title: Total RNA from tomato fruit 3 days post breaker

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 3 days post breaker

source_name: breaker +3 days fruit

value: Whole tomato fruit 3 days post breaker

value: breaker +3 days fruit


title: Total RNA from tomato breaker stage fruit

status: Public on Aug 29 2012

type: RNA

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato breaker stage fruit

hyb_protocol: The samples were hybridised in the standard way, 16hrs at 45C and stainned with the Affymetix hyb wash and stain kit.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: The data were analyzed with Bioconductor affy package, using for background correction - RMA, normalization - quantiles, summarization - median polish. The default probe groupping was used.

label: biotin

molecule: total RNA

organism: Solanum lycopersicum

source_name: breaker stage fruit

label_protocol: GeneChip 3' IVT Express kit. the user manual is P/N 702646 Rev.1

growth_protocol: Plants were grown in pots with soil in a growth chamber having a photoperiod of 16/8h day/night, a thermoperiod 23/ 18ºC  day/night and humidity of 40%.

extract_protocol: Total RNA was extracted from Solanum lycopersicum cv. Micro-Tom using a phenol chloroform procedure.

tag: tissue

value: Whole tomato breaker stage fruit

tag: genotype

value: Solanum lycopersicum cv. Micro-Tom

tag: developmental stage

value: breaker stage fruit


title: Total RNA from tomato mature green fruit

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato mature green fruit

source_name: mature green fruit

value: Whole tomato mature green fruit

value: mature green fruit


title: Total RNA from tomato fruit 5 days post breaker

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 5 days post breaker

source_name: breaker +5 days fruit

value: Whole tomato fruit 5 days post breaker

value: breaker +5 days fruit


title: Total RNA from tomato fruit 11mm to 14mm in diameter

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 11mm to 14mm in diameter

source_name: 11-14mm fruit

value: Whole tomato fruit 11mm to 14mm in diameter

value: 11-14mm fruit


title: Exerimental (nhr-23 RNAi), biological rep2

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

country: USA

institute: NIDDK/NIH

description:
08-02-04_Krause_Celegans_E2
Gene expression data from synchronized larvae - inhibited for nhr-23 function by feeding them with bacteria dsRNA (LBD of NHR-23)  from L4440 vector

hyb_protocol: C. elegans whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

scan_protocol: Chips were scanned with an Affymetrix Scanner with standard settings

data_processing: Data was analyzed by Micrarray Suite 5.0 (MAS5) and by RMA using the program Partek

organism: Caenorhabditis elegans

source_name: L2 larvae inhibited by nhr-23 RNAi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

growth_protocol: 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.

extract_protocol: Total RNA was isolated from frozen pellets using a Mixer-Mill (Miller-Mill 300) following an RNeasy Mini Kit (Qiagen, Germantown, MD) according to manufacturer protocol.  Aliquots of cultures used for RNA isolation were kept on nhr-23 RNAi plates to confirm the knockdown phenotypic changes occurred during subsequent molts.

treatment_protocol: Synchronized populations of L1 larvae were plated with two sets of HT115 bacteria, one that had been transformed with the RNAi vector only (L4440 plasmid) and another that had been transformed with a vector targeting nhr-23 (clone 5174) [Proc Natl Acad Sci USA 98 (2001) 7360-7365].  Worms were kept on 2% agarose plates for 21 hr at 20C, collected, and approximately 200ml of worms resuspended in PBS were used in each individual experiment.

tag: strain background

tag: genotype/variation

value: inhibited by nhr-23 RNAi

tag: age

value: L2 Larvae

value: harvested synchronized larvae


title: Control, biological rep2

description:
08-02-04_Krause_Celegans_C2
Gene expression data from synchronized larvae - controls treated as controls by feeding them with bacteria expresing short nonspecific dsRNA from L4440 vector

source_name: L2 larvae control treated with LL4440 empty plasmid processed similarly as corresponding experimental samples

value: treated with LL4440 empty plasmid


title: Total RNA from tomato fruit 5mm to 7mm in diameter

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 5mm to 7mm in diameter

source_name: 5-7mm fruit

value: Whole tomato fruit 5mm to 7mm in diameter

value: 5-7mm fruit


title: Control, biological rep3

description:
08-02-04_Krause_Celegans_C3
Gene expression data from synchronized larvae - controls treated as controls by feeding them with bacteria expresing short nonspecific dsRNA from L4440 vector


title: Exerimental (nhr-23 RNAi), biological rep1

description:
08-02-04_Krause_Celegans_E1
Gene expression data from synchronized larvae - inhibited for nhr-23 function by feeding them with bacteria dsRNA (LBD of NHR-23)  from L4440 vector


title: Total RNA from open flower

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from open flower

source_name: Open flower

value: open flower (sepals, petals, stamens and carpels)

