 mM IPTG in NZYM broth harvested in exponential phase


title: C4-2 scrambled shRNA control -DOX replicate 1

city: Vancouver

middle: SW

last: Cheng

state: BC

address: 2660 Oak Street

institute: The Prostate Centre at VGH

description: C4-2 scrambled control -DOX replicate 1 versus Universal Reference RNA.

hyb_protocol: Microarrays were hybridized with 10 ug of total RNA from samples of scrambled shRNA expressing cells in the absence of DOX, labeled with Cy5 against 10 ug of Universal Human Reference RNA labeled with Cy3 followed by overnight hybridization and washings.

scan_protocol: Arrays were scanned on a Scan Array Express Microarray Scanner (Perkin Elmer Applied Biosystems).

data_processing: Signal quality and quantity were determined using ImaGene 8.0 software (BioDiscovery, San Diego, CA). Data from Imagene were analyzed using GeneSpring GX 7.3 software with a per spot and per chip intensity-dependent (LOWESS) normalization (Silicon Genetics, Redwood City, CA) for profiling significant changes in gene expression. Data were subsequently filtered using the raw signal strength value. Measurements with higher signal strength values are relatively more precise than measurements with lower signal. Consequently, genes with expression that did not reach the minimum signal (50 arbitrary units) in at least one out of two conditions were discarded.

source_name: C4-2 scrambled shRNA control -DOX

label_protocol: Total RNA was labeled with Cy5 and assessed using the 3DNA Array 350™Expression Array Detection Kit according to the manufacturer’s instructions (Genisphere, Hatfield, PA)

growth_protocol: C4-2 cells expressing inducible shRNAs were plated in 10 cm tissue culture dishes in RPMI containing 5% charcoal-stripped serum (CSS; HyClone, VWR, West Chester, PA) and allowed to grow for 3 days in CSS without R1881 supplement and without DOX.

extract_protocol: Total RNA was extracted using Trizol reagent following the manufacturer’s instructions (Invitrogen) with phenol/chloroform extraction and RNA precipitated with isopropanol.

treatment_protocol: Grown in the absence of androgens in the absence of DOX.

tag: Castration-resistant C4-2 human prostate cancer cells stably expressing a tetracycline-inducible scrambled short hairpin RNA (shRNA) were generated as a control for AR knock down.

source_name: Universal Human Reference RNA

label_protocol: Total RNA from Universal Human Reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.

extract_protocol: Done by Stratagene.

tag: The Universal Human Reference RNA (Stratagene, Cedar Creek, TX) is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.


title: S. aureus_mvaS+IPTG-1

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, + IPTG, rep1


title: Vehicle, rat 3, 35 day exposure

description: biological replicate, 3 of 4, vehicle-treated rat


title: Vehicle, rat 1, 35 day exposure

description: biological replicate, 1 of 4, vehicle-treated rat


title: Sa_Stage1_D

description: Pool of seabream larvae collected at 24 hours post-hatching


title: C4-2 scrambled shRNA control -DOX, replicate 2

description: C4-2 scrambled control -DOX replicate 2 versus Universal Reference RNA.


title: S. aureus_WT-IPTG-3

description:
Gene expression data from exponentially growing cells
wildtype RN4220, - IPTG, rep3

source_name: S. aureus RN4220 grown without IPTG in NZYM broth harvested in exponential phase

tag: typical RN4220 lab strain


title: C4-2 scrambled shRNA control +DOX, replicate 3

description: C4-2 scrambled control +DOX replicate 3 versus Universal Reference RNA.

hyb_protocol: Microarrays were hybridized with 10 ug of total RNA from samples of scrambled shRNA expressing cells treated + DOX, labeled with Cy5 against 10 ug of Universal Human Reference RNA labeled with Cy3 followed by overnight hybridization and washings.

source_name: C4-2 scrambled shRNA control +DOX

growth_protocol: C4-2 cells expressing inducible shRNAs were plated in 10 cm tissue culture dishes in RPMI containing 5% charcoal-stripped serum (CSS; HyClone, VWR, West Chester, PA) and allowed to grow for 3 days. For shRNA induction, 2 ug/mL of the tetracycline analogue, doxycycline hyclase (DOX; Sigma Chemicals, St. Louis, MO), were added for 2 days and cells were grown in CSS without R1881 supplement.

treatment_protocol: Grown in the absence of androgens in the presence of DOX.


