title: Cr_L_11-2

description: Gene Expression after 24h exposed to Cr_L_11-2 in rat liver cell

value: Chromium (sodium chromate)_0.03-2


title: 7_Copper_90-2_R

status: Public on Jan 05 2010

type: RNA

city: Vicksburg

first: Xin

last: Guan

address: 3909 Halls Ferry Rd

department: EPP

country: USA

institute: USACE-ERDC

description: Gene Expression after 24h exposed to 7_Copper_90-2 in rat liver cell

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned at PMT levels 350 using GenePix 4200AL scanner (Molecular Device Inc.),

data_processing: The Feature extraction software (V. 9.5.1) from Agilent was used to automatically find and place microarray grids, reject outlier pixels, accurately determine feature intensities and ratios, flag outlier pixels, and calculate statistical confidences. First normalize be median perchip, then by median per gene, which means normalization by median value across all samples, then transformed to log2 based value.

molecule: total RNA

organism: Rattus norvegicus

label_protocol: Rat whole genome oligo arrays in the format of 4X44K were purchased from Agilent. Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 1.0). 1ug of total RNA was used. The Agilent One-Color Spike-Mix (part number 5188-5282) was diluted 5000-fold and 5 μL of the diluted spike-in mix was added to 1000 ng of each of the total RNA samples prior to labeling reactions. The labeling reactions were performed using the Agilent Low RNA Input Linear Amplification Kit in the presence of cyanine 3-CTP.

growth_protocol: The primary rat hepatocytes, rtNHeps (AC-2630), isolated from male Sprague Dawley and its hepatocyte culture medium (HCM), and supplements and growth factors (CC-3198) were purchased from Cambrex BioScience (Walkersville, MD).  Freshly isolated hepatocytes were shipped overnight on ice and processed immediately upon receipt.  These cells were seeded on BioCoat Type 1 Collagen-coated T-25 (BD356484) or T-75 (BD356485) flasks, or clear, flat-bottom, 96-well plates (BD356407) that were purchased from BD Biosciences (Palo Alto, CA).  Phosphate buffered saline (PBS, 21600-010), Trypsin-EDTA (15400-054), Trypan Blue stain (15250-061), Leibovitz medium (12448-015) were obtained from GIBCO-InVitrogen (Grand Island, NY).

extract_protocol: Total RNA was extracted from primary rat hepatocytes cell pellet.  Cell pellet were homogenized in the lysis buffer with FAST Prep-24 from MP at speed 6.0/s twice, each last 30s before using RNeasy kits (Qiagen). Total RNA concentrations were measured using NanoDrop® ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity and quality of total RNA was checked on an Agilent 2100 Bioanalyzer (Palo Alto, CA). The gel-like images generated by the Bioanalyzer show that total RNAs have two bands, represent 18S and 26S RNA of mammalian RNA . Nuclease-free water (Ambion) was used to elute total RNA.

treatment_protocol: The chemicals for the entire OMICS study were purchased from various sources:  Energetics from Chem Service (West Chester, PA) and SRI International (Menlo Park, CA); remaining chemicals from Sigma-Aldrich (St. Louis, MO) and Fisher Scientific (Fair Lawn, NJ).  The purity of all these compounds was equal or greater than 98%.  Prior to testing, the compounds were made up and serially diluted in dimethyl sulfoxide, DMSO (Fisher Scientific, Fair Lawn, NJ).  Metal compounds were made up and serially diluted in 0.1Fm-filtered, ultra-pure water before testing.  The 24-h toxicity of each OMICS compound was first determined in the human hepatocyte cell line HepG2 using the Neutral Red cytotoxicity kit (In Vitro Toxicology Kit Tox-4) obtained from Sigma-Aldrich.Primary rtNHeps cells collected at the end of the 24h chemical exposure were immediately stored in RNA Later (7021) purchased from Ambion (Austin, TX).  The primary rtN Heps cells were reconstituted in HCM supplemented with ascorbic acid, fatty acid-free bovine serum albumin, transferrin, insulin, recombinant human epidermal growth factor, hydrocortisone 21 hemisuccinate, Gentamicin sulfate, and Amphotericin B immediately upon receipt.  An aliquot of the cell suspension was stained in a 0.05% Trypan Blue solution and counted under an inverted microscope.  The cells were then seeded at 3 x 106 cells per (Type 1 collagen-coated) T-75 flask.   The flasks were left in a 37C, 5% CO2 incubator overnight to allow for cell attachment.    The cells were replenished with fresh HCM and dosed in triplicate flasks with the non-toxic concentration of each compound (pre-determined in the HepG2 cells) at 1% DMSO (v/v) or with solution at 1% water (v/v).  Another set of triplicate flasks were dosed with the appropriate solvent control.  Hence, for every 3 chemicals and a solvent control, a total of 12 flasks were used.After dosing, the flasks were returned to the incubator and incubated for 24 hours. The cells were washed with 1x PBS and detached with 1x trypsin-EDTA.  The cells were left in tryspin-EDTA no longer than 5 minutes.  Freshly warmed HCM was then added to neutralize the trypsin.  The cells were then transferred into a tube and centrifuged.  RNA Later was added the cell pellet and stored at –20C until genomic analysis

tag: treatment

value: Copper (copper II chloride dihydrate, CuCl2.2HO)_2

tag: dose

value: 10  ppm

tag: time

tag: cell type

value: primary rat hepatocytes, rtNHeps

tag: gender

value: Male


title: 7_Tungsten_90-2

description: Gene Expression after 24h exposed to 7_Tungsten_90-2 in rat liver cell

value: Tungsten (sodium tungstate dihydrate, Na2WO4.2H2O)_3

value: 100 ppm


title: 8_Nickel_90-2_R

description: Gene Expression after 24h exposed to 8_Nickel_90-2 in rat liver cell

value: Nickel (nickel (II) chloride, NiCl2)_3


title: 7_Copper_90-2

value: Copper (copper II chloride dihydrate, CuCl2.2HO)_1


title: 8_c_90-2

description: Gene Expression after 24h exposed to 8_control set_90-2 in rat liver cell

value: Solvent Control (Water)_1


title: 8_Zinc_90-1

description: Gene Expression after 24h exposed to 8_Zinc _90-1 in rat liver cell

value: Zinc (zinc sulfate heptahydrate, ZnSO4.7H2O)_2


title: 9_DEHP_90-1

description: Gene Expression after 24h exposed to 9_DEHP_90-1 in rat liver cell

value: DEHP (di-(2-ethylhexyl)phthalate)_1

value: 1 ppm


title: 8_Selenium_90-2

description: Gene Expression after 24h exposed to 8_Selenium_90-2 in rat liver cell

value: Selenium (sodium selenite, Na2SeO3)_2

value: 0.1 ppm


title: 8_c_90-2_R

value: Solvent Control (Water)_2


title: 8_Nickel_90-1

description: Gene Expression after 24h exposed to 8_Nickel _90-1 in rat liver cell

value: Nickel (nickel (II) chloride, NiCl2)_1


title: 7_Tungsten_90-2_R

value: Tungsten (sodium tungstate dihydrate, Na2WO4.2H2O)_1


title: 9_c_90-1

description: Gene Expression after 24h exposed to 9_control set_90-1 in rat liver cell

value: Solvent Control set9 (DMSO)_1


title: 8_Nickel_90-2

value: Nickel (nickel (II) chloride, NiCl2)_2

value: 10  ppm


title: 8_Selenium_90-2_R

value: Selenium (sodium selenite, Na2SeO3)_3

value: primary rat hepatocytes, rtNHeps

value: Male


title: 7_Copper_90-1

description: Gene Expression after 24h exposed to 7_Copper_90-1 in rat liver cell

value: Copper (copper II chloride dihydrate, CuCl2.2HO)_3


title: 8_c_90-1

description: Gene Expression after 24h exposed to 8_control set_90-1 in rat liver cell

value: Solvent Control set8 (Water)_3


title: 6_TNFa_90-1

description: Gene Expression after 24h exposed to 6_TNFa_90-1 in rat liver cell

value: TNFa (Cachectin) - rat_1

value: 10 ppb


title: 6_IL-3_90-2_R

description: Gene Expression after 24h exposed to 6_IL-3_90-2 in rat liver cell

value: IL-3 - human_2


title: 7_c_90-2

description: Gene Expression after 24h exposed to 7_control set_90-2 in rat liver cell


title: 7_c_90-2_R

value: Solvent Control (Water)_3


title: 6_TNFa_90-2

description: Gene Expression after 24h exposed to 6_TNFa_90-2 in rat liver cell

value: TNFa (Cachectin) - rat_2


title: 7_Cadmium_90-2_R

description: Gene Expression after 24h exposed to 7_Cadmium_90-2 in rat liver cell

value: Cadmium (cadmium chloride anhydrous, CdCl2)_2

value: 0.1 ppm


title: 6_LPS_90-1

description: Gene Expression after 24h exposed to 6_LPS_90-1 in rat liver cell

value: LPS (lipopolysaccharides)_1

value: 100 ppb


title: 7_Tungsten_90-1

description: Gene Expression after 24h exposed to 7_Tungsten_90-1 in rat liver cell

value: Tungsten (sodium tungstate dihydrate, Na2WO4.2H2O)_1

value: 100 ppm


title: 7_Cadmium_90-2

value: Cadmium (cadmium chloride anhydrous, CdCl2)_1


title: 6_TNFa_90-2_R

value: TNFa (Cachectin) - rat_3


title: 6_LPS_90-2_R

description: Gene Expression after 24h exposed to 6_LPS_90-2 in rat liver cell

value: LPS (lipopolysaccharides)_2

value: primary rat hepatocytes, rtNHeps


title: 6_LPS_90-2

value: LPS (lipopolysaccharides)_3

value: Male


title: 6_IL-3_90-1

description: Gene Expression after 24h exposed to 6_IL-3_90-1 in rat liver cell

value: IL-3 - human_1


title: 5_Naphthalene_90-2_R

description: Gene Expression after 24h exposed to 5_Naphthalene_90-2 in rat liver cell

value: 10 ppm


title: 6_IL-3_90-2

value: IL-3 - human_3

value: 10 ppb


title: 6_c_90-2_R

description: Gene Expression after 24h exposed to 6_control set_90-2 in rat liver cell

value: Solvent Control (Water)_2


title: 6_c_90-1

description: Gene Expression after 24h exposed to 6_control set_90-1 in rat liver cell