value: Open flower


title: Exerimental (nhr-23 RNAi), biological rep3

description:
08-02-04_Krause_Celegans_E3
Gene expression data from synchronized larvae - inhibited for nhr-23 function by feeding them with bacteria dsRNA (LBD of NHR-23)  from L4440 vector


title: Total RNA from tomato fruit 1mm to 3mm in diameter

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from tomato fruit 1mm to 3mm in diameter

source_name: 1-3mm fruit

value: Whole tomato fruit 1mm to 3mm in diameter

value: 1-3mm fruit


title: Total RNA from closed bud before flower blooming

description: Total RNAs from Solanum lycopersicum cv. Micro-Tom from closed bud before flower opens

source_name: Closed bud before flower opens

value: closed bud before flower opens (including developing sepals, stamens petals and carpels)

value: Solanum lycopersicum cv. Micro-Tom

value: Closed bud before flower opens


title: Jagged1-OE3

status: Public on Aug 28 2012

city: Chiba

first: Yohko

last: Yoshida

address: 1-8-1, Inohana, Chuo-ku

country: Japan

institute: Chiba University Graduate school of medicine

description: gene expression of Jagged1 over-expressing HUVEC

hyb_protocol: 1.5 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: HUVEC infected retroviral vector encoding Jagged1, passage 8, line3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human umbilical vein endothelial cells were purchased from Lonza, and cultured according to the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from endothelial cells with RNAZol-B(Molecular Research Center).

treatment_protocol: HUVEC were infected with retroviral vectors encoding Jagged1, Jagged1-shRNA, or Notch1-shRNA, or  empty vector as control.

tag: cell type

value: human unbilical endothelial vein cells (HUVEC)


title: control-1

description: gene expression of control HUVEC

source_name: HUVEC infected retroviral vector encoding empty vector, passage 8, line1


title: Control, biological rep1

description:
08-02-04_Krause_Celegans_C1
Gene expression data from synchronized larvae - controls treated as controls by feeding them with bacteria expresing short nonspecific dsRNA from L4440 vector


title: control-3

description: gene expression of control HUVEC

source_name: HUVEC infected retroviral vector encoding empty vector, passage 8, line3


title: Notch1-KD3

description: gene expression of Notch1 knockdown HUVEC

source_name: HUVEC infected retroviral vector encoding Notch1-shRNA, passage 8, line3


title: Jagged1-KD1

description: gene expression of Jagged1 knockdown HUVEC

source_name: HUVEC infected retroviral vector encoding Jagged1-shRNA, passage 8, line1


title: Jagged1-KD3

source_name: HUVEC infected retroviral vector encoding Jagged1-shRNA, passage 8, line3


title: control-2

description: gene expression of control HUVEC

source_name: HUVEC infected retroviral vector encoding empty vector, passage 8, line2


title: Notch1-KD1

source_name: HUVEC infected retroviral vector encoding Notch1-shRNA, passage 8, line1


title: Notch1-KD2

source_name: HUVEC infected retroviral vector encoding Notch1-shRNA, passage 8, line2


title: Jagged1-KD2

source_name: HUVEC infected retroviral vector encoding Jagged1-shRNA, passage 8, line2


title: Jagged1-OE2

source_name: HUVEC infected retroviral vector encoding Jagged1, passage 8, line2


title: Jagged1-OE1

source_name: HUVEC infected retroviral vector encoding Jagged1, passage 8, line1


title: pLV-miR-16-treated HSCs 2

city: Shanghai

first: Qin

last: Pan

address: 1665 Kongjiang Rd.

country: China

institute: Xin Hua hospital

description:
HSCs are derived from the liver of adult male Sprague-Dawley rats
Gene expression data from activated HSCs treated by pLV-miR-16

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: quiescent hepatic stellate cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: HSCs were cultured in cultured in Dulbecco’s modified Eagle medium (DMEM) containing 5 % fetal calf serum, penicillin (100 IU/ ml) and st reptomycin (100 mg/ ml).

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The pLV-miR-16-treated group, pLV-GFP-treated group were infected with pLV-miR-16 and pLV-GFP, respectively.

tag: strain

value: Sprague-Dawley

value: adult

tag: gender

value: male

tag: infection


title: Human in vivo, environmental exposure, subject 8

city: Tuxedo

first: Adriana

last: Arita

address: 57 Old Forge Road

institute: New York University

hyb_protocol: Samples were hybridized to a GeneChip Human Gene 1.0 ST Array (Affymetrix) that contains 28,869 well annotated genes.

