title: M3-S2(0.1):hcf-1(pk924) vs N2 (YA)

description: Purpose: to compare gene expression profiles of N2 vs. hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy5 and N2-Cy3 from RNA batch MA3 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 739 Pixel Size : 5 Laser on time : 27732 Laser Power : 2.04 Scan Date : 2008-08-20 Scan Temperature : 33.53 Scan Time : 13:23:55 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 6 a1

status: Public on Jul 23 2011

type: genomic

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

country: USA

institute: UT Southwestern

hyb_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).

scan_protocol: Arrays were scanned on a the Axon Genepix 4000B scanner at 5 microns for both 532nm and 635nm channels

data_processing: Scanned images were processed using NimbleScan

molecule: genomic DNA

organism: Homo sapiens

source_name: CTCF ChIP DNA

growth_protocol: H1 hESCs were grown on matrigel in mTeSR1

extract_protocol: Chromatin extraction, sonication, ChIP and LM-PCR were performed following previously published protocols from the Ren Lab (Li et al., 2005; Heintzman et al., 2007 & 2009).

tag: cell type

value: hESC

tag: chip antibody

value: CTFC

tag: cell line

tag: chip antibody manufacturer

value: in house

tag: chip antibody catalog #

source_name: input DNA


title: M2-S2(0.1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

type: RNA

city: Ithaca

first: Gizem

last: Rizki

state: NY

address: 526 Campus Road, 341 Biotech

institute: Cornell University

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA2 compared in this experiment. Scan settings=AutoPMT 0.1%

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Scan Power : 100 PMT Volts : 752 Pixel Size : 5 Laser on time : 26824 Laser Power : 2.11 Scan Date : 2008-08-08 Scan Temperature : 34.63 Scan Time : 13:47:19 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1040, 34280

molecule: total RNA

organism: Caenorhabditis elegans

label_protocol:
Type of label : Cy3
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636

growth_protocol:
Culture Methods : Synchronized by hatching in M9 at 16C and developed at 25C
Developmental Stage : Young adult

extract_protocol: Extraction method : Trizol/Qiagen Rneasy Kit

tag: strain name

label_protocol:
Type of label : Cy5
reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=32636


title: DFC H3K4me3 Hs35b_P02R

description: H3K4me3 ChIP on H1 hESCs treated w. BMP4 for 5d

hyb_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following  Affymetrix specifications.

data_processing: data aligned to hg17

label: biotin

source_name: ChIP DNA

treatment_protocol: H1 hESCs were grown on matrigel in mTeSR1 supplemented with 200ng/mL BMP4 for 5 days

value: differentiated hESC

value: Upstate


title: M2-S2(1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA2 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 962 Pixel Size : 5 Laser on time : 26881 Laser Power : 2.19 Scan Date : 2008-08-08 Scan Temperature : 36.61 Scan Time : 14:44:13 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 34280


title: brain_14d_273 ng/L diazepam_replicate 3

city: Muttenz

first: Daniela

middle: Maria

last: Oggier

address: Gründenstrasse 40

department: School of Lifesciences

country: Switzerland

institute: University of Applied Sciences Northwestern Switzerland

description: Gene expression after 14 d exposure to 273 ng/L diazepam

hyb_protocol: Cy-3-labeled cRNA samples (1.65 µg) were mixed with Agilent blocking solution, subsequently fragmented randomly to 100-200 bp at 65 °C with fragmentation buffer and resuspended in hybridization buffer as provided by the gene expression hybridization Kit (Agilent Technologies). Target cRNA samples (100 µL) were hybridized to the Agilent Zebrafish 4x44K Gene Expression Microarray for 17 h at 65 °C. The hybridized arrays were then washed using Agilent GE wash buffers 1 and 2 according to the manufacturer's instructions.

scan_protocol: Slides were scanned by an Agilent Microarray Scanner (Agilent p/n G2565BA) at 5 μm resolution with the green photomultiplier tube set to 100% and a scan area of 61 x 21.6 mm.

data_processing: Image generation and feature extraction was performed using the Agilent Feature Extraction (FE) software version 9.5.3. Quality control was additionally considered before performing the statistical analysis. These included array hybridization pattern inspection: absence of scratches, bubbles, areas of non-hybridization, proper grid alignment, spike performance in controls with a linear dynamic range of 5 orders of magnitude and the number of green-feature non-uniformity outliers which should be below 100 for all samples.

organism: Danio rerio

source_name: Male zebrafish, 14 d, 273 ng/L diazepam, replicate 3

label_protocol: Total RNA samples (600 ng) were reverse-transcribed into double-strand cDNA in the presence of RNA poly-A controls with the Agilent One-Color RNA Spike-In Kit. Cy3 labeling and hybridization were performed according to the manufacturer's manual. After reverse-transcription of RNA into double-stranded cDNA, double-strand cDNA was in vitro transcribed into cRNA in the presence of Cy3 labeled nucleotides using a Low RNA Input Linear Amp Kit +Cy dye (Agilent Technologies, Basel, Switzerland). The Cy3-labeled cRNA was purified using an RNeasy mini kit (Qiagen, Basel, Switzerland), and quality and quantity was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively. Only cRNA samples with a total cRNA yield higher than 2 µg and a dye incorporation rate between 9 pmol/µg and 20 pmol/µg were used for hybridization.

extract_protocol: Total RNA was extracted from male zebrafish brains using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). Total RNA concentrations were measured spectrophotometrically using a NanoDrop ND-1000 UV-VIS Spectrophotometer at 260 nm. The integrity of each RNA sample was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Basel, Switzerland). Only samples containing a 260/280 nm ratio between 1.8-2.1, a 28S/18S ratio between 1.5-2 and an RNA integrity number (RIN) > 8 were processed further.

treatment_protocol: The experimental setup consisted of four replicates of water controls and two diazepam doses. Twenty male zebrafish per replicate were held in 20-L stainless steel tanks in well-aerated exposure water. Fish were exposed for 14 d to the nominal concentrations of 273 ng/L and 273 μg/L diazepam, respectively. The lower concentration (273 ng/L) was assumed to represent the worst case environmental concentration, and 273 μg/L refers to the NOEC in the early life stages test (12). During the experiment fish survival, appearance and behavior were determined.   A 48 h static-renewal procedure was used to minimize handling stress for the fish. Thereby after 24 h, food remains and feces were removed by siphoning 1/3 of the water and replacement by new exposure water containing the appropriate diazepam concentrations. After 48 h, the water renewal procedure was repeated, but this time by replacing total tank water (20 L). The quality of the exposure water was continuously monitored by the oxygen concentration determination (>70%), the pH value (6.7-7.2) and the temperature (27±1 °C).

tag: tissue

value: brain

tag: developmental stage

value: male

tag: age

value: adult

tag: treatment

value: 273 ng/L diazepam


title: DFC H3K4me1 Hs35b_P02R

description: H3K4me1 ChIP on H1 hESCs treated w. BMP4 for 5d

scan_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following  Affymetrix specifications.

value: Abcam


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 4 a1

label_protocol: ChIP-DNA samples were labeled and hybridized to NimbleGen HD microarrays (NimbleGen Systems). DNA was labeled according to NimbleGen Systems’ protocol. Samples were hybridized at 42°C for 16 hours on a MAUI 12-bay hybridization station (BioMicro Systems).


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 6 a3


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 4 a3


title: brain_14d_273 ng/L diazepam_replicate 1

source_name: Male zebrafish, 14 d, 273 ng/L diazepam, replicate 1


title: Atherogenic diet, male pig number 2200

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

hyb_protocol: Following fragmentation, 15 cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA), using CEL files obtained from GCOS software (Affymetrix).

organism: Sus scrofa

source_name: male pig, AD group

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 4 μg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Pigs' heparinised blood was processed within two hours after extraction and used to isolate PBMNCs. Isolation was carried out under sterile conditions to avoid the activation of monocytes. Blood was diluted 1:1 with RPMI 1640 cell culture medium and processed by density gradient centrifugation with Histopaque-1077 (Sigma Aldrich) according to the manufacturer instructions. After washing the cells (x2) with phosphate buffer solution (PBS), the PBMNCs were lysed using RLT Buffer (Qiagen) and stored at –80 C for RNA extraction.

extract_protocol: Total RNA was isolated using an RNeasy  Plus Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water, aliquoted and stored at –80C.

treatment_protocol: PBMNCs were isolated from the following groups: i) CT (animals fed a standard commercial pig chow for 4 months), n=4 arrays (2 females, 2 males); ii) AD (animals fed an atherogenic diet containing 5.5% beef tallow, 10% coconut oil and 1% cholic acid for 4 months), n=4 arrays (2 females, 2 males); iii) AD-GE (animals fed an atherogenic diet supplemented with grape extract 1 g GE/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); iv) AD-GE-RES (animals fed an atherogenic diet supplemented with resveratrol-enriched grape extract 1 g GE/70 Kg animal body weight equivalent to 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); v) AD-RES (animals fed an atherogenic diet supplemented with resveratrol, 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males); vi) CT-GE-RES (animals fed a standard commercial pig chow supplemented with resveratrol-enriched grape extract 1 g GE/70 Kg animal body weight equivalent to 18 mg RES/70 Kg animal body weight for 4 months), n=4 arrays (2 females, 2 males).

tag: gender

value: Peripheral blood mononuclear cells (PBMNCs)

tag: diet

value: Atherogenic diet (AD)


title: M2-S1(1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA1 compared in this experiment. Scan settings=AutoPMT 1%

scan_protocol: Scan Power : 100 PMT Volts : 945 Pixel Size : 5 Laser on time : 26894 Laser Power : 2.20 Scan Date : 2008-08-08 Scan Temperature : 36.98 Scan Time : 14:57:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1120, 50040


title: M2-S2(0.005):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plates and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA2 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 673 Pixel Size : 5 Laser on time : 26772 Laser Power : 2.00 Scan Date : 2008-08-08 Scan Temperature : 32.58 Scan Time : 12:54:49 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 34200


title: brain_14d_273 ng/L diazepam_replicate 4

source_name: Male zebrafish, 14 d, 273 ng/L diazepam, replicate 4


title: M2-S1(0.1):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA1 compared in this experiment. Scan settings=AutoPMT 0.1%

scan_protocol: Scan Power : 100 PMT Volts : 734 Pixel Size : 5 Laser on time : 26836 Laser Power : 2.13 Scan Date : 2008-08-08 Scan Temperature : 35.02 Scan Time : 14:00:11 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1120, 50000


title: M2-S1(0.005):daf-16(RX5);hcf-1(pk924) vs. hcf-1(pk924) (YA)DF

description: Purpose: to compare gene expression profiles of hcf1 vs. daf16;hcf1 mutants. Worms were eggprepped, hatched at 16C, o/n, L1s plated and grown at 25C until young adult stage. Hcf1-Cy3 and d16;hcf1-Cy5 from RNA batch MA1 compared in this experiment. Scan settings=AutoPMT 0.005%

scan_protocol: Scan Power : 100 PMT Volts : 649 Pixel Size : 5 Laser on time : 26784 Laser Power : 2.04 Scan Date : 2008-08-08 Scan Temperature : 33.10 Scan Time : 13:07:09 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [83882] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0 Auto PMT setting (%) : 0.005