title: OP-treated, rat 4, single exposure, sacrifice 24 hours later

description: biological replicate, 4 of 4, OP-treated rat

source_name: Pooled liver RNA, female 77 day old Sprague-Dawley rat, single exposure to solvent or OP, sacrifice 24 hour later

treatment_protocol: tissue weighed then frozen in liquid nitrogen

source_name: Uterus RNA, Sprague-Dawley rat, 24 hour OP exposure

tag: female 77 day old Sprague-Dawley rat, single exposure to 125 mg/kg OP sacrifice 24 hours later


title: C4-2 scrambled shRNA control +DOX, replicate 1

description: C4-2 scrambled control +DOX replicate 1 versus Universal Reference RNA.


title: OP-treated, rat 2, single exposure, sacrifice 24 hours later


title: C4-2 scrambled shRNA control +DOX, replicate 2

description: C4-2 scrambled control +DOX replicate 2 versus Universal Reference RNA.


title: C4-2 inducible AR shRNA -DOX control, replicate 3

description: C4-2 AR inducible shRNA -DOX replicate 3 versus Universal Reference RNA.

hyb_protocol: Microarrays were hybridized with 10 ug of total RNA from control samples of AR shRNA inducible cells treated - DOX, labeled with Cy5 against 10 ug of Universal Human Reference RNA labeled with Cy3 followed by overnight hybridization and washings.

source_name: C4-2 inducible AR shRNA -DOX control

growth_protocol: C4-2 cells expressing inducible shRNAs were plated in 10 cm tissue culture dishes in RPMI containing 5% charcoal-stripped serum (CSS; HyClone, VWR, West Chester, PA) and allowed to grow for 3 days. Cells were grown in CSS without R1881 supplement and without DOX.

tag: Castration-resistant C4-2 human prostate cancer cells stably expressing a tetracycline-inducible AR-targeted short hairpin RNA (shRNA) were generated to directly test the effects of AR knockdown in C4-2 human prostate cancer cells. shRNA not induced by omitting DOX.


title: C4-2 scrambled shRNA control -DOX, replicate 3

description: C4-2 scrambled control -DOX replicate 3 versus Universal Reference RNA.


title: S. aureus_mvaS-IPTG-2

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, - IPTG, rep2


title: S. aureus_WT-IPTG-2

description:
Gene expression data from exponentially growing cells
wildtype RN4220, - IPTG, rep2


title: S. aureus_mvaS+IPTG-3

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, + IPTG, rep3


title: S. aureus_mvaS-IPTG-1

description:
Gene expression data from exponentially growing cells
mvaS regulated mutant RN4220, - IPTG, rep1


title: Vehicle, rat 4, 35 day exposure

description: biological replicate, 4 of 4, vehicle-treated rat

source_name: Pooled liver RNA, female Sprague-Dawley rat, 35 day exposure, combined OP- and solvent-treated samples (n=8 rats)


title: S. aureus_WT-IPTG-1

description:
Gene expression data from exponentially growing cells
wildtype RN4220, - IPTG, rep1


title: S. aureus_WT+IPTG-3

description:
Gene expression data from exponentially growing cells
wildtype RN4220, + IPTG, rep3

source_name: S. aureus RN4220 grown with 1 mM IPTG in NZYM broth harvested in exponential phase


title: S. aureus_WT+IPTG-2

description:
Gene expression data from exponentially growing cells
wildtype RN4220, + IPTG, rep2


title: OP-treated, rat 1, single exposure, sacrifice 24 hours later

description: biological replicate, 1 of 4, OP-treated rat


title: C4-2 inducible AR shRNA -DOX control, replicate 2

description: C4-2 AR inducible shRNA -DOX replicate 2 versus Universal Reference RNA.


title: OP-treated, rat 3, single exposure, sacrifice 24 hours later

description: biological replicate, 3 of 4, OP-treated rat


title: C4-2 inducible AR shRNA -DOX control, replicate 1

description: C4-2 AR inducible shRNA -DOX replicate 1 versus Universal Reference RNA.


title: Vehicle, rat 3, single exposure, sacrifice 24 hours later

description: biological replicate, 3 of 4, vehicle-treated rat

source_name: Uterus RNA, Sprague-Dawley rat, 24 hour vehicle exposure

tag: female 77 day old Sprague-Dawley rat, single exposure to solvent, sacrifice 24 hours later


title: C4-2 AR knock down using shRNA +DOX, replicate 3

description: C4-2 AR knock down using shRNA +DOX replicate 3 versus Universal Reference RNA.

hyb_protocol: Microarrays were hybridized with 10 ug of total RNA from samples of AR shRNA expressing cells treated + DOX, labeled with Cy5 against 10 ug of Universal Human Reference RNA labeled with Cy3 followed by overnight hybridization and washings.

