title: HV3-20-53CGH

description: male DNA

source_name: LNCaP


title: HV3-20-58CGH

status: Public on Oct 23 2007

type: genomic

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

country: USA

institute: National Cancer Institute

description: DU145 NIH

hyb_protocol: DNA samples were hybridized onto the array for 16-18 hours at 42°C utilizing the MAUI 4-bay hybridization system and MAUI Mixer A0 (BioMicro System, Salt Lake City, UT, USA). After hybridization arrays and MAUI Mixer were disassembled in 42°C 1xSSC and 0.05% SDS (wash solution 1) and subsequently washed two times in wash solution 1 for 5 minutes followed by two washes in 0.1xSSC (wash solution 2) for 5 minutes.

scan_protocol: Dried array slides were scanned using a ScanLite Express microarray scanner (Perkin Elmer, Wellesley, MA, USA). Raw image files of the arrays were processed using DeArray software (Chen et al, 1997) and resulting image data were imported into R environment using bioconductor packages (Gentleman RC et al., 2004) for further analysis.

data_processing: Loess normalization

molecule: genomic DNA

organism: Homo sapiens

source_name: DU145 NIH

label_protocol: 10 µg of amplified and purified DNA were labeled using the BioPrime Array CGH Genomic Labeling kit (Invitrogen) according to the manufacturer¢â¬â„¢s instructions in a volume of 50 µl with a modified dNTP mix containing 120 µM each of dATP, dGTP, and dCTP; 60 µM dTTP; and 60 µM Cy5-dUTP or Cy3-dUTP. Labeled DNA was purified using QIAquick PCR purification columns (Qiagen). Tumor and reference DNA were pooled, mixed with 50 µg Cot-1 DNA (Invitrogen) and concentrated to a volume of 20 µl in a vacuum centrifuge. DNA was then mixed with an equal amount of 2x formamide buffer, denaturated at 95°C for 5 min and preincubated at 37°C for 30 min in a waterbath.

extract_protocol: DNA was isolated using the QiAmp DNA isolation kit (Qiagen, Hilden, Germany) and subsequently quantified by a fluorometric assay (Quant-iT Pico Green dsDNA Kit, Invitrogen, Karlsruhe, Germany). Fluorescence was measured using a TECAN (Salzburg, Austria) SpectrafluorPLUS microplate fluorescence reader with an excitation wavelength at 485 nm and an emission wavelength at 535 nm. DNA concentrations were calculated from a standard curve of double-stranded control DNA provided with the kit that was measured in triplicate at the concentrations 30, 3, 0.3, and 0.03 ng/µl (measured by fluorometry).A volume of 2.5 µl out of 4 ng/µl dilutions from cell lines and control DNA was used as starting material for the amplification. The phi29-amplification was carried out according to the Repli-G kit manufacturer's instructions (Qiagen) using an incubation time of 16 h. Repli-G reactions were checked by a real time based intra Alu-PCR assay. Additionally DNA concentration was fluorimetrically measured with Quant-iT Pico Green dsDNA Kit (Invitrogen) and ranged between 10-30 Ž¼g.

tag: DU145 NIH

source_name: male DNA


title: TS#9/AdGFP day3 in GM Grp A

status: Public on Nov 07 2007

type: RNA

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: TS#9/AdGFP day3 in GM; GrpA replicate

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by Illumina using the Illumina scanner.

data_processing: None: raw data from Beadstudio

label: Streptavidin Cy3

molecule: total RNA

organism: Mus musculus

source_name: Mouse TS#9/AdGFP day3 in GM

label_protocol: As described in the illumina Mouse-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

growth_protocol: TS cells were isolated from blastocysts and grown as previously described (Tanaka et al., 1998). Briefly, Growth medium (GM) was RPMI 1640 supplemented with 20% FBS, 1 mM sodium pyruvate, 100 μM b-mercaptoethanol, 100 U/ml penicillin, 100μg/ml streptomycin, 2 mM L-glutamine, 25 ng/ml human recombinant FGF4 (Sigma), 1 μg/ml heparin, and 70% EFCM. TS cell differentiation was induced by withdrawal of FGF4 and EFCM after trypsinization and replating at appropriate density. For TS colony formation assay, optimally growing TS cells were trypsinized and replated at 500-2000 cells per 6-cm dish onto feeder cells, and fed with fresh GM every 2-3 days for 1-2 weeks.

extract_protocol: Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)

tag: Ets2 type

value: f/f; medium GM; AdenoGFP; TS#9/AdGFP day3 in GM


title: TS#9/AdCreGFP day1 in GM Grp B

description: TS#9/AdCreGFP day1 in GM; GrpB replicate

source_name: Mouse TS#9/AdCreGFP day1 in GM

tag: Ets2 type f/f; medium GM; Adeno CreGFP; TS#9/AdCreGFP day1 in GM


title: PC31_Hind

status: Public on Oct 22 2007

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Cancer Research UK

description: Several serial frozen tissue sections (20 µm thickness) were prepared for tissue microdissection. An additional 4-µm section was also made for detailed histological examination by hematoxylin-eosin staining. Only PDAC regions were microdissected under visualization with an inverted microscope (Nikon 66906, Tokyo, Japan) using a sterile 26-gauge needle.

hyb_protocol: Hybridization was performed at 45°C for 16h in a hybridization machine (Affymetrix).

scan_protocol: The arrays were washed and stained on the Affymetrix fluidics Station 450 and the signal intensities were measured using the Affymetrix GeneChip® Scanner 3000.

data_processing: The raw images were analyzed using the Affymetrix GCOS (Ver1.4) software. For genotyping analysis, we used the Affymetrix GTYPE (Ver4.1) software that implements an accurate genotyping algorithm, BRLMM (http://www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx).

label: biotin

source_name: Pancreatic ductal adenocarcinoma (PDAC)

label_protocol: The experiments were performed according to the manufacturer's instructions (GeneChip® Mapping 50K HindIII or XbaI Assay Kit). Briefly, 250 ng of tumor DNA was digested by either HindIII or XbaI restriction enzyme (New England Biolabs, Boston, MA, USA). After ligation to an appropriate adaptor for each enzyme, PCR reaction was carried out using a generic primer that recognizes the adapter sequence. The PCR products from four reactions were pooled, concentrated, fragmented by DNase I and then, labeled with biotin.

extract_protocol: Microdissected tumor DNA was extracted using a SePaGene DNA extraction kit (SankoJunyaku Co., Ltd., Tokyo, Japan).