scan_protocol: Hybridization and scanning of the arrays was performed using a standard procedure

data_processing: Gene expression analyses were performed using R. Gene expression data were imported and normalized in batches using the Affymetrix package and robust multichip average (RMA) [Affy package v.1.30.0. in R v.2.13.2 GUI 1.42 Leopard build 32-bit]. Samples were then batch normalized and log-transformed using an empirical Bayes approach with the R package COMBAT [VA 3.0.2 in R 2.14.0 GUI 1.42 Leopard build 32-bit]. Significance of gene expression changes between the exposed and referent populations was assessed using a gene-wise linear model approach with LIMMA, which utilizes an empirical Bayes approach to generate moderated t-statistics by taking into account the standard errors and estimated log-fold changes.

source_name: Human PMBC_environmental exposure nickel

label_protocol: cRNA probes were synthesized and labeled using GeneChip Whole Transcript Terminal Labeling Expression Kit (Affymetrix).

extract_protocol: 50 mL of blood was collected from each subject by venipuncture by a local registered nurse. PBMC were isolated from blood using a standard Ficoll-Gradient procedure. PBMCs were frozen Trizol at -80C. Total RNA was extracted from each sample according to the TRIzol (Invitrogen) manufacturer's protocol

tag: subject group

value: reference

tag: exposure to nickel

value: environmental

value: blood

value: peripheral blood mononuclear cells

tag: batch


title: Human in vivo, environmental exposure, subject 3


title: Human in vivo, environmental exposure, subject 7


title: pLV-miR-16-treated HSCs 1


title: pLV-GFP-treated HSCs 2

description:
HSCs are derived from the liver of adult male Sprague-Dawley rats
Gene expression data from activated HSCs treated by pLV-GFP

value: pLV-GFP


title: pLV-GFP-treated HSCs 1


title: pLV-miR-16-treated HSCs 3


title: Human in vivo, environmental exposure, subject 1


title: Human in vivo, environmental exposure, subject 2


title: Human in vivo, environmental exposure, subject 6


title: Human in vivo, environmental exposure, subject 5


title: Human in vivo, environmental exposure, subject 9


title: pLV-GFP-treated HSCs 3


title: Human in vivo, environmental exposure, subject 10


title: Methapyrilene HCl 48hr 1% DMSO GSS171_Overmann_Rat_IV_28_75-184

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Time Course/Dose Response Study

hyb_protocol: Twenty micrograms of labeled cRNA was fragmented and hybridized to Affymetrix Rat Genome 230 2.0 array (Santa Clara, CA) for 16 h at 45°C. Hybridized arrays were washed using a GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

source_name: Primary Rat Hepatocytes

label_protocol: Labeled cRNA was synthesized from 1 g of total RNA from the 24 h and 48 h time point samples using the MessageAmpII Biotin-Enhanced labeling kit (Ambion, Austin, TX) and Agencourt RNAClean beads according to manufacturer’s instructions (Beckman Coulter Inc., Danvers, MA).

growth_protocol: Frozen male Sprague Dawley primary rat hepatocytes were purchased from XenoTech (Lenexa, KS) and stored in the vapor phase of liquid N2, until use. Cells were thawed using supplier’s protocol and XenoTech cell isolation kit (Lenexa, KS). Briefly, one, 4.5 ml cryovial containing 17 x 106 rat hepatocytes was removed from liquid N2 and immediately placed in a shaking 37oC water bath for 2 min.  Hepatocytes were transferred to a 50 ml conical tube containing 40 ml of solution A (XenoTech Dulbecco’s Modified Eagles Media supplemented with isotonic Percoll, no pen/strep). The cryovial was rinsed with 4.5 ml of Solution B (XenoTech Dulbecco’s Modified Eagles Media supplemented with isotonic Percoll, no pen/strep) and transferred to the 50 ml conical tube containing cells in solution A.  Hepatocytes were centrifuged at 60 g (1000 rpm) using an International Equipment Company Centra-8R Centrifuge (Chattanooga, TN) for 5 min at room temperature.  Following centrifugation the supernatant was aspirated and hepatocytes were resuspended in 35 ml of Solution B and centrifuged at 60 g (1000 rpm) for another 3 min at room temperature. The resulting cell pellet was resuspended in 30 ml of XenoTech resuspension media (Lenexa, KS) and cell viability was evaluated by trypan blue exclusion.  Following the assessment of viability, cells were resuspended in Modified Chee’s culture media (XenoTech, Lenexa, KS) at a concentration of 0.7 - 1.0 x 106cells/ml, and 2 ml of cell suspension was transferred to each well of 6 well collagen coated plates (Corning Corning, NY) and placed in a 37oC incubator (5% CO2, 80% humidity). Following 3 to 4 hours of incubation to allow hepatocytes to attach, media was removed and 2 ml of ice cold modified Chee’s culture media (XenoTech, Lenexa, KS) supplemented with 0.25 mg/ml BD Matrigel, (BD Biosciences, Bedford, MA) was added to each well using pipets chilled to 4oC. Hepatocytes were incubated at 37oC, 5% CO2, media was replaced every day for the next 2 days with Modified Chee’s culture media (XenoTech, Lenexa, KS).