source_name: C4-2 AR knock down using shRNA +DOX

label_protocol: Total RNA from AR shRNA expressing cells treated + DOX was labeled with Cy5 and assessed using the 3DNA Array 350™Expression Array Detection Kit according to the manufacturer’s instructions (Genisphere, Hatfield, PA)

tag: Castration-resistant C4-2 human prostate cancer cells stably expressing a tetracycline-inducible AR-targeted short hairpin RNA (shRNA) were generated to directly test the effects of AR knockdown in C4-2 human prostate cancer cells.


title: Vehicle, rat 4, single exposure, sacrifice 24 hours later


title: S. aureus_WT+IPTG-1

description:
Gene expression data from exponentially growing cells
wildtype RN4220, + IPTG, rep1


title: Vehicle, rat 2, single exposure, sacrifice 24 hours later

description: biological replicate, 2 of 4, vehicle-treated rat


title: NtlChIP_gastrula_rep2

status: Public on Feb 19 2009

first: Fiona

last: Wardle

address: Downing Street

department: Physiology, Development and Neuroscience

institute: University of Cambridge

hyb_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).

scan_protocol: Slides were scanned using an Agilent scanner

data_processing:
Images were quantified using Genepix.
Data was analysed using Whitehead error model as described in Wardle et al 2006 (Genome Biology 7:R71).

organism: Danio rerio

source_name: Immunoprecipitated chromatin

growth_protocol: embryos grown to 75-85% epiboly

extract_protocol: Chromatin  immunoprecipitation assay

treatment_protocol: Embryos at 75%-85% epiboly were collected and used in  a ChIP assay to generate the Cy5 (ChIPed DNA) and Cy3 (whole cell input DNA) labelled probes for hybridisation to the gene arrays.

tag: gastrula embryo

source_name: Whole cell chromatin


title: NtlChIP_gastrula_rep3

label_protocol: Protocol as described in Wardle et al 2006 (Genome Biology 7:R71).


title: C4-2 AR knock down using shRNA +DOX, replicate 1

description: C4-2 AR knock down using shRNA +DOX replicate 1 versus Universal Reference RNA.


title: Vehicle, rat 1, single exposure, sacrifice 24 hours later

description: biological replicate, 1 of 4, vehicle-treated rat


title: C4-2 AR knock down using shRNA +DOX, replicate 2

description: C4-2 AR knock down using shRNA +DOX replicate 2 versus Universal Reference RNA.


title: NtlChIP_gastrula_rep1


title: Liver_D1100_Replicate 3

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

description: The Type column in the raw file indicates whether the spot corresponds to background (50% DMSO alone), to a mouse transcript (mouse cDNA fragment in 50% DMSO) or to a yeast spiked-in mRNA (yeast cDNA fragment in 50% DMSO)

hyb_protocol: The arrays were prehybridized for 6h at 65°C in a rotating oven (Qbiogen) in 60 ml individual polypropylene tubes (Nalge Nunc) containing 4 ml of hybridization solution (5X SSC, 5X Denhardt’s solution, 0.5% SDS, 100 μg salmon sperm DNA). 33P-labeled cDNAs were added to the hybridization solution (5ml final volume). Arrays were hybridized for 24h at 65°C. Arrays were washed twice for 30 min and once for 1h at 65°C in 10 ml 0.1X SSC, 0.1% SDS.

scan_protocol: The arrays were exposed for 72 h to a phosphor screen (Molecular Dynamics) and scanned on a STORM 860 phosphorimager (Amersham Biosciences). Images were quantified using Image Master Array v.2.0 (Amersham Biosciences).

data_processing: All data were log10 transformed. For each array, outlier background spots (50% DMSO alone) were detected and filtered out using boxplots. The normality of the background was evaluated using a Shapiro-Wilk test. Each spot on each array was declared present only when its signal exceeded the mean background + 2 standard deviations. The 246 spots declared present on at least 25% of the arrays were kept for further analysis. Data were normalized using the mean log signal of the yeast spiked-in mRNAs. All analyses were done under R (www.r-project.org) using the functions available at http://www.inra.fr/internet/Centres/toulouse/pharmacologie/pharmaco-moleculaire/technologie/fonctions.R. Due to a high and heterogeneous background the data for 5 arrays out of the 24 (=4 groups x 6 mice/group) were excluded.