tag: Age

tag: Sex

value: Male

tag: Tissue

value: PDAC

tag: Stage

tag: Call rate


title: HV3-20-59CGH

description: male DNA

tag: male DNA

source_name: DU145 HOM


title: PC33_Hind

value: Female


title: PC36_Hind

value: IVb


title: PC30_Hind


title: PC34_Hind


title: PC32_Hind


title: PC21_Hind


title: PC20_Hind


title: PC14_Hind


title: PC17_Hind


title: PC6_Hind

value: IVa


title: PC16_Hind


title: LIVER_GRANISETRON_175mg/kg_5days_exp4527_rep2_19893

status: Public on Mar 28 2008

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 19893
treated sample for experiment (RepID) 4527
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM222232: LIVER_GRANISETRON_175mg/kg_5days_exp4527_rep3_19892
Replicate experimental sample: GSM222230: LIVER_GRANISETRON_175mg/kg_5days_exp4527_rep1_81424
Matched control sample: GSM204608: LIVER_vehicle_NA_.25days_control_NA_18857
Matched control sample: GSM204708: LIVER_vehicle_NA_1days_control_NA_18859
Matched control sample: GSM204742: LIVER_vehicle_NA_3days_control_NA_18863
Matched control sample: GSM204602: LIVER_vehicle_NA_.25days_control_NA_18865
Matched control sample: GSM204691: LIVER_vehicle_NA_1days_control_NA_18868
Matched control sample: GSM204760: LIVER_vehicle_NA_3days_control_NA_18872
Matched control sample: GSM204663: LIVER_vehicle_NA_1days_control_NA_18986
Matched control sample: GSM204604: LIVER_vehicle_NA_.25days_control_NA_19233
Matched control sample: GSM204677: LIVER_vehicle_NA_1days_control_NA_19236
Matched control sample: GSM204771: LIVER_vehicle_NA_3days_control_NA_19238
Matched control sample: GSM204642: LIVER_vehicle_NA_1days_control_NA_80157
Matched control sample: GSM204718: LIVER_vehicle_NA_1days_control_NA_80159
Matched control sample: GSM204621: LIVER_vehicle_NA_.25days_control_NA_80565
Matched control sample: GSM204768: LIVER_vehicle_NA_3days_control_NA_80570
Matched control sample: GSM204868: LIVER_vehicle_NA_5days_control_NA_80573
Matched control sample: GSM204669: LIVER_vehicle_NA_1days_control_NA_80683
Matched control sample: GSM204629: LIVER_vehicle_NA_.25days_control_NA_81664
Matched control sample: GSM204782: LIVER_vehicle_NA_3days_control_NA_81665
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

hyb_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. 12.5 ug of cRNA sample was fragmented in 40 mM Tris-acetate (TrisOAc) pH7.9, 100 mM KOAc and 31.5 mM MgOAc at 94oC for 20 min. This typically resulted in a fragmented cRNA with a size range between 100 to 200 bases. 10 ug of the fragmented cRNA was used for hybridization of each Rat-Uniset I (RU1) Expression BioArray (Amersham Biosciences, Piscataway, NJ) in a volume of 260 ul, containing 78 ul of CodeLink Hyb buffer component A and 130 ul of CodeLink Hyb buffer component B (Amersham Biosciences, Piscataway, NJ). The hybridization solution was denatured at 90oC for 5 min then chilled on ice. The sample was vortexed at maximum speed for 5 sec and centrifuged at maximum speed for 5 min before 250 ul of the solution was injected into the inlet port of the flex-hybridization chamber, and placed in a CodeLink 12-slide shaker tray. The hybridization ports were sealed with 1 cm sealing strips (Amersham Biosciences, Piscataway, NJ), and the shaker tray(s) containing the slides was loaded into a New Brunswick Innova 4080 shaking incubator, with the hybridization chambers facing up. Slides were incubated for 20 hr at 37oC, while shaking at 300 rpm. The 12-slide shaker tray was removed from the shaker, and the hybridization chamber removed from each slide. Each slide was placed into the BioArray Rack of the Parallel Processing Tool (Amersham Biosciences, Piscataway, NJ) and incubated with 0.75x TNT (0.075 M Tris-HCl, pH7.6, 0.1125 M NaCl, 0.0375 % Tween-20) at 46oC for 1hr. The BioArray Rack was moved from the TNT containing reservoir to the small reagent reservoir containing 1:500 dilution of streptavidin-Alexa 647 (Molecular Probes, Eugene, OR). The signal was developed for 30 min at room temperature, before the reaction was stopped and slides were washed four times for 5 min each in TNT buffer (0.1 M Tris-HCl, pH7.6, 0.15 M NaCl, 0.05% Tween-20) using a large reagent reservoir. The slides were rinsed in ddH2O with 0.05% Tween-20 twice for 5 sec each before they were dried by centrifugation with a Qiagen Sigma 4-15C centrifuge (Valencia, CA) using a swinging bucket rotor (2x96) for exactly 3 min at 2000rpm (acceleration at position 9 and deceleration at position 9). The dried slides were stored in light protective slide boxes at room temperature prior to scanning.

scan_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The Axon GenePix Scanner (Axon Instrument, Union City, CA) was calibrated using the Calibration Slide supplied by Axon Instrument with GenePix 4.0 at 635 nm using the Calibration System. After calibration of the scanner, all processed slides were scanned with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 microns. For consistency all slides were scanned the same day of color development, within an hour after dry spinning them and the data was analyzed using the CodeLink Expression Analysis Software version 2.2.25 (Amersham Biosciences, Piscataway, NJ).

data_processing: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44, supplemental methods.  Prior to statistical computation, the spot reading data was normalized. For this purpose a new nonlinear normalization procedure, similar to the centralization approach reported in the literature (Zien et al., 2001) was developed for the CodeLink array platform. The normalization procedure uses proprietary algorithm that assumes that in general, for an array with many probes, the majority of the signal represents genes that have unchanged expressions compared to controls, with the extreme values representing the true biology of the process and not some artifact due to measurement noise. The algorithm does not make the assumption that the true mRNA abundance being measured is linearly proportional to the spot reading signal or any assumption about the error distribution of such signals or their differential. Rather, the assumption of unchanged signals representing the bulk of the signal measurements is used to center a nonlinear curve fit to a reference template. This reference template is constructed for a large set of time matched, same tissue and same vehicle, control arrays, computing a median log signal for each probe. The replicate size of this set is adequate to ensure very small random error in the ensemble signal level for each reference probe. The curve fit corrects for some array processing problems, such as partial signal saturation, and improves the overall quality of the data compared to simple linear normalization methods. Essentially the curve tracks the mode of the signal distribution for sets of genes against the expected value for that set.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: LIVER, GRANISETRON, 175mg/kg, 5 days

label_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. The methods used for cRNA preparation (cDNA synthesis, cRNA preparation, and cRNA purification) are essentially as described in the CodeLink™ manual v2.1 as supplied by Amersham Biosciences (Piscataway, NJ) using the Qiagen BioRobot 9604 (Valencia, CA). cDNA synthesis, cRNA preparation, and cRNA purification were completely processed in a 96-well format using the automated Qiagen BioRobot 9604 procedure. 0.6 – 20 ìg of enriched RNA from different tissue sources were added to a reaction mixture in a final volume of 12 ìl, containing bacterial control RNA (1.5pg FixA, 5pgYjeK, 5pg AraB, 15pg EntF, 50pg FixB, 150pg HisB, 500pg LeuB, 1500pg gnd) and 1.0 ìl of 100 pmol ìl-1 T7-(dT)24 oligonucleotide primer (Proligo, Boulder, CO). The T7-(dT)24 oligonucleotide primer used, is an HPLC purified 63-mer with the sequence : 5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTTTTTTTTTTTTTTTTTT-3'. The mixture was incubated for 10 min at 70oC and chilled on ice. On ice, 4 ul of 5x first-strand buffer, 2 ul 0.1 M DTT, 1 ul of 10 mM dNTP mix and 1 ul Superscript™II RNaseH-reverse transcriptase (200 U/ul) were added to the mixture to make a final volume of 20 ul. The mixture was incubated for 1 hr at 37oC. Second-strand cDNA was synthesized in a volume of 150 ul, containing 92 ul nuclease-free water, 30 ul of 5x second-strand buffer, 3 ul of 10 mM dNTP mix, 4 ul of Escherichia coli DNA polymerase I (10 U/ìl) and 1 ul of RNase H (2 U/ul) for 2 hr at 16oC. The cDNA was purified using a Qiagen QIAquick purification kit, and completely dried down using a Speed-Vac concentrator (45oC) for 2 hr. The dried product was resuspended in IVT reaction mix containing 3.0 ul of nuclease-free water, 4.0 ul 10x reaction buffer, 4.0 ul 75 mM ATP, 4.0 ul 75 mM GTP, 3.0 ul 75 mM CTP, 3.0 ul 75 mM UTP, 7.5 ul 10 mM Biotin 11-CTP, 7.5 ul 10 mM Biotin 11-UTP and 4.0 ul enzyme mix. The reaction mix was incubated for 14 hr at 37oC using an MJ Research 96-well PTC-200 Thermal Cycler (MJ Research, Waltham, MA), before the cRNA was purified using a Qiagen RNeasy® kit. The resulting cRNA yield was quantified using the 96-well ìQuan Universal Microplate Spectrophotometer Model MQX200 (BIO-TEK Instruments Inc., Winooski, VT) at a wavelength of 260 nm. Conformance of the cRNA sample to historical size distributions (the bulk of the cRNA product should be between 500 and 3,000 bases in size) was confirmed using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). Samples not near the historical norm were reprocessed starting from tissue or RNA.