extract_protocol: Total RNA was isolated at 24 and 48 h post treatment, using Tri-Reagent (Molecular Research Center, Inc., Cincinnati, OH), further purified using a Qiagen RNeasy kit (Valencia, CA) and RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).

treatment_protocol: On day 3 of culture, cells were dosed with chemical:  Fresh 100X chemical dosing solutions in 1% DMSO were prepared 24 h before exposure for all chemical doses. Cells were treated with two concentrations of chemical or vehicle on the morning of day 3 and harvested for RNA at 24 and 48 h post treatment. Prior to RNA isolation all treatments were examined under a light microscope for signs of visible cytotoxicity (i.e. cell death). Five independent cell-cultures (1 well of 6 well plate X 5) per each time point/dose combination were performed to obtain 5 separate biological replicates.

tag: agent

value: DMSO

tag: concentration

tag: time

value: 48 hours

value: Male

value: Sprague Dawley


title: Methapyrilene HCl 24hr 1% DMSO GSS171_Overmann_Rat_IV_25_75-184

description: Time Course/Dose Response Study

value: 24 hours


title: Methapyrilene HCl 48hr 100 uM GSS171_Overmann_Rat_IV_30_75-184

description: Time Course/Dose Response Study

value: Methapyrilene HCl


title: Methapyrilene HCl 48hr 3 uM GSS171_Overmann_Rat_IV_29_75-184

description: Time Course/Dose Response Study

value: 3 uM


title: Human in vivo, environmental exposure, subject 4


title: Methapyrilene HCl 48hr 1% DMSO GSS171_Overmann_Rat_IV_22_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 3 uM GSS171_Overmann_Rat_IV_26_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 3 uM GSS171_Overmann_Rat_IV_23_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 1% DMSO GSS171_Overmann_Rat_IV_19_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 100 uM GSS171_Overmann_Rat_IV_27_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 100 uM GSS171_Overmann_Rat_IV_24_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 3 uM GSS171_Overmann_Rat_IV_20_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 100 uM GSS171_Overmann_Rat_IV_18_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 100 uM GSS171_Overmann_Rat_IV_21_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 3 uM GSS171_Overmann_Rat_IV_17_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 1% DMSO GSS171_Overmann_Rat_IV_16_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 3 uM GSS171_Overmann_Rat_IV_14_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 100 uM GSS171_Overmann_Rat_IV_12_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 100 uM GSS171_Overmann_Rat_IV_09_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 100 uM GSS171_Overmann_Rat_IV_15_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 1% DMSO GSS171_Overmann_Rat_IV_01_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 1% DMSO GSS171_Overmann_Rat_IV_07_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 3 uM GSS171_Overmann_Rat_IV_08_75-184

description: Time Course/Dose Response Study


title: WY-14643 48hr 8 uM GSS0214_Overmann_X_23_1806-031

description: Time Course/Dose Response Study

label_protocol: Labeled cRNA was synthesized from 1 ug of total RNA from the 24 h and 48 h time point samples using the MessageAmpII Biotin-Enhanced labeling kit (Ambion, Austin, TX) and Agencourt RNAClean beads according to manufacturer’s instructions (Beckman Coulter Inc., Danvers, MA).

value: 8 uM


title: WY-14643 24hr 200 uM GSS0214_Overmann_X_21_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 1% DMSO GSS0214_Overmann_X_22_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 1% DMSO GSS0214_Overmann_X_28_1806-031

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 1% DMSO GSS171_Overmann_Rat_IV_04_75-184

description: Time Course/Dose Response Study


title: WY-14643 48hr 200 uM GSS0214_Overmann_X_24_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 8 uM GSS0214_Overmann_X_29_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 8 uM GSS0214_Overmann_X_20_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 8 uM GSS0214_Overmann_X_26_1806-031

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 3 uM GSS171_Overmann_Rat_IV_02_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 100 uM GSS171_Overmann_Rat_IV_06_75-184

description: Time Course/Dose Response Study


title: WY-14643 24hr 1% DMSO GSS0214_Overmann_X_25_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 200 uM GSS0214_Overmann_X_30_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 200 uM GSS0214_Overmann_X_18_1806-031

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 1% DMSO GSS171_Overmann_Rat_IV_13_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 24hr 100 uM GSS171_Overmann_Rat_IV_03_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 1% DMSO GSS171_Overmann_Rat_IV_10_75-184

description: Time Course/Dose Response Study


title: WY-14643 24hr 200 uM GSS0214_Overmann_X_27_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 1% DMSO GSS0214_Overmann_X_19_1806-031

