title: E6.25_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51113.gif
Developmental Stage: E6.25

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.06; Parameter Scan Time = 16:51:32; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 22902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E8.0a_rep1

status: Public on Nov 06 2007

type: RNA

city: Stanford

first: Nesanet

last: Mitiku

state: CA

address: 300 Pasteur Drive Alway M313

department: Genetics

country: USA

institute: Stanford University

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51112.gif
Developmental Stage: E8

hyb_protocol: see channel 2 labeling protocol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 16:41:21; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 23513; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Mus musculus

source_name: REF

label_protocol: see channel 2 labeling protocol

extract_protocol: Reference RNA extraction: The common reference used in this work was comprised of a mixture of maternal brain, E17.5 embryo, E17.5 placenta, and CGR8 ES cells.  All tissues used in the reference RNA pool, with the exception of CGR8 ES cells, were ground via mortar and pestle in the presence of liquid nitrogen.  The resulting powder was put through one acid phenol extraction, two Trizol (Invitrogen) extractions, DNAse I (Ambion) treated, and then re-purified over RNAqueous Midi columns (Ambion).  The ES cell component of the reference pool was purified similarly beginning with the acid phenol extraction.  In lieu of mortar and pestle grinding, ES cells were spun down and directly resuspended in solution D.  Total RNA from all four sources was combined at a proportion of 1:1.5:2:2.5 (brain:placenta:ES cells:E17.5 embryos, according to mass) and linearly amplified (mMessageAmp, Ambion).  All reference amplification reactions were then pooled. This reference aRNA pool was used for all hybridizations.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku

tag: REF

source_name: EXP

label_protocol: Microarray Methods: Labeling and Hybridization  Each labeling reaction was carried out using 4 mcg of aRNA , 10 mcg of pDN6 (Amersham), 0.6 mcL 50X dNTPs (Invitrogen), 3 mcL 0.1M DTT, 3 mcL Cy3 or Cy5 dUTP and 2mcL Superscript II (Invitrogen) reverse transcriptase in the supplied buffer.  Samples were incubated at 42°C for 2 hours in an Eppendorf cycler with the lid heated to 47°C.  Each labeling reaction was stopped via the addition of 15 mcL of 0.1N NaOH + 2mM EDTA followed by incubation at 70°C for 10 min.  15 mcL of 0.1N HCL was added to neutralize each sample.  Cy3 and Cy5 samples for a single hybridization were combined.  Labeled aRNA samples were then purified over Microcon YM-30 columns (Millipore); samples were washed 5X with TE buffer and suspended in a volume of 10.14 mcl TE by the end of purification.; Protocol Type = Labeling; Performer: Nesanet,,Mitiku