growth_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Sprague-Dawley (Crl:CD®(SD)|GS BR) rats (aged 6-8 weeks and weighing 200 - 260 g), were purchased from Charles River Laboratories (Wilmington, MA). They were housed in plastic cages for 1 week for acclimation to the laboratory environment of a ventilated room (temperature, 22oC ±3oC; humidity, 30 - 70%; light/dark cycle, 12 h d-1, 6:00am - 6:00pm) until use. Certified Rodent Diet #5002 (PMI Feeds Inc.) and chlorinated tap water was available ad libitum.

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

treatment_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44.  Compounds were administered via the route of administration (ROA) that corresponds to that by which humans receive the drug. Compounds were typically administered orally (PO) (83%), intravenously (IV) (9.4%), subcutaneously (SC) (5.7%), or intraperitoneally (IP) (2%). If the compound is a toxicant or a biochemical standard, it was administered orally. For oral dosing, the vehicle choice largely depends on the solubility of the compound in water. Water-soluble compounds were administered in water. Insoluble compounds are administered in either corn oil or 0.5% carboxymethylcellulose (CMC) using the best literature recommendation as a guide. IV administered compounds were usually dissolved in saline and SC administered compounds in corn oil. The highest dose the rats receive is the Maximum Tolerated Dose (MTD). The dosing of animals was staggered based on intended harvest order to ensure that sacrifice occurred within 30 minutes of the recorded time point. Dosing frequency was as described in Sample_characteristics for the particular treatment.

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

value: male

tag: tissue

value: LIVER

tag: treatment compound

value: GRANISETRON

tag: dose

value: 175 mg/kg

tag: solvent

value: WATER

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 5 days

tag: experiment date


title: PC18_Hind

tag: Age


title: PC12_Hind

tag: Sex


title: PC4_Hind

tag: Tissue

value: III


title: PC28_Hind

tag: Stage


title: PC10_Hind

tag: Call rate


title: PC9_Hind


title: PC7_Hind


title: PC2_Hind


title: PC8_Hind


title: PC36_Xba


title: PC33_Xba


title: PC1_Hind

value: II


title: PC25_Hind


title: PC34_Xba


title: PC19_Xba


title: PC20_Xba


title: PC14_Xba


title: PC31_Xba


title: PC30_Xba

label_protocol: The experiments were performed according to the manufacturer's instructions (GeneChip® Mapping 50K HindIII or XbaI Assay Kit). Briefly, 250 ng of tumor DNA was digested by either HindIII or XbaI restriction enzyme (New England Biolabs, Boston, MA, USA). After ligation to an appropriate adaptor for each enzyme, PCR reaction was carried out using a generic primer that recognizes the adapter sequence. The PCR products from four reactions were pooled, concentrated, fragmented by DNase I and then, labeled with biotin.n.


title: PC28_Xba


title: PC3_Hind


title: PC17_Xba


title: PC12_Xba


title: PC25_Xba


title: PC15_Hind


title: PC18_Xba


title: PC15_Xba


title: PC10_Xba


title: PC6_Xba


title: MLP-29 KrasG12D Clone2

status: Public on Sep 17 2007

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: Oncogenic G12D mutation inserted by AAV-driven homologous recombination at the Kras gene in one allele.

hyb_protocol: 0.85 microgram of biotin-labeled cRNA was hybridized to Illumina Mouse Ref-8 BeadChips at 55 °C overnight. BeadChips were incubated with Cy3 streptavidin and washed according to the manufacturer’s protocol.

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan confocal scanner

data_processing: Illumina BeadStudio version 1.5.1.3

source_name: MLP-29, knock-in of G12D mutation in one Kras allele, Clone2

label_protocol: Five hundred ng of total RNA was reverse transcribed and amplified overnight with T7 RNA polymerase and labeled with biotin following the manufacturer’s protocol.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

tag: Liver progenitor cell line derived from E13 mouse embryo


title: PC2_Xba


title: PC9_Xba


title: PC7_Xba


title: PC16_Xba


title: PC11_Xba


title: MLP-29 KrasG12D Clone1

source_name: MLP-29, knock-in of G12D mutation in one Kras allele, Clone1


title: PC21_Xba


title: PC1_Xba


title: PC8_Xba


title: MLP-29 Wild-type

description: Control cells

source_name: MLP-29, control wild-type cells


title: PC3_Xba


title: SCLC NCI-H187 cell line (NCI-H187.s12)

status: Public on Apr 12 2007

city: Abbott Park

first: Mark

last: Anderson

state: IL

address: 100 Abbott Park Road

institute: Abbott Laboratories

hyb_protocol: Affy protocol, midi_euk_2v3

data_processing: GCOS

label: Biotin

source_name: SCLC NCI-H187 cell line

label_protocol: Enzo kit

extract_protocol: Trizol

value: 0.21 ± 0.05 (3 replicates)


title: autism with FMR1-FM AU046708

status: Public on Jun 01 2007

city: Los Angeles

first: Yuhei

last: Nishimura

address: 2309 Gonda 695 Charles E Young Dr. South

department: Neuropsychiatric Institute

institute: University of California Los Angeles

hyb_protocol: The generated cRNAs were mixed and subjected to hybridization to the Agilent Whole Human Genome Array G4112A according to the manufacture's protocol.

scan_protocol: Scanning of the microarray was done by Agilent DNA microarray scanner.

data_processing: Scanner output image file was normalized and filtered using Feature Extraction Software ver 8.5. Normalization was performed so that overall intensity ratio of Cy5 to Cy3 was equal to one.

source_name: pool

label_protocol: cRNA synthesis was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.

growth_protocol: A total of 9x10(6) of lymphoblastoid cells were seeded in a T75 flask in 30 ml of fresh medium. Medium was RPMI1640 with 2 mM L glutamine and 25 mM HEPES and 10 percent fetal bovine serum and 1x Anitbiotic Antimicotic solution. After 24 hours total RNA was extracted.

extract_protocol: Total RNA was extracted from lymphoblastoid cells of 14 individuals using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: Pooled total RNAs from lymphoblastoid cells of 14 individuals

source_name: Autism with FMR1-FM AU046708

label_protocol: Target preparation was performed using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) according to the manufacture's protocol.