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 3 uM GSS171_Overmann_Rat_IV_11_75-184

description: Time Course/Dose Response Study


title: Methapyrilene HCl 48hr 3 uM GSS171_Overmann_Rat_IV_05_75-184

description: Time Course/Dose Response Study


title: WY-14643 48hr 1% DMSO GSS0214_Overmann_X_16_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 200 uM GSS0214_Overmann_X_15_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 200 uM GSS0214_Overmann_X_12_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 8 uM GSS0214_Overmann_X_17_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 8 uM GSS0214_Overmann_X_14_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 8 uM GSS0214_Overmann_X_11_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 1% DMSO GSS0214_Overmann_X_13_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 1% DMSO GSS0214_Overmann_X_10_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 8 uM GSS0214_Overmann_X_08_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 1% DMSO GSS0214_Overmann_X_07_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 1% DMSO GSS0214_Overmann_X_04_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 200 uM GSS0214_Overmann_X_06_1806-031

description: Time Course/Dose Response Study


title: WY-14643 48hr 8 uM GSS0214_Overmann_X_05_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 200 uM GSS0214_Overmann_X_03_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 8 uM GSS0214_Overmann_X_02_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 1% DMSO GSS0214_Overmann_X_01_1806-031

description: Time Course/Dose Response Study


title: WY-14643 24hr 200 uM GSS0214_Overmann_X_09_1806-031

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1000 uM GSS0204_Overmann_IX_27

description: Time Course/Dose Response Study

value: Clofibrate


title: Clofibrate 48hr 1000 uM GSS0204_Overmann_IX_18

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1000 uM GSS0204_Overmann_IX_30

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1% DMSO GSS0204_Overmann_IX_28

description: Time Course/Dose Response Study


title: Clofibrate 48hr 60 uM GSS0204_Overmann_IX_29

description: Time Course/Dose Response Study

value: 60 uM


title: Clofibrate 48hr 1% DMSO GSS0204_Overmann_IX_22

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1000 uM GSS0204_Overmann_IX_12

description: Time Course/Dose Response Study


title: Clofibrate 24hr 60 uM GSS0204_Overmann_IX_26

description: Time Course/Dose Response Study


title: Clofibrate 24hr 60 uM GSS0204_Overmann_IX_08

description: Time Course/Dose Response Study


title: Clofibrate 48hr 60 uM GSS0204_Overmann_IX_17

description: Time Course/Dose Response Study


title: Clofibrate 48hr 60 uM GSS0204_Overmann_IX_23

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1% DMSO GSS0204_Overmann_IX_10

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1000 uM GSS0204_Overmann_IX_15

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1% DMSO GSS0204_Overmann_IX_16

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1000 uM GSS0204_Overmann_IX_21

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1% DMSO GSS0204_Overmann_IX_07

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1000 uM GSS0204_Overmann_IX_06

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1% DMSO GSS0204_Overmann_IX_19

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1% DMSO GSS0204_Overmann_IX_25

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1000 uM GSS0204_Overmann_IX_24

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1% DMSO GSS0204_Overmann_IX_13

description: Time Course/Dose Response Study


title: Clofibrate 24hr 60 uM GSS0204_Overmann_IX_20

description: Time Course/Dose Response Study


title: Clofibrate 48hr 60 uM GSS0204_Overmann_IX_11

description: Time Course/Dose Response Study


title: Clofibrate 24hr 60 uM GSS0204_Overmann_IX_14

description: Time Course/Dose Response Study


title: Clofibrate 48hr 60 uM GSS0204_Overmann_IX_05

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1000 uM GSS0204_Overmann_IX_09

description: Time Course/Dose Response Study


title: Clofibrate 24hr 60 uM GSS0204_Overmann_IX_02

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1% DMSO GSS0204_Overmann_IX_01

description: Time Course/Dose Response Study


title: Clofibrate 48hr 1% DMSO GSS0204_Overmann_IX_04

description: Time Course/Dose Response Study


title: Clofibrate 24hr 1000 uM GSS0204_Overmann_IX_03

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 100 mM GSS0197_Overmann_VIII_30_1806-014

description: Time Course/Dose Response Study

value: Diisononyl Phthalate


title: Diisononyl Phthalate 48hr 1% DMSO GSS0197_Overmann_VIII_28_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 100 mM GSS0197_Overmann_VIII_27_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 100 mM GSS0197_Overmann_VIII_24_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 25 mM GSS0197_Overmann_VIII_14_1806-014