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 1080, 49960


title: hESC H3K4me1 Hs35b_P02R

description: H3K4me1 ChIP on H1 hESCs

label_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following  Affymetrix specifications.


title: brain_14d_273 ng/L diazepam_replicate 2

source_name: Male zebrafish, 14 d, 273 ng/L diazepam, replicate 2


title: DFC H3K4me1 Hs35b_P01R


title: DFC H3K4me3 Hs35b_P01R


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 4 a2


title: hESC H3K4me1 Hs35b_P01R

description: H3K4me1 ChIP on H1 hESCs


title: hESC H3K4me3 Hs35b_P01R

description: H3K4me3 ChIP on H1 hESCs


title: brain_14d_water_replicate 2

description: Gene expression after 14 d exposure to water control

source_name: Male zebrafish, 14 d, water control, replicate 2

value: water control


title: brain_14d_water_replicate 3

source_name: Male zebrafish, 14 d, water control, replicate 3


title: brain_14d_water_replicate 1

source_name: Male zebrafish, 14 d, water control, replicate 1


title: wholebody_40ug/L_6dpf_4

description: Gene expression after 6 dpf exposure to 40 ug/L PKC416

source_name: Eleuthero-embryo whole body, 6 dpf, 40 ug/L PKC412, replicate 4

extract_protocol: Total RNA was extracted from zebrafish eleuthero-embryos using the RNeasy Mini Kit (Qiagen, Basel, Switzerland). Total RNA concentrations were measured spectrophotometrically using a NanoDrop ND-1000 UV-VIS Spectrophotometer at 260 nm. The integrity of each RNA sample was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Basel, Switzerland). Only samples containing a 260/280 nm ratio between 1.8-2.1, a 28S/18S ratio between 1.5-2 and an RNA integrity number (RIN) > 8 were processed further.

treatment_protocol: All zebrafish embryos used in the experiments were at blastula stage. They were placed in 750 mL covered glass beakers of reconstituted water (total hardness of 125 mg/L as CaCO3 and a conductivity of 270 μS/cm) and the appropriate concentration of PKC412 or DMSO (0.01 %, solvent control). The water temperature was held constant at 27±1 °C with the photoperiod set at 16:8 h light/dark. The static exposure setup consisted of six replicates of water control, solvent control (0.01 % DMSO) and two PKC412 doses. A total of 100 fertilized eggs per replicate (n = 6) were exposed up to 6 days post fertilization (dpf) to nominal concentrations of 2 μg/L and 40 μg/L PKC412, respectively. Every 24 h, lethal and sublethal effects were evaluated, dead embryos or eleuthero-embryos were removed and the water was changed. The quality of the exposure water was continuously monitored by oxygen concentration determination (>70%), the pH value (6.7-7.2) and the temperature (27±1 °C). At the end of exposure, eleuthero-embryos were anaesthetized in a clove oil solution (Fluka AG, Buchs, Switzerland). A total of 80 eleuthero-embryos per replicate were pooled in RNAlater for microarray and qRT-PCR.

value: whole body

value: eleuthero-embryo

value: 6 days post fertilization

value: 40 ug/L PKC412


title: wholebody_40ug/L_6dpf_2

description: Gene expression after 6 dpf exposure to 40 ug/L PKC414

source_name: Eleuthero-embryo whole body, 6 dpf, 40 ug/L PKC412, replicate 2


title: brain_14d_273 ug/L diazepam_replicate 1

description: Gene expression after 14 d exposure to 273 ug/L diazepam

source_name: Male zebrafish, 14 d, 273 ug/L diazepam, replicate 1

value: 273 ug/L diazepam


title: wholebody_40ug/L_6dpf_3

description: Gene expression after 6 dpf exposure to 40 ug/L PKC415

source_name: Eleuthero-embryo whole body, 6 dpf, 40 ug/L PKC412, replicate 3


title: Egr1 A

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

description: custom array design 4845

hyb_protocol: Hybridization was performed by Nimblegen

scan_protocol: Arrays were scanned by Nimblegen

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Rattus norvegicus

source_name: Egr1 ChIP DNA from H4IIE cells treated with insulin for 1h

label_protocol: ChIP DNA was amplified by whole genome amplification (Sigma), and then sent to Nimblegen for labeling with Cy3 or Cy5 per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: H4IIE cells in Growth Medium

extract_protocol: ChIP assays were performed on H4IIE rat liver cell lines grown in standard growth media and passaged twice weekly.  Cells were treated with 0.1uM insulin for 1h or untreated and cross linked 1% formaldehyde in PBS for 20min as described (Jang et al., J. Neurochemistry, 2006; Jang and Svaren, JBC 2009, Gokey et al., JBC, 201).

treatment_protocol: 1h insulin

value: H4IIE liver cells

tag: antibody

value: Egr1, Santa Cruz, sc-189

tag: sample type

value: WGA-amplified ChIP DNA

value: treated with insulin for 1h

source_name: Egr1 ChIP DNA from H4IIE cells untreated

treatment_protocol: untreated


title: Muscle_AQM_9-14d UU57

city: Uppsala

first: Monica

last: Llano-Diez

address: Akademiska sjukhuset, Ing.85, 3tr

department: Neuroscience

country: Sweden

institute: Uppsala university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip  Scanner 3000.

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 800. The RMA algorithm was then used to generate the Sample data table values.

source_name: gastrocnemius muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA) and mechanically ventilated, 9 to 14d group

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 g total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

extract_protocol: Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and Rneasy column cleanup

treatment_protocol: Briefly, the following surgery and instrumentation was completed with sterile technique: 1) Precordial silver wire electrocardiogram (ECG) electrodes were implanted subcutaneously.  2) An aortic catheter (28-gauge Teflon) was inserted via the left carotid artery to record arterial blood pressure.  3) A 0.9-mm Renathane catheter was threaded into the left jugular vein to administer parental solutions.  4) Three subcutaneous EEG needle electrodes were placed into the skull above the right and left temporal lobes, and a third reference electrode was placed in the neck region.  5) Temperature was measured by a vaginal thermistor and servo-regulated at 37°C.  6) A silicone cannula was inserted in the urethra to continuously record urine output.  During surgery or any possible irritating manipulation, the anesthetic isoflurane level was at >1.5%, which maintained the following states: 1) the electroencephalogram (EEG) was synchronized and dominated by high-voltage slow-wave activity; 2) mean arterial pressure was 100 mmHg, the heart rate, 420 beats/min, and 3) there were no evident EEG, blood pressure or heart rate responses to surgical manipulation.  Isoflurane was delivered into the inspiratory gas stream by a precision mass-flow controller.  After the initial surgery, Isoflurane was gradually lowered (over 1-2 days) and maintained at <0.5% during the remaining experimental period.  Rats were ventilated through a per os coaxial tracheal cannula at 72 breaths/min with an inspiratory and expiratory ratio of 1:2 and a minute volume of 180–200 ml and gas concentrations of 50% O2, 47% N2, and 3% CO2, delivered by a precision volumetric respirator.  Intermittent respiratory hyperinflations (6 per hour at 15 cmH2O), positive end-expiratory pressure (1.5 cmH2O), and expiratory CO2 monitoring were continuous.  Neuromuscular blockade (NMBA) was induced on the first day (100 µg iv. alpha-cobrotoxin) and maintained by continuous infusion (250 µg/day, iv). Mechanical ventilation was initiated immediately after the NMBA induction.

tag: strain

value: Sprague-Dawley

value: female

value: gactrocnemius muscle

tag: disease state

value: AQM


title: Muscle_AQM_9-14d UU59


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 6 a2

source_name: CTCF ChIP DNA

value: hESC

value: CTFC

value: in house

source_name: input DNA


title: heart Ovx + Late estrogen rep2

city: Davis

first: Li

last: Lin

address: 451 Health Sciences Way

department: Department of Medicine

institute: University of California, Davis

description: total RNA was pooled from three rat hearts in equal amounts, and analyzed with gene expression chip

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: heart of aged Norway Brown rat receiving ovariectomy plus delayed estrogen replacement

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

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

value: Norway Brown

value: 18-22 months-old

value: heart

value: ovariectomy + late estrogen


title: heart Ovx + Late estrogen rep1


title: Muscle_AQM_9-14d UU51


title: wholebody_2ug/L_6dpf_4

description: Gene expression after 6 dpf exposure to 2 ug/L PKC412

source_name: Eleuthero-embryo whole body, 6 dpf, 2 ug/L PKC412, replicate 4

value: whole body

value: eleuthero-embryo

value: 6 days post fertilization

value: 2 ug/L PKC412


title: heart Ovx + Early estrogen rep1

source_name: heart of aged Norway Brown rat receiving ovariectomy plus immediate estrogen replacement

value: ovariectomy + early estrogen


title: heart Ovx + Early estrogen rep2


title: hESC H3K4me3 Hs35b_P02R

description: H3K4me3 ChIP on H1 hESCs

source_name: ChIP DNA

value: Upstate


title: wholebody_2ug/L_6dpf_3

source_name: Eleuthero-embryo whole body, 6 dpf, 2 ug/L PKC412, replicate 3


title: wholebody_40ug/L_6dpf_1

description: Gene expression after 6 dpf exposure to 40 ug/L PKC413

source_name: Eleuthero-embryo whole body, 6 dpf, 40 ug/L PKC412, replicate 1

value: 40 ug/L PKC412


title: Muscle_AQM_9-14d UU47

value: Sprague-Dawley

value: female


title: Muscle_AQM_9-14d UU49

value: gactrocnemius muscle

value: AQM


title: wholebody_2ug/L_6dpf_1

source_name: Eleuthero-embryo whole body, 6 dpf, 2 ug/L PKC412, replicate 1


title: heart Ovx rep2

source_name: heart of aged Norway Brown rat receiving ovariectomy

value: ovariectomy


title: heart Sham rep2

source_name: heart of aged Norway Brown rat receiving sham-operation

value: sham


title: wholebody_DMSO_6dpf_4

description: Gene expression after 6 dpf exposure to 0.01% DMSO

source_name: Eleuthero-embryo whole body, 6 dpf, solvent control 0.01% DMSO, replicate 4


title: heart Ovx rep1

value: Norway Brown


title: Muscle_AQM_9-14d UU45


title: wholebody_2ug/L_6dpf_2

source_name: Eleuthero-embryo whole body, 6 dpf, 2 ug/L PKC412, replicate 2


title: DFC H3K4me3 Hs35b_P06R

description: H3K4me3 ChIP on H1 hESCs treated w. BMP4 for 5d

value: differentiated hESC

value: hESC


title: heart Sham rep1

value: 18-22 months-old

value: heart


title: Muscle_AQM_5-8d UU53

source_name: gastrocnemius muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA) and mechanically ventilated, 5 to 8d group


title: DFC H3K4me1 Hs35b_P06R

value: Abcam


title: Muscle_AQM_5-8d UU43


title: wholebody_DMSO_6dpf_3

source_name: Eleuthero-embryo whole body, 6 dpf, solvent control 0.01% DMSO, replicate 3

value: whole body

value: eleuthero-embryo

value: 6 days post fertilization


title: Muscle_AQM_5-8d UU41


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 8 a1

value: CTFC

value: in house


title: wholebody_DMSO_6dpf_2

source_name: Eleuthero-embryo whole body, 6 dpf, solvent control 0.01% DMSO, replicate 2