value: Solvent Control set6 (Water)_1


title: 6_c_90-2

value: Solvent Control (Water)_3


title: 5_Naphthalene_90-1

description: Gene Expression after 24h exposed to 5_Naphthalene_90-1 in rat liver cell


title: 7_c_90-1

description: Gene Expression after 24h exposed to 7_control set_90-1 in rat liver cell

value: Solvent Control set7 (Water)_1


title: 5_Naphthalene_90-2


title: 5_Anthracene_90-2_R

description: Gene Expression after 24h exposed to 5_Anthracene_90-2 in rat liver cell


title: Aceto_L_11-1

description: Gene Expression after 24h exposed to Aceto_L_11-1 in rat liver cell

value: 1 mM


title: Aceto_C_11-2

description: Gene Expression after 24h exposed to Aceto_control set_11-2 in rat liver cell


title: 5_c_90-2

description: Gene Expression after 24h exposed to 5_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_1


title: AS_H_11-2

description: Gene Expression after 24h exposed to AS_H_11-2 in rat liver cell

value: Arsenic (sodium (meta) arsenite)_1-2

value: 1 ppm


title: 5_Anthracene_90-2


title: 5_3-Methylcholanthrene_90-1

description: Gene Expression after 24h exposed to 5_3-Methylcholanthrene_90-1 in rat liver cell


title: 5_3-Methylcholanthrene_90-2

description: Gene Expression after 24h exposed to 5_3-Methylcholanthrene_90-2 in rat liver cell


title: 4_Perchlorate_90-1

description: Gene Expression after 24h exposed to 4_Perchlorate _90-1 in rat liver cell

source_name: 4_Perchlorate _90-1

value: Perchlorate (sodium perchlorate, NaClO4)_2

value: 100 ppm


title: 4_Perchlorate_90-2

description: Gene Expression after 24h exposed to 4_Perchlorate_90-2 in rat liver cell

value: Perchlorate (sodium perchlorate, NaClO4)_3

value: primary rat hepatocytes, rtNHeps


title: 5_3-Methylcholanthrene_90-2_R

value: Male


title: 4_Lead_90-1

description: Gene Expression after 24h exposed to 4_Lead _90-2 in rat liver cell

value: Lead (lead nitrate, Pb(NO3)2)_1


title: 4_Lead_90-2_R

description: Gene Expression after 24h exposed to 4_Lead_90-1 in rat liver cell

value: Lead (lead nitrate, Pb(NO3)2)_2

value: 10 ppm


title: 5_Anthracene_90-1

description: Gene Expression after 24h exposed to 5_Anthracene_90-1 in rat liver cell


title: 4_Cr_90-2

description: Gene Expression after 24h exposed to 4_Cr_90-2 in rat liver cell

value: Chromium (hexavalent chromium, K2CrO4)_2

value: 0.1 ppm


title: 4_Perchlorate_90-2_R

value: Perchlorate (sodium perchlorate, NaClO4)_1


title: 5_c_90-2_R

value: Solvent Control (DMSO)_2


title: 4_c_90-2_R

description: Gene Expression after 24h exposed to 4_control set_90-2 in rat liver cell

value: Solvent Control (Water)_3


title: 4_Lead_90-2

value: Lead (lead nitrate, Pb(NO3)2)_3


title: 4_Cr_90-1

description: Gene Expression after 24h exposed to 4_Cr_90-1 in rat liver cell

value: Chromium (hexavalent chromium, K2CrO4)_1


title: 4_c_90-1

description: Gene Expression after 24h exposed to 4_control set_90-1 in rat liver cell

value: Solvent Control set4 (Water)_1


title: 33_Fluoranthene_90-2_R

description: Gene Expression after 24h exposed to 33_Fluoranthene_90-2 in rat liver cell

value: Fluoranthene (aka Benzo[j,k]fluorene)_3


title: 33_Piperonyl-Butoxide_90-2_R

description: Gene Expression after 24h exposed to 33_Piperonyl Butoxide_90-2 in rat liver cell

source_name: 33_Piperonyl Butoxide_90-2

value: Piperonyl Butoxide (PBO)_2


title: 4_c_90-2

value: Solvent Control (Water)_2


title: 33_Piperonyl-Butoxide_90-1

description: Gene Expression after 24h exposed to 33_Piperonyl Butoxide _90-1 in rat liver cell

source_name: 33_Piperonyl Butoxide _90-1

value: Piperonyl Butoxide (PBO)_3


title: 33_Fluoranthene_90-1

description: Gene Expression after 24h exposed to 33_Fluoranthene_90-1 in rat liver cell

value: Fluoranthene (aka Benzo[j,k]fluorene)_1

value: primary rat hepatocytes, rtNHeps


title: 33_c_90-2

description: Gene Expression after 24h exposed to 33_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_1

value: Male


title: 33_Fluoranthene_90-2

value: Fluoranthene (aka Benzo[j,k]fluorene)_2

value: 10 ppm


title: 4_Cr_90-2_R

value: Chromium (hexavalent chromium, K2CrO4)_3

value: 0.1 ppm


title: 33_Benzo_90-1

description: Gene Expression after 24h exposed to 33_Benzo_90-1 in rat liver cell

value: Benzo(a)pyrene (BaP)_1

value: 1 ppm


title: 32_PCB_90-2

description: Gene Expression after 24h exposed to 32_PCB_90-2 in rat liver cell

value: PCB 126 (co-planar PCB)_1

value: 100 ppb


title: 33_Benzo_90-2_R

description: Gene Expression after 24h exposed to 33_Benzo_90-2 in rat liver cell

value: Benzo(a)pyrene (BaP)_3


title: 33_c_90-1

description: Gene Expression after 24h exposed to 33_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_3


title: 32_PCB_90-2_R

value: PCB 126 (co-planar PCB)_3


title: 32_2-3-7-8-TCDD_90-1

description: Gene Expression after 24h exposed to  32_2-3-7-8-TCDD_90-1  in rat liver cell

value: 0.1 ppb


title: 33_c_90-2_R

value: Solvent Control (DMSO)_2


title: 32_c_90-2_R

description: Gene Expression after 24h exposed to 32_control set_90-2 in rat liver cell

value: Solvent Control (Iso-octane)_2


title: 32_c_90-2

value: Solvent Control (Iso-octane)_1

value: primary rat hepatocytes, rtNHeps


title: 33_Benzo_90-2

value: Benzo(a)pyrene (BaP)_2

value: Male


title: 33_Piperonyl-Butoxide_90-2

value: Piperonyl Butoxide (PBO)_1

value: 10 ppm


title: 32_2-3-7-8-TCDD_90-2

description: Gene Expression after 24h exposed to  32_2-3-7-8-TCDD_90-2  in rat liver cell


title: 32_PCB_90-1

description: Gene Expression after 24h exposed to 32_PCB_90-1 in rat liver cell

value: PCB 126 (co-planar PCB)_2


title: 32_2-3-7-8-TCDD_90-2_R


title: 32_c_90-1

description: Gene Expression after 24h exposed to 32_control set_90-1 in rat liver cell

value: Solvent Control (Iso-octane)_3


title: 32_2-3-7-8-TBDD_90-2_R

description: Gene Expression after 24h exposed to  32_2-3-7-8-TBDD_90-2  in rat liver cell


title: 32_2-3-7-8-TBDD_90-2


title: 31_Phenobarbital_90-2_R

description: Gene Expression after 24h exposed to 31_Phenobarbital_90-2 in rat liver cell


title: 32_2-3-7-8-TBDD_90-1

description: Gene Expression after 24h exposed to  32_2-3-7-8-TBDD_90-1  in rat liver cell


title: 31_Phenobarbital_90-2


title: 7_Cadmium_90-1

description: Gene Expression after 24h exposed to 7_Cadmium _90-1 in rat liver cell

source_name: 7_Cadmium _90-1

value: Cadmium (cadmium chloride anhydrous, CdCl2)_3

value: 0.1 ppm


title: 31_Carbon-Tetrachloride_90-1

description: Gene Expression after 24h exposed to 31_Carbon Tetrachloride_90-1 in rat liver cell

source_name: 31_Carbon Tetrachloride_90-1

value: Carbon Tetrachloride_3


title: 31_Carbon-Tetrachloride_90-2

description: Gene Expression after 24h exposed to 31_Carbon Tetrachloride_90-2 in rat liver cell

source_name: 31_Carbon Tetrachloride_90-2

value: Carbon Tetrachloride_1


title: 31_Carbon-Tetrachloride_90-2_R

value: Carbon Tetrachloride_2


title: 31_Beta-Naphthoflavone_90-2_R

description: Gene Expression after 24h exposed to 31_Beta-Naphthoflavone_90-2 in rat liver cell

value: 1 ppm


title: 31_c_90-1

description: Gene Expression after 24h exposed to 31_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_3


title: 30_TNX_90-2

description: Gene Expression after 24h exposed to 30_TNX_90-2 in rat liver cell


title: 31_c_90-2

description: Gene Expression after 24h exposed to 31_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_1


title: 31_Phenobarbital_90-1

description: Gene Expression after 24h exposed to 31_Phenobarbital_90-1 in rat liver cell


title: 31_c_90-2_R

value: Solvent Control (DMSO)_2


title: 31_Beta-Naphthoflavone_90-1

description: Gene Expression after 24h exposed to 31_Beta-Naphthoflavone_90-1 in rat liver cell


title: 31_Beta-Naphthoflavone_90-2


title: 30_TNX_90-1

description: Gene Expression after 24h exposed to 30_TNX_90-1 in rat liver cell


title: 30_MNX_90-2_R

description: Gene Expression after 24h exposed to 30_MNX_90-2 in rat liver cell


title: 30_Methotrexate_90-2

description: Gene Expression after 24h exposed to 30_Methotrexate_90-2 in rat liver cell

value: ~14 ppm


title: 30_TNX_90-2_R

value: primary rat hepatocytes, rtNHeps


title: 30_Methotrexate_90-2_R


title: 30_MNX_90-2


title: 30_c_90-1

description: Gene Expression after 24h exposed to 30_control set_90-1 in rat liver cell


title: 30_Methotrexate_90-1

description: Gene Expression after 24h exposed to 30_Methotrexate_90-1 in rat liver cell


title: 30_c_90-2

description: Gene Expression after 24h exposed to 30_control set_90-2 in rat liver cell


title: 3_RDX_90-2_R

description: Gene Expression after 24h exposed to 3_RDX_90-2 in rat liver cell


title: 30_c_90-2_R


title: 3_c_90-2

description: Gene Expression after 24h exposed to 3_control set_90-2 in rat liver cell