description: Time Course/Dose Response Study

value: 25 mM


title: Diisononyl Phthalate 48hr 100 mM GSS0197_Overmann_VIII_18_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 25 mM GSS0197_Overmann_VIII_26_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 25 mM GSS0197_Overmann_VIII_23_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 1% DMSO GSS0197_Overmann_VIII_16_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 100 mM GSS0197_Overmann_VIII_12_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 1% DMSO GSS0197_Overmann_VIII_13_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 1% DMSO GSS0197_Overmann_VIII_04_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 25 mM GSS0197_Overmann_VIII_08_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 1% DMSO GSS0197_Overmann_VIII_25_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 100 mM GSS0197_Overmann_VIII_09_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 1% DMSO GSS0197_Overmann_VIII_10_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 1% DMSO GSS0197_Overmann_VIII_07_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 25 mM GSS0197_Overmann_VIII_29_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 100 mM GSS0197_Overmann_VIII_15_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 1% DMSO GSS0197_Overmann_VIII_01_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 100 mM GSS0197_Overmann_VIII_21_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 25 mM GSS0197_Overmann_VIII_11_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 25 mM GSS0197_Overmann_VIII_17_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 100 mM GSS0197_Overmann_VIII_03_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 100 mM GSS0197_Overmann_VIII_06_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 1% DMSO GSS0197_Overmann_VIII_19_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 25 mM GSS0197_Overmann_VIII_02_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 24hr 25 mM GSS0197_Overmann_VIII_20_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 1% DMSO GSS0197_Overmann_VIII_22_1806-014

description: Time Course/Dose Response Study


title: Diisononyl Phthalate 48hr 25 mM GSS0197_Overmann_VIII_05_1806-014

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 20 uM GSS0190_Overmann_Rat_VII_21_1806-006

description: Time Course/Dose Response Study

value: Chlorpromazine HCl

value: 20 uM


title: Chlorpromazine HCl 48hr 0.8 uM GSS0190_Overmann_Rat_VII_29_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 1% DMSO GSS0190_Overmann_Rat_VII_13_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 1% DMSO GSS0190_Overmann_Rat_VII_28_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 20 uM GSS0190_Overmann_Rat_VII_27_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 0.8 uM GSS0190_Overmann_Rat_VII_14_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 1% DMSO GSS0190_Overmann_Rat_VII_16_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 20 uM GSS0190_Overmann_Rat_VII_12_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 0.8 uM GSS0190_Overmann_Rat_VII_17_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 20 uM GSS0190_Overmann_Rat_VII_18_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 20 uM GSS0190_Overmann_Rat_VII_09_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 0.8 uM GSS0190_Overmann_Rat_VII_20_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 20 uM GSS0190_Overmann_Rat_VII_24_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 1% DMSO GSS0190_Overmann_Rat_VII_10_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 20 uM GSS0190_Overmann_Rat_VII_15_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 1% DMSO GSS0190_Overmann_Rat_VII_22_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 0.8 uM GSS0190_Overmann_Rat_VII_26_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 1% DMSO GSS0190_Overmann_Rat_VII_01_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 0.8 uM GSS0190_Overmann_Rat_VII_11_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 0.8 uM GSS0190_Overmann_Rat_VII_02_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 20 uM GSS0190_Overmann_Rat_VII_06_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 0.8 uM GSS0190_Overmann_Rat_VII_23_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 0.8 uM GSS0190_Overmann_Rat_VII_08_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 2hr 1% DMSO GSS0190_Overmann_Rat_VII_07_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 1% DMSO GSS0190_Overmann_Rat_VII_25_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 1% DMSO GSS0190_Overmann_Rat_VII_19_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 24hr 20 uM GSS0190_Overmann_Rat_VII_03_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 0.8 uM GSS0190_Overmann_Rat_VII_05_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 1% DMSO GSS0190_Overmann_Rat_VII_04_1806-006

description: Time Course/Dose Response Study


title: Chlorpromazine HCl 48hr 20 uM GSS0190_Overmann_Rat_VII_30_1806-006

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1% DMSO GSS183_Overmann_Rat_VI_25_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 100uM GSS183_Overmann_Rat_VI_24_1806-001

description: Time Course/Dose Response Study

value: Beta-Naphthoflavone


title: Beta-Naphthoflavone 24hr 100uM GSS183_Overmann_Rat_VI_21_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 100uM GSS183_Overmann_Rat_VI_27_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 100uM GSS183_Overmann_Rat_VI_30_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1uM GSS183_Overmann_Rat_VI_23_1806-001