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 10 a1


title: hESC H3K4me1 Hs35b_P06R

description: H3K4me1 ChIP on H1 hESCs


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 8 a2


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 8 a3


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 10 a3


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 9 a1


title: wholebody_water_6dpf_3

description: Gene expression after 6 dpf exposure to water control

source_name: Eleuthero-embryo whole body, 6 dpf, water control, replicate 3

value: water control


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 10 a2

source_name: CTCF ChIP DNA


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 9 a2

source_name: input DNA


title: wholebody_water_6dpf_4

source_name: Eleuthero-embryo whole body, 6 dpf, water control, replicate 4


title: wholebody_water_6dpf_2

source_name: Eleuthero-embryo whole body, 6 dpf, water control, replicate 2


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 9 a3


title: wholebody_DMSO_6dpf_1

source_name: Eleuthero-embryo whole body, 6 dpf, solvent control 0.01% DMSO, replicate 1


title: Muscle_AQM_6h-4d UU31

source_name: gastrocnemius muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA) and mechanically ventilated, 6h to 4d group

value: Sprague-Dawley

value: female


title: DFC H3K4me3 Hs35b_P07R

source_name: ChIP DNA

value: Upstate


title: Muscle_AQM_6h-4d UU35

value: gactrocnemius muscle

value: AQM


title: hESC H3K27ac (Nimblegen 2.1M HD2 #2)

source_name: H3K27ac ChIP DNA


title: Muscle_AQM_5-8d UU55


title: wholebody_water_6dpf_1

source_name: Eleuthero-embryo whole body, 6 dpf, water control, replicate 1


title: Muscle_AQM_6h-4d UU33


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #10)

source_name: H3K27me3 ChIP DNA

growth_protocol: H1 hESCs were grown on matrigel in mTeSR1 supplemented with 200ng/mL BMP4 for 5 days


title: DFC H3K4me1 Hs35b_P07R


title: hESC H3K4me3 Hs35b_P07R

description: H3K4me3 ChIP on H1 hESCs


title: hESC H3K4me1 Hs35b_P07R

description: H3K4me1 ChIP on H1 hESCs


title: Muscle_AQM_6h-4d UU23


title: hESC H3K27ac (Nimblegen 2.1M HD2 #10)


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #12)


title: Muscle_AQM_6h-4d UU29


title: DFC H3K27ac (Nimblegen 2.1M HD2 #12)


title: hESC H3K4me3 Hs35b_P06R

description: H3K4me3 ChIP on H1 hESCs


title: DFC H3K4me3 Hs35b_P05R


title: Muscle_AQM_6h-4d UU27


title: Muscle_AQM_6h-4d UU21


title: DFC H3K4me1 Hs35b_P05R


title: Muscle_AQM_6h-4d UU19


title: Muscle_AQM_6h-4d UU37


title: hESC H3K4me3 Hs35b_P05R

description: H3K4me3 ChIP on H1 hESCs


title: DFC H3K27ac (Nimblegen 2.1M HD2 #10)


title: hESC H3K27ac (Nimblegen 2.1M HD2 #12)


title: Muscle_AQM_6h-4d UU17


title: DFC H3K27ac (Nimblegen 2.1M HD2 #1)


title: hESC H3K4me1 Hs35b_P05R

description: H3K4me1 ChIP on H1 hESCs


title: Muscle_AQM_6h-4d UU15


title: Muscle_AQM_6h-4d UU13


title: MIAPaCa-2 NDRG1 cells (rep 2)

city: Sydney

first: Zaklina

last: Kovacevic

state: NSW

address: Level 5 Blackburn Building D06, University of Sydney

department: Pathology

country: Australia

institute: University of Sydney

description:
NDRG1 2
Gene expression data from MIAPaCa-2 cells transfected with NDRG1 vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

source_name: MIAPaCa-2 cells NDRG1

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

growth_protocol: Cell were grown in DMEM media at 37oC

extract_protocol: RNA was extracted using Trizol (Invitrogen) following manufacturers protocol.

treatment_protocol: Cell were stably transfected with either a vector control or NDRG1 vector.

value: Cultured cells

value: MIAPaCa-2 pancreatic cancer cells

tag: transfectant

value: NDRG1 transfected


title: hESC H3K27ac (Nimblegen 2.1M HD2 #1)

tag: cell type

value: hESC


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #2)

value: differentiated hESC

tag: chip antibody


title: MIAPaCa-2 control cells (rep 2)

description:
Con 2
Gene expression data from MIAPaCa-2 cells transfected with empty vector control

source_name: MIAPaCa-2 cells vector control

value: vector control


title: Muscle_AQM_6h-4d U11


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #3)

tag: cell line


title: DFC H3K27ac (Nimblegen 2.1M HD2 #3)

tag: chip antibody manufacturer

value: Abcam


title: Muscle_AQM_Control UU9

source_name: gastrocnemius muscle, treated with non-depolarizing neuromuscular blocking agents (NMBA) and mechanically ventilated,control

value: control


title: DFC H3K27ac (Nimblegen 2.1M HD2 #2)

tag: chip antibody catalog #


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #7)


title: hESC H3K27ac (Nimblegen 2.1M HD2 #3)


title: Muscle_AQM_Control UU7


title: MIAPaCa-2 NDRG1 cells (rep 1)

description:
NDRG1 1
Gene expression data from MIAPaCa-2 cells transfected with NDRG1 vector


title: MIAPaCa-2 control cells (rep 1)

description:
Con 1
Gene expression data from MIAPaCa-2 cells transfected with empty vector control


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #11)


title: Muscle_AQM_Control UU5


title: DFC H3K27ac (Nimblegen 2.1M HD2 #9)


title: Muscle_AQM_Control UU3


title: hESC H3K27ac (Nimblegen 2.1M HD2 #9)


title: DFC H3K27ac (Nimblegen 2.1M HD2 #7)


title: Muscle_AQM_Control UU1


title: DFC H3K27ac (Nimblegen 2.1M HD2 #11)


title: Mutant in the presence of tetracycline, rep3

city: Gwangju

first: Byoung-Cheol

last: Lee

address: 1 Oryong-dong Buk-gu

department: Life science

country: South Korea

institute: Gwangju Institutue Science and Technology

description:
Gene expression data from HEK cells expressing mutant TRPM7 channel
Mutant tet3

hyb_protocol: Fragmented cRNA was hybridized to the Human Genome UI133 Plus 2.0 Array (Affymetrix) at 45°C for 16 h according to the Affymetrix standard protocol.

scan_protocol: After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner 3000 (Affymetrix), controlled by GCOS Affymetrix software.

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.

source_name: HEK cell lines expressing mutant channel

label_protocol: 5 ug of total RNA from each cell-lines was used for labeling. Probe synthesis from total RNA samples, hybridization, detection, and scanning were performed according to standard protocols from Affymetrix, Inc..

growth_protocol: Stabel cell-lines were grown in in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and an antibiotic, 5 ug/mL blasticidin (Invitrogen). Cells were cultured in a humidified atmosphere of 5% CO2 at 37 °C.

treatment_protocol: 1 ug of tetracycline was treated to stabel cell-lines which overexressing WT and mutant TRPM7 channel for 72 hours

value: Embryonic kidney cell line HEK

tag: genotype/variation

value: mutant channel

tag: agent

value: tetracycline


title: DFC H3K4me3 Hs35b_P04R


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #8)


title: Mutant in the presence of tetracycline, rep2

description:
Gene expression data from HEK cells expressing mutant TRPM7 channel
Mutant tet2


title: hESC H3K27ac (Nimblegen 2.1M HD2 #7)


title: DFC H3K27me6 (Nimblegen 2.1M HD2 #4)


title: Mutatn in the absence of tetracycline, rep3

description:
Gene expression data from HEK cells non-expressing mutant TRPM7 channel
Mutant no3

source_name: HEK cell lines non-expressing mutant channel

value: untreated


title: hESC H3K27ac (Nimblegen 2.1M HD2 #11)


title: DFC H3K27ac (Nimblegen 2.1M HD2 #8)


title: Mutant in the presence of tetracycline, rep1

description:
Gene expression data from HEK cells expressing mutant TRPM7 channel
Mutant tet1


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 7 a2

value: CTFC

value: in house


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 7 a1


title: hESC H3K27ac (Nimblegen 2.1M HD2 #8)


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #9)

value: Upstate


title: DFC H3K27ac (Nimblegen 2.1M HD2 #4)


title: hESC H3K4me1 Hs35b_P04R

description: H3K4me1 ChIP on H1 hESCs


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 7 a3


title: DFC H3K4me3 Hs35b_P03R


title: Mutant in the absence of tetracycline, rep1

description:
Gene expression data from HEK cells non-expressing mutant TRPM7 channel
Mutant no1


title: DFC H3K4me1 Hs35b_P03R

description: H3K4me1 ChIP on H1 hESCs treated w. BMP4 for 5d


title: Mutant in the absence of tetracycline, rep2

description:
Gene expression data from HEK cells non-expressing mutant TRPM7 channel
Mutant no2


title: hESC H3K4me3 Hs35b_P04R

description: H3K4me3 ChIP on H1 hESCs


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 5 a1


title: WT in the presence of tetracycline, rep2

description:
Gene expression data from HEK cells expressing WT TRPM7 channel
WT tet2

source_name: HEK cell lines expressing WT channel

value: WT channel


title: hESC H3K4me1 Hs35b_P03R

description: H3K4me1 ChIP on H1 hESCs


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #1)


title: hESC H3K27ac (Nimblegen 2.1M HD2 #4)


title: DFC H3K4me1 Hs35b_P04R


title: WT in the presence of tetracycline, rep3

description:
Gene expression data from HEK cells expressing WT TRPM7 channel
WT tet3


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #5)