source_name: Liver of high dose DEHP-treated mouse

label_protocol: Five µg of total RNA and a mix of 13 selected yeast spiked-in mRNAs were reverse-transcribed with SuperScript II reverse transcriptase (Invitrogen) using 2µg oligo-dT primers (Invitrogen) and 1.5µg random hexamers in the presence of 40 µCi of [33P]dCTP (Perkin). The RNA matrix was degraded by alkaline lysis (SDS 0.2%, EDTA 50 mM, and NaOH 300 mM final, 68°C, 45 min). Following neutralization (Tris-HCl, pH 7.5, 500 mM final), unincorporated nucleotides were removed on Sephadex G50 columns (Amersham Biosciences). 33P-labeled cDNAs were denatured for 5 min at 95°C and incubated in 1 ml of hybridization solution (5X SSC, 5X Denhardt’s solution, 0.5% SDS, 100μg salmon sperm DNA) in the presence of 6µg of dA60.

growth_protocol: Seven-week-old male C57BL/6J mice were purchased from Charles River (Les Oncins, France). Mice were acclimatized for eight weeks, housed in polycarbonate cages at 22+2°C on a 12 hour light/dark cycle and allowed free access to water and food. The in vivo study was conducted under the European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, liver was removed, weighted, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Fifteen week-old mice were randomly divided into four groups (vehicle-treated, or DEHP-treated at doses 30, 180 or 1100 mg/kg/day, n=6 per group). Di-(2-ethylhexyl)-phthalate (DEHP, 30, 180 or 1100 mg/kg/day) in solution into corn oil (low, medium or high dose DEHP-treated groups respectively) or corn oil (vehicle-treated group) were administered for 14 days by daily gavage.

tag: STRAIN

tag: GENDER

value: Male

tag: AGE

value: 17 weeks

tag: DOSE

value: 1100 mg DEHP/kg/day

tag: TREATMENT LENGTH

tag: ADMINISTRATION

value: daily gavage

tag: TISSUE

value: liver


title: Liver_D1100_Replicate 5

value: 14 days


title: Liver_D1100_Replicate 2


title: NtlChIP_gastrula_rep2


title: Liver_D1100_Replicate 4


title: Liver_D1100_Replicate 1


title: Liver_D180_Replicate 4

source_name: Liver of medium dose DEHP-treated mouse

value: 180 mg DEHP/kg/day


title: Liver_D180_Replicate 3


title: Liver_D180_Replicate 2


title: Liver_D180_Replicate 1


title: Liver_D30_Replicate 2

source_name: Liver of low dose DEHP-treated mouse

value: 30 mg DEHP/kg/day


title: Liver_D30_Replicate 1


title: Liver_D30_Replicate 3


title: Liver_Control_Replicate 6

source_name: Liver of vehicle-treated mouse

value: 0 mg DEHP/kg/day


title: Liver_D30_Replicate 4


title: Liver_Control_Replicate 4


title: Liver_Control_Replicate 3


title: Liver_Control_Replicate 5


title: Liver_Control_Replicate 1


title: B4 Monoclonal IgM Antibody

city: La Jolla

first: Gregg

last: Silverman

address: 9500 Gilman Dr

institute: UC San Diego School of Medicine

description: Hybridoma-derived monoclonal B4 antibody

hyb_protocol: On each slide were two nitrocellulose pads, with most antigens printed at 200 mg/ml on each pad in six replicates at known positions that alternated with printing of buffer alone to eliminate carry-over. Slides were then blocked (Whatman blocking buffer) and incubated for 2 h with 400 ml of serum diluted at 1 : 200 in phosphate-buffered saline (PBS), pH 7·4.

scan_protocol: Slides were washed with PBS, water-rinsed and then scanned (Genepix 4000B; Molecular Devices, Sunnyvale, CA, USA) using Genepix Pro version 6·0 software at 532 and 635 nm to detect IgG and IgM reactivity, respectively, with images saved as tiff files.

data_processing: Genepix Pro version 6·0 software was used to analyse the intensity of each spot with foreground and background fluorescence intensities determined for each spot on the slide, with output as a gpr file. Data were extracted from the gpr files with r software (http://www.r-project.org). Background correction used a Matlab script, and the mean values for replicate spots determined with jmp version 7·0 software (http://www.jmp.com). Comparisons of array data for subjects and controls were performed and visual depictions generated with Cluster version 3·0 (Stanford University)  and Java TreeView (http://rana.lbl.gov/EisenSoftware.htm). Background levels were therefore determined based on replicate slides developed without antibodies, and with sera from healthy adult controls (not shown). In these studies, a level of 600 digital fluorescence intensity units was set as a threshold for significant reactivity, which was greater than the mean background plus 2 standard deviations (s.d.).