extract_protocol:
Embryonic RNA extraction/preparation (experimental sample):  Total RNA was prepared using a variation on the acid phenol method of Chomczynski et al(Chomczynski and N. 1987).  The method of sample homogenization in solution D (4M guanidinium thiocyanate, 100mM NaOAc, 0.5% Sarkosyl, 0.1M beta-mercaptoethanol)  varied according to the composition of the sample from which RNA was being extracted. Early post-implantation embryos were transferred into microfuge tubes containing solution D immediately following dissection and staging; homogenization was achieved by flicking until complete dissolution.  Homogenized samples were stored at -80degC until RNA isolation.   On the day of RNA isolation, solution D-homogenized samples were defrosted and vortexed to ensure complete mixing.  As the initial volume of lysate was in accordance to the initial sample quantity, lysate volumes were variable, and solution volumes throughout the RNA isolation were adjusted for the initial lysate volume.  Initial lysate volumes were one of the following: 650 mcL/400 mcL/300 mcL/100 mcL.  Lysates were stored at -80degC.  65 mcL/40 mcL/30 mcL/10mcL NaOAc pH 4.0 was added to each defrosted sample, followed by 650 mcL/400 mcL/300 mcL/100 mcL H20-saturated phenols.  130 mcL/80 mcL/60 mcL/20 mcL of chloroform:isoamyl alcohol was added to each sample.  Samples were mixed via inversion then incubated on ice for 15 minutes.  After this incubation, samples were centrifuged at 20817g for 15 minutes at room temperature.  The top phase of each sample was removed carefully, so as not to disturb the cloudy interphase layer, and deposited in a fresh nuclease-free tube.  In order to precipitate the RNA, the following were added to each sample: 65 mcL/40 mcL/30 mcL/10 mcL NaOAc, 5 mcL linear acrylamide (Ambion), and 650 mcL/400 mcL/300 mcL/100 mcL isopropanol.   After the first round of RNA purification, all samples were stored at -80degC.  Prior to starting the second round of purifications, the samples were first defrosted on ice, and then centrifuged at 20817g for 30 minutes at room temperature.  The isopropanol was carefully aspirated, and the remaining pellet was resuspended in sample lysis buffer (RNAqueous Mini kit, Ambion).  During this step, the provided silica-based filter cartridges were assembled in microfuge tubes.  Following dissolution of the pellet, 400mcL of 64% ethanol was added.  Mixing was achieved through pipeting 2-3 times.  The resulting mixture was immediately applied to the previously prepared filter cartridges.  After centrifugation at 13000g for 1 minute, the flow-through was discarded.  Subsequently, each cartridge was washed once with 700mcL of Wash Solution #1 and twice with 500 mcL of Wash Solution #2.  Cartridges were spun for 1 minute in the absence of wash solution in order to remove any residual ethanol.  Purified RNA was eluted into a fresh nuclease free tube with nuclease-free H20 preheated to 75degC.  RNA integrity was assessed by examining 5mcL of each sample by gel electrophoresis. RNA was quantified using Ribogreen reagent (Molecular Probes).  Experimental samples were diluted 1:10 or 1:20, as needed to avoid signal saturation, prior to quantification.  RNA dilutions for standard curve generation were freshly prepared from the manufacturer supplied stock.  Each sample was prepared for measurement as follows: 2 mcL diluted experimental sample + 98 mcL nuclease-free TE + 100 mcL of freshly diluted Ribogreen reagent.  All measurements were conducted in 96 well format.  All embryonic samples were linearly amplified.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku
embryo samples; Outbred timed pregnant Swiss Webster mice were used for all experiments. Mice were sacrificed by cervical dislocation and uteri removed by caesarian section.  Uteri were washed in PBS and then transferred into Petri dishes containing fresh cold PBS.  Individual decidua were removed from each uterus and then transferred to fresh PBS with 10% Fetal Bovine Serum (FBS).  Embryos were dissected out of their implantation decidual tissue with fine watchmakers forceps under a light microscope.  Embryonic stage was determined by coupling gestational age to morphologic landmarks. After staging, embryos were either transferred into solution D (see sample extraction).; Protocol Type = Amplification; Performer: Nesanet,,Mitiku

tag: EXP


title: W3110 lsrK mutants, biological rep2

status: Public on Nov 02 2007

city: Bethesda

first: Jun

last: Li

state: MD

address: Rm 173, Building 14 A

institute: NIH

description: Gene expression data from embryos in slow phase of cellularisation.

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

scan_protocol: 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.

label: biotin

organism: Escherichia coli

source_name: W3110  lsrK mutants

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: E. coli grow in LB rich medium to OD600=2.4

extract_protocol: RNA samples were extracted via Invitrogen RNAeasy Kit and treated with DNaseI to remove all DNA

treatment_protocol: Cells treated with bacterial protect reagent and freeze at -70 C

tag: Genotype

value: E. coli K12


title: W3110 lsrR mutants, biological rep2

source_name: W3110 lsrR  mutants


title: E8.0a_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48018.gif
Developmental Stage: E8

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.80; Parameter Scan Time = 21:18:33; Parameter PMT Volts = 540; Parameter Scan Date = 2003-11-20; Parameter Pixel Size = 10; Parameter Laser on time = 22401; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: W3110 wild type, biological rep1