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 5 a3


title: DFC H3K27ac (Nimblegen 2.1M HD2 #5)


title: hESC H3K4me3 Hs35b_P03R

description: H3K4me3 ChIP on H1 hESCs


title: WT in the presence of tetracycline, rep1

description:
Gene expression data from HEK cells expressing WT TRPM7 channel
WT tet1


title: SAMPLE 229

status: Public on Jul 22 2011

city: Seattle

first: Chu

last: Chen

state: Washington

address: 1100 Fairview Ave. N, PO Box 19024, M/S M5-C800

department: PHS

institute: Fred Hutchinson Cancer Research Center

description: Gene expression data from oral dysplasia tissue

hyb_protocol: The cRNA was hybridized to an Affymetrix U133 2.0 Plus GeneChip arrays per Affymetrix protocols

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip arrays Scanner 3000 7G in the Fred Hutchinson Cancer Research Center's Genomics Shared Resources

data_processing: We used gcRMA algorithm from Bioconductor to extract gene expression values and perform normalization. The data were analyzed using a regression-based, estimating equations approach implemented in GenePlus software. The hierarchical clustering was performed using Affymetrix GeneSpring software GX 7.3.1.

source_name: oral tissue

label_protocol: Biotin-labeled cRNA were prepared from 1.0 to 2.5 ug of total RNA using the GeneChip Expression 3'-Amplification Reagents Kit per manufacturer's protocol

extract_protocol: The RNA and DNA from each specimen were simultaneously extracted using TRIzol method.

tag: status

value: dysplasia

tag: Sex

value: M


title: WT in the absence of tetracycline, rep1

description:
Gene expression data from HEK cells non-expressing WT TRPM7 channel
WT no1

source_name: HEK cell lines non-expressing WT channel


title: WT in the absence of tetracycline, rep3

description:
Gene expression data from HEK cells non-expressing WT TRPM7 channel
WT no3


title: WT in the absence of tetracycline, rep2

description:
Gene expression data from HEK cells non-expressing WT TRPM7 channel
WT no2


title: SAMPLE 228

tag: age


title: SAMPLE 227

value: F


title: SAMPLE 226


title: SAMPLE 224


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 5 a2

source_name: CTCF ChIP DNA

source_name: input DNA


title: SAMPLE 219


title: SAMPLE 225


title: SAMPLE 220


title: Egr1 C

description: custom array design 081105

source_name: Egr1 ChIP DNA from H4IIE cells treated with insulin for 1h

tag: tissue

value: H4IIE liver cells

value: Egr1, Santa Cruz, sc-189

value: WGA-amplified ChIP DNA

tag: treatment

value: treated with insulin for 1h

source_name: Egr1 ChIP DNA from H4IIE cells untreated


title: Egr1 B

description: custom array design 081105

tag: antibody


title: SAMPLE 222


title: SAMPLE 217


title: hESC H3K27ac (Nimblegen 2.1M HD2 #5)

value: hESC

value: Abcam


title: SAMPLE 214


title: SAMPLE 216


title: SAMPLE 215


title: SAMPLE 213


title: hESC H3K27ac (Nimblegen 2.1M HD2 #6)


title: SAMPLE 211

description: Gene expression data from normal oral tissue

value: control


title: SAMPLE 221


title: SAMPLE 210


title: SAMPLE 223


title: SAMPLE 209


title: SAMPLE 203


title: SAMPLE 208


title: SAMPLE 206


title: SAMPLE 202


title: SAMPLE 205


title: SAMPLE 204


title: SAMPLE 218


title: SAMPLE 212


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 1 a2


title: SAMPLE 199


title: SAMPLE 195


title: SAMPLE 207


title: DFC H3K27me3 (Nimblegen 2.1M HD2 #6)

value: differentiated hESC


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 3 a2


title: DFC H3K27ac (Nimblegen 2.1M HD2 #6)