title: 3_RDX_90-2


title: 30_MNX_90-1

description: Gene Expression after 24h exposed to 30_MNX_90-1 in rat liver cell


title: 3_RDX_90-1

description: Gene Expression after 24h exposed to 3_RDX_90-1 in rat liver cell


title: 3_c_90-1

description: Gene Expression after 24h exposed to 3_control set_90-1 in rat liver cell

value: Solvent Control set3 (DMSO)_2


title: 3_4-amino-2-6-DNT_90-1

description: Gene Expression after 24h exposed to  3_4-amino-2-6-DNT_90-1  in rat liver cell

value: Male


title: 3_4-amino-2-6-DNT_90-2

description: Gene Expression after 24h exposed to  3_4-amino-2-6-DNT_90-2  in rat liver cell


title: 3_c_90-2_R


title: 5_c_90-1

description: Gene Expression after 24h exposed to 5_control set_90-1 in rat liver cell

value: Solvent Control set5 (DMSO)_3


title: 3_1-3-5-TNB_90-2_R

description: Gene Expression after 24h exposed to  3_1-3-5-TNB_90-2  in rat liver cell


title: 29_HMX_90-2_R

description: Gene Expression after 24h exposed to 29_HMX_90-2 in rat liver cell

value: 10 ppm


title: 3_1-3-5-TNB_90-2


title: 3_4-amino-2-6-DNT_90-2_R


title: 29_HMX_90-2


title: 29_HMX_90-1

description: Gene Expression after 24h exposed to 29_HMX_90-1 in rat liver cell


title: 3_1-3-5-TNB_90-1

description: Gene Expression after 24h exposed to  3_1-3-5-TNB_90-1  in rat liver cell


title: 29_DDT_90-1

description: Gene Expression after 24h exposed to 29_DDT_90-1 in rat liver cell


title: 29_DDT_90-2_R

description: Gene Expression after 24h exposed to 29_DDT_90-2 in rat liver cell


title: 29_CL-20_90-2

description: Gene Expression after 24h exposed to 29_CL-20_90-2 in rat liver cell


title: 29_DDT_90-2


title: 28_c_90-2

description: Gene Expression after 24h exposed to 28_control set_90-2 in rat liver cell


title: 28_Pentachlorophenol_90-2_R

description: Gene Expression after 24h exposed to 28_Pentachlorophenol_90-2 in rat liver cell


title: 29_CL-20_90-2_R


title: 29_c_90-2

description: Gene Expression after 24h exposed to 29_control set_90-2 in rat liver cell


title: 28_4-Hydroxynonenal_90-2_R

description: Gene Expression after 24h exposed to 28_4-Hydroxynonenal_90-2 in rat liver cell

value: 4-Hydroxynonenal (HNE-DMA)*_3

value: (5 uM ) 1 ppm


title: 28_c_90-1

description: Gene Expression after 24h exposed to 28_control set_90-1 in rat liver cell


title: 28_Pentachlorophenol_90-2


title: 28_Trichloroethylene_90-1

description: Gene Expression after 24h exposed to 28_Trichloroethylene_90-1 in rat liver cell

value: Trichloroethylene (TCE)_3

value: 100 ppm


title: 28_4-Hydroxynonenal_90-1

description: Gene Expression after 24h exposed to 28_4-Hydroxynonenal_90-1 in rat liver cell

value: 4-Hydroxynonenal (HNE-DMA)*_1


title: 28_c_90-2_R


title: 29_c_90-1

description: Gene Expression after 24h exposed to 29_control set_90-1 in rat liver cell


title: 28_Pentachlorophenol_90-1

description: Gene Expression after 24h exposed to 28_Pentachlorophenol_90-1 in rat liver cell


title: 29_c_90-2_R


title: 27_Spectromycin_90-1

description: Gene Expression after 24h exposed to 27_Spectromycin _90-1 in rat liver cell

source_name: 27_Spectromycin _90-1

value: Spectromycin (sulfate)_1


title: 28_4-Hydroxynonenal_90-2

value: 4-Hydroxynonenal (HNE-DMA)*_2


title: 28_Trichloroethylene_90-2_R

description: Gene Expression after 24h exposed to 28_Trichloroethylene_90-2 in rat liver cell

value: Trichloroethylene (TCE)_2


title: 29_CL-20_90-1

description: Gene Expression after 24h exposed to 29_CL-20_90-1 in rat liver cell


title: 27_Spectromycin_90-2

description: Gene Expression after 24h exposed to 27_Spectromycin_90-2 in rat liver cell

value: Spectromycin (sulfate)_2


title: 27_Spectromycin_90-2_R

value: Spectromycin (sulfate)_3


title: 27_Penicillin-G_90-2_R

description: Gene Expression after 24h exposed to 27_Penicillin G_90-2 in rat liver cell

source_name: 27_Penicillin G_90-2

value: Penicillin G_3


title: 27_Penicillin-G_90-1

description: Gene Expression after 24h exposed to 27_Penicillin G_90-1 in rat liver cell

source_name: 27_Penicillin G_90-1

value: Penicillin G_2


title: 27_Paraquat_90-2

description: Gene Expression after 24h exposed to 27_Paraquat_90-2 in rat liver cell

value: Paraquat (Cl Tetrahydrate)_2

value: primary rat hepatocytes, rtNHeps


title: 27_Paraquat_90-2_R

value: Paraquat (Cl Tetrahydrate)_3

value: Male


title: 27_c_90-2_R

description: Gene Expression after 24h exposed to 27_control set_90-2 in rat liver cell

value: Solvent Control (Water)_3


title: 27_Penicillin-G_90-2

value: Penicillin G_1


title: 26_Musk-xylene_90-2

description: Gene Expression after 24h exposed to 26_Musk xylene_90-2 in rat liver cell

source_name: 26_Musk xylene_90-2

value: Musk xylene_2

value: 1 ppm


title: 26_Musk-xylene_90-2_R

value: Musk xylene_3


title: 28_Trichloroethylene_90-2

value: Trichloroethylene (TCE)_1

value: 100 ppm


title: 27_c_90-1

description: Gene Expression after 24h exposed to 27_control set_90-1 in rat liver cell

value: Solvent Control (Water)_1


title: 27_c_90-2

value: Solvent Control (Water)_2


title: 26_DIM_90-2

description: Gene Expression after 24h exposed to 26_DIM_90-2 in rat liver cell

value: DIM (3',3-diindolylmethane) (CAS 1968-05-4)_2


title: 26_DIM_90-2_R

value: DIM (3',3-diindolylmethane) (CAS 1968-05-4)_3


title: 26_Chlorpyrifos_90-1

description: Gene Expression after 24h exposed to 26_Chlorpyrifos_90-1 in rat liver cell

value: 10 ppm


title: 25_Etoposide_90-2_R

description: Gene Expression after 24h exposed to 25_Etoposide_90-2 in rat liver cell

value: Etoposide (VP16)_3


title: 26_Chlorpyrifos_90-2

description: Gene Expression after 24h exposed to 26_Chlorpyrifos_90-2 in rat liver cell

value: 0.1 ppm


title: 26_DIM_90-1

description: Gene Expression after 24h exposed to 26_DIM _90-1 in rat liver cell

value: DIM (3',3-diindolylmethane) (CAS 1968-05-4)_1

value: primary rat hepatocytes, rtNHeps


title: 26_Chlorpyrifos_90-2_R

value: Male


title: 25_Cytochalasin_90-2

description: Gene Expression after 24h exposed to 25_Cytochalasin_90-2 in rat liver cell

value: Cytochalasin D_1


title: 26_c_90-2_R

description: Gene Expression after 24h exposed to 26_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_3


title: 25_Etoposide_90-2

value: Etoposide (VP16)_2


title: 25_Doxorubicin_90-1

description: Gene Expression after 24h exposed to 25_Doxorubicin_90-1 in rat liver cell

value: Doxorubicin (Adriamycin) (HCl)_2

value: 0.3 ppm


title: 26_c_90-2

value: Solvent Control (DMSO)_2


title: 26_c_90-1

description: Gene Expression after 24h exposed to 26_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_1


title: 25_Etoposide_90-1

description: Gene Expression after 24h exposed to 25_Etoposide_90-1 in rat liver cell

value: Etoposide (VP16)_1

value: 1 ppm


title: 25_Cytochalasin_90-2_R

value: Cytochalasin D_2


title: 25_Doxorubicin_90-2

description: Gene Expression after 24h exposed to 25_Doxorubicin_90-2 in rat liver cell

value: Doxorubicin (Adriamycin) (HCl)_1


title: 25_Doxorubicin_90-2_R

value: Doxorubicin (Adriamycin) (HCl)_3


title: 25_c_90-1

description: Gene Expression after 24h exposed to 25_control set_90-1 in rat liver cell


title: 25_Cytochalasin_90-1

description: Gene Expression after 24h exposed to 25_Cytochalasin_90-1 in rat liver cell

value: Cytochalasin D_3

value: 10 ppm


title: 25_c_90-2_R

description: Gene Expression after 24h exposed to 25_control set_90-2 in rat liver cell


title: 25_c_90-2


title: 27_Paraquat_90-1

description: Gene Expression after 24h exposed to 27_Paraquat_90-1 in rat liver cell

value: Paraquat (Cl Tetrahydrate)_1


title: 24_Rosiglitazone_90-2

description: Gene Expression after 24h exposed to 24_Rosiglitazone_90-2 in rat liver cell

value: 3 ppm

value: primary rat hepatocytes, rtNHeps


title: 24_PFDA_90-1

description: Gene Expression after 24h exposed to 24_PFDA_90-1 in rat liver cell

value: PFDA (perfluorodecanoic acid)_2

value: 30 ppm

value: Male


title: 24_WY_90-1

description: Gene Expression after 24h exposed to 24_WY_90-1 in rat liver cell

value: WY-14643 (Pirixinic Acid)_1

value: 10  ppm


title: 24_PFDA_90-2_R

description: Gene Expression after 24h exposed to 24_PFDA_90-2 in rat liver cell

value: PFDA (perfluorodecanoic acid)_3


title: 23_Clofibrate_90-2_R

description: Gene Expression after 24h exposed to 23_Clofibrate_90-2 in rat liver cell

value: 100  ppm


title: 24_Rosiglitazone_90-1

description: Gene Expression after 24h exposed to 24_Rosiglitazone_90-1 in rat liver cell