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

source_name: W3110 wild type


title: W3110 wild type, biological rep2


title: W3110 lsrR mutants, biological rep1


title: E8.5a_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50643.gif
Developmental Stage: E8.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 7080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.98; Parameter Scan Time = 19:57:56; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 23847; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep3_12950

status: Public on Jun 23 2007

city: Mountain View

first: Jeremy

last: Gollub

address: 325 E. Middlefield Rd.

institute: Iconix Biosciences

description:
HybID: 12950
treated sample for experiment (RepID) 2674
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204543: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep1_12949
Replicate experimental sample: GSM204544: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep2_14246
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

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, KETOCONAZOLE, 227mg/kg, 3 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: age

value: 6 to 8 weeks

tag: sex

value: male

tag: tissue

value: LIVER

tag: treatment compound

value: KETOCONAZOLE

tag: dose

value: 227 mg/kg

tag: solvent

value: CORN OIL

tag: administration route

value: ORAL GAVAGE

tag: frequency of dosing

value: DAILY

tag: treatment duration

value: 3 days

tag: experiment date


title: E7.0_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50638.gif
Developmental Stage: E7

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 18:06:18; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 23735; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep2_13526

description:
HybID: 13526
treated sample for experiment (RepID) 2977
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204567: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep3_13525
Replicate experimental sample: GSM204565: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep1_13527
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, LOVASTATIN, 1500mg/kg, 1 days

value: LOVASTATIN

value: 1 days


title: E7.25_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50639.gif
Developmental Stage: E7.25

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 19:15:00; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 23215; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 4.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep1_13527

description:
HybID: 13527
treated sample for experiment (RepID) 2977
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204567: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep3_13525
Replicate experimental sample: GSM204566: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep2_13526
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


title: E9.0_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51120.gif
Developmental Stage: E

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.34; Parameter Scan Time = 18:18:53; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 22989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E7.0_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48016.gif
Developmental Stage: E7

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 7080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.92; Parameter Scan Time = 21:49:11; Parameter PMT Volts = 540; Parameter Scan Date = 2003-11-20; Parameter Pixel Size = 10; Parameter Laser on time = 22432; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep3_13525

description:
HybID: 13525
treated sample for experiment (RepID) 2977
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204566: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep2_13526
Replicate experimental sample: GSM204565: LIVER_LOVASTATIN_1500mg/kg_1days_exp2977_rep1_13527
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


title: E8.5b_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50644.gif
Developmental Stage: E8.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.19; Parameter Scan Time = 17:21:13; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 23553; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.82; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E8.5a_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48015.gif
Developmental Stage: E8.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 19:42:23; Parameter PMT Volts = 540; Parameter Scan Date = 2003-11-20; Parameter Pixel Size = 10; Parameter Laser on time = 22305; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E6.5_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50636.gif
Developmental Stage: E6.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 15:21:59; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 23433; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E7.5_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48017.gif
Developmental Stage: E7.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.52; Parameter Scan Time = 20:48:49; Parameter PMT Volts = 540; Parameter Scan Date = 2003-11-20; Parameter Pixel Size = 10; Parameter Laser on time = 22372; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E6.25_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50634.gif
Developmental Stage: E6.25

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 7440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 18:49:05; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 23189; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.26; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E7.5_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50640.gif
Developmental Stage: E7.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 15:52:07; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 23464; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E7.75_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50641.gif
Developmental Stage: E7.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 7080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.13; Parameter Scan Time = 18:42:49; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 23772; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 4.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E8.75_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50645.gif
Developmental Stage: E8.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.19; Parameter Scan Time = 20:37:57; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 23887; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E8.0b_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50642.gif
Developmental Stage: E8.25