title: SAMPLE 198


title: SAMPLE 200


title: SAMPLE 196


title: SAMPLE 197


title: SAMPLE 192


title: SAMPLE 188


title: SAMPLE 189


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 3 a1


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 1 a1


title: SAMPLE 193


title: SAMPLE 190


title: SAMPLE 194


title: SAMPLE 191


title: SAMPLE 185


title: SAMPLE 187


title: SAMPLE 183


title: SAMPLE 182


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 2 a3


title: SAMPLE 184


title: SAMPLE 181


title: SAMPLE 180


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 2 a1


title: SAMPLE 179


title: SAMPLE 177


title: SAMPLE 176


title: SAMPLE 174


title: SAMPLE 178


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 1 a3


title: SAMPLE 173


title: SAMPLE 171


title: SAMPLE 175


title: SAMPLE 170


title: SAMPLE 168


title: SAMPLE 167

description: Gene expression data from OSCC tissue

value: cancer


title: SAMPLE 165

description: Gene expression data from OSCC tissue


title: SAMPLE 164

description: Gene expression data from OSCC tissue


title: SAMPLE 166

description: Gene expression data from OSCC tissue


title: SAMPLE 172


title: SAMPLE 201


title: SAMPLE 163

description: Gene expression data from OSCC tissue


title: SAMPLE 186


title: SAMPLE 162

description: Gene expression data from OSCC tissue


title: SAMPLE 159

description: Gene expression data from OSCC tissue


title: SAMPLE 161

description: Gene expression data from OSCC tissue


title: SAMPLE 153

description: Gene expression data from OSCC tissue


title: SAMPLE 147

description: Gene expression data from OSCC tissue


title: SAMPLE 158

description: Gene expression data from OSCC tissue


title: SAMPLE 152

description: Gene expression data from OSCC tissue


title: SAMPLE 144

description: Gene expression data from OSCC tissue


title: SAMPLE 151

description: Gene expression data from OSCC tissue


title: SAMPLE 145

description: Gene expression data from OSCC tissue


title: SAMPLE 148

description: Gene expression data from OSCC tissue


title: SAMPLE 157

description: Gene expression data from OSCC tissue


title: SAMPLE 156

description: Gene expression data from OSCC tissue


title: SAMPLE 154

description: Gene expression data from OSCC tissue


title: SAMPLE 138

description: Gene expression data from OSCC tissue


title: SAMPLE 155

description: Gene expression data from OSCC tissue


title: SAMPLE 142

description: Gene expression data from OSCC tissue


title: SAMPLE 160

description: Gene expression data from OSCC tissue


title: SAMPLE 140

description: Gene expression data from OSCC tissue


title: SAMPLE 139

description: Gene expression data from OSCC tissue


title: SAMPLE 169


title: SAMPLE 149

description: Gene expression data from OSCC tissue


title: SAMPLE 150

description: Gene expression data from OSCC tissue


title: SAMPLE 141

description: Gene expression data from OSCC tissue


title: SAMPLE 146

description: Gene expression data from OSCC tissue


title: SAMPLE 137

description: Gene expression data from OSCC tissue


title: SAMPLE 143

description: Gene expression data from OSCC tissue


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 3 a3


title: SAMPLE 133

description: Gene expression data from OSCC tissue


title: SAMPLE 135

description: Gene expression data from OSCC tissue


title: SAMPLE 132

description: Gene expression data from OSCC tissue


title: hESC CTCF NimbleGen Human Whole-Genome Tiling Array Set 2 a2


title: SAMPLE 125

description: Gene expression data from OSCC tissue


title: SAMPLE 130

description: Gene expression data from OSCC tissue


title: SAMPLE 117

description: Gene expression data from OSCC tissue


title: SAMPLE 114

description: Gene expression data from OSCC tissue


title: SAMPLE 123

description: Gene expression data from OSCC tissue


title: SAMPLE 113

description: Gene expression data from OSCC tissue


title: SAMPLE 111

description: Gene expression data from OSCC tissue


title: SAMPLE 126

description: Gene expression data from OSCC tissue


title: SAMPLE 120

description: Gene expression data from OSCC tissue


title: SAMPLE 122

description: Gene expression data from OSCC tissue


title: SAMPLE 124

description: Gene expression data from OSCC tissue


title: SAMPLE 134

description: Gene expression data from OSCC tissue


title: SAMPLE 129

description: Gene expression data from OSCC tissue


title: SAMPLE 136

description: Gene expression data from OSCC tissue


title: SAMPLE 119

description: Gene expression data from OSCC tissue


title: SAMPLE 115

description: Gene expression data from OSCC tissue


title: SAMPLE 121

description: Gene expression data from OSCC tissue


title: SAMPLE 110

description: Gene expression data from OSCC tissue


title: SAMPLE 116

description: Gene expression data from OSCC tissue


title: SAMPLE 127

description: Gene expression data from OSCC tissue


title: SAMPLE 109

description: Gene expression data from OSCC tissue


title: SAMPLE 112

description: Gene expression data from OSCC tissue


title: SAMPLE 131

description: Gene expression data from OSCC tissue


title: SAMPLE 108

description: Gene expression data from OSCC tissue


title: SAMPLE 94

description: Gene expression data from OSCC tissue


title: SAMPLE 101

description: Gene expression data from OSCC tissue


title: SAMPLE 87

description: Gene expression data from OSCC tissue


title: SAMPLE 107

description: Gene expression data from OSCC tissue


title: SAMPLE 104

description: Gene expression data from OSCC tissue


title: SAMPLE 91

description: Gene expression data from OSCC tissue


title: SAMPLE 98

description: Gene expression data from OSCC tissue


title: SAMPLE 95

description: Gene expression data from OSCC tissue


title: SAMPLE 92

description: Gene expression data from OSCC tissue


title: SAMPLE 88

description: Gene expression data from OSCC tissue


title: SAMPLE 102

description: Gene expression data from OSCC tissue


title: SAMPLE 90

description: Gene expression data from OSCC tissue


title: SAMPLE 99

description: Gene expression data from OSCC tissue


title: SAMPLE 89

description: Gene expression data from OSCC tissue


title: SAMPLE 93

description: Gene expression data from OSCC tissue


title: SAMPLE 97

description: Gene expression data from OSCC tissue


title: SAMPLE 83

description: Gene expression data from OSCC tissue


title: SAMPLE 100

description: Gene expression data from OSCC tissue


title: SAMPLE 86

description: Gene expression data from OSCC tissue


title: SAMPLE 106

description: Gene expression data from OSCC tissue


title: SAMPLE 84

description: Gene expression data from OSCC tissue


title: SAMPLE 81

description: Gene expression data from OSCC tissue


title: SAMPLE 96

description: Gene expression data from OSCC tissue


title: SAMPLE 82

description: Gene expression data from OSCC tissue


title: SAMPLE 103

description: Gene expression data from OSCC tissue


title: SAMPLE 85

description: Gene expression data from OSCC tissue


title: SAMPLE 80

description: Gene expression data from OSCC tissue


title: SAMPLE 77

description: Gene expression data from OSCC tissue


title: SAMPLE 73

description: Gene expression data from OSCC tissue


title: SAMPLE 75

description: Gene expression data from OSCC tissue


title: SAMPLE 65

description: Gene expression data from OSCC tissue


title: SAMPLE 63

description: Gene expression data from OSCC tissue


title: SAMPLE 70

description: Gene expression data from OSCC tissue


title: SAMPLE 79

description: Gene expression data from OSCC tissue


title: SAMPLE 74

description: Gene expression data from OSCC tissue


title: SAMPLE 67

description: Gene expression data from OSCC tissue


title: SAMPLE 78

description: Gene expression data from OSCC tissue


title: SAMPLE 76

description: Gene expression data from OSCC tissue


title: SAMPLE 66

description: Gene expression data from OSCC tissue


title: SAMPLE 71

description: Gene expression data from OSCC tissue


title: SAMPLE 128

description: Gene expression data from OSCC tissue


title: SAMPLE 68

description: Gene expression data from OSCC tissue


title: SAMPLE 59

description: Gene expression data from OSCC tissue


title: SAMPLE 55

description: Gene expression data from OSCC tissue


title: SAMPLE 62

description: Gene expression data from OSCC tissue


title: SAMPLE 58

description: Gene expression data from OSCC tissue


title: SAMPLE 60

description: Gene expression data from OSCC tissue


title: SAMPLE 69

description: Gene expression data from OSCC tissue


title: SAMPLE 61

description: Gene expression data from OSCC tissue


title: SAMPLE 72

description: Gene expression data from OSCC tissue


title: SAMPLE 64

description: Gene expression data from OSCC tissue


title: SAMPLE 57

description: Gene expression data from OSCC tissue


title: SAMPLE 54

description: Gene expression data from OSCC tissue


title: SAMPLE 52

description: Gene expression data from OSCC tissue


title: SAMPLE 56

description: Gene expression data from OSCC tissue


title: SAMPLE 51

description: Gene expression data from OSCC tissue


title: SAMPLE 41

description: Gene expression data from OSCC tissue


title: SAMPLE 49

description: Gene expression data from OSCC tissue


title: SAMPLE 45

description: Gene expression data from OSCC tissue


title: SAMPLE 47

description: Gene expression data from OSCC tissue


title: SAMPLE 39

description: Gene expression data from OSCC tissue


title: SAMPLE 44

description: Gene expression data from OSCC tissue


title: SAMPLE 118

description: Gene expression data from OSCC tissue


title: SAMPLE 48

description: Gene expression data from OSCC tissue


title: SAMPLE 36

description: Gene expression data from OSCC tissue


title: SAMPLE 38

description: Gene expression data from OSCC tissue


title: SAMPLE 46

description: Gene expression data from OSCC tissue


title: SAMPLE 43

description: Gene expression data from OSCC tissue


title: SAMPLE 42

description: Gene expression data from OSCC tissue


title: SAMPLE 50

description: Gene expression data from OSCC tissue


title: SAMPLE 40

description: Gene expression data from OSCC tissue


title: SAMPLE 27

description: Gene expression data from OSCC tissue


title: SAMPLE 30

description: Gene expression data from OSCC tissue


title: SAMPLE 33

description: Gene expression data from OSCC tissue


title: SAMPLE 53

description: Gene expression data from OSCC tissue


title: SAMPLE 37

description: Gene expression data from OSCC tissue


title: SAMPLE 35

description: Gene expression data from OSCC tissue


title: SAMPLE 34

description: Gene expression data from OSCC tissue


title: SAMPLE 32

description: Gene expression data from OSCC tissue


title: SAMPLE 25

description: Gene expression data from OSCC tissue


title: SAMPLE 31

description: Gene expression data from OSCC tissue


title: SAMPLE 24

description: Gene expression data from OSCC tissue


title: SAMPLE 28

description: Gene expression data from OSCC tissue


title: SAMPLE 29

description: Gene expression data from OSCC tissue


title: SAMPLE 21

description: Gene expression data from OSCC tissue


title: SAMPLE 26

description: Gene expression data from OSCC tissue


title: SAMPLE 20

description: Gene expression data from OSCC tissue


title: SAMPLE 105

description: Gene expression data from OSCC tissue


title: SAMPLE 16

description: Gene expression data from OSCC tissue


title: SAMPLE 10

description: Gene expression data from OSCC tissue


title: SAMPLE 14

description: Gene expression data from OSCC tissue


title: SAMPLE 13

description: Gene expression data from OSCC tissue


title: SAMPLE 17

description: Gene expression data from OSCC tissue


title: SAMPLE 7

description: Gene expression data from OSCC tissue


title: SAMPLE 11

description: Gene expression data from OSCC tissue


title: SAMPLE 9

description: Gene expression data from OSCC tissue


title: SAMPLE 12

description: Gene expression data from OSCC tissue


title: SAMPLE 6

description: Gene expression data from OSCC tissue


title: SAMPLE 4

description: Gene expression data from OSCC tissue


title: SAMPLE 5

description: Gene expression data from OSCC tissue


title: SAMPLE 23

description: Gene expression data from OSCC tissue


title: SAMPLE 19

description: Gene expression data from OSCC tissue


title: SAMPLE 15

description: Gene expression data from OSCC tissue


title: P49/5mg/kg/W30 (36521)

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 11 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GCOS 1.4 (GeneChip Operating System) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: colonic biopsy

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

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: Colonoscopic punch biopsy was collected from lesions, 15 to 20 cm from the anal verge, and stored in RNAlater at  80oC.

tag: dose

tag: time

tag: subject

tag: wk8 response

value: Yes

tag: wk30 response


title: SAMPLE 2

description: Gene expression data from OSCC tissue


title: SAMPLE 3

description: Gene expression data from OSCC tissue


title: SAMPLE 22

description: Gene expression data from OSCC tissue


title: P47/5mg/kg/W0 (36517)

value: No


title: SAMPLE 8

description: Gene expression data from OSCC tissue


title: P48/Placebo/W0 (36518)

value: placebo


title: P48/Placebo/W30 (36520)


title: P46/Placebo/W30 (36516)


title: P45/5mg/kg/W30 (36513)


title: P46/Placebo/W8 (36515)


title: P42/5mg/kg/W8 (36504)


title: P44/Placebo/W30 (36510)


title: P45/5mg/kg/W0 (36511)


title: Microdissected Lobules_006_Post-treatment_Tamoxifen

first: David

last: Euhus

address: 5323 Harrry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Analysis was performed using GeneSpring 11.0.1 as follows.  Flags were set to present for entities with detection P-values < 0.2 and absent for entities with detection P-values > 0.4.  Raw signal values < 1 were reset to 1. Quantile normalization was used and baseline transformation performed based on the median expression level for all entities. Matrix non-normalized is average raw intensity; Matrix normalized is thresholded, median transformed, and quantile normalized mean intensity. The microdissected lobule data was normalized and processed independent of the whole breast tissue core data.

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

extract_protocol: RNA was extracted from snap frozen breast tissue core samples (Qiazol and the RNeasy Micro Kit, Qiagen) and amplified once, (TargetAmp Biotin-aRNA Amplification Kit, Epicentre Biotechnologies).

tag: subjectid

value: Microdissected Lobules

value: Post-treatment

value: Tamoxifen

value: POST


title: P43/5mg/kg/W0 (36506)


title: P41/10mg/kg/W8 (36503)


title: P44/Placebo/W8 (36509)


title: Microdissected Lobules_021_Baseline_Tamoxifen

value: Baseline

value: PRE


title: Microdissected Lobules_017_Baseline_Tamoxifen


title: P46/Placebo/W0 (36514)


title: P45/5mg/kg/W8 (36512)


title: Microdissected Lobules_003_Baseline_Tamoxifen


title: Microdissected Lobules_057_Post-treatment_Tamoxifen


title: Microdissected Lobules_021_Post-treatment_Tamoxifen


title: P42/5mg/kg/W30 (36505)


title: P44/Placebo/W0 (36508)


title: Microdissected Lobules_003_Post-treatment_Tamoxifen


title: Microdissected Lobules_057_Baseline_Tamoxifen


title: Microdissected Lobules_017_Post-treatment_Tamoxifen


title: P40/5mg/kg/W30 (36501)


title: P41/10mg/kg/W0 (36502)


title: P40/5mg/kg/W8 (36500)


title: Benign Breast Core_060_Baseline_Tamoxifen

source_name: Benign Breast Core,Baseline,Tamoxifen

value: Benign Breast Core


title: Benign Breast Core_060_Post-treatment_Tamoxifen


title: Microdissected Lobules_006_Baseline_Tamoxifen


title: P40/5mg/kg/W0 (36499)


title: Benign Breast Core_058_Baseline_Placebo

source_name: Benign Breast Core,Baseline,Placebo

value: Placebo


title: Benign Breast Core_058_Post-treatment_Placebo


title: P36/10mg/kg/W30 (36473)


title: P36/10mg/kg/W8 (36472)


title: Benign Breast Core_025_Post-treatment_Tamoxifen


title: Benign Breast Core_057_Post-treatment_Tamoxifen


title: P35/Placebo/W30 (36470)


title: P38/5mg/kg/W8 (36494)


title: Benign Breast Core_057_Baseline_Tamoxifen


title: Benign Breast Core_041_Baseline_Tamoxifen


title: P36/10mg/kg/W0 (36471)


title: P39/Placebo/W0 (36497)


title: Benign Breast Core_022_Post-treatment_Placebo


title: P38/5mg/kg/W0 (36493)


title: P38/5mg/kg/W30 (36495)


title: Benign Breast Core_041_Post-treatment_Tamoxifen


title: SAMPLE 18

description: Gene expression data from OSCC tissue

value: M


title: P35/Placebo/W0 (36469)


title: P34/10mg/kg/W8 (36467)


title: P34/10mg/kg/W30 (36468)


title: P33/5mg/kg/W8 (36465)


title: P48/Placebo/W8 (36519)


title: Benign Breast Core_025_Baseline_Tamoxifen


title: Benign Breast Core_062_Baseline_Placebo


title: Benign Breast Core_022_Baseline_Placebo


title: Benign Breast Core_062_Post-treatment_Placebo


title: P33/5mg/kg/W0 (36464)


title: Benign Breast Core_052_Post-treatment_Tamoxifen


title: Benign Breast Core_047_Post-treatment_Placebo


title: Benign Breast Core_047_Baseline_Placebo


title: SAMPLE 1

description: Gene expression data from OSCC tissue

value: F


title: Benign Breast Core_052_Baseline_Tamoxifen


title: P32/10mg/kg/W8 (36463)


title: Benign Breast Core_045_Post-treatment_Tamoxifen


title: P30/Placebo/W0 (36459)


title: Benign Breast Core_1000_Post-treatment_Placebo


title: Benign Breast Core_1000_Baseline_Placebo


title: P32/10mg/kg/W0 (36462)


title: P30/Placebo/W30 (36460)


title: Benign Breast Core_038_Baseline_Tamoxifen


title: P31/Placebo/W8 (36461)


title: P29/5mg/kg/W8 (36457)