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU046708 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU046708 is a male with autism and full mutation of FMR1.


title: SCLC NCI-H345 cell line (NCI-H345.s9)

source_name: SCLC NCI-H345 cell line

value: 2.16 ± 0.58 (3 replicates)


title: SCLC NCI-H345 cell line (NCI-H345.s8)


title: autism with FMR1-FM AU046707

source_name: Autism with FMR1-FM AU046707

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU046707 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU046707 is a male with autism and full mutation of FMR1.


title: SCLC NCI-H187 cell line (NCI-H187.s10)


title: MLP-29 Control NEO+

description: Neo resistance inserted by AAV-driven homologous recombination at the Kras gene in one allele, not affecting Kras sequence.

source_name: MLP-29, control clone with knock-in NEO+ (not affecting Kras sequence)


title: PC4_Xba

value: PDAC


title: SCLC NCI-H209 cell line (NCI-H209.3)

source_name: SCLC NCI-H209 cell line

value: 1.15 ± 0.23 (3 replicates)


title: control AU1165305

source_name: control AU1165305

extract_protocol: Total RNA was extracted from lymphoblastoid cells of AU1165305 using RNeasy Mini Kit (QIAGEN) with DNase I treatment according to the manufacture's protocol.

tag: AU1165305 is a control male without autism.


title: SCLC NCI-H187 cell line (NCI-H187.s11)


title: SCLC NCI-H209 cell line (NCI-H209.1)


title: SCLC NCI-H196 cell line (NCI-H196.1)

source_name: SCLC NCI-H196 cell line

value: 38.6 ± 6.2 (3 replicates)


title: SCLC NCI-H146 cell line (NCI-H146.2)

source_name: SCLC NCI-H146 cell line


title: SCLC NCI-H82 cell line (NCI-H82.2)

source_name: SCLC NCI-H82 cell line

value: 22.4 ± 2.8 (3 replicates)


title: SCLC H69AR cell line (H69AR.0)

source_name: SCLC H69AR cell line

value: 22.3 ± 1.97 (6 replicates)


title: SCLC NCI-H82 cell line (NCI-H82.3)


title: PC32_Xba

source_name: Pancreatic ductal adenocarcinoma (PDAC)

value: Male


title: SCLC NCI-H196 cell line (NCI-H196.2)


title: SCLC cell line NCI-H146 (NCI-H146.0)

source_name: SCLC cell line NCI-H146


title: SCLC SW-1271 cell line (SW-1271.3)

source_name: SCLC SW-1271 cell line

value: 33.9 ± 4.95 (3 replicates)


title: NCI-H1963 cell line (NCI-H1963c)

source_name: NCI-H1963 cell line

value: 0.18 ± 0.06 (3 replicates)


title: SCLC SW-1271 cell line (SW-1271.1)


title: SCLC NCI-H209 cell line (NCI-H209.2)


title: SCLC cell line DMS-53 (DMS-53.3)

source_name: SCLC cell line DMS-53

value: 1.6 ± 0.2 (4 replicates)


title: SCLC cell line DMS-53 (DMS-53.2)


title: NCI-H889 cell line (NCI-H889c)

source_name: NCI-H889 cell line

value: 0.14 ± 0.04 (3 replicates)


title: NCI-H1963 cell line (NCI-H1963a)


title: NCI-H1417 cell line (NCI-H1417a)

source_name: NCI-H1417 cell line

value: 0.36 ± 0.09 (3 replicates)


title: NCI-H510 cell line (NCI-H510a)

source_name: NCI-H510 cell line

value: 1.22 ± 0.54 (3 replicates)


title: NCI-H889 cell line (NCI-H889a)


title: NCI-H1417 cell line (NCI-H1417c)


title: yeastcells_treatment6hrsafterO.D.1.0_250ug/ml T1

status: Public on Jan 22 2007

city: College Station

first: Coran

middle: MH

last: Watanabe

state: TX

address: Texas A&M Dept. Chemistry MS 3255

department: Chemistry

institute: Texas A*M University

description: We have examined the transcriptional response of S. cerevisiae to exposure to pyocyanin at 25 and 250 ?g/ml concentrations.  Our analysis indicates that the changes are consistent with an oxidative stress response, as observed in other studies of the mode of action of pyocyanin toxicity.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip YeastS98 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

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

growth_protocol: Cells were grown in YPD media at 30 degrees Celsius at 250 rpm shaker.

extract_protocol: SDS/double phenol RNA extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were grown to O.D. of 1.0, given 250?g/ml pyocyanin in minimal ethanol, and grown for 6 hours, then collected by centrifugation, frozen in liquid nitrogen, thawed before proecessing.

tag: Saccharomyces cerevisiae, wt, maintianed on YPD plates, started from 48 hrs growth on a new YPD agar plate


title: NCI-H510 cell line (NCI-H510c)


title: NCI-H211 cell line (NCI-H211c)

source_name: NCI-H211 cell line

value: 0.41 ± 0.2 (3 replicates)


title: yeastcells_treatment6hrsafterO.D.1.0_250ug/ml T2


title: liver Pol2 Nimblegen 14.4M Mouse tiling array of mm5 at 100bp resolution v1.0 3 of 4

status: Public on Jul 28 2007

first: Bing

last: Ren

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against Pol2 and formaldehyde crosslinked chromatin from liver cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI33 build of the mouse genome (mm5) that contains non-overlapping 50-mer oligonucleotides, positioned at every 100 basepairs (bp)

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: Condensed array sets (1-4) for all tissues were either loess normalized or median normalized using the R package limma with the normalization using the RANDOM_GC probes.

source_name: Chromatin immunoprecipitated DNA from liver cells using Pol2 antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: liver immunoprecipitated chromatin

source_name: Input Chromatin liver cells.

extract_protocol: input chromatin

value: liver input chromatin


title: NCI-H211 cell line (NCI-H211a)


title: liver, WT mouse, sample WT6

status: Public on Dec 19 2006

city: Portland

first: Svetlana

last: Lutsenko

state: OR

address: 3181 SW Sam Jackson Pk Rd L224

institute: OHSU

description:
*Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5' and 3' ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged.
An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.

hyb_protocol: *Array hybridization and processing. *Labeled target is fragmented at 95^o C in the presence of high magnesium concentration. The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer. Ten mg of target is hybridized with the GeneChip /(insert array name) /array (Affymetrix) overnight, followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 400 (Affymetrix).

scan_protocol: The distribution of fluorescent material on the processed array is determined using the Agilent GeneArray laser scanner (Affymetrix). Image inspection is performed manually immediately following each scan.

data_processing: MAS 5.0 absolute expression analysis, target intensity 350

label: Enzo BioArray High Yield RNA labeling kit

source_name: Liver RNA, WT mice

extract_protocol: TRIZOL RNA purification followed by RNaesy Mini kit clean up

tag: WT mice, 6 weeks old


title: liver, ATP7B KO mouse, sample KO905

source_name: liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671)

label_protocol: Enzo BioArray High Yield RNA labeling kit

tag: ATP7B -/- Ko mice, 6 weeks old


title: liver, wt mouse, sample WT5

source_name: liver RNA, WT  mouse

tag: 6 weeks old


title: Uterus Menstruating Progesterone withdrawn T3

status: Public on Dec 01 2006

city: Cambridge

first: Ching-wen

last: Cheng

address: Robinson Way

department: Obstetrics and Gynaecology

institute: University of Cambridge

description: Pooled RNA sample from 4 experimental animals.

hyb_protocol: Hybridisation according to Affymetrix protocols by Geneservice, Cambridge, UK.

scan_protocol: Microarray images were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Numerified using MAS 5.0 software (Affymetrix)

source_name: Menstruating uterus 60 hours after Progesterone withdrawn

label_protocol: Labelling according to Affymetrix protocols by Geneservice, Cambridge, UK.

extract_protocol: Total RNA from individual uteri was isolated by homogenising one of uterine horn in TRIZOL (Invitrogen, Paisley, United Kingdom) and further purified using Qiagen RNeasy Mini kit (Qiagen, West Sussex, United Kingdom) following the manufacturer’s instructions. The Quality of purified RNA was examined using Agilent 2100 Bioanalyzer (Agilent Technologies UK, Stockport, United Kingdom).