source_name: Hybridoma

label_protocol: After washing with Tris-buffered saline/0·1% Tween 20, the slides were reacted with  Cy-3- labelled Abs, West Grove, PA, USA) for 1 h incubation, then washed with PBS/0·05% Tween20.

growth_protocol: Monoclonal Ab B4  were developed by the fusion of peritoneal, lymph node and spleen cells from unmanipulated wild-type C57BL/6 mice with the SP2/0-AG14 myeloma cell line. Successful fusions were screened by Western blot analysis using IEC lysates and by flow cytometric analysis of isolated IEC. from the exhausted supernatants of cultured B4 hybridomas was affinity purified on a column of agarose beads with goat anti-human IgM (Sigma-Aldrich). Bound Ab was eluted with a buffer containing 0.1 M glycine, pH 2.3, and collected into a buffer containing 1.5 M Tris, pH 8.8. Eluted mAb was dialyzed against PBS, pH 7.4, for 48 h and concentrated using centrifugal filtration on Centricon Plus-20 (Millipore). Ab concentration was determined by measuring the A280 of the sample, and purity was confirmed by analysis on a 10% SDS-PAGE gel.

extract_protocol: To purify mAbs, Ab from the exhausted supernatants of cultured B4  hybridomas was affinity purified on a column of agarose beads with goat anti-human IgM (Sigma-Aldrich). Bound Ab was eluted with a buffer containing 0.1 M glycine, pH 2.3, and collected into a buffer containing 1.5 M Tris, pH 8.8. Eluted mAb was dialyzed against PBS, pH 7.4, for 48 h and concentrated using centrifugal filtration on Centricon Plus-20 (Millipore). Ab concentration was determined by measuring the A280 of the sample, and purity was confirmed by analysis on a 10% SDS-PAGE gel.

tag: genotype

tag: cell type

value: peritoneal/lymph node/spleen cells + SP2/0-AG14 myeloma cell line


title: Polyclonal IgM Antibody

description: Polyclonal IgM antibodies derived from serum

source_name: Polyclonal

value: peritoneal/lymph node/spleen cells


title: NC17-D8 B4 Isotype Monoclonal IgM Antibody

description: Hybridoma-derived monoclonal Isotype antibody


title: No Antibody (Negative Control)

type: other

description: No antibody hybridized to slide; Buffer only

molecule: other

organism: unidentified

source_name: control


title: Liver_Control_Replicate 2


title: MyD88 KO_macrophages_1h

city: Kyoto

first: Osamu

last: Takeuchi

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku,

department: Grad School of Medicine

institute: Kyoto University

hyb_protocol: The cRNA product was purified using an RNeasy kit (Qiagen), fragmented, and hybridized to Affymetrix mouse expression array A430A microarray chips, according to the manufacturer's protocol (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix Gene CHIP scanner 3000.

data_processing: The data were analyzed with RMA using the arrayassist program (Stratagene).

source_name: MyD88 KO macrophages stimulated with LPS for 1 h

label_protocol: cDNAs were used to prepare biotin-labeled cRNA by an in vitro transcription reaction performed using T7 RNA polymerase in the presence of biotinylated-ribonucleotides, according to the manufacturer's protocol (Enzo Diagnostics, Farmingdale, NY).

growth_protocol: peritoneal macrophages were preprared from thioglycollate-injected mice.

treatment_protocol: stimulated with 100 ng/ml LPS for indicated periods

tag: strain

value: MyD88 KO


title: MyD88 KO_macrophages_0h

source_name: MyD88 KO macrophages unstimulated


title: H3 K56Ac ChIP in HSF6 cells treated with retinoic acid

city: Los Angeles

first: Wei

last: Xie

address: 611 Young Dr. East, Boyer Hall Rm 332, UCLA

institute: UCLA

description: H3 K56Ac + retinoic acid IP vs. input

hyb_protocol: Hybridization was done according to manufacturer's protocol.

scan_protocol: Scanning was done according to manufacturer's protocol.

data_processing:
Data was processed first using Agilent Feature Extraction, and then using Agilent ChIP-Analytics software v1.3, which produced one file that combined the hybridization data from Agilent Human Promoter ChIP-on-Chip Set 244K Microarrays 1 and 2. Data was not used directly from Feature Extraction.
The IP and Input channels were normalized after both inter- and intra- array normalization according to manufacturer's instructions.

source_name: H3 K56Ac IP, HSF6 cells treated with retinoic acid

label_protocol: Labeling was performed according to manufacturer's protocol.

extract_protocol: Chromatin was isolated using standard procedures and an immunoprecipitation was performed using an antibody against H3 K56Ac. DNA was then extracted using standard protocols.