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.64; Parameter Scan Time = 19:24:49; Parameter PMT Volts = 540; Parameter Scan Date = 2004-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 23815; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 4.03; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: E8.5b_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51119.gif
Developmental Stage: E8.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 18:05:56; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 22977; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.99; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep1_12949

description:
HybID: 12949
treated sample for experiment (RepID) 2674
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204545: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep3_12950
Replicate experimental sample: GSM204544: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep2_14246
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


title: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep3_13394

description:
HybID: 13394
treated sample for experiment (RepID) 2853
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204489: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep2_13610
Replicate experimental sample: GSM204488: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep1_14835
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, FLUCONAZOLE, 394mg/kg, 1 days

value: FLUCONAZOLE

value: 394 mg/kg


title: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep1_13395

description:
HybID: 13395
treated sample for experiment (RepID) 2784
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204493: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep3_13216
Replicate experimental sample: GSM204492: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep2_13788
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, FLUCONAZOLE, 394mg/kg, 3 days


title: E6.75_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50637.gif
Developmental Stage: E6.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 19:02:23; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 23203; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep2_14246

description:
HybID: 14246
treated sample for experiment (RepID) 2674
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204543: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep1_12949
Replicate experimental sample: GSM204545: LIVER_KETOCONAZOLE_227mg/kg_3days_exp2674_rep3_12950
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


title: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep3_13216

description:
HybID: 13216
treated sample for experiment (RepID) 2784
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204491: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep1_13395
Replicate experimental sample: GSM204492: LIVER_FLUCONAZOLE_394mg/kg_3days_exp2784_rep2_13788
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


title: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep1_14835

description:
HybID: 14835
treated sample for experiment (RepID) 2853
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204490: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep3_13394
Replicate experimental sample: GSM204489: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep2_13610
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


title: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep2_15031

description:
HybID: 15031
treated sample for experiment (RepID) 3005
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204482: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep1_13553
Replicate experimental sample: GSM204484: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep3_14060
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, FINASTERIDE, 800mg/kg, 3 days

value: FINASTERIDE

value: 800 mg/kg


title: E6.5_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48014.gif
Developmental Stage: E6.5

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 20:09:17; Parameter PMT Volts = 540; Parameter Scan Date = 2003-11-20; Parameter Pixel Size = 10; Parameter Laser on time = 22332; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.79; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep3_15836

description:
HybID: 15836
treated sample for experiment (RepID) 2905
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204479: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep1_13551
Replicate experimental sample: GSM204480: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep2_13552
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

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).

source_name: LIVER, FINASTERIDE, 800mg/kg, 1 days


title: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep3_14060

description:
HybID: 14060
treated sample for experiment (RepID) 3005
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204482: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep1_13553
Replicate experimental sample: GSM204483: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep2_15031
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep2_13610

description:
HybID: 13610
treated sample for experiment (RepID) 2853
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204490: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep3_13394
Replicate experimental sample: GSM204488: LIVER_FLUCONAZOLE_394mg/kg_1days_exp2853_rep1_14835
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


title: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep1_13551

description:
HybID: 13551
treated sample for experiment (RepID) 2905
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204480: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep2_13552
Replicate experimental sample: GSM204481: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep3_15836
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


title: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep2_13552

description:
HybID: 13552
treated sample for experiment (RepID) 2905
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204479: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep1_13551
Replicate experimental sample: GSM204481: LIVER_FINASTERIDE_800mg/kg_1days_exp2905_rep3_15836
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


title: LIVER_FLUCONAZOLE_394mg/kg_5days_exp2997_rep1_15732

description:
HybID: 15732
treated sample for experiment (RepID) 2997
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204496: LIVER_FLUCONAZOLE_394mg/kg_5days_exp2997_rep3_13396
Replicate experimental sample: GSM204495: LIVER_FLUCONAZOLE_394mg/kg_5days_exp2997_rep2_13936
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, FLUCONAZOLE, 394mg/kg, 5 days

value: 5 days


title: E9.0_rep1

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50646.gif
Developmental Stage: E9