title: Benign Breast Core_038_Post-treatment_Tamoxifen


title: P29/5mg/kg/W0 (36456)


title: Benign Breast Core_045_Baseline_Tamoxifen


title: P28/10mg/kg/W30 (36455)


title: Benign Breast Core_037_Post-treatment_Placebo


title: Benign Breast Core_021_Post-treatment_Tamoxifen


title: Benign Breast Core_013_Baseline_Placebo


title: Benign Breast Core_037_Baseline_Placebo


title: Benign Breast Core_013_Post-treatment_Placebo


title: P28/10mg/kg/W0 (36453)


title: Benign Breast Core_021_Baseline_Tamoxifen


title: P28/10mg/kg/W8 (36454)


title: Benign Breast Core_001_Baseline_Tamoxifen


title: Benign Breast Core_001_Post-treatment_Tamoxifen


title: P27/10mg/kg/W30 (36452)


title: P27/10mg/kg/W8 (36451)


title: P25/Placebo/W30 (36446)


title: P27/10mg/kg/W0 (36450)


title: P24/10mg/kg/W8 (36442)


title: P24/10mg/kg/W30 (36443)


title: Benign Breast Core_059_Baseline_Placebo


title: Benign Breast Core_056_Post-treatment_Placebo


title: Benign Breast Core_059_Post-treatment_Placebo


title: P25/Placebo/W8 (36445)


title: P26/Placebo/W0 (36447)


title: P25/Placebo/W0 (36444)


title: P26/Placebo/W30 (36448)


title: P29/5mg/kg/W30 (36458)


title: Benign Breast Core_042_Baseline_Tamoxifen


title: Benign Breast Core_056_Baseline_Placebo


title: Benign Breast Core_042_Post-treatment_Tamoxifen


title: Benign Breast Core_032_Post-treatment_Placebo


title: Benign Breast Core_032_Baseline_Placebo


title: P23/5mg/kg/W8 (36439)


title: Benign Breast Core_024_Baseline_Tamoxifen


title: P24/10mg/kg/W0 (36441)


title: P23/5mg/kg/W30 (36440)


title: P22/10mg/kg/W30 (36438)


title: Benign Breast Core_017_Post-treatment_Tamoxifen


title: Benign Breast Core_015_Post-treatment_Placebo


title: Benign Breast Core_024_Post-treatment_Tamoxifen


title: P22/10mg/kg/W0 (36437)


title: Benign Breast Core_017_Baseline_Tamoxifen


title: P19/10mg/kg/W0 (36430)


title: P20/Placebo/W30 (36434)


title: P20/Placebo/W0 (36433)


title: Benign Breast Core_027_Baseline_Tamoxifen


title: P19/10mg/kg/W30 (36432)


title: P19/10mg/kg/W8 (36431)


title: P21/10mg/kg/W0 (36435)


title: Benign Breast Core_004_Baseline_Placebo


title: Benign Breast Core_015_Baseline_Placebo


title: Benign Breast Core_006_Post-treatment_Tamoxifen


title: P18/Placebo/W30 (36429)


title: Benign Breast Core_027_Post-treatment_Tamoxifen


title: Benign Breast Core_006_Baseline_Tamoxifen


title: P21/10mg/kg/W30 (36436)


title: P18/Placebo/W8 (36427)


title: P18/Placebo/W0 (36426)


title: Benign Breast Core_003_Baseline_Tamoxifen


title: Benign Breast Core_004_Post-treatment_Placebo


title: P16/5mg/kg/W8 (36420)


title: P17/10mg/kg/W8 (36424)


title: P34/10mg/kg/W0 (36466)


title: Benign Breast Core_040_Post-treatment_Tamoxifen


title: Benign Breast Core_026_Post-treatment_Tamoxifen


title: Benign Breast Core_003_Post-treatment_Tamoxifen


title: P17/10mg/kg/W30 (36425)


title: Benign Breast Core_040_Baseline_Tamoxifen


title: P17/10mg/kg/W0 (36423)


title: Benign Breast Core_026_Baseline_Tamoxifen


title: Benign Breast Core_029_Post-treatment_Placebo


title: P16/5mg/kg/W0 (36419)


title: Benign Breast Core_035_Baseline_Placebo


title: P15/10mg/kg/W30 (36417)


title: Benign Breast Core_035_Post-treatment_Placebo


title: P14/5mg/kg/W8 (36414)


title: Benign Breast Core_028_Post-treatment_Placebo


title: Benign Breast Core_053_Baseline_Tamoxifen


title: Benign Breast Core_028_Baseline_Placebo


title: Benign Breast Core_053_Post-treatment_Tamoxifen


title: P14/5mg/kg/W0 (36413)


title: P13/5mg/kg/W8 (36387)


title: P15/10mg/kg/W0 (36415)


title: P13/5mg/kg/W0 (2) (36386)


title: Benign Breast Core_030_Baseline_Placebo


title: Benign Breast Core_031_Post-treatment_Tamoxifen


title: Benign Breast Core_030_Post-treatment_Placebo


title: P12/5mg/kg/W0 (36384)


title: Benign Breast Core_029_Baseline_Placebo


title: Benign Breast Core_031_Baseline_Tamoxifen


title: P11/10mg/kg/W8 (36383)


title: P15/10mg/kg/W8 (36416)


title: P13/5mg/kg/W0 (36385)


title: P10/10mg/kg/W8 (36380)


title: P11/10mg/kg/W0 (36382)


title: P10/10mg/kg/W0 (36379)


title: Cdc45-IP_alpha_factor_wt, Replicate 1

city: Cambridge

first: Stephen

middle: P

last: Bell

state: MA

address: 68-630, 77 Massachusetts Ave.

department: Biology

institute: MIT

description:
Cdc45-myc CDC7wt.1
Cdc45-myc ChIP in wild-type CDC7 cells arrested in G1 at 25°C.

hyb_protocol: Standard Agilent hybridization and wash protocols.

scan_protocol: Agilent scanner.

data_processing: For each cohybridization, Cy3 and Cy5 levels were calculated using Agilent Feature Extractor CGH software. Log2 ratios for each experiment and scale normalizations across each set of duplicated experiments were calculated using the sma package (Yang et al. 2002) in R, a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

organism: Saccharomyces cerevisiae

source_name: Cdc45-myc ChIP, anti-Myc antibody, CDC7 cells

label_protocol: Half of the immunoprecipitated DNA and 5 μg of ChIP input DNA were differentially labeled with 2 nmol of either Cy3-dUTP or Cy5-dUTP (GE Healthcare) using 4 μg random nonomer oligo (IDT) and 0.5 μl 50,000 u/ml Klenowexo- (NEB) in 40 μl. IP and input samples were mixed after labeling and unincorporated dyes were removed using a microcon filter (Millipore YM-30) by washing the samples three times with 0.4 ml TE.

growth_protocol: Cells were grown in YPD at 25 degrees to log phase.

extract_protocol: ChIP assays were performed as described previously (Aparicio et al., 1997 (PMID 9335335)). 50 ml of culture was collected for each ChIP sample. Half of the resulting cell lysate was used for a Cdc45-13Myc IP using an anti-Myc monoclonal antibody (9E11; Abcam ab56).

treatment_protocol: Log-phase cells were arrested in alpha-factor for three hours prior to ChIP analysis.

tag: background/strain

tag: genotype

value: wild type

tag: cell cycle phase

tag: chip antibody

value: anti-Myc monoclonal antibody (9E11)

tag: antibody vendor

value: Abcam

tag: antibody catalog number

tag: antibody lot number

source_name: ChIP input DNA, CDC7 cells


title: Cdc45-IP_alpha_factor_wt, Replicate 2

description:
Cdc45-myc CDC7wt.2
Cdc45-myc ChIP in wild-type CDC7 cells arrested in G1 at 25°C.


title: Cdc45-IP_alpha_factor_cdc7-4, Replicate 2

description:
Cdc45-myc cdc7-4.2
Cdc45-myc ChIP in cdc7-4 cells arrested in G1 at 25°C.

source_name: Cdc45-myc ChIP, anti-Myc antibody, cdc7-4 cells

source_name: ChIP input DNA, cdc7-4 cells


title: P10/10mg/kg/W30 (36381)


title: Cdc45-IP_alpha_factor_cdc7-4, Replicate 1

description:
Cdc45-myc cdc7-4.1
Cdc45-myc ChIP in cdc7-4 cells arrested in G1 at 25°C.


title: P9/5mg/kg/W8 (36377)


title: Distal lung fibroblasts_NC9

city: Pittsburgh

first: XIUXIA

last: ZHOU

address: 3459 fifth ave

department: Medicine

institute: University of Pittsburgh

hyb_protocol: Cy3 labeled cRNA was hybridized to Agilent 4X44K Whole Human Genome Microarrays

scan_protocol: The hybridized slides were scanned with Agilent scanner (Agilent Technologies, Santa, Clara, CA) as recommended by the manufacturer and previously described

data_processing: The data were extracted using Agilent Feature Extraction software. The generation of the gene expression data was performed as described.  For analysis we filtered out genes that did not pass manufacturer recommendation for quality control.

source_name: Distal lung fibroblasts

label_protocol: Complementary RNA (cRNA) labeled with the Cy3 fluorescent dye was generated

growth_protocol: Endo- and transbronchial biopsy lung tissue was processed as described before. Briefly, the biopsy pieces were cultured until fibroblasts grown out from the tissue. Fibroblasts were passed to the next passage during the proliferate state, and only third or 4th passage primary AF or DLF were plated in 24 or 6 well plates and grown to near confluence in DMEM/10% FBS. To compare the differences between AF and DLF, parallel experiments were performed on paired fibroblasts (AF compared with DLF from the same subject). Following serum starvation for 24 hours, grow the cells in DMEM and the cells and supernatants harvested at various time points depending on the experiment. Although samples from a total of 18 subjects were utilized in the study, samples varied for each individual experiment on the basis of availability of cells.

extract_protocol: Total RNA in Trizol was extracted from cultured fibroblasts using Qiagen RNeasy kit (Qiagen Inc. Valencia, CA).

treatment_protocol: third passage cultured matched pairs of AF and DLF were grown to 80% confluency, serum deprived for 24 hours and continue to grow for 15 hours.