treatment_protocol: Ovariectomized mice were treated sequentially with steroid hormones and then, to induce decidualization, oil was injected into the uterine lumen.The menstruation was induced by progesterone withdrawal after the induction of decidualization.

tag: Strain

value: Female

value: Uterus / decidualized and mentruating


title: liver, wt mouse, sample WT4

source_name: liver RNA, wt mouse


title: liver, ATP7B KO mouse, sample KO903

description:
*Data analysis. *The array image scan is processed with Affymetrix Microarray Suite, version 5.0 (MAS 5.0) software. The GeneChip expression arrays contain control probe sets for both spiked and endogenous RNA transcripts (e.g., BioB, BioC, BioD, CreX and species-specific actin and GAPDH). Following image processing and absolute analysis of the array pattern with MAS, six values are examined to assess overall assay performance: background, noise, average Signal, % Present, ratio of Signal values for probe sets representing the 5’ and 3’ ends of actin and GAPDH transcripts, and total Signal for probe sets for BioC, BioD and CreX. Assays demonstrating poor or marginal performance are flagged.
An MAS 5.0 absolute expression analysis was performed for each GeneChip genome array hybridization. Following the initial analysis, the absolute analyses were rerun using global scaling to an average target intensity of */350/*. The scaling allows for the direct comparison of hybridization values from the different targets analyzed in this project (and with any additional GeneChip sample assays you run using the same array type). For each analysis, scaled or unscaled, the parameters a_1 and a_2 are set to 0.1 and 0.15 respectively. These parameters set the point at which a probeset is called present(P), marginal(M), or undetectable(A). This call is based on the Detection p-value of the probeset.


title: Uterus Menstruating Progesterone withdrawn T1

source_name: Menstruating uterus 36 hours after Progesterone withdrawn


title: Uterus Menstruating Progesterone withdrawn T4

source_name: Menstruating uterus 84 hours after Progesterone withdrawn


title: NMRI mouse embryonic fibroblasts

status: Public on Oct 03 2006

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: This sample presents the control for FGF2-treated NMRI mouse embryonic fibroblasts.

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degC

scan_protocol: Using an Illumina scanner; gain factor: 2.5

data_processing: In BeadStudio 1.0 raw data were background subtracted and normalised using the "rank invariant" algorithm. Value = "null" denotes expression below background (p < 0.01).

source_name: NMRI MEFs

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 300ng of total RNA; IVT: 6h

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium without FGF2 supplementation. RNA was isolated one day later.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions

treatment_protocol: inactivated NMRI MEFs incubated with basic human embryonic stem cell medium for 24h

tag: primary mouse embryonic fibroblasts of strain NMRI


title: Folate Depletion Experiment 1, p79s33

status: Public on Nov 02 2006

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: 25 µg of total RNA was used for cDNA synthesis.  The microarray used in this study was the NIEHS Human Oligo chip containing approximately 17,000 70mer oligonucleotides from the Operon Human Oligo Set V1.1.  The gene list can be found at http://dir.niehs.nih.gov/microarray/inhousearrays.htm.  Fluorescent intensities were measured with an Agilent DNA Microarray scanner (Palo Alto, CA).

data_processing: The signal intensities were quantified and normalized from the spots on the image files utilizing IPLabs image-processing software (Scanalytics, Inc., Fairfax, VA) with the Array Suite 2.0 extension (National Human Genome Research Institute, NHGRI, Bethesda, MD) (Chen et al., 1997).

source_name: Folate Depletion #1, p79s33

tag: human fibroblast culture, GM03349, folate depleted for 7 days before harvest for gene expression

source_name: Control Folate Depletion #1, p79s33

tag: human fibroblast culture, GM03349, sham folate depleted for 7 days before harvest for gene expression


title: Folate Depletion Experiment 1, p79s32

source_name: Folate Depletion #1, p79s32

source_name: Control Folate Depletion #1, p79s32


title: 150mg/kg Acetaminophen 24hr rat 3069 liver vs. Mock Acetaminophen 24hr rat control liver

status: Public on Sep 19 2006

description: Gene expression analysis was conducted using Rattus Norvegicus Agilent Arrays.Starting with 1ug of total RNA, Cy3 and Cy5 labeled cRNA was produced using the Agilent low input labeling and amplification kit according to manufacturer’s protocol.  The labeled cRNA samples from individual treated animals and control pools were mixed and hybridized for 16 hr at 60?C to the oligonucleotide probes on the Agilent Rat Oligo Microarray (Agilent #G4130A).Chips were scanned with an Agilent G2565 AA Scanner and processed with the Agilent G2566AA Feature Extraction Software.

data_processing: Rosetta Resolver Error Model

source_name: RNA prepared from left liver lobes

label_protocol: One ug of RNA per sample was converted to cDNA with reverse transcriptase and then amplified using T7 RNA polymerase while labeling with either Cy3-dUTP or Cy5-dUTP. The labeled cRNA’s from treated individuals and control pools were hybridized together twice, with Cy3 and Cy5 dye swap.

growth_protocol: Rats were housed in groups of 3 in polycarbonate cages (Lab Products, Inc., Maywood, NJ) with Sani-Chips® (P.J. Murphy Forest Products Corp., Montville, NJ) bedding. The animal rooms were maintained at 21-22° C and 48-53% relative humidity with a 12-hr dark-light cycle with lights coming on at 6 a.m. and room air changes of 10/hour. Cages were changed twice per week. NIH-07 diet and tap water was provided ad libitum.

extract_protocol: Total hepatic RNA was isolated from individual rat livers using QIAGEN RNeasy Maxi Kits® (QIAGEN, Valencia, CA). Equal amounts of RNA from each of the control animals at every dose and time period were pooled for control gene expression and compared with individual rats at each dose and time period.  The samples were hybridized in duplicate for each individual rat.

treatment_protocol: Rats were exposed to vehicle alone by oral gavage

tag: control

treatment_protocol: Rats were exposed to acetaminophen in methyl cellulose by oral gavage

tag: treated


title: 150mg/kg Acetaminophen 24hr rat 3074 liver vs. Mock Acetaminophen 24hr rat control liver

hyb_protocol: The labeled cRNA samples from individual treated animals and control pools were mixed and hybridized for 16 hr at 60?C to the oligonucleotide probes on the Agilent Rat Oligo Microarray (Agilent #G4130A)

scan_protocol: Chips were scanned with an Agilent G2565 AA Scanner and processed with the Agilent G2566AA Feature Extraction Software.


title: 150mg/kg Acetaminophen 24hr rat 3070 liver vs. Mock Acetaminophen 24hr rat control liver


title: NMRI mouse embryonic fibroblasts treated with FGF2

description: Non-stimulated NMRI mouse embryonic fibroblasts were used as control.