description: Time Course/Dose Response Study

value: 1 uM


title: Beta-Naphthoflavone 48hr 100uM GSS183_Overmann_Rat_VI_06_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 100uM GSS183_Overmann_Rat_VI_18_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1uM GSS183_Overmann_Rat_VI_26_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1% DMSO GSS183_Overmann_Rat_VI_04_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1uM GSS183_Overmann_Rat_VI_17_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1% DMSO GSS183_Overmann_Rat_VI_19_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1% DMSO GSS183_Overmann_Rat_VI_13_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1uM GSS183_Overmann_Rat_VI_08_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1uM GSS183_Overmann_Rat_VI_11_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1uM GSS183_Overmann_Rat_VI_29_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 100uM GSS183_Overmann_Rat_VI_03_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1% DMSO GSS183_Overmann_Rat_VI_10_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1% DMSO GSS183_Overmann_Rat_VI_07_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 100uM GSS183_Overmann_Rat_VI_15_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1% DMSO GSS183_Overmann_Rat_VI_22_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1uM GSS183_Overmann_Rat_VI_02_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1% DMSO GSS183_Overmann_Rat_VI_16_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1uM GSS183_Overmann_Rat_VI_20_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 100uM GSS183_Overmann_Rat_VI_12_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1uM GSS183_Overmann_Rat_VI_14_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 100uM GSS183_Overmann_Rat_VI_09_1806-001

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 24hr 1% DMSO GSS183_Overmann_Rat_VI_01_1806-001

description: Time Course/Dose Response Study


title: Phenobarbital 48hr Water GSS173_Overmann_Rat_V_28_75-187

description: Time Course/Dose Response Study

treatment_protocol: On day 3 of culture, cells were dosed with chemical:  Fresh 100X chemical dosing solutions in Culture Media were prepared 24 h before exposure for all chemical doses. Cells were treated with two concentrations of chemical or vehicle on the morning of day 3 and harvested for RNA at 24 and 48 h post treatment. Prior to RNA isolation all treatments were examined under a light microscope for signs of visible cytotoxicity (i.e. cell death). Five independent cell-cultures (1 well of 6 well plate X 5) per each time point/dose combination were performed to obtain 5 separate biological replicates.

value: Culture Media

value: Water


title: Phenobarbital 24hr 3000 uM GSS173_Overmann_Rat_V_27_75-187

description: Time Course/Dose Response Study

value: Phenobarbital


title: Phenobarbital 48hr 3000 uM GSS173_Overmann_Rat_V_24_75-187

description: Time Course/Dose Response Study

value: 48 hours

value: Male


title: Phenobarbital 48hr 3000 uM GSS173_Overmann_Rat_V_30_75-187

description: Time Course/Dose Response Study

value: Sprague Dawley


title: Beta-Naphthoflavone 48hr 1% DMSO GSS183_Overmann_Rat_VI_28_1806-001

description: Time Course/Dose Response Study

value: DMSO


title: Phenobarbital 48hr 300 uM GSS173_Overmann_Rat_V_29_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 3000 uM GSS173_Overmann_Rat_V_21_75-187

description: Time Course/Dose Response Study

value: 24 hours


title: Phenobarbital 24hr Water GSS173_Overmann_Rat_V_25_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 3000 uM GSS173_Overmann_Rat_V_06_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 300 uM GSS173_Overmann_Rat_V_14_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr Water GSS173_Overmann_Rat_V_10_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 3000 uM GSS173_Overmann_Rat_V_12_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr Water GSS173_Overmann_Rat_V_07_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr Water GSS173_Overmann_Rat_V_04_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 300 uM GSS173_Overmann_Rat_V_26_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 300 uM GSS173_Overmann_Rat_V_11_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 3000 uM GSS173_Overmann_Rat_V_18_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr Water GSS173_Overmann_Rat_V_22_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 3000 uM GSS173_Overmann_Rat_V_15_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 300 uM GSS173_Overmann_Rat_V_20_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr Water GSS173_Overmann_Rat_V_16_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 300 uM GSS173_Overmann_Rat_V_23_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr Water GSS173_Overmann_Rat_V_19_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 3000 uM GSS173_Overmann_Rat_V_09_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 3000 uM GSS173_Overmann_Rat_V_03_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 300 uM GSS173_Overmann_Rat_V_17_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 300 uM GSS173_Overmann_Rat_V_08_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 48hr 300 uM GSS173_Overmann_Rat_V_05_75-187

description: Time Course/Dose Response Study


title: Phenobarbital 24hr Water GSS173_Overmann_Rat_V_13_75-187

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 10 mM GSS164_Overmann_Rat_III_27_75-181

description: Time Course/Dose Response Study

treatment_protocol: On day 3 of culture, cells were dosed with chemical:  Fresh 100X chemical dosing solutions in water were prepared 24 h before exposure for all chemical doses. Cells were treated with two concentrations of chemical or vehicle on the morning of day 3 and harvested for RNA at 24 and 48 h post treatment. Prior to RNA isolation all treatments were examined under a light microscope for signs of visible cytotoxicity (i.e. cell death). Five independent cell-cultures (1 well of 6 well plate X 5) per each time point/dose combination were performed to obtain 5 separate biological replicates.