title: 24_PFDA_90-2

value: PFDA (perfluorodecanoic acid)_1


title: 24_Rosiglitazone_90-2_R


title: 24_WY_90-2

description: Gene Expression after 24h exposed to 24_WY_90-2 in rat liver cell

value: WY-14643 (Pirixinic Acid)_2


title: 24_c_90-2_R

description: Gene Expression after 24h exposed to 24_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_3


title: 24_c_90-1

description: Gene Expression after 24h exposed to 24_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_1


title: 24_WY_90-2_R

value: WY-14643 (Pirixinic Acid)_3


title: 23_c_90-2

description: Gene Expression after 24h exposed to 23_control set_90-2 in rat liver cell


title: 23_Chlorpheniramine_90-2_R

description: Gene Expression after 24h exposed to 23_Chlorpheniramine_90-2 in rat liver cell


title: 23_Chlorpheniramine_90-1

description: Gene Expression after 24h exposed to 23_Chlorpheniramine_90-1 in rat liver cell


title: 23_Atorvastatin_90-2

description: Gene Expression after 24h exposed to 23_Atorvastatin_90-2 in rat liver cell

value: 1 ppm


title: 23_Clofibrate_90-2


title: 23_Clofibrate_90-1

description: Gene Expression after 24h exposed to 23_Clofibrate_90-1 in rat liver cell


title: 24_c_90-2

value: Solvent Control (DMSO)_2


title: 23_Atorvastatin_90-2_R


title: 23_c_90-1

description: Gene Expression after 24h exposed to 23_control set_90-1 in rat liver cell


title: 23_c_90-2_R


title: 23_Chlorpheniramine_90-2

value: 10 ppm


title: 23_Atorvastatin_90-1

description: Gene Expression after 24h exposed to 23_Atorvastatin_90-1 in rat liver cell


title: 22_Cyclosporin-A_90-2

description: Gene Expression after 24h exposed to 22_Cyclosporin A_90-2 in rat liver cell

source_name: 22_Cyclosporin A_90-2

value: Cyclosporin A_2

value: 3 ppm


title: 22_Cyclosporin-A_90-2_R

value: Cyclosporin A_3

value: primary rat hepatocytes, rtNHeps


title: 22_Cyclophosphamide_90-2_R

description: Gene Expression after 24h exposed to 22_Cyclophosphamide_90-2 in rat liver cell

value: 100 ppm

value: Male


title: 22_c_90-1

description: Gene Expression after 24h exposed to 22_control set_90-1 in rat liver cell


title: 22_c_90-2

description: Gene Expression after 24h exposed to 22_control set_90-2 in rat liver cell


title: 22_Chlorpromazine_90-1

description: Gene Expression after 24h exposed to 22_Chlorpromazine_90-1 in rat liver cell

value: Chlorpromazine (HCl)_3


title: 22_Chlorpromazine_90-2

description: Gene Expression after 24h exposed to 22_Chlorpromazine_90-2 in rat liver cell

value: Chlorpromazine (HCl)_1


title: 21_Permethrin_90-2

description: Gene Expression after 24h exposed to 21_Permethrin_90-2 in rat liver cell


title: 22_c_90-2_R


title: 21_Toxaphene_90-2_R

description: Gene Expression after 24h exposed to 21_Toxaphene_90-2 in rat liver cell


title: 22_Cyclophosphamide_90-1

description: Gene Expression after 24h exposed to 22_Cyclophosphamide_90-1 in rat liver cell


title: 22_Cyclophosphamide_90-2


title: 22_Cyclosporin-A_90-1

description: Gene Expression after 24h exposed to 22_Cyclosporin A_90-1 in rat liver cell

source_name: 22_Cyclosporin A_90-1

value: Cyclosporin A_1


title: 21_Toxaphene_90-2


title: 21_Permethrin_90-1

description: Gene Expression after 24h exposed to 21_Permethrin_90-1 in rat liver cell


title: 21_Permethrin_90-2_R


title: 22_Chlorpromazine_90-2_R

value: Chlorpromazine (HCl)_2


title: 20_Oltipraz_90-1

description: Gene Expression after 24h exposed to 20_Oltipraz_90-1 in rat liver cell


title: 21_Methoxychlor_90-2

description: Gene Expression after 24h exposed to 21_Methoxychlor_90-2 in rat liver cell


title: 21_Methoxychlor_90-2_R


title: 21_Methoxychlor_90-1

description: Gene Expression after 24h exposed to 21_Methoxychlor_90-1 in rat liver cell


title: 21_c_90-2

description: Gene Expression after 24h exposed to 21_control set_90-2 in rat liver cell


title: 21_c_90-1

description: Gene Expression after 24h exposed to 21_control set_90-1 in rat liver cell


title: 20_c_90-2_R

description: Gene Expression after 24h exposed to 20_control set_90-2 in rat liver cell


title: 21_c_90-2_R


title: 20_Ethoxyquin_90-1

description: Gene Expression after 24h exposed to 20_Ethoxyquin_90-1 in rat liver cell


title: 20_Oltipraz_90-2

description: Gene Expression after 24h exposed to 20_Oltipraz_90-2 in rat liver cell


title: 20_Oltipraz_90-2_R


title: 20_Ethoxyquin_90-2

description: Gene Expression after 24h exposed to 20_Ethoxyquin_90-2 in rat liver cell


title: 20_c_90-1

description: Gene Expression after 24h exposed to 20_control set_90-1 in rat liver cell


title: 20_2-4-Dinitrophenol_90-2

description: Gene Expression after 24h exposed to  20_2-4-Dinitrophenol_90-2  in rat liver cell


title: 20_c_90-2


title: 20_Ethoxyquin_90-2_R


title: 20_2-4-Dinitrophenol_90-1

description: Gene Expression after 24h exposed to  20_2-4-Dinitrophenol_90-1  in rat liver cell


title: 2_2-amino-4-4-DNT_90-2

description: Gene Expression after 24h exposed to  2_2-amino-4-4-DNT_90-2  in rat liver cell


title: 21_Toxaphene_90-1

description: Gene Expression after 24h exposed to 21_Toxaphene_90-1 in rat liver cell


title: 2_2-4-diamino-6-nitrotoluene_90-1

description: Gene Expression after 24h exposed to  2_2-4-diamino-6-nitrotoluene_90-1  in rat liver cell


title: 2_2-amino-4-6-DNT_90-2_R

description: Gene Expression after 24h exposed to  2_2-amino-4-6-DNT_90-2  in rat liver cell


title: 2_2-4-diamino-6-nitrotoluene_90-2_R

description: Gene Expression after 24h exposed to  2_2-4-diamino-6-nitrotoluene_90-2  in rat liver cell


title: 2_2-amino-4-6-DNT_90-1

description: Gene Expression after 24h exposed to  2_2-amino-4-6-DNT_90-1  in rat liver cell


title: 2_2-4-diamino-6-nitrotoluene_90-2


title: 2_2-amino-4-4-DNT_90-1

description: Gene Expression after 24h exposed to  2_2-amino-4-4-DNT_90-1  in rat liver cell


title: 2_2-amino-4-6-DNT_90-2


title: 2_c_90-2_R

description: Gene Expression after 24h exposed to 2_control set_90-2 in rat liver cell


title: 2_2-amino-4-4-DNT_90-2_R


title: 20_2-4-Dinitrophenol_90-2_R


title: 19_Fipronil_90-2

description: Gene Expression after 24h exposed to 19_Fipronil_90-2 in rat liver cell


title: 19_Fipronil_90-2_R


title: 2_c_90-1

description: Gene Expression after 24h exposed to 2_control set_90-1 in rat liver cell

value: Solvent Control set2 (DMSO)_3


title: 2_c_90-2


title: 19_DEET_90-2

description: Gene Expression after 24h exposed to 19_DEET_90-2 in rat liver cell


title: 19_DEET_90-2_R


title: 19_DEET_90-1

description: Gene Expression after 24h exposed to 19_DEET_90-1 in rat liver cell


title: 19_c_90-2_R

description: Gene Expression after 24h exposed to 19_control set_90-2 in rat liver cell


title: 19_4-Bromophenyl_90-1

description: Gene Expression after 24h exposed to 19_4-Bromophenyl_90-1 in rat liver cell

value: 4-Bromophenyl phenyl ether_2


title: 19_c_90-2

value: Solvent Control (DMSO)_3


title: 18_Vinblastine-sulfate_90-2

description: Gene Expression after 24h exposed to  18_Vinblastine- sulfate_90-2  in rat liver cell

source_name: 18_Vinblastine- sulfate_90-2

value: Vinblastine, sulfate_1


title: 19_4-Bromophenyl_90-2_R

description: Gene Expression after 24h exposed to 19_4-Bromophenyl_90-2 in rat liver cell

value: 4-Bromophenyl phenyl ether_3


title: 18_Vinblastine-sulfate_90-1

description: Gene Expression after 24h exposed to  18_Vinblastine- sulfate_90-1  in rat liver cell

source_name: 18_Vinblastine- sulfate_90-1

value: Vinblastine, sulfate_3


title: 19_c_90-1

description: Gene Expression after 24h exposed to 19_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_1


title: 18_Vinblastine-sulfate_90-2_R

value: Vinblastine, sulfate_2

value: 10 ppm


title: 18_Camptothecin_90-2_R

description: Gene Expression after 24h exposed to 18_Camptothecin_90-2 in rat liver cell

value: 10 ppb


title: 19_4-Bromophenyl_90-2

value: 4-Bromophenyl phenyl ether_1

value: primary rat hepatocytes, rtNHeps


title: 18_Clotrimazole_90-1

description: Gene Expression after 24h exposed to 18_Clotrimazole_90-1 in rat liver cell

value: 1  ppm

value: Male


title: 17_SR12813_90-1

description: Gene Expression after 24h exposed to 17_SR12813_90-1 in rat liver cell


title: 17_Hyperforin_90-2_R

description: Gene Expression after 24h exposed to 17_Hyperforin_90-2 in rat liver cell

value: 0.3 ppm


title: 17_Hyperforin_90-2


title: 18_c_90-2_R

description: Gene Expression after 24h exposed to 18_control set_90-2 in rat liver cell


title: 17_Taxol_90-1

description: Gene Expression after 24h exposed to 17_Taxol_90-1 in rat liver cell

value: Taxol  (Placitaxel)_3


title: 17_SR12813_90-2_R

description: Gene Expression after 24h exposed to 17_SR12813_90-2 in rat liver cell