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium plus 40 ng/ml of FGF2. RNA was isolated one day later.

treatment_protocol: inactivated NMRI MEFs incubated with basic human embryonic stem cell medium plus 40 ng/ml of FGF2 for 24h


title: 150 mg/kg Acetaminophen 6hr rat 3083 liver vs. Mock Acetaminophen 6hr rat control liver


title: Folate Depletion Experiment 1, p79s34

source_name: Folate Depletion #1, p79s34

source_name: Control Folate Depletion #1, p79s34


title: 150mg sham 24 hour vs. 150mg/kg Acetaminophen 24hr rat 3074 liver


title: CD1 mouse embryonic fibroblasts

description: This sample presents the control for FGF2-treated CD1 mouse embryonic fibroblasts.

source_name: CD1 MEFs

treatment_protocol: inactivated CD1 MEFs incubated with basic human embryonic stem cell medium for 24h

tag: primary mouse embryonic fibroblasts of strain CD1


title: Folate Depletion Experiment 1, p79s35

source_name: Folate Depletion #1, p79s35

source_name: Control Folate Depletion #1, p79s35


title: Folate Depletion Experiment 2, p103s92

source_name: Folate Depletion #2, p103s92

source_name: Control Folate Depletion #2, p103s92


title: Uterus Menstruating Progesterone withdrawn T2

source_name: Menstruating uterus 48 hours after Progesterone withdrawn

tag: Sex

tag: Age

tag: Tissue


title: Folate Depletion Experiment 2, p103s93

source_name: Folate Depletion #2, p103s93

source_name: Control Folate Depletion #2, p103s93


title: liver, ATP7B KO mouse, sample KO904

source_name: liver RNA, ATP 7B KO mouse (first described Hum. Mol. Genet. (1999) 8:1665-1671)

tag: ATP7B -/- KO mice, 6 weeks old


title: 150mg/kg Acetaminophen 6 hr rat 3081 liver vs. Mock Acetaminophen 6hr rat control liver


title: Folate Depletion Experiment 2, p103s87

source_name: Folate Depletion #2, p103s87

source_name: Control Folate Depletion #2, p103s87


title: 150 mg/kg Acetaminophen 6hr rat 3082 liver vs. Mock Acetaminophen 6hr rat control liver


title: 1500mg Acetaminophen 48h Rat Pool vs. 1500mg Acetaminophen 48h Rat 3008


title: 2000mg Acetaminophen 48h Rat Pool vs. 2000mg Acetaminophen 48h Rat 3119


title: Folate Depletion Experiment 2, p103s85

data_processing: The signal intensities were quantified and normalized from the spots on the image files utilizing IPLabs image-processing software (Scanalytics, Inc., Fairfax, VA) with the Array Suite 2.0 extension (National Human Genome Research Institute, NHGRI, Bethesda, MD)

source_name: Folate Depletion #2, p103s85

tag: human fibroblast culture, GM03349, folate depleted for 7 days before harvest for gene expression.

source_name: Control Folate Depletion #2, p103s85

tag: human fibroblast culture, GM03349, sham folate depleted for 7 days before harvest for gene expression.


title: 1500mg Acetaminophen 48h Rat Pool vs. 1500mg Acetaminophen 48h Rat 3007


title: 2000mg Acetaminophen 48h Rat Pool vs. 2000mg Acetaminophen 48h Rat 3117


title: 2000mg Acetaminophen 48h Rat Pool vs. 2000mg Acetaminophen 48h Rat 3118


title: CD1 mouse embryonic fibroblasts treated with FGF2

description: Non-stimulated CD1 mouse embryonic fibroblasts were used as control.

treatment_protocol: inactivated CD1 MEFs incubated with basic human embryonic stem cell medium plus 40 ng/ml of FGF2 for 24h


title: 2000mg Acetaminophen 24h Rat Pool vs. 2000mg Acetaminophen 24h Rat 3107


title: 1500mg Acetaminophen 24h Rat Pool vs. 1500mg Acetaminophen 24h Rat 3020


title: 1500mg Acetaminophen 24h Rat Pool vs. 1500mg Acetaminophen 24h Rat 3019


title: 2000mg Acetaminophen 24h Rat Pool vs. 2000mg Acetaminophen 24h Rat 3105


title: 2000mg Acetaminophen 6h Rat Pool vs. 2000mg Acetaminophen 6h Rat 3094


title: 150mg Acetaminophen 48h Rat Pool vs. 150mg Acetaminophen 48h Rat 3057


title: 2000mg Acetaminophen 6h Rat Pool vs. 2000mg Acetaminophen 6h Rat 3095


title: 1500mg Acetaminophen 48h Rat Pool vs. 1500mg Acetaminophen 48h Rat 3006


title: 2000mg Acetaminophen 24h Rat Pool vs. 2000mg Acetaminophen 24h Rat 3106


title: 1500mg Acetaminophen 6h Rat Pool vs. 1500mg Acetaminophen 6h Rat 3032


title: 1500mg Acetaminophen 24h Rat Pool vs. 1500mg Acetaminophen 24h Rat 3018


title: 1500mg Acetaminophen 6h Rat Pool vs. 1500mg Acetaminophen 6h Rat 3031


title: 50mg Acetaminophen 24h Rat Pool vs. 50mg Acetaminophen 24h Rat 3138


title: 50mg Acetaminophen 48h Rat Pool vs. 50mg Acetaminophen 48h Rat 3150


title: 150mg Acetaminophen 48h Rat Pool vs. 150mg Acetaminophen 48h Rat 3058


title: 2000mg Acetaminophen 6h Rat Pool vs. 2000mg Acetaminophen 6h Rat 3093


title: 50mg Acetaminophen 48h Rat Pool vs. 50mg Acetaminophen 48h Rat 3149


title: 150mg Acetaminophen 48h Rat Pool vs. 150mg Acetaminophen 48h Rat 3059


title: 50mg Acetaminophen 24h Rat Pool vs. 50mg Acetaminophen 24h Rat 3139


title: 2000mg Acetaminophen 48h Rat 3118 vs. 2000mg Acetaminophen 48h Rat Pool


title: 2000mg Acetaminophen 48h Rat 3119 vs. 2000mg Acetaminophen 48h Rat Pool


title: 1500mg Acetaminophen 48h Rat 3008 vs. 1500mg Acetaminophen 48h Rat Pool


title: 1500mg Acetaminophen 6h Rat Pool vs. 1500mg Acetaminophen 6h Rat 3030


title: 1500mg Acetaminophen 48h Rat 3007 vs. 1500mg Acetaminophen 48h Rat Pool


title: 2000mg Acetaminophen 48h Rat 3117 vs. 2000mg Acetaminophen 48h Rat Pool


title: 1500mg Acetaminophen 24h Rat 3020 vs. 1500mg Acetaminophen 24h Rat Pool


title: 1500mg Acetaminophen 24h Rat 3019 vs. 1500mg Acetaminophen 24h Rat Pool


title: 2000mg Acetaminophen 24h Rat 3106 vs. 2000mg Acetaminophen 24h Rat Pool


title: 2000mg Acetaminophen 24h Rat 3105 vs. 2000mg Acetaminophen 24h Rat Pool


title: 50mg Acetaminophen 24h Rat Pool vs. 50mg Acetaminophen 24h Rat 3137


title: 2000mg Acetaminophen 24h Rat 3107 vs. 2000mg Acetaminophen 24h Rat Pool


title: 150mg sham 24 hour vs. 150mg/kg Acetaminophen 24hr rat 3070 liver


title: Mock Acetaminophen 6hr rat control liver vs. 150 mg/kg Acetaminophen 6hr rat 3083 liver


title: 1500mg Acetaminophen 24h Rat 3018 vs. 1500mg Acetaminophen 24h Rat Pool


title: 150mg Acetaminophen 48h Rat 3059 vs. 150mg Acetaminophen 48h Rat Pool


title: 50mg Acetaminophen 48h Rat 3151 vs. 50mg Acetaminophen 48h Rat Pool


title: 150mg Acetaminophen 48h Rat 3058 vs. 150mg Acetaminophen 48h Rat Pool


title: 150mg sham 24 hour vs. 150mg/kg Acetaminophen 24hr rat 3069 liver


title: 1500mg Acetaminophen 48h Rat 3006 vs. 1500mg Acetaminophen 48h Rat Pool


title: 50mg Acetaminophen 24h Rat 3139 vs. 50mg Acetaminophen 24h Rat Pool


title: Mock Acetaminophen 6hr rat control liver vs. 150 mg/kg Acetaminophen 6hr rat 3082 liver