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.61; Parameter Scan Time = 19:50:15; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-17; Parameter Pixel Size = 10; Parameter Laser on time = 23251; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.73; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep1_13553

description:
HybID: 13553
treated sample for experiment (RepID) 3005
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204484: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep3_14060
Replicate experimental sample: GSM204483: LIVER_FINASTERIDE_800mg/kg_3days_exp3005_rep2_15031
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf


title: LIVER_CYTARABINE_487mg/kg_3days_exp3053_rep3_13892

description:
HybID: 13892
treated sample for experiment (RepID) 3053
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204375: LIVER_CYTARABINE_487mg/kg_3days_exp3053_rep2_13893
Replicate experimental sample: GSM204374: LIVER_CYTARABINE_487mg/kg_3days_exp3053_rep1_13894
Matched control sample: GSM204626: LIVER_vehicle_NA_.25days_control_NA_13650
Matched control sample: GSM204603: LIVER_vehicle_NA_.25days_control_NA_13655
Matched control sample: GSM204679: LIVER_vehicle_NA_1days_control_NA_13657
Matched control sample: GSM204743: LIVER_vehicle_NA_3days_control_NA_13660
Matched control sample: GSM204617: LIVER_vehicle_NA_.25days_control_NA_13855
Matched control sample: GSM204756: LIVER_vehicle_NA_3days_control_NA_13867
Matched control sample: GSM204825: LIVER_vehicle_NA_5days_control_NA_13875
Matched control sample: GSM204615: LIVER_vehicle_NA_.25days_control_NA_13923
Matched control sample: GSM204658: LIVER_vehicle_NA_1days_control_NA_13925
Matched control sample: GSM204736: LIVER_vehicle_NA_3days_control_NA_13932
Matched control sample: GSM204846: LIVER_vehicle_NA_5days_control_NA_14006
Matched control sample: GSM204614: LIVER_vehicle_NA_.25days_control_NA_14066
Matched control sample: GSM204661: LIVER_vehicle_NA_1days_control_NA_14072
Matched control sample: GSM204762: LIVER_vehicle_NA_3days_control_NA_14076
Matched control sample: GSM204612: LIVER_vehicle_NA_.25days_control_NA_14190
Matched control sample: GSM204818: LIVER_vehicle_NA_5days_control_NA_14279
Matched control sample: GSM204655: LIVER_vehicle_NA_1days_control_NA_14288
Matched control sample: GSM204823: LIVER_vehicle_NA_5days_control_NA_14298
Matched control sample: GSM204645: LIVER_vehicle_NA_1days_control_NA_14306
Matched control sample: GSM204735: LIVER_vehicle_NA_3days_control_NA_14311
Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf

source_name: LIVER, CYTARABINE, 487mg/kg, 3 days

value: CYTARABINE

value: 487 mg/kg

value: SALINE

value: INTRAVENOUS


title: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep3_13296

description:
HybID: 13296
treated sample for experiment (RepID) 2854
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204403: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep1_13297
Replicate experimental sample: GSM204404: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep2_13298
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, DIETHYLSTILBESTROL, 280mg/kg, 3 days

value: 6 to 8 weeks

value: male

value: LIVER

value: DIETHYLSTILBESTROL

value: 280 mg/kg


title: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep1_13297

description:
HybID: 13297
treated sample for experiment (RepID) 2854
replicate 1 of 3
Experimental sample
Replicate experimental sample: GSM204405: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep3_13296
Replicate experimental sample: GSM204404: LIVER_DIETHYLSTILBESTROL_280mg/kg_3days_exp2854_rep2_13298
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

value: CORN OIL

value: ORAL GAVAGE

value: DAILY

value: 3 days


title: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep3_13301

description:
HybID: 13301
treated sample for experiment (RepID) 2861
replicate 3 of 3
Experimental sample
Replicate experimental sample: GSM204399: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep1_13299
Replicate experimental sample: GSM204400: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep2_13300
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, DIETHYLSTILBESTROL, 280mg/kg, 1 days

value: 1 days


title: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep2_13300

description:
HybID: 13300
treated sample for experiment (RepID) 2861
replicate 2 of 3
Experimental sample
Replicate experimental sample: GSM204399: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep1_13299
Replicate experimental sample: GSM204401: LIVER_DIETHYLSTILBESTROL_280mg/kg_1days_exp2861_rep3_13301
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