title: 17_Taxol_90-2_R

description: Gene Expression after 24h exposed to 17_Taxol_90-2 in rat liver cell

value: Taxol  (Placitaxel)_2


title: 18_Clotrimazole_90-2

description: Gene Expression after 24h exposed to 18_Clotrimazole_90-2 in rat liver cell


title: 17_Taxol_90-2

value: Taxol  (Placitaxel)_1


title: 18_c_90-1

description: Gene Expression after 24h exposed to 18_control set_90-1 in rat liver cell


title: 18_Camptothecin_90-1

description: Gene Expression after 24h exposed to 18_Camptothecin_90-1 in rat liver cell


title: 18_Clotrimazole_90-2_R


title: 18_Camptothecin_90-2


title: 18_c_90-2

value: Solvent Control (DMSO)_2


title: 17_SR12813_90-2


title: 17_c_90-2_R

description: Gene Expression after 24h exposed to 17_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_3


title: 19_Fipronil_90-1

description: Gene Expression after 24h exposed to 19_Fipronil_90-1 in rat liver cell

value: 3 ppm


title: 16_Tamoxifen_90-2

description: Gene Expression after 24h exposed to 16_Tamoxifen_90-2 in rat liver cell

value: 3  ppm


title: 16_Rifampicin_90-2

description: Gene Expression after 24h exposed to 16_Rifampicin_90-2 in rat liver cell

value: Rifampicin (Rifampin, Rifamycin AMP)_1

value: 1 0 ppm


title: 17_Hyperforin_90-1

description: Gene Expression after 24h exposed to 17_Hyperforin_90-1 in rat liver cell


title: 16_Tamoxifen_90-2_R


title: 17_c_90-1

description: Gene Expression after 24h exposed to 17_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_1


title: 16_Rifampicin_90-2_R

value: Rifampicin (Rifampin, Rifamycin AMP)_2


title: 16_Rifampicin_90-1

description: Gene Expression after 24h exposed to 16_Rifampicin_90-1 in rat liver cell

value: Rifampicin (Rifampin, Rifamycin AMP)_3


title: 17_c_90-2


title: 16_PCN_90-2_R

description: Gene Expression after 24h exposed to 16_PCN_90-2 in rat liver cell

value: PCN (pregnenolone-16alpha-nitrile)_3


title: 16_PCN_90-2

value: PCN (pregnenolone-16alpha-nitrile)_1

value: primary rat hepatocytes, rtNHeps


title: 16_Tamoxifen_90-1

description: Gene Expression after 24h exposed to 16_Tamoxifen_90-1 in rat liver cell

value: Male


title: 16_c_90-2

description: Gene Expression after 24h exposed to 16_control set_90-2 in rat liver cell


title: 16_c_90-2_R


title: 15_Genistein_90-1

description: Gene Expression after 24h exposed to 15_Genistein_90-1 in rat liver cell

value: 10 ppm


title: 15_Bisphenol-A_90-2

description: Gene Expression after 24h exposed to 15_Bisphenol A_90-2 in rat liver cell

source_name: 15_Bisphenol A_90-2

value: Bisphenol A_3


title: 15_Genistein_90-2

description: Gene Expression after 24h exposed to 15_Genistein_90-2 in rat liver cell


title: 15_Atrazine_90-2_R

description: Gene Expression after 24h exposed to 15_Atrazine_90-2 in rat liver cell


title: 15_c_90-1

description: Gene Expression after 24h exposed to 15_control set_90-1 in rat liver cell


title: 15_c_90-2

description: Gene Expression after 24h exposed to 15_control set_90-2 in rat liver cell


title: 15_c_90-2_R


title: 15_Bisphenol-A_90-1

description: Gene Expression after 24h exposed to 15_Bisphenol A_90-1 in rat liver cell

source_name: 15_Bisphenol A_90-1

value: Bisphenol A_1


title: 15_Atrazine_90-1

description: Gene Expression after 24h exposed to 15_Atrazine_90-1 in rat liver cell


title: 15_Genistein_90-2_R


title: 14_Nonylphenol_90-1

description: Gene Expression after 24h exposed to 14_Nonylphenol _90-1 in rat liver cell

source_name: 14_Nonylphenol _90-1

value: Nonylphenol (9-nonylphenol) Tergitol NP-9_1

value: 1 ppm


title: 14_c_90-2

description: Gene Expression after 24h exposed to 14_control set_90-2 in rat liver cell


title: 14_Aldosterone_90-1

description: Gene Expression after 24h exposed to 14_Aldosterone_90-1 in rat liver cell


title: 14_Spironolactone_90-1

description: Gene Expression after 24h exposed to 14_Spironolactone_90-1 in rat liver cell


title: 14_Aldosterone_90-2_R

description: Gene Expression after 24h exposed to 14_Aldosterone_90-2 in rat liver cell


title: 14_c_90-2_R

value: Solvent Control (DMSO)_3


title: 14_c_90-1

description: Gene Expression after 24h exposed to 14_control set_90-1 in rat liver cell

value: Solvent Control (DMSO)_2


title: 14_Nonylphenol_90-2

description: Gene Expression after 24h exposed to 14_Nonylphenol_90-2 in rat liver cell

value: Nonylphenol (9-nonylphenol) Tergitol NP-9_2


title: 13_Metyrapone_90-2_R

description: Gene Expression after 24h exposed to 13_Metyrapone_90-2 in rat liver cell

value: 100 ppm


title: 14_Spironolactone_90-2_R

description: Gene Expression after 24h exposed to 14_Spironolactone_90-2 in rat liver cell


title: 14_Spironolactone_90-2


title: 14_Aldosterone_90-2


title: 15_Bisphenol-A_90-2_R

value: Bisphenol A_2


title: 15_Atrazine_90-2


title: 13_Metyrapone_90-2


title: 13_Metyrapone_90-1

description: Gene Expression after 24h exposed to 13_Metyrapone_90-1 in rat liver cell


title: 13_EE2_90-2

description: Gene Expression after 24h exposed to 13_EE2_90-2 in rat liver cell

value: EE2 (ethinyl estradiol), 17alpha_1


title: 13_EE2_90-2_R

value: EE2 (ethinyl estradiol), 17alpha_3


title: 13_c_90-1

description: Gene Expression after 24h exposed to 13_control set_90-1 in rat liver cell

value: Solvent Control set13 (DMSO)_3


title: 13_Cortisone_90-2

description: Gene Expression after 24h exposed to 13_Cortisone_90-2 in rat liver cell

value: 30 ppm


title: 13_c_90-2

description: Gene Expression after 24h exposed to 13_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_1


title: 13_Cortisone_90-2_R

value: primary rat hepatocytes, rtNHeps


title: 26_Musk-xylene_90-1

description: Gene Expression after 24h exposed to 26_Musk xylene_90-1 in rat liver cell

source_name: 26_Musk xylene_90-1

value: Musk xylene_1

value: Male


title: 13_c_90-2_R


title: 12_PFAA-PFOA_90-2_R

description: Gene Expression after 24h exposed to 12_PFAA/PFOA_90-2 in rat liver cell

value: PFAA/PFOA (Perfluorooctanoic acid)_3


title: 12_PFAA-PFOA_90-2

value: PFAA/PFOA (Perfluorooctanoic acid)_1


title: 12_Ibuprofen_90-2_R

description: Gene Expression after 24h exposed to 12_Ibuprofen_90-2 in rat liver cell


title: 11_Troglitazone_90-2_R

description: Gene Expression after 24h exposed to 11_Troglitazone_90-2 in rat liver cell

value: 3 ppm


title: 12_Aspirin_90-1

description: Gene Expression after 24h exposed to 12_Aspirin_90-1 in rat liver cell


title: 12_Ibuprofen_90-1

description: Gene Expression after 24h exposed to 12_Ibuprofen_90-1 in rat liver cell


title: 12_c_90-2_R

description: Gene Expression after 24h exposed to 12_control set_90-2 in rat liver cell


title: 12_Ibuprofen_90-2


title: 12_PFAA-PFOA_90-1

description: Gene Expression after 24h exposed to 12_PFAA/PFOA_90-1 in rat liver cell

value: PFAA/PFOA (Perfluorooctanoic acid)_2


title: 12_c_90-2


title: 12_Aspirin_90-2_R

description: Gene Expression after 24h exposed to 12_Aspirin_90-2 in rat liver cell


title: 11_Indomethacin_90-2_R

description: Gene Expression after 24h exposed to 11_Indomethacin_90-2 in rat liver cell

value: 10 ppm


title: 12_c_90-1

description: Gene Expression after 24h exposed to 12_control set_90-1 in rat liver cell

value: Solvent Control set12 (DMSO)_3


title: 11_Troglitazone_90-2


title: 12_Aspirin_90-2


title: 11_Troglitazone_90-1

description: Gene Expression after 24h exposed to 11_Troglitazone_90-1 in rat liver cell


title: 13_Cortisone_90-1

description: Gene Expression after 24h exposed to 13_Cortisone_90-1 in rat liver cell


title: 11_Fenoprofen_90-2_R

description: Gene Expression after 24h exposed to 11_Fenoprofen_90-2 in rat liver cell

value: Fenoprofen (calcium salt hydrate)_2


title: 11_Indomethacin_90-1

description: Gene Expression after 24h exposed to 11_Indomethacin_90-1 in rat liver cell


title: 11_Fenoprofen_90-2

value: Fenoprofen (calcium salt hydrate)_1


title: 16_PCN_90-1

description: Gene Expression after 24h exposed to 16_PCN_90-1 in rat liver cell

value: PCN (pregnenolone-16alpha-nitrile)_2

value: 1 0 ppm


title: 11_Fenoprofen_90-1

description: Gene Expression after 24h exposed to 11_Fenoprofen_90-1 in rat liver cell

value: Fenoprofen (calcium salt hydrate)_3


title: 11_Indomethacin_90-2


title: 11_c_90-2_R

description: Gene Expression after 24h exposed to 11_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_3


title: 10_Lovastatin_90-2_R

description: Gene Expression after 24h exposed to 10_Lovastatin_90-2 in rat liver cell

value: Lovastatin (Mevinolin)_3

value: 1 ppm


title: 11_c_90-1

description: Gene Expression after 24h exposed to 11_control set_90-1 in rat liver cell