tag: cell line

value: cultured human embryonic stem cell line HSF6

tag: treatment

value: retinoic acid

source_name: H3 K56Ac Input, HSF6 cells treated with retinoic acid

extract_protocol: Genomic DNA was isolated using standard procedures without immunoprecipitations.


title: MyD88 KO_macrophages_4h

source_name: MyD88 KO macrophages stimulated with LPS for 4 h


title: TRIF KO_macrophages_1h

source_name: TRIF KO macrophages stimulated with LPS for 1 h

value: TRIF KO


title: Wild-type_macrophages_0h

source_name: wild-type macrophages unstimulated

value: wild-type


title: NtlChIP_gastrula_rep2


title: TRIF KO_macrophages_0h

source_name: TRIF KO macrophages unstimulated


title: Wild-type_macrophages_1h

source_name: wild-type macrophages stimulated with LPS for 1 h


title: TRIF KO_macrophages_4h

source_name: TRIF KO macrophages stimulated with LPS for 4 h


title: NtlChIP_gastrula_rep3

source_name: Immunoprecipitated chromatin

source_name: Whole cell chromatin


title: Wild-type_macrophages_4h

source_name: wild-type macrophages stimulated with LPS for 4 h


title: NtlChIP_gastrula_rep1


title: GPR30-antisense Transfection, OHT Induction 1h, A

city: Geneva

first: Deo Prakash

last: Pandey

address: 30 Quai Ernest-Ansmert

department: Cell Biology

country: Switzerland

institute: University of Geneva

description: Gene expression analyses were carried out to identify genes regulated by 17-beta estradiol (E2) and Hydroxytamoxifen (OHT) through GPR30 in SKBR3 cells.

data_processing: Illumina Bead Studio, No background subtraction, No normalization

label: biotin UTP

label_protocol: As suggested by the manufacturer, Illumina for beadchip Illumina human-6 v2.0 expression beadchip, Illumina TotalPrep RNA Amplification Kit from Ambion, Catalog #IL1791

growth_protocol: SKBR3 cells were grown in RPMI-1640 media supplemented with 10% FCS and L-Glutamine. Cells were switched to media without serum 24 h before transfection.

extract_protocol: Total RNA was extracted using TriZOL.

treatment_protocol: SKBR3 cells were transfected in 10 cm plates at roughly 60% density with Fugene for 30 hours (3microl/microgram). Cells were induced for 1 h with respective treatment.

tag: Estrogen Receptor alpha and beta negative breast cancer cells


title: Control Transfection, E2 Induction 1h, C

hyb_protocol: As suggested by the manufacturer, Illumina for beadchip Illumina human-6 v2.0 expression beadchip


title: GPR30-antisense Transfection, OHT Induction 1h, B

scan_protocol: As suggested by the manufacturer, Illumina for beadchip Illumina human-6 v2.0 expression beadchip


title: Control Transfection, E2 Induction 1h, B


title: GPR30-antisense Transfection, OHT Induction 1h, C


title: Control Transfection, No Induction 1h, C


title: Control Transfection, OHT Induction 1h, A


title: T6 vs T0 third biological replica

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

institute: UNIL

description: Digestive gland responses to okadaic acid treatment, loop design

hyb_protocol: labelled cDNAs were hybridised in SSC 5X, Sarcosile 0.1%, Denhardt sol 1X overnight at 48°C, the slides were washed with decreasing stringency buffer untill SSC 0.05X.

scan_protocol: Bio-Rad Chip Reader, laser powers 100% and detector sensitivity varied to balance the two channel intensities spots were inspected and quantified with Bio-Rad Cheap Reader's software.

data_processing: Raw data was first background subtracted then normalized with the LOESS algorithm. Finally a quantile normalization was apply. R software was used implemented with LIMMA package

organism: Mytilus galloprovincialis

label_protocol: Total RNA was retro-transcribed using Superscript II Reverse Transcriptase (Invitrogen) with aminoallyl-dUTP and then labelled with Cy5 or Cy3 fluorescent dyes (GE Healthcare)

growth_protocol: Mussels were maintained in tanks provided with oxygen-pump and water-lively pump in sea water. To prevent additional environmental stress, the seasonal photoperiod (L 10-D 14) and water temperature (17°C) were maintained. Sea water was changed weekly and water salinity (37 PSU) was controlled daily.