value: lung

tag: disease state

value: normal


title: Distal lung fibroblasts_NLD1

tag: tissue


title: Airway fibroblasts_NC9

source_name: Airway fibroblasts


title: P9/5mg/kg/W30 (36378)

value: Yes


title: P6/Placebo/W8 (36369)

value: placebo

value: No


title: Airway fibroblasts_865I

value: asthmatic


title: P6/Placebo/W30 (36370)


title: Airway fibroblasts_NLD1


title: Airway fibroblasts_NC3.31.05


title: P7/Placebo/W0 (36371)


title: P9/5mg/kg/W0 (36376)


title: Airway fibroblasts_NC7


title: P8/Placebo/W0 (36373)


title: P6/Placebo/W0 (36368)


title: Distal lung fibroblasts_NC3.31.05


title: P5/10mg/kg/W30 (36367)


title: P8/Placebo/W8 (36374)


title: P7/Placebo/W8 (36372)


title: P5/10mg/kg/W0 (36366)


title: Distal lung fibroblasts_1257Q


title: Distal lung fibroblasts_283B


title: Distal lung fibroblasts_865I


title: Airway fibroblasts_283B


title: P4/10mg/kg/W0 (36364)


title: P4/10mg/kg/W8 (36365)


title: Distal lung fibroblasts_1226S


title: Airway fibroblasts_1226S


title: P3/5mg/kg/W0 (36362)


title: P3/5mg/kg/W8 (36363)


title: Airway fibroblasts_1257Q


title: P2/10mg/kg/W30 (36361)


title: P2/10mg/kg/W8 (36360)


title: Airway fibroblasts_1084L


title: Airway fibroblasts_0944E


title: Distal lung fibroblasts_0944E


title: P1/5mg/kg/W0 (36357)


title: P1/5mg/kg/W8 (36358)


title: Airway fibroblasts_0021X


title: Airway fibroblasts_0349Q


title: Distal lung fibroblasts_1084L


title: Distal lung fibroblasts_0349Q


title: Distal lung fibroblasts_0021X


title: AirwayFibroblast_1257Q

hyb_protocol: Cy5 labeled cRNA was hybridized to Agilent 4X44K Whole Human Genome Microarrays

data_processing:
The data were extracted using Agilent Feature Extraction software. The generation of the gene expression data was performed as described.  For analysis we filtered out genes that did not pass manufacturer recommendation for quality control.
Normalized/processed_data: Raw microarray data were preprocessed using a protocol previously described (Wu, et al. Physiol Genomics 36(1):24-34, 2008). The processed microarray data was log2-transformed, and normalized using a statistical method CyclicLoess to minimize unwanted noise in the data. The log2-transformed, normalized data were used as input to the downstream computational analyses.

source_name: Airway fibroblast

label_protocol: Complementary RNA (cRNA) labeled with the Cy5 fluorescent dye was generated


title: DistalLungFibroblast_1257Q

source_name: Distal lung fibroblast


title: P2/10mg/kg/W0 (36359)


title: PTC1_SDD (rep1)

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

country: Japan

institute: National Food Rsearch Institute

description: Gene expression data from S. cerevisiae PTC1 mutant yeast strain grown in YPD with chemicals

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: CEL files were normalized with MAS5. Signals were calculated by Affymetrix GeneChip Operating Software Version 1.4. Benjamini-Hochberg was used as multiple testing correction.

source_name: PTC1 with SDS and DON

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets using Affymetrix 3' IVT Express kit.

growth_protocol: Precultured yeast mutant strain (OD650 = ~0.9) was diluted 100 times by YPD media with 0.01% SDS, and then incubated for 1-2 days at 25 °C.

extract_protocol: Each sample of total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Both strains were grown in YPD medium including 0.01% SDS, or 0.01% SDS with 50 ppm deoxynivalenol.

tag: growth protocol

value: SDS and DON


title: DistalLungFibroblast_0944E


title: AirwayFibroblast_0944E


title: P16/5mg/kg/W30 (36421)


title: PTC1_SDD (rep3)


title: PTC1_SDD (rep2)


title: PTC1_SD (rep2)

source_name: PTC1 with SDS

value: SDS


title: AirwayFibroblast_0349Q


title: DistalLungFibroblast_0349Q


title: PTC1_SD (rep1)


title: PTC1_SD (rep3)


title: Distal lung fibroblasts_NC7


title: AKXD subline 9 biological rep_2 [MOE430B]

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

state: MD

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2710sub9B

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit: (Affymetrix, P/N 900720) following manufacture’s protocol for One-Cycle cDNA Synthesis Kit Protocol for Eukaryotic Target Prepartion, Affymetrix)

scan_protocol: GCOSv1.4, Affymetrix Fluidics Station 450 (FS450_0001), Gene ChIP Scanner 3000 7G

data_processing: GCOSv1.4, Scaling: default (500), Normalization: User defined=1, RMA normalization using BioConductor

organism: Mus musculus

source_name: AKXD subline 9

label_protocol: GeneChip® One-Cycle Target Labeling and Control Reagents (Affymetrix, P/N 900493) following manufacture’s protocol.

extract_protocol: Trizol (Invitrogen), following manufacturers protocol, RNeasy Mini Kit (Qiagen)

tag: strain background

value: AKXD x PyMT

value: AKXD x PyMT mammary tumor


title: AKXD subline 28 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2815sub28B

source_name: AKXD subline 28


title: AKXD subline 9 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2685sub9B


title: AKXD subline 9 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2949sub9B


title: AKXD subline 28 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2809sub28B


title: AKXD subline 7 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2543sub7B

source_name: AKXD subline 7


title: AKXD subline 3 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3446sub3B

source_name: AKXD subline 3


title: AKXD subline 3 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD4225sub3B


title: AKXD subline 7 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3336sub7B


title: AKXD subline 28 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3432sub28B


title: AKXD subline 3 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1747sub3B


title: AKXD subline 7 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2967sub7B


title: AKXD subline 27 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1757sub27B

source_name: AKXD subline 27


title: AKXD subline 25 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2326sub25B

source_name: AKXD subline 25


title: AKXD subline 27 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1756sub27B


title: AKXD subline 27 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2968sub27B


title: AKXD subline 25 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2328sub25B


title: AKXD subline 25 biological rep_4 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2629sub25B


title: AKXD subline 25 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1607sub25B


title: AKXD subline 24 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1880sub24B

source_name: AKXD subline 24


title: AKXD subline 23 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3955sub23B

source_name: AKXD subline 23


title: AKXD subline 24 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1494sub24B


title: AKXD subline 22 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2461sub22B

source_name: AKXD subline 22


title: AKXD subline 21 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2918sub21B

source_name: AKXD subline 21


title: AKXD subline 24 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3030sub24B


title: AKXD subline 23 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2976sub23B


title: AKXD subline 22 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2460sub22B


title: AKXD subline 2 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2957sub2B

source_name: AKXD subline 2


title: AKXD subline 20 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2554sub20B

source_name: AKXD subline 20


title: AKXD subline 2 biological rep_4 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2959sub2B


title: AKXD subline 21 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2611sub21B


title: AKXD subline 18 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2804sub18B

source_name: AKXD subline 18


title: AKXD subline 2 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1948sub2B


title: AKXD subline 20 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2456sub20B


title: AKXD subline 16 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1636sub16B

source_name: AKXD subline 16


title: AKXD subline 20 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2829sub20B


title: AKXD subline 14 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2632sub14B

source_name: AKXD subline 14


title: AKXD subline 18 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1647sub18B


title: AKXD subline 2 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1950sub2B


title: AKXD subline 18 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2616sub18B


title: AKXD subline 21 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1610sub21B


title: AKXD subline 16 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD4152sub16B


title: AKXD subline 14 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3444sub14B


title: AKXD subline 14 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2640sub14B


title: AKXD subline 22 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2463sub22B


title: AKXD subline 13 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2721sub13B

source_name: AKXD subline 13


title: AKXD subline 16 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3688sub16B


title: AKXD subline 11 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2824sub11B

source_name: AKXD subline 11


title: AKXD subline 13 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2718sub13B


title: AKXD subline 11 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD1910sub11B


title: AKXD subline 11 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2825sub11B


title: AKXD subline 10 biological rep_2 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2620sub10B

source_name: AKXD subline 10


title: AKXD subline 10 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2618sub10B


title: AKXD subline 9 biological rep_2 [MOE430A]

description:
AKXD2710sub9A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 9

growth_protocol: Spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 23 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2975sub23B


title: AKXD subline 10 biological rep_3 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD3023sub10B


title: AKXD subline 9 biological rep_3 [MOE430A]

description:
AKXD2949sub9A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 7 biological rep_3 [MOE430A]

description:
AKXD3336sub7A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 7


title: AKXD subline 7 biological rep_2 [MOE430A]

description:
AKXD2967sub7A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 3 biological rep_1 [MOE430A]

description:
AKXD1747sub3A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 3


title: AKXD subline 3 biological rep_2 [MOE430A]

description:
AKXD3446sub3A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 7 biological rep_1 [MOE430A]

description:
AKXD2543sub7A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 9 biological rep_1 [MOE430A]

description:
AKXD2685sub9A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 3 biological rep_3 [MOE430A]

description:
AKXD4225sub3A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 28 biological rep_3 [MOE430A]

description:
AKXD3432sub28A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 28


title: AKXD subline 27 biological rep_2 [MOE430A]

description:
AKXD1757sub27A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 27


title: AKXD subline 27 biological rep_3 [MOE430A]

description:
AKXD2968sub27A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 27 biological rep_1 [MOE430A]

description:
AKXD1756sub27A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 28 biological rep_2 [MOE430A]

description:
AKXD2815sub28A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 25 biological rep_4 [MOE430A]

description:
AKXD2629sub25A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 25


title: AKXD subline 25 biological rep_2 [MOE430A]

description:
AKXD2326sub25A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 25 biological rep_3 [MOE430A]

description:
AKXD2328sub25A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 22 biological rep_2 [MOE430A]

description:
AKXD2461sub22A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 24 biological rep_2 [MOE430A]

description:
AKXD1880sub24A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 24


title: AKXD subline 23 biological rep_2 [MOE430A]

description:
AKXD2976sub23A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 23


title: AKXD subline 28 biological rep_1 [MOE430A]

description:
AKXD2809sub28A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 22 biological rep_3 [MOE430A]

description:
AKXD2463sub22A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 22


title: AKXD subline 13 biological rep_1 [MOE430B]

description:
Spontaneous mammary tumors induced by MMTV-PyMT transgene
AKXD2635sub13B


title: AKXD subline 25 biological rep_1 [MOE430A]

description:
AKXD1607sub25A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 23 biological rep_3 [MOE430A]

description:
AKXD3955sub23A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 24 biological rep_3 [MOE430A]

description:
AKXD3030sub24A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 23 biological rep_1 [MOE430A]

description:
AKXD2975sub23A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 21 biological rep_3 [MOE430A]

description:
AKXD2918sub21A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 21


title: AKXD subline 22 biological rep_1 [MOE430A]

description:
AKXD2460sub22A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 24 biological rep_1 [MOE430A]

description:
AKXD1494sub24A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 21 biological rep_2 [MOE430A]

description:
AKXD2611sub21A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep13

city: Bethesda

first: Mark

last: Cookson

address: 35 CONVENT DR RM 1A116

department: Lab of Neuorgenetics

institute: NIA, NIH

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Illumina BeadStudio software suite: quantile normalization with background subtraction on a per brain region basis to generate expression values for each probe.