value: Solvent Control set11 (DMSO)_1

value: primary rat hepatocytes, rtNHeps


title: 11_c_90-2

value: Solvent Control (DMSO)_2

value: Male


title: 10_Lovastatin_90-2

value: Lovastatin (Mevinolin)_2


title: 10_Lovastatin_90-1

description: Gene Expression after 24h exposed to 10_Lovastatin _90-1 in rat liver cell

source_name: 10_Lovastatin _90-1

value: Lovastatin (Mevinolin)_1


title: 10_Bezafibrate_90-2_R

description: Gene Expression after 24h exposed to 10_Bezafibrate_90-2 in rat liver cell

value: 100 ppm


title: 10_c_90-2_R

description: Gene Expression after 24h exposed to 10_control set_90-2 in rat liver cell


title: 10_Bezafibrate_90-2


title: 1_c_90-1

description: Gene Expression after 24h exposed to 1_control set_90-1 in rat liver cell

value: Solvent Control set1 (DMSO)_3


title: 16_c_90-1

description: Gene Expression after 24h exposed to 16_control set_90-1 in rat liver cell


title: 1_2-6-DNT_90-2_R

description: Gene Expression after 24h exposed to  1_2-6-DNT_90-2  in rat liver cell

value: 10 ppm


title: 10_Amiodarone_90-2

description: Gene Expression after 24h exposed to 10_Amiodarone_90-2 in rat liver cell


title: 1_2-4-DNT_90-2_R

description: Gene Expression after 24h exposed to  1_2-4-DNT_90-2  in rat liver cell


title: 10_Amiodarone_90-1

description: Gene Expression after 24h exposed to 10_Amiodarone_90-1 in rat liver cell


title: 1_2-4-DNT_90-2


title: 10_Bezafibrate_90-1

description: Gene Expression after 24h exposed to 10_Bezafibrate_90-1 in rat liver cell


title: 1_2-6-DNT_90-2


title: 10_c_90-2


title: 1_c_90-2_R

description: Gene Expression after 24h exposed to 1_control set_90-2 in rat liver cell

value: Solvent Control (DMSO)_1


title: 1_2-4-DNT_90-1

description: Gene Expression after 24h exposed to  1_2-4-DNT_90-1  in rat liver cell


title: 1_2-4-6-TNT_90-1

description: Gene Expression after 24h exposed to  1_2-4-6-TNT_90-1  in rat liver cell


title: 1_c_90-2


title: 10_Amiodarone_90-2_R


title: 10_c_90-1

description: Gene Expression after 24h exposed to 10_control set_90-1 in rat liver cell

value: Solvent Control set10 (DMSO)_1


title: 14_Nonylphenol_90-2_R

description: Gene Expression after 24h exposed to 14_Nonylphenol_90-2 in rat liver cell

value: Nonylphenol (9-nonylphenol) Tergitol NP-9_3


title: 1_2-4-6-TNT_90-2_R

description: Gene Expression after 24h exposed to  1_2-4-6-TNT_90-2  in rat liver cell


title: 1_2-4-6-TNT_90-2


title: SFA vs. Control, replicate 5

status: Public on Jan 01 2010

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

description: Biological replicate 5

hyb_protocol: The labeled aRNA was hybridized overnight to 44K 60mer oligonucleotide spotted microarray slides (Agilent Technologies). Hybridization and subsequent washing of the slides was performed following the Agilent hybridization protocol for cDNA, version 4.1. Slides were dried by gentle centrifugation.

scan_protocol: Slides were scanned using the GenePix 4100A scanner (Axon Instruments, Downingtown, PA). ).Image analysis was performed with GenePix Pro 5.0 software, and calculated values for all spots were saved as GenePix results files

data_processing: MA data was calculated from the Genepix data and lowess-nomalized using R (http://www.R-project.org)

organism: Homo sapiens

source_name: control

label_protocol: 1µg total RNA per sample were amplified and labeled using the T7 Low Input RNA kit (Agilent, Waldbronn, Germany) according to the kit protocol. Cy-CTP from Perkin Elmer (Rodgau, Germany) were used with the amplification kit to obtain Cy-labeled aRNA.

growth_protocol: Human PBMC were isolated from buffy coats of healthy blood donors by Ficoll-Paque (Pharmacia, Freiburg, Germany) density gradient centrifugation.  CD14+ monocytes were purified (>95%) using CD14 immunomagnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and 3 million cells were cultured in six-well flat-bottom plates, in 3ml of DC medium, comprising RPMI 1640, L-glutamine, penicillin/streptomycin, sodium-pyruvate, nonessential amino acids, 10% heat-inactivated FCS Gold (PAA Laboratories, Linz, Austria), 1000 IU/ml recombinant human (rh) GM-CSF (Novartis Pharmaceuticals) and 1000 IU/ml rhIL-4 (Promo Cell, Heidelberg, Germany).

extract_protocol: RNA from 15 million was extracted using the RNeasy Midi Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The RNA from four donors was pooled and the volume elution volume was reduced with the help of the speed vac. 18µl of the RNA was stored at -70°C until use.

treatment_protocol: On day 5, PBS was added to the DC medium. After one hour 1µg/ml Lipopolysaccharid (LPS, Sigma-Aldrich) was added to the culture.

value: PBMC

tag: stimulation

value: no

value: m,m,f,f

source_name: stimulated

treatment_protocol: On day 5, SFA was added to the DC medium. After one hour 1µg/ml Lipopolysaccharid (LPS, Sigma-Aldrich) was added to the culture.

value: SFA


title: SFA vs. Control, replicate 2

description: Biological replicate 2

value: f,f,m,m


title: SFA vs. Control, replicate 4

description: Biological replicate 4

value: m,f,f,f


title: SFA vs. Control, replicate 3

description: Biological replicate 3

value: m,m,m,m


title: SFA vs. Control, replicate 6

description: Biological replicate 6


title: SFA vs. Control, replicate 7

description: Biological replicate 7

value: m,f,f,m


title: SFA vs. Control, replicate 1

description: Biological replicate 1

value: f,m,f,m


title: patient161;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

status: Public on Aug 15 2009

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: breast tumor biopsy

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on U133 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-2v4.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: dChip version2006

label: biotin

source_name: posttreatment; human breast tumor

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

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

value: female

tag: tissue

value: breast tumor

value: Letrozole, 2.5mg/day,oral, 3 months


title: patient126;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient137;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient114;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient190;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient159;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient136;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient116;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient152;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient133;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient193;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: 13_EE2_90-1

description: Gene Expression after 24h exposed to 13_EE2_90-1 in rat liver cell

value: EE2 (ethinyl estradiol), 17alpha_2

value: 1 ppm

value: primary rat hepatocytes, rtNHeps

value: Male


title: patient109;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient173;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: patient195;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: MAFB_E13.5_1

status: Public on Apr 25 2009

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11686

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 5ug

scan_protocol: Affymetrix standard protocol

data_processing:
Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs.
GCOS Tgt value: 1500.

label: Biotin

organism: Mus musculus

source_name: visceral epithelium (syn: podocyte layer)

extract_protocol: Potter protocol: 'RNA purification'

treatment_protocol:
pool size: approx 5-10 E13.5 kidneys
Pooled sample: Yes
Dissection Method: Podocyte cells were isolated from E13.5 Mafb transgenic mice kidneys using a combination of tyrpsinization and FACS.
Mafb transgenic mice are time-mated.  Pregnant Mafb transgenic mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are killed by decapitation with a scalpel.  Fetal kidneys are dissected from fetuses and placed in ice-cold PBS.  Embryonic kidneys are incubated in the presence of 300µl of trypsin for 5 minutes at 37 ºC.  Kidneys are then dissociated by titurating in the presence of 600µl of ice-cold 10%FBS/PBS.  The dissociated cells from the kidneys are pelleted at 5000 rpm, 4 ºC for 5 minutes.  The media is aspirated and the cell pellet is resuspended in 200µl of ice-cold 2%FBS/PBS.  Filter cells through 70 micron mesh filter and the GFP positive cells are further isolated using FACS.

tag: gene reported

value: Tg(Mafb-EGFP)79Gsat / MMRRC:011834-UCD

value: visceral epithelium

tag: strain

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: MAFB_E13.5_2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11687


title: ureter8_200309

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11684

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10ug

data_processing: Analysis method: Affymetrix GCOS and Gene Spring and Avadis programs GCOS Tgt value: 1500

source_name: ureter

treatment_protocol:
pool size: NA
Pooled sample: no
Dissection Method: Ureter microdissected and snap frozen in liquid nitrogen.
FVB/N mice were time mated. At embryonic day 15 mice were euthanized by decapitation and the ureters were micro-dissected, cut from pelvis to the bladder insertion point and snap frozen in liquid nitrogen. Total RNA was isolated for gene expression analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

value: wild-type

value: ureter

value: FVB/N

tag: Sex

tag: developmental landmark:


title: patient112;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: mesenchyme3_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11682

hyb_protocol: Affymetrix standard protocol Amount labeled target hybridization to array: 10µg

source_name: bladder neck/urethral mesenchyme

treatment_protocol:
pool size: NA
Pooled sample: no
Dissection Method: Bladder neck/urethra microdissected by cutting the specimen at the level of ureter insertion and treated with 1 mg/ml trypsin in Tyrode's solution to dissociate the mesenchyme from the epithelium.
FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were micro-dissected, cut just above the ureters and treated with 1 mg/ml trypsin in Tyrode’s solution for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder neck with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

value: bladder neck/urethral mesenchyme

value: embryonic day 13


title: MAFB_E13.5_3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11688


title: patient117;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy


title: urothelium5_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11679

hyb_protocol: Affymetrix standard protocol Amount labeled  target hybridization to array: 10µg

source_name: bladder neck/urethral epithelium

value: bladder neck/urethral epithelium


title: 1_2-6-DNT_90-1

description: Gene Expression after 24h exposed to  1_2-6-DNT_90-1  in rat liver cell

value: 10 ppm


title: urothelium2_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit:
TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11678


title: ureter9_200309

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11685


title: mesenchyme2_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11681


title: mesenchyme1_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11680


title: urothelium1_200209

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11677


title: ureter3_200309

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplified protocol: Potter Protocols
Rounds of amplification: 2
URL: http://www.gudmap.org/gudmap/pages/mic_submission.html?id=GUDMAP:11683


title: XX_DPY27-N_042807_B

status: Public on Mar 01 2009

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 30007G.