extract_protocol: Total RNA extracted using RNAtidy G following manufacturer's instructions plus an additional LiCl precipitation

treatment_protocol: 6.5 µg of Okadaic acid (Sigma Chemical Co.) diluted in 1 mL ethanol every two days for a time span of 5 weeks

value: Control

tag: age

value: 0 days post treatment

tag: biological replica

tag: tissue

value: digestive gland

value: Okadaic acod

value: 5 weeks post treatment


title: T4 vs T6 third biological replica

value: Okadaic acid

value: 3 weeks post treatment


title: Control Transfection, OHT Induction 1h, B


title: Control Transfection, OHT Induction 1h, C


title: T1 vs T4 third biological replica

value: 3 days post treatment


title: T0 vs T2 third biological replica

value: 1 week post treatment


title: T2 vs T4 third biological replica


title: T1 vs T2 third biological replica


title: Control Transfection, No Induction 1h, A


title: T6 vs T2 third biological replica


title: Leydig cells: Vehicle-treated Sample 4 vs. DEHP-treated Sample 4

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec)

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1).

data_processing: Data were analyzed under R (www.r-project.org) using the limma package of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {  okType<-x[,ControlType]==0  okFoundRed<-x[,rIsFound]==1  okFoundGreen<-x[,gIsFound]==1  okPixRed<-((x[,rNumPixOLHi]+x[,rNumPixOLLo])/x[,rNumPix])<=0.1  okPixGreen<-((x[,gNumPixOLHi]+x[,gNumPixOLLo])/x[,gNumPix])<=0.1  okBGRed1<-(x[,rMedianSignal]/x[,rBGMedianSignal])>=1.5  okBGRed2<-(x[,rMeanSignal]/x[,rBGMeanSignal])>=1.5  okBGRed3<-(x[,rMedianSignal]-x[,rBGMedianSignal])/x[,rBGPixSDev]>=2  okBGRed4<-(x[,rMeanSignal]-x[,rBGMeanSignal])/x[,rBGPixSDev]>=2  okBGGreen1<-(x[,gMedianSignal]/x[,gBGMedianSignal])>=1.5  okBGGreen2<-(x[,gMeanSignal]/x[,gBGMeanSignal])>=1.5  okBGGreen3<-(x[,gMedianSignal]-x[,gBGMedianSignal])/x[,gBGPixSDev]>=2  okBGGreen4<-(x[,gMeanSignal]-x[,gBGMeanSignal])/x[,gBGPixSDev]>=2  okSatRed<-x$rIsSaturated==0  okSatGreen<- x$gIsSaturated==0  okUnifRed<-x$rIsFeatNonUnifOL==0  okUnifGreen<-x$gIsFeatNonUnifOL==0  okUnifBGRed<-x$rIsBGNonUnifOL==0  okUnifBGGreen<-x$gIsBGNonUnifOL==0  okPopRed<-x$rIsFeatPopnOL==0  okPopGreen<-x$gIsFeatPopnOL==0  okPopBGRed<-x$rIsBGPopnOL==0  okPopBGGreen<-x$gIsBGPopnOL==0  okManualFlag<-x$IsManualFlag==0  okAbBGRed<-x$rIsWellAboveBG==1  okAbBGGreen<-x$gIsWellAboveBG==1  as.numeric(okType & okFoundRed & okFoundGreen & okPixRed & okPixGreen & ((okBGRed1 & okBGRed2 & okBGRed3 & okBGRed4) | (okBGGreen1 & okBGGreen2 & okBGGreen3 & okBGGreen4)) &  okSatRed & okSatGreen & okUnifRed & okUnifGreen & okUnifBGRed & okUnifBGGreen & okPopRed & okPopGreen & okPopBGRed & okPopBGGreen & okManualFlag & okAbBGRed & okAbBGGreen) }. Only the spots that had a weight of 1 on at least 6 microarrays corresponding to 3 dye-swap experiments were further analyzed. Additionally, we deleted the spots that were called present only on the 3 dye-swaps corresponding to a single DEHP-treated biological replicates. Local background was substracted on Cy3 and Cy5 data and a lowess normalization was applied to the log(Cy5/Cy3) data using the normalizeWithinArrays function.