title: 50mg Acetaminophen 48h Rat 3150 vs. 50mg Acetaminophen 48h Rat Pool


title: 50mg Acetaminophen 24h Rat 3138 vs. 50mg Acetaminophen 24h Rat Pool


title: 50mg Acetaminophen 48h Rat 3149 vs. 50mg Acetaminophen 48h Rat Pool


title: 2000mg Acetaminophen 6h Rat 3095 vs. 2000mg Acetaminophen 6h Rat Pool


title: 1500mg Acetaminophen 6h Rat 3032 vs. 1500mg Acetaminophen 6h Rat Pool


title: 150mg Acetaminophen 48h Rat 3057 vs. 150mg Acetaminophen 48h Rat Pool


title: 50mg Acetaminophen 24h Rat 3137 vs. 50mg Acetaminophen 24h Rat Pool


title: 1500mg Acetaminophen 6h Rat 3030 vs. 1500mg Acetaminophen 6h Rat Pool


title: 2000mg Acetaminophen 6h Rat 3093 vs. 2000mg Acetaminophen 6h Rat Pool


title: 50mg Acetaminophen 6h Rat Pool vs. 50mg Acetaminophen 6h Rat 3127


title: 50mg Acetaminophen 6h Rat 3126 vs. 50mg Acetaminophen 6h Rat Pool


title: 50mg Acetaminophen 6h Rat 3125 vs. 50mg Acetaminophen 6h Rat Pool


title: 1500mg Acetaminophen 6h Rat 3031 vs. 1500mg Acetaminophen 6h Rat Pool


title: Mock Acetaminophen 6hr rat control liver vs. 150mg/kg Acetaminophen 6 hr rat 3081 liver


title: 50mg Acetaminophen 6h Rat 3127 vs. 50mg Acetaminophen 6h Rat Pool


title: 50mg Acetaminophen 6h Rat Pool vs. 50mg Acetaminophen 6h Rat 3125


title: 2000mg Acetaminophen 6h Rat 3094 vs. 2000mg Acetaminophen 6h Rat Pool


title: 50mg Acetaminophen 6h Rat Pool vs. 50mg Acetaminophen 6h Rat 3126


title: 100nM Anti-miR-134 transfection plus 100nM RA treatment, 72hr, replicate 1

status: Public on Apr 08 2006

city: Singapore

last: Lim

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Stem Cell and Developmental Biology

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: All Hybridisation and Wash procedures were performed following instructions in the Experienced User Card #2,  Hybridize/Wash 8-sample BeadChip protocol (Illumina). Briefly, 34ul of the Hyb mix with labeled cRNA sample was dispensed onto the center of each array and allowed to hyb with rotations in a pre-heated oven for 16-20h at 55*C. Washes were done with Wash E1BC solution, Block E1 solution was used for blocking and detection performed by Block E1 solution+Streptavidin-Cy3/5.

scan_protocol: standard Illumina procedures

data_processing: RMA normalization

source_name: E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)

label_protocol: First & Second strand cDNA synthesis, cRNA Biotin-labelling and cRNA purification were performed using the Illumina TotalPrepRNA Amplification kit (Ambion;#IL1791). 850ng labeled cRNA were mixed with Hyb Mix (Hyb E1+Formamide) as according to instructions in BeadStation 500X Gene Expression System (Illumina) and used for microarray (Illumina Mouse Refseq-8 Array) staining.

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Anti-miR-134 (Ambion;#17000, ID:AM10341) oligomer using Lipofectamine 2000 (Invitorgen protocol), 100nM all-trans retinoic acid induction started 24h post-transfection and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).

tag: mouse embryonic stem cell


title: 50mg Acetaminophen 48h Rat Pool vs. 50mg Acetaminophen 48h Rat 3151

source_name: RNA prepared from left liver lobes


title: 100nM Anti-miR-134 transfection plus 100nM RA treatment, 48hr, replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Anti-miR-134 (Ambion;#17000, ID:AM10341) oligomer using Lipofectamine 2000 (Invitorgen protocol), 100nM all-trans retinoic acid induction started 24h post-transfection and total RNA extracted after 48h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Scrambled oligo transfection plus 100nM RA treatment, 72hr, replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Scrambled (Ambion; AGACUAGCGGUAUCUUUAUCCC) oligomer using Lipofectamine 2000 (Invitorgen protocol), 100nM all-trans retinoic acid induction started 24h post-transfection and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Scrambled oligo transfection plus 100nM RA treatment, 48hr, replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Scrambled (Ambion; AGACUAGCGGUAUCUUUAUCCC) oligomer using Lipofectamine 2000 (Invitorgen protocol), 100nM all-trans retinoic acid induction started 24h post-transfection and total RNA extracted after 48h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Scrambled oligo transfection plus 100nM RA treatment, 72hr, replicate 1


title: 100nM miR134-mimetic transfection replicate 1

status: Public on Mar 24 2006

extract_protocol: Mouse embryonic stem cells were transfected with 100nM miR-134 Mimetic precursor (Ambion;#17100, ID:PM10341) using Lipofectamine 2000 (Invitorgen protocol) and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Let7i-Pre-miR transfection replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Let7i Pre-miR (Ambion;#17100, ID:PM10517) using Lipofectamine 2000 (Invitorgen protocol) and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Scrambled oligo transfection plus 100nM RA treatment, 48hr, replicate 1


title: 100nM Scrambled oligo transfection replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with 100nM Scrambled (Ambion; AGACUAGCGGUAUCUUUAUCCC) oligomer using Lipofectamine 2000 (Invitorgen protocol) and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Anti-miR-134 transfection plus 100nM RA treatment, 48hr, replicate 1


title: plus 100nM RA treatment, 144h, replicate 1

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 144h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Scrambled oligo transfection replicate 1


title: plus 100nM RA treatment, 96h, replicate 1

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 96h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: 100nM Let7i-Pre-miR transfection replicate 1


title: plus 100nM RA treatment, 96h, replicate 2


title: mock transfection; Lipofectamine only replicate 2

extract_protocol: Mouse embryonic stem cells were transfected with Lipofectamine 2000 (Invitorgen protocol) only and total RNA extracted after 72h using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: mock transfection; Lipofectamine only replicate 1


title: 100nM miR134-mimetic transfection replicate 2

hyb_protocol: All Hybridisation and Wash procedures were performed following instructions in the Experienced User Card #2,  Hybridize/Wash 8-sample BeadChip protocol (Illumina). Briefly, 34ul of the Hyb mix with labeled cRNA sample was dispensed onto the center of each array and allowed to hyb with rotations in a pre-heated oven for 16-20h at 55*C. Washes were done with Wash E1BC solution, Block E1 solution was used for blocking and detection performed by Block E1 solution+Streptavidin-Cy3/5.	!Sample_hyb_protocol =All Hybridisation and Wash procedures were performed following instructions in the Experienced User Card #2,  Hybridize/Wash 8-sample BeadChip (Illumina). Briefly, 34ul of the Hyb mix with labeled cRNA sample was dispensed onto the center of each array and allowed to hyb with rotations in a pre-heated oven for 16-20h at 55*C. Washes were done with Wash E1BC solution, Block E1 solution was used for blocking and detection  performed by Block E1+Streptavidin-Cy3/5.