source_name: Brain tissue (medulla), PD

label_protocol: RNA was amplified using the Illumina TotalPrep RNA amplification kit, resulting in biotin-labeled cRNA.

extract_protocol: RNA from different brain regions was extracted from flash-frozen tissue using Trizol (Invitrogen) and stored at -80°C until use.

value: brain

tag: brain region

value: medulla

value: Parkinson's disease

tag: gender

value: female

tag: age

tag: individual identifier

value: IPD 14


title: PD_brain_MED_rep14

value: IPD 15


title: AKXD subline 20 biological rep_1 [MOE430A]

description:
AKXD2456sub20A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 20


title: PD_brain_MED_rep12

value: male

value: IPD 13


title: AKXD subline 2 biological rep_4 [MOE430A]

description:
AKXD2959sub2A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 2


title: AKXD subline 20 biological rep_2 [MOE430A]

description:
AKXD2554sub20A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 20 biological rep_3 [MOE430A]

description:
AKXD2829sub20A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep11

value: IPD 12


title: AKXD subline 2 biological rep_1 [MOE430A]

description:
AKXD1948sub2A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep10

value: IPD 11


title: AKXD subline 2 biological rep_2 [MOE430A]

description:
AKXD1950sub2A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 16 biological rep_2 [MOE430A]

description:
AKXD3688sub16A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 16


title: AKXD subline 2 biological rep_3 [MOE430A]

description:
AKXD2957sub2A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep7

value: IPD 8


title: PD_brain_MED_rep6

value: IPD 7


title: AKXD subline 18 biological rep_1 [MOE430A]

description:
AKXD1647sub18A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 18


title: AKXD subline 16 biological rep_3 [MOE430A]

description:
AKXD4152sub16A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep3

value: IPD 4


title: AKXD subline 18 biological rep_2 [MOE430A]

description:
AKXD2616sub18A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep9

value: IPD 10


title: PD_brain_MED_rep4

value: IPD 5


title: PD_brain_MED_rep2

value: IPD 3


title: AKXD subline 18 biological rep_3 [MOE430A]

description:
AKXD2804sub18A
spontaneous mammary tumors induced by MMTV-PyMT transgene

value: AKXD x PyMT

value: AKXD x PyMT mammary tumor


title: AKXD subline 21 biological rep_1 [MOE430A]

description:
AKXD1610sub21A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep15

source_name: Brain tissue (medulla), control

value: brain

value: medulla

value: control

value: Control 21


title: PD_brain_MED_rep1

value: Parkinson's disease

value: female

value: IPD 1


title: PD_brain_MED_rep5

value: IPD 6


title: AKXD subline 14 biological rep_3 [MOE430A]

description:
AKXD3444sub14A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 14


title: AKXD subline 16 biological rep_1 [MOE430A]

description:
AKXD1636sub16A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 13 biological rep_2 [MOE430A]

description:
AKXD2718sub13A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 13


title: Control_brain_MED_rep12

value: Control 15


title: AKXD subline 13 biological rep_3 [MOE430A]

description:
AKXD2721sub13A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep11

value: Control 14


title: Control_brain_MED_rep14

value: Control 20


title: Control_brain_MED_rep13

value: Control 17


title: AKXD subline 11 biological rep_3 [MOE430A]

description:
AKXD2825sub11A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 11


title: AKXD subline 13 biological rep_1 [MOE430A]

description:
AKXD2635sub13A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep9

value: male

value: Control 12


title: AKXD subline 11 biological rep_2 [MOE430A]

description:
AKXD2824sub11A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 14 biological rep_2 [MOE430A]

description:
AKXD2640sub14A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: PD_brain_MED_rep8

value: IPD 9


title: Control_brain_MED_rep10

value: Control 13


title: Control_brain_MED_rep7

value: Control 9


title: AKXD subline 10 biological rep_3 [MOE430A]

description:
AKXD3023sub10A
spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: AKXD subline 10

value: AKXD x PyMT

value: AKXD x PyMT mammary tumor


title: AKXD subline 14 biological rep_1 [MOE430A]

description:
AKXD2632sub14A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep5

value: brain

value: medulla

value: control

value: Control 6


title: AKXD subline 11 biological rep_1 [MOE430A]

description:
AKXD1910sub11A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep6

value: Control 8


title: Control_brain_MED_rep3

value: Control 4


title: Control_brain_MED_rep8

value: female

value: Control 11


title: Control_brain_MED_rep4

value: Control 5


title: NZB Backcross animal 5000

description: Spontaneous mammary tumors induced by MMTV-PyMT transgene

source_name: PyMT-induced mammary tumor

value: ((NZB x PyMT) x FVB) backcross

value: NZB x PyMT backcross mammary tumor


title: AKXD subline 10 biological rep_1 [MOE430A]

description:
AKXD2618sub10A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: AKXD subline 10 biological rep_2 [MOE430A]

description:
AKXD2620sub10A
spontaneous mammary tumors induced by MMTV-PyMT transgene


title: Control_brain_MED_rep1

value: male

value: Control 1


title: PD_brain_STR_rep15

source_name: Brain tissue (striatum), PD

value: striatum

value: Parkinson's disease

value: IPD 15


title: NZB Backcross animal 4980


title: Control_brain_MED_rep2

value: Control 2


title: PD_brain_STR_rep13

value: brain

value: IPD 13


title: NZB Backcross animal 4975


title: NZB Backcross animal 4967


title: NZB Backcross animal 4973


title: NZB Backcross animal 4978


title: PD_brain_STR_rep9

value: IPD 9


title: PD_brain_STR_rep10

value: IPD 10


title: NZB Backcross animal 4963


title: NZB Backcross animal 4979R


title: PD_brain_STR_rep14

value: IPD 14


title: NZB Backcross animal 4971


title: PD_brain_STR_rep8

value: IPD 8


title: PD_brain_STR_rep11

value: IPD 11


title: PD_brain_STR_rep12

value: female

value: IPD 12


title: NZB Backcross animal 4966

value: ((NZB x PyMT) x FVB) backcross


title: NZB Backcross animal 4977

value: NZB x PyMT backcross mammary tumor


title: PD_brain_STR_rep5

value: male

value: IPD 5


title: NZB Backcross animal 4960


title: PD_brain_STR_rep3

value: striatum

value: IPD 3


title: PD_brain_STR_rep7

value: Parkinson's disease

value: IPD 7


title: NZB Backcross animal 4956


title: PD_brain_STR_rep4

value: brain

value: IPD 4


title: PD_brain_STR_rep1

value: IPD 1


title: PD_brain_STR_rep2

value: IPD 2


title: Control_brain_STR_rep15

source_name: Brain tissue (striatum), control

value: control

value: Control 22


title: NZB Backcross animal 3890R


title: NZB Backcross animal 3868


title: NZB Backcross animal 4950


title: NZB Backcross animal 4946


title: NZB Backcross animal 3891


title: NZB Backcross animal 4955


title: Control_brain_STR_rep14

value: Control 20


title: PD_brain_STR_rep6

value: female

value: IPD 6


title: NZB Backcross animal 3867

value: ((NZB x PyMT) x FVB) backcross


title: NZB Backcross animal 3864

value: NZB x PyMT backcross mammary tumor


title: NZB Backcross animal 4958


title: NZB Backcross animal 4957R


title: Control_brain_STR_rep10

value: Control 14


title: Control_brain_STR_rep13

value: Control 19


title: Control_brain_STR_rep11

value: striatum

value: Control 17


title: Control_brain_STR_rep12

value: Control 18


title: NZB Backcross animal 3855


title: NZB Backcross animal 3854R


title: Control_brain_STR_rep8

value: male

value: Control 10


title: Control_brain_STR_rep9

value: brain

value: Control 11


title: NZB Backcross animal 3853


title: Control_brain_STR_rep7

value: Control 9


title: NZB Backcross animal 3827


title: NZB Backcross animal 3852R


title: NZB Backcross animal 3825


title: NZB Backcross animal 3830R


title: Control_brain_STR_rep4

value: control

value: Control 5


title: Control_brain_STR_rep6

value: Control 8


title: NZB Backcross animal 3739


title: NZB Backcross animal 3824


title: Control_brain_STR_rep5

value: Control 7


title: NZB Backcross animal 3769


title: NZB Backcross animal 3570


title: Control_brain_STR_rep3

value: Control 3


title: NZB Backcross animal 3738

value: ((NZB x PyMT) x FVB) backcross


title: Control_brain_STR_rep2

value: Control 2


title: NZB Backcross animal 3572

value: NZB x PyMT backcross mammary tumor


title: NZB Backcross animal 3568


title: PD_brain_CB_rep15

source_name: Brain tissue (cerebellum), PD

value: cerebellum

value: Parkinson's disease

value: female

value: IPD 15


title: PD_brain_CB_rep12

value: IPD 12


title: Control_brain_STR_rep1

value: striatum

value: male

value: Control 1


title: PD_brain_CB_rep14

value: brain

value: IPD 14


title: NZB Backcross animal 3567


title: NZB Backcross animal 3569


title: PD_brain_CB_rep7

value: IPD 7


title: PD_brain_CB_rep8

value: IPD 8


title: PD_brain_CB_rep11

value: IPD 11


title: PD_brain_CB_rep9

value: IPD 9


title: PD_brain_CB_rep6

value: IPD 6


title: NZB Backcross animal 3546

value: ((NZB x PyMT) x FVB) backcross


title: NZB Backcross animal 3547

value: NZB x PyMT backcross mammary tumor


title: PD_brain_CB_rep10

value: cerebellum

value: IPD 10


title: PD_brain_CB_rep13

value: Parkinson's disease

value: IPD 13


title: NZB Backcross animal 3548


title: NZB Backcross animal 3550


title: NZB Backcross animal 3394


title: PD_brain_CB_rep4

value: female

value: IPD 4


title: NZB Backcross animal 3397


title: PD_brain_CB_rep2

value: IPD 2


title: NZB Backcross animal 3353


title: PD_brain_CB_rep1

value: IPD 1


title: PD_brain_CB_rep3

value: brain

value: male

value: IPD 3


title: NZB Backcross animal 3355


title: PD_brain_CB_rep5

value: IPD 5


title: Control_brain_CB_rep14

source_name: Brain tissue (cerebellum), control

value: control

value: Control 22


title: NZB Backcross animal 3351R


title: Control_brain_CB_rep13

value: Control 20


title: NZB Backcross animal 3299R

value: ((NZB x PyMT) x FVB) backcross


title: NZB Backcross animal 3351

value: NZB x PyMT backcross mammary tumor


title: Control_brain_CB_rep12

value: cerebellum

value: Control 19


title: NZB Backcross animal 3291


title: NZB Backcross animal 3296


title: Control_brain_CB_rep7

value: Control 11


title: NZB Backcross animal 3295


title: Control_brain_CB_rep9

value: Control 16