source_name: Laser capture microdissected Leydig cells from vehicle-treated mouse

label_protocol: For each sample, 1µg of amplified RNA was labelled using the Agilent Low Input Linear Amplification Labelling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Fourteen-week-old male C57BL/6J mice were purchased from Charles River (Les Oncins, France). Mice were acclimatized for four weeks, housed in polycarbonate cages at 22+2°C on a 12 hour light/dark cycle and allowed free access to water and food. In vivo studies were conducted under European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, the right testis of DEHP-treated or vehicle-treated C57BL/6J male mice were embedded in Tissue-Tek O.C.T. compound (Sankura Finetek, Torrance,CA) and snap frozen with isopentane cooled in liquid nitrogen. Sections of 10µm (Leica CM3050S cryostat) were mounted on microscope slides which were immediately fixed, stained with hematoxylin-eosin, dehydrated by sequential baths in ice-cold 70%, 95% and 100% ethanol and stored under vacuum. Laser capture microdissection of Leydig cells was performed with the Arcturus PixCell IIe (Arcturus, California, USA) using CapSure® Macro LCM Caps (Molecular Devices Corporation). To avoid contaminations, the laser power and duration was adjusted for each section (ranging from 50 to 70 mW and 0.6 to 0.8 ms respectively). Approximately 1500 laser shots were performed per tissue section. Total RNA was isolated from single caps obtained from independent mice using the PicoPure® RNA Isolation Kit (Molecular Devices Corporation) and was amplified for two rounds with RiboAmp® RNA Amplification Kit (Molecular Devices Corporation) according to the manufacturers instructions.

treatment_protocol: corn oil was administered for 21 days by daily gavage

tag: Strain

tag: Gender

value: male

tag: Age

value: 21 weeks

tag: Tissue

value: laser-capture microdissected Leydig cells

source_name: Laser capture microdissected Leydig cells from DEHP-treated mouse

treatment_protocol: Eighteen week-old mice were randomly divided into two groups (DEHP-treated and vehicle-treated, n=4 per group). di-(2-ethylhexyl)-phthalate (DEHP, 200 mg/Kg/day) in solution into corn oil (DEHP-treated group) or corn oil (vehicle-treated group) were administered for 21 days by daily gavage


title: CUMC19

city: Houston

first: Federico

middle: A

last: Monzon

state: TX

address: 6565 Fannin St., MS205

institute: The Methodist Hospital Research Institute

hyb_protocol: Affymetrix Mapping 10K Xba 2.0 Assay

scan_protocol: Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner

data_processing: Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0

label: Biotin

source_name: Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue

label_protocol: Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)

extract_protocol: Deparaffinization followed by Qiagen DNeasy Blood and Tissue kit by manufacturer's instructions

tag: Furhman Nuclear Grade:	4

tag: TNM Stage:	pT3b Nx Mx

tag: LymphoVascular Invasion:	FALSE


title: Control Transfection, No Induction 1h, B


title: CUMC18

tag: Furhman Nuclear Grade:	1

tag: TNM Stage:	pT1b Nx Mx


title: CUMC20

tag: Furhman Nuclear Grade:	3

tag: TNM Stage:	pT3a Nx Mx


title: CUMC17


title: Leydig cells: Vehicle-treated Sample 4 vs. DEHP-treated Sample 1


title: CUMC16

source_name: Renal Cell Carcinoma, Papillary Type, DNA from Paraffin Embedded Tissue

tag: TNM Stage:	pT2 Nx Mx


title: T0 vs T1 third biological replica

tag: treatment


title: Leydig cells: DEHP-treated Sample 1 vs. Vehicle-treated Sample 4

treatment_protocol: di-(2-ethylhexyl)-phthalate (DEHP) in solution into corn oil was administered at 200 mg/Kg/day for 21 days by daily gavage


title: Leydig cells: DEHP-treated Sample 4 vs. Vehicle-treated Sample 4


title: CUMC15

tag: Furhman Nuclear Grade:	2


title: CUMC13


title: CUMC12

hyb_protocol: Affymetrix Mapping 250K_Nsp Assay

scan_protocol: Affymetrix Mapping 250K Nsp Assay with an Affymetrix GeneChip 3000 7G scanner

label_protocol: Standard labeling protocol for FFPE tissue based on Affymetrix Mapping 250K Nsp Assay. Startup DNA amount is 1ug


title: Leydig cells: Vehicle-treated Sample 2 vs. DEHP-treated Sample 4


title: Leydig cells: Vehicle-treated Sample 2 vs. DEHP-treated Sample 1


title: CUMC11


title: Leydig cells: Vehicle-treated Sample 1 vs. DEHP-treated Sample 4


title: T6 vs T2 second biological replica

tag: age


title: T4 vs T6 second biological replica

tag: biological replica


title: T1 vs T4 second biological replica

tag: tissue


title: CUMC14

source_name: Renal Neoplasm, Unclassified, DNA from Paraffin Embedded Tissue

tag: TNM Stage:	pT3a N2 Mx


title: T1 vs T2 second biological replica


title: Leydig cells: Vehicle-treated Sample 1 vs. DEHP-treated Sample 1

tag: Strain

tag: Gender