data_processing: Arrays were normalized by RMA (Robust Multichip Average) using Affymetrix Expression Consol software (Irizarry et al. 2003).    Data were analyzed by ArrayStar.  Statistical analysis was performed using a moderated t-test with FDR multiple testing correction (Benjamini-Hochberg method). Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U., and Speed, T.P. 2003. Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics 4: 249-264.

organism: Caenorhabditis elegans

source_name: embryo from worms grown on NG plates

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

growth_protocol: sdc-2(-) XX animals were prepared by growing sdc-2(y93) XX animals on Ahringer feeding library bacteria (Kamath et al. 2003) bearing an sdc-2 plasmid.  The wild-type control for the sdc-2 RNAi was N2 worms fed Ahringer library feeding bacteria bearing a plasmid lacking an insert.  Feeding bacteria was prepared by seeding 1L LB cultures with a single colony, growing overnight at 37∞C, inducing for 2hr with 5 mM IPTG, pelleting, and resuspending in 1 volume (w/v) of LB with 20% glycerol.

extract_protocol: Gravid adults were bleached and embryos harvested as described (Portman, D.S, Wombook, Profiling C. elegans gene expression with DNA microarrays) and 100 µl aliquots snap frozen in liquid nitrogen and stored at -80∞C.  An aliquot was thawed at 65∞C for 10 minutes, resuspended in 1ml Trizol (Invitrogen, Carlsbad, CA), vortexed vigorously to resuspend, and incubated for 20 minutes at room temperature. The sample was then centrifuged for 15 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and 100 µl of BCP (1-bromo-3-chloropropane) (MRC, Cincinnati, OH) was added, the sample was mixed by vortexing, incubated for 15 minutes at room temperature, and centrifuged for 10 minutes at 12,000xg at 4∞C.  The aqueous phase was transferred to a new tube and nucleic acid was precipitated by addition of 500 µl of isopropanol. The sample was incubated for 10 minutes at room temperature, centrifuged at 12,000xg for 8 minutes, washed in 70% ethanol and air dried for 5 minutes.  Nucleic acid was resuspended in 100 µl nuclease-free water and RNA quantified with a UV spectrophotometer. One hundred micrograms of RNA was then treated with 3 µl RQ1-DNAse (Promega, Madison, WI) and RNA isolated with the RNAeasy kit as per the manufacturer's protocol (Qiagen, Valencia, CA). RNA was again quantified with a UV spectrophotometer and cDNA was prepared from 5 µg RNA using the Protoscript Kit (NEB, Ipswich, MA) and diluted 1:15 in water.

treatment_protocol: Embryos used for microarray analysis were obtained from bleached gravid adults.

tag: dpy-27(y57) XX embryos


title: XX_WT-N_080307_A

tag: Wild Type control for dpy-27


title: XX_DPY27-N_042807_C


title: XX_WT-N_080307_B


title: XX_SDC2Y93R-P-022208_B

source_name: embryo from worms grown on RNAi plates

tag: sdc-2(y93, RNAi) XX embryos


title: XX_SDC2Y93R-P-022208_C


title: XX_WT-P_081407_C

tag: Wild Type controls for sdc-2


title: XX_WT-N_080307_C


title: XX_DPY27-N_042807_A


title: patient50;female;breast tumor;Letrozole, 2.5mg/day,oral, 3 months

description: breast tumor biopsy

value: female

tag: treatment


title: Patient_538_Never_Smoker

status: Public on Jan 29 2009

city: Gaithersburg

first: Sriram

last: Sridhar

state: MD

address: 1 MedImmune Way

department: Translational Medicine

institute: MedImmune

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B538N.CEL [Embargoed due to pending publication]

hyb_protocol: cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase. Five and a half micrograms of biotinylated cDNA was added to a hybridization cocktail, loaded on a Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing: The approximately 230,000 “core” exon probesets on the Exon array were used for transcript level analysis, which map to approximately 17,500 empirically supported transcripts (RefSeq and full-length GenBank mRNAs) with a high degree of confidence. Transcript-level expression values were derived using the model-based iterPLIER algorithm as implemented in the ExACT software package (Affymetrix, Santa Clara, CA). The gene annotations used for each probe set were from the annotation file obtained from Affymetrix (http://www.affymetrix.com).

label: biotin labeled

source_name: epithelial cells from right mainstem bronchus

label_protocol: Ribosomal RNA was first removed from the High molecular weight RNA fraction using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). This treated RNA was then converted to cDNA and subsequently processed and biotin-labeled.

extract_protocol: Epithelial cells were obtained from brushing the right mainstem bronchus of current and never smoker volunteers at bronchoscopy. Epithelial cell content yields were generally approximately 90%. RNA was size fractionated, and high molecular weight RNA ( > 200 nucleotides) was obtained from each sample for mRNA microarray analysis.

value: Female

tag: Race

value: Caucasian

tag: Age

tag: PKYRS

tag: Never smoker


title: Patient_536_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B536N-1.CEL [Embargoed due to pending publication]


title: Patient_537_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B537N.CEL [Embargoed due to pending publication]


title: XX_SDC2Y93R-P-022208_A


title: Patient_525_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B525N.CEL [Embargoed due to pending publication]


title: Patient_527_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B527N.CEL [Embargoed due to pending publication]


title: Patient_536_Never_Smoker_tech_replicate

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B536N-tech.CEL [Embargoed due to pending publication]


title: Patient_128_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B128N.CEL [Embargoed due to pending publication]

value: African American


title: Patient_142_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B142N.CEL [Embargoed due to pending publication]

value: Hispanic


title: Patient_531_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B531N.CEL [Embargoed due to pending publication]


title: Patient_533_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B533C.CEL [Embargoed due to pending publication]

tag: Current smoker


title: Patient_530_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B530C.CEL [Embargoed due to pending publication]


title: Patient_529_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B529N.CEL [Embargoed due to pending publication]


title: Patient_535_Never_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B535N.CEL [Embargoed due to pending publication]


title: Patient_534_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B534C.CEL [Embargoed due to pending publication]


title: Patient_526_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B526C.CEL [Embargoed due to pending publication]


title: Patient_459_Current_Smoker_temp_replicate

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B459C-temp2.CEL [Embargoed due to pending publication]


title: Patient_539_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B539C.CEL [Embargoed due to pending publication]


title: Patient_528_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B528C.CEL [Embargoed due to pending publication]


title: Patient_532_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B532C.CEL [Embargoed due to pending publication]


title: CHP, t=6 min, biological replicate 3

status: Public on Oct 24 2007

city: Blacksburg

first: Vladimir

last: Shulaev

state: VA

address: Virginia Bioinformatics Inst., Virginia Tech, Washington st.

institute: Virginia Bioinformatics Institute

description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast S98 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 640.

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

data_processing: The data were normalized with RMA.

organism: Saccharomyces cerevisiae

source_name: yeast, CHP, t=6 min, replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast cultures were grown in controlled batch conditions, in 1 L fermentors at 30C, pH 6.0, 500 rpm, and dO2> 80%.

extract_protocol: RNA was extracted with a procedure modified from the hot phenol protocol, as described (Martins, A. et al (2007) Yeast 24, 181-188)

treatment_protocol: In mid-exponential phase (OD600 ~ 1.5), three replicate cultures were treated with 0.19 mM CHP, while three untreated cultures were used as controls.

tag: Strain BY4743

tag: Mid-exponental phase


title: CHP, t=20 min, biological replicate 3

description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 3

source_name: yeast, CHP, t=20 min, replicate 3


title: CHP, t=12 min, biological replicate 3

description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 3

source_name: yeast, CHP, t=12 min, replicate 3


title: CHP, t=3 min, biological replicate 3

description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 3

source_name: yeast, CHP, t=3 min, replicate 3


title: Patient_462_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B462C.CEL [Embargoed due to pending publication]


title: Patient_524_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B524C.CEL [Embargoed due to pending publication]


title: CHP, t=0 min, biological replicate 3

description: Culture to be treated with CHP 0.19 mM, collected at t=0 (immediately before adding CHP), biological replicate 3

source_name: yeast, CHP, t=0, replicate 3


title: CHP, t=12 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=12 min, replicate 2


title: Patient_459_Current_Smoker

description:
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B459C-1.CEL [Embargoed due to pending publication]


title: CHP, t=6 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=6 min, replicate 2


title: CHP, t=12 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=12 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=12 min, replicate 1


title: CHP, t=20 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=20 min, replicate 2


title: CHP, t=20 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=20 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=20 min, replicate 1


title: Total MCF10AT-YB-1

status: Public on Oct 31 2008

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

description: Probeset RMA summarized expression data from total mRNA MCF10AT-YB-1 cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip Human Exon 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Genetrix software used for data processing. First the data was normalized using RMA sketch quantile normalization on PSRs with CORE level annotation (~283K PSRs) generating both summarized gene-level and individual normalized PSR-level expression matrices. Gene-level summarized expression data was determined using CORE annotation level PSRs only using the core-mapping file that maps HuExon 1.0 st exon probesets to HG-U133 2.0 probesets (see Series supplementary file).

source_name: MCF10AT-YB-1 fraction 1

label_protocol: Biotinlabelled target for the microarray experiment were prepared using 1 ug of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix).

growth_protocol: Low-passage MCF10AT (also known as MCF10AT1k.cl2) cell lines were provided by Dr. S.J. Kim (National Cancer Institute, Bethesda) and cultured on tissue culture plastic (Falcon) or on Matrigel-coated plates in defined medium, as previously described (Debnath et al., 2003; Janda et al., 2002; Roskelley et al., 1994).

treatment_protocol: Total cell extracts from monolayer cultured cells were prepared using the NP-40 lysis buffer containing 20 mM Hepes-KOH, pH 7.6, 100 mM KCl, 5 mM MgCl2, 2 mM dithiothreitol, 0.25% Nonidet P-40, 2 ug/ml leupeptin, 2 ug/ml pepstatin and 10 ug/ml cycloheximide. Cell fractionation, purification of polysomal and post-polysomal mRNA fractions using differential centrifugation on sucrose gradients.