title: plus 100nM RA treatment, 48h, replicate 2

extract_protocol: Total RNA from Mouse embryonic stem cells with 100nM all-trans retinoic acid induction for 48h were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: plus 100nM RA treatment, 144h, replicate 2


title: minus RA treatment replicate 2

description: minus RA treatment replicate 2

extract_protocol: Total RNA from Mouse embryonic stem cells without all-trans retinoic acid induction were extracted using TRIzol reagent (Invitrogen) and further purified by Rneasy column (Qiagen;#75144).


title: minus RA treatment replicate 1

description: minus RA treatment replicate 1


title: plus 100nM RA treatment, 48h, replicate 1


title: 100nM Anti-miR-134 transfection plus 100nM RA treatment, 72hr, replicate 2


title: LIVER_ALLYL_ALCOHOL_16mg/kg_1days_exp2935_rep2_13484

description:
HybID: 13484
treated sample for experiment (RepID) 2935
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM220501: LIVER_ALLYL_ALCOHOL_16mg/kg_1days_exp2935_rep1_13483
Replicate experimental sample: GSM220503: LIVER_ALLYL_ALCOHOL_16mg/kg_1days_exp2935_rep3_13485
Matched control sample: GSM204723: LIVER_vehicle_NA_3days_control_NA_12836
Matched control sample: GSM204878: LIVER_vehicle_NA_7days_control_NA_12838
Matched control sample: GSM204611: LIVER_vehicle_NA_.25days_control_NA_12903
Matched control sample: GSM204729: LIVER_vehicle_NA_3days_control_NA_12905
Matched control sample: GSM204835: LIVER_vehicle_NA_5days_control_NA_13027
Matched control sample: GSM204877: LIVER_vehicle_NA_7days_control_NA_13034
Matched control sample: GSM204761: LIVER_vehicle_NA_3days_control_NA_13051
Matched control sample: GSM204849: LIVER_vehicle_NA_5days_control_NA_13053
Matched control sample: GSM204625: LIVER_vehicle_NA_.25days_control_NA_13077
Matched control sample: GSM204656: LIVER_vehicle_NA_1days_control_NA_13085
Matched control sample: GSM204840: LIVER_vehicle_NA_5days_control_NA_13086
Matched control sample: GSM204744: LIVER_vehicle_NA_3days_control_NA_13153
Matched control sample: GSM204683: LIVER_vehicle_NA_1days_control_NA_13223
Matched control sample: GSM204599: LIVER_vehicle_NA_.25days_control_NA_13369
Matched control sample: GSM204665: LIVER_vehicle_NA_1days_control_NA_13371
Matched control sample: GSM204601: LIVER_vehicle_NA_.25days_control_NA_13424
Matched control sample: GSM204672: LIVER_vehicle_NA_1days_control_NA_13427
Matched control sample: GSM204595: LIVER_vehicle_NA_.25days_control_NA_13505
Matched control sample: GSM204755: LIVER_vehicle_NA_3days_control_NA_13509
Matched control sample: GSM204827: LIVER_vehicle_NA_5days_control_NA_13512
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, ALLYL ALCOHOL, 16mg/kg, 1 days

extract_protocol: See Ganter et al., J Biotechnol. 2005 Sep 29;119(3):219-44. Following sacrifice, 6 mm disposable biopsy punches (#REF 33-36 Miltex, Inc. Bethpage, NY) were used to obtain tissue samples of approximately 100 mg. Samples were placed in cryogenic tubes and snap frozen. Poly A(+)-RNA from tissue samples was isolated using the MagNA Pure LC robot (Roche, Basel, Switzerland) in combination with the MagNA Pure LC mRNA Isolation kit I and II (Roche, Basel, Switzerland) for cells (see supplemental methods section) and tissues, respectively. Tissue samples were completely homogenized directly from ~100 mg punches stored on dry ice prior to application of lysis buffer to a final concentration of 65 mg tissue per ml of buffer. After complete homogenization, using disposable Omni Tip Disposable Generator Probes (Omni Inc, Warrenton, VA) and before loading of the samples into the 32-well MagNA Pure plate, the samples were drawn up 5-6 times through a 20-gauge needle attached to a 3-ml syringe to ensure any tissue pieces or clumps were removed from the lysate prior to robotic processing. Tissue sample processing was performed in duplicate wells (loading 150 ul of homogenized sample to each well) of the MagNA Pure LC, which is programmed to extract mRNA using the oligo-dT selection method into a final elution volume of 100 ul. Poly A(+) RNA sample concentration was performed manually using a standard ethanol precipitation protocol in the presence of glycogen (50 ug/ml). After precipitation the final purified RNA sample was resuspended in 7 ìl DEPC-H2O and quantified using a Ribogreen high-range assay (Molecular Probes) on the Wallac Victor2 Fluorometer (Perkin-Elmer, Fremont, CA). Additionally, the integrity of each RNA sample was determined, by comparison to historical standards (no gross degradation should be visible as suggested by clear 18S and 28S peaks on top of a hump of complex RNA, with lower amounts of RNA below 18S than under and above the 18S peak), using the Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA) in combination with the RNA 6000 Nano Lab Chip kit (Agilent Technologies).

tag: Sprague-Dawley

tag: age

value: 6 to 8 weeks

tag: sex

value: male

tag: tissue

value: LIVER

tag: treatment compound

value: ALLYL ALCOHOL

tag: dose

value: 16 mg/kg

tag: solvent

value: SALINE

tag: administration route

value: INTRAPERITONEAL

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 1 days

tag: experiment date


title: Cancer tissue from patient 771522-2

status: Public on Feb 18 2008

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

description: the microRNA expression in the tissue

hyb_protocol: Hybridization was performed at 42C under LifterSlipTM (Erie, Portsmouth, NH) in a hybridization chamber which was placed in a 3D-tilting agitator BioMixerTM  II (CapitalBio) to provide continuous mixing of the hybridization buffer that results in more uniform hybridization across the entire slide surface, preventing edge effects and giving improved signal intensity, the efficiency of which has been demonstrated with our genome-wide mRNA expression profiling (Patterson et al., Nat Biotechnol. 2006, 24:1140-1150).The array was then washed with two consecutive washing solutions of 0.2% SDS, 2X SSC at 42C for 5 min, and 0.2% SSC for 5 min at room temperature.

scan_protocol: Arrays were scanned with a LuxScanTM 10K-A laser confocal scanner and the images obtained were then analyzed using LuxScan 3.0TM software (both from CapitalBio, Beijing, China).

data_processing: After average values of the replicate spots of each miRNA were background subtracted, faint spots were filtered out when expression signal were lower than 800 in all samples.  Signal was normalized using the median center tool for genes in the Cluster 3.0 software before performing the unsupervised clustering with complete linkage and uncentered Pearson correlation to underlying the structure of the miRNA expression (Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns (Proc Natl Acad Sci U S A 1998;95:14863-8).

source_name: Cancer tissue from patient 771522-2

label_protocol: 4 ug of low-molecular-weight RNA was labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon, Lafayette, CO) with 2 units T4 RNA ligase (New England Biolabs, Ipswich, MA).  The labeling reaction was performed at 4C for 2 h.  Labeled RNA was precipitated with 0.3 M sodium acetate and 2.5 volumes ethanol and after washing with ethanol and drying was resuspended in 15 ul of hybridization buffer containing 3X SSC, 0.2% SDS and 15% formamide.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Carlsbad, CA) and the low-molecular-weight RNA was isolated by using the Ambion miRNA Isolation Kit

tag: Cancer tissue from patient 771522-2


title: Adjacent normal tissue from patient 200303-2

description: the microRNA expression in the tissue