tag: female; breast cancer cell line MCF10-AT

tag: total mRNA


title: CHP, t=0 min, biological replicate 1

description: Culture to be treated with CHP 0.19 mM, collected at t=0 (immediately before adding CHP), biological replicate 2

source_name: yeast, CHP, t=0, replicate 1


title: CHP, t=3 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=3 min, replicate 1


title: CHP, t=6 min, biological replicate 1

description: Culture treated with CHP 0.19 mM, collected at t=6 min (after adding CHP), biological replicate 1

source_name: yeast, CHP, t=6 min, replicate 1


title: Control, t=20 min, biological replicate 3

description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=20 min, replicate 3


title: Control, t=0 min, biological replicate 3

description: Culture to serve as a control, collected at t=0 (immediately before adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=0, replicate 3


title: Control, t=3 min, biological replicate 3

description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=3 min, replicate 3


title: Control, t=12 min, biological replicate 2

description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=12 min, replicate 2


title: Control, t=6 min, biological replicate 3

description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=6 min, replicate 3


title: Control, t=12 min, biological replicate 3

description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 3

source_name: yeast, Control, t=12 min, replicate 3


title: Control, t=20 min, biological replicate 2

description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=20 min, replicate 2


title: Control, t=6 min, biological replicate 2

description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=6 min, replicate 2


title: Control, t=3 min, biological replicate 2

description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 2

source_name: yeast, Control, t=3 min, replicate 2


title: Control, t=0 min, biological replicate 2

source_name: yeast, Control, t=0, replicate 2


title: Control, t=12 min, biological replicate 1

description: Control (untreated culture), collected at t=12 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=12 min, replicate 1


title: Control, t=6 min, biological replicate 1

description: Control (untreated culture), collected at t=6 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=6 min, replicate 1


title: Control, t=3 min, biological replicate 1

description: Control (untreated culture), collected at t=3 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=3 min, replicate 1


title: Control, t=20 min, biological replicate 1

description: Control (untreated culture), collected at t=20 min (after adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=20 min, replicate 1


title: CHP, t=3 min, biological replicate 2

description: Culture treated with CHP 0.19 mM, collected at t=3 min (after adding CHP), biological replicate 2

source_name: yeast, CHP, t=3 min, replicate 2


title: Control, t=0 min, biological replicate 1

description: Culture to serve as a control, collected at t=0 (immediately before adding CHP to treated cultures), biological replicate 1

source_name: yeast, Control, t=0, replicate 1


title: XX_WT-P_081407_B

source_name: embryo from worms grown on RNAi plates


title: renal vesicle - xrv2

status: Public on Nov 18 2006

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification:  2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7057

hyb_protocol: Amount labeled  target hybridization to array: 15 ug Hybridization/Wash/Stain protocol: EukGE-WS2v4

data_processing: Analysis method: Affymetrix GCOS and Rosetta Resolver GCOS Tgt value: 500

source_name: renal vesicle

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA extracted using TRIzol.  Two round amplification using the Arcturus kit according to the manufacturer protocol.

treatment_protocol:
pool size: 20 renal vesicles
Pooled sample: Yes
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system, were microdissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.

tag: gene reported

tag: strain

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: wnt4_mut2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7055

hyb_protocol: Amount labeled target hybridization to array: 15 ug Hybridization/Wash/Stain protocol: EukGE-WS2v4

source_name: Metanephros

extract_protocol: Disruption in liguid nitrogen, total RNA isolation with Qiagen Rneasy, followed by homogenization with QiaShredder columns (two 30ul elutions).

treatment_protocol:
pool size: 8-10 Wnt4 mutant kidneys (pooled from 4-5 mutant embryos)
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction.  Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants.  At E14.5, these structures are present in wildtype kidneys.  Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates.  CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug.  Presence of a plug is taken as day 0.5 post coitum.  Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation.  All fetuses are euthanized by decapitation with scissors.  Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

tag: sex


title: renal vesicle - xrv3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7058

tag: Sex


title: s-shaped body - xs01

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7059

source_name: s-shaped body

treatment_protocol:
pool size: 20 s-shaped bodies
Pooled sample: Yes
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system, were microdissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.


title: s-shaped body - xs02

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7060


title: collecting duct - xur2

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7063

source_name: collecting duct

treatment_protocol:
pool size: 1 collecting duct
Pooled sample: No
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system, were microdissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.


title: SKI-DLCL cells_AraC 20nM_24h_rpt3

status: Public on Sep 15 2006

city: New Brunswick

first: Pravin

last: Mishra

state: NJ

address: 195 Little Albany St.

department: Pharmacology

institute: UMDNJ

description: Samples were processed in CINJ Core Expression Array Facility according to Affymetrix protocol.

hyb_protocol: Hybridization  Water, Molecular Biology Grade or DEPC-treated Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL) Herring Sperm DNA GeneChip Eukaryotic Hybridization Control Kit 5M NaCl, RNase-free, DNase-free MES Free Acid Monohydrate MES Sodium Salt EDTA Disodium Salt  Miscellaneous Reagents/Supplies  Surfact-Amps 20 (Tween-20), 10% Hybridization Oven 640 Sterile, RNase-free, microcentrifuge tubes, 1.5mL Micropipettors Sterile-barrier pipette tips and non-barrier tips Heatblock

scan_protocol: Washing, Staining, and Scanning  Water, Molecular Biology Grade Distilled water Acetylated Bovine Serum Albumin (BSA) solution (50 mg/mL) R-Phycoerythrin Streptavidin 20X SSPE (3M NaCl, 0.2M NaH2PO4, 0.02M EDTA) Goat IgG, Reagent Grade Anti-streptavidin antibody (goat), biotinylated 10% surfact-Amps 20 (Tween-20)

data_processing: scanned fluorescence intensity, no normalization

source_name: SKI-DLCL cells

label_protocol:
Synthesis of Biotin-Labeled cRNA/Purification

ENZO BioArray RNA Transcript Labeling Kit
GeneChip Sample Cleanup Module

Miscellaneous Reagents/Supplies

100% ethanol ? room temperature
80%   ethanol ? room temperature
Water, Molecular Biology Grade or DEPC-treated
Ethidium Bromide
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier, RNase-free pipette tips
Mini agarose gel electrophoresis unit with appropriate buffers
UV Spectrophotometer
Cooling water bath

growth_protocol: Cells were grown under standard cell culture condition (95% air, 5% CO2, 37C)

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen.

treatment_protocol: AraC alone at concentration 20 nM

tag: SKI-DLCL cells were treated with AraC alone at concentration 20nM for 24h. Total RNA was isolated.


title: wnt4_mut1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7054

treatment_protocol:
pool size: 8-10 Wnt4 mutant kidneys (pooled from 4-5 mutant embryos)
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction. Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants. At E14.5, these structures are present in wildtype kidneys. Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates. CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug. Presence of a plug is taken as day 0.5 post coitum. Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are euthanized by decapitation with scissors. Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.


title: s-shaped body - xs03

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7061


title: CHP, t=0 min, biological replicate 2

description: Culture to be treated with CHP 0.19 mM, collected at t=0 (immediately before adding CHP), biological replicate 3

source_name: yeast, CHP, t=0, replicate 2


title: SKI-DLCL cells_Aplidin 1.5 nM AraC 5nM_24h_rpt2

treatment_protocol: Combination of Aplidin 1.5 nM and AraC 5 nM

tag: SKI-DLCL cells were treated with Aplidin 1.5nM and AraC 5.0 nM combination for 24h. Total RNA will be extracted.


title: SKI-DLCL cells_Aplidin 1.5 nM AraC 5.0 nM_24h_rpt3

tag: SKI-DLCL cells were treated with Aplidin 1.5 nM and AraC 5.0 nM combination for 24h. Total RNA was isolated.


title: SKI-DLCL cells_Aplidin 3nM_24h_rpt1

label_protocol:
Synthesis of Biotin-Labeled cRNA/Purification

ENZO BioArray RNA Transcript Labeling Kit
GeneChip Sample Cleanup Module

Miscellaneous Reagents/Supplies

100% ethanol room temperature
80%   ethanol room temperature
Water, Molecular Biology Grade or DEPC-treated
Ethidium Bromide
Sterile, RNase-free, microcentrifuge tubes, 1.5mL
Micropipettors
Sterile-barrier, RNase-free pipette tips
Mini agarose gel electrophoresis unit with appropriate buffers
UV Spectrophotometer
Cooling water bath

treatment_protocol: Aplidin alone at concentration 3 nM

tag: SKI-DLCL cells treated with Aplidin (3nM) for 24h. Total RNA was extracted.


title: collecting duct - xur1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7062


title: SKI-DLCL cells_Aplidin 3.0nM_24h_rpt2

tag: SKI-DLCL cells treated with Aplidin 3.0nM for 24h. Total RNA was isolated using RNeasy kit.


title: SKI-DLCL cells_Aplidin 1.5nM AraC 5nM_24h_rpt1

tag: SKI-DLCL cells were treated with Aplidin 1.5nM and AraC 5 nM combination for 24h. Total RNA was isolated.


title: SKI-DLCL cells_untreated_24h_rpt3

description: Sample processed by CINJ core expression array facility according to Affymetrix protocol.

data_processing: scanned fluorescence intensity values, not normalized

growth_protocol: Cells were grown under standard cell culture condition (95% air, 5%CO2, 37 C)

extract_protocol: RNeasy kit from Qiagen

treatment_protocol: Cells were not treated, control

tag: SKI-DLCL cells, not treated and cultured for 24h. Total RNA was isolated using RNeasy kit


title: SKI-DLCL cells_untreated_24h_1rpt

source_name: SKI-DLCL cells untreated

tag: SKI-DLCL cells cultured for 24h


title: wnt4_wt3

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)
Target Amplified protocol: Affymetrix Standard
Rounds of amplification: 1
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7052

treatment_protocol:
pool size: 2 wild-type kidneys
Pooled sample: Yes
Dissection Method: Whole organ excision
Experimental Design: Wnt4 is required for renal vesicle (RV) induction. Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants. At E14.5, these structures are present in wildtype kidneys. Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates. CD-1 mice are mated overnight and examined the following morning for the presence of a copulatory plug. Presence of a plug is taken as day 0.5 post coitum. Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are euthanized by decapitation with scissors. Fetal kidneys are removed from stage E14.5 embryos and stored in RNAlater at 4°C until RNA isolation (<4 days). Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

value: wild-type (PMID:18346943)


title: SKI-DLCL cells_AraC 20nM_24h_rpt2


title: SKI-DLCL cells_untreated_24h_2rpt

tag: SKI-DLCL cells untreated, cultured for 24h, total RNA was isolated using RNeasy kit


title: SKI-DLCL cells_AraC 20nM_24h_rpt1

tag: SKI-DLCL cells were treated with AraC alone in concentration 20nM for 24h. Total RNA was extracted


title: renal vesicle - xrv1

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7056

tag: gene reported

tag: strain