value: Sodium Valproate

value: 10 mM


title: Sodium Valproate 24hr 0.5 mM GSS164_Overmann_Rat_III_20_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 0.5 mM GSS164_Overmann_Rat_III_26_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 0.5 mM GSS164_Overmann_Rat_III_23_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 0.5 mM GSS164_Overmann_Rat_III_17_75-181

description: Time Course/Dose Response Study


title: Phenobarbital 24hr Water GSS173_Overmann_Rat_V_01_75-187

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr Water GSS164_Overmann_Rat_III_16_75-181

description: Time Course/Dose Response Study

value: Vehicle Control


title: Sodium Valproate 48hr 10 mM GSS164_Overmann_Rat_III_30_75-181

description: Time Course/Dose Response Study


title: Phenobarbital 24hr 300 uM GSS173_Overmann_Rat_V_02_75-187

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr Water GSS164_Overmann_Rat_III_28_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr Water GSS164_Overmann_Rat_III_22_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr Water GSS164_Overmann_Rat_III_19_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 0.5 mM GSS164_Overmann_Rat_III_14_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr Water GSS164_Overmann_Rat_III_13_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr Water GSS164_Overmann_Rat_III_25_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 0.5 mM GSS164_Overmann_Rat_III_29_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 10 mM GSS164_Overmann_Rat_III_24_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 10 mM GSS164_Overmann_Rat_III_21_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 10 mM GSS164_Overmann_Rat_III_18_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 10 mM GSS164_Overmann_Rat_III_15_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr Water GSS164_Overmann_Rat_III_10_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 10 mM GSS164_Overmann_Rat_III_12_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 10 mM GSS164_Overmann_Rat_III_09_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 0.5 mM GSS164_Overmann_Rat_III_11_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr Water GSS164_Overmann_Rat_III_07_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 0.5 mM GSS164_Overmann_Rat_III_08_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 0.5 mM GSS164_Overmann_Rat_III_05_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr Water GSS164_Overmann_Rat_III_04_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 48hr 10 mM GSS164_Overmann_Rat_III_06_75-181

description: Time Course/Dose Response Study


title: Beta-Naphthoflavone 48hr 1uM GSS183_Overmann_Rat_VI_05_1806-001

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1% DMSO GSS164_Overmann_Rat_II_28_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1% DMSO GSS164_Overmann_Rat_II_22_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1000uM GSS164_Overmann_Rat_II_27_75-180

description: Time Course/Dose Response Study

value: Dioctyl Phthalate


title: Sodium Valproate 24hr Water GSS164_Overmann_Rat_III_01_75-181

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 10 mM GSS164_Overmann_Rat_III_03_75-181

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 250uM GSS164_Overmann_Rat_II_29_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1000uM GSS164_Overmann_Rat_II_21_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1000uM GSS164_Overmann_Rat_II_30_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 250uM GSS164_Overmann_Rat_II_23_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1% DMSO GSS164_Overmann_Rat_II_19_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1000uM GSS164_Overmann_Rat_II_18_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1000uM GSS164_Overmann_Rat_II_24_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 250uM GSS164_Overmann_Rat_II_17_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1% DMSO GSS164_Overmann_Rat_II_25_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1000uM GSS164_Overmann_Rat_II_12_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1% DMSO GSS164_Overmann_Rat_II_13_75-180

description: Time Course/Dose Response Study


title: Sodium Valproate 24hr 0.5 mM GSS164_Overmann_Rat_III_02_75-181

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1% DMSO GSS164_Overmann_Rat_II_16_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1000uM GSS164_Overmann_Rat_II_09_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 250uM GSS164_Overmann_Rat_II_11_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1000uM GSS164_Overmann_Rat_II_15_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 250uM GSS164_Overmann_Rat_II_26_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1% DMSO GSS164_Overmann_Rat_II_10_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 250uM GSS164_Overmann_Rat_II_08_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 250uM GSS164_Overmann_Rat_II_20_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 250uM GSS164_Overmann_Rat_II_14_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1% DMSO GSS164_Overmann_Rat_II_04_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 250uM GSS164_Overmann_Rat_II_05_75-180

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 1% DMSO GSS_161_25_75-173

description: Time Course/Dose Response Study


title: Dioctyl Phathalate 48hr 1000uM GSS164_Overmann_Rat_II_06_75-180

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 5000uM GSS_161_27_75-173

description: Time Course/Dose Response Study

value: Acetaminophen


title: Acetaminophen 24hr 500uM GSS_161_20_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 500uM GSS_161_23_75-173

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1% DMSO GSS164_Overmann_Rat_II_01_75-180

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 500uM GSS_161_29_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 5000uM GSS_161_24_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 5000uM GSS_161_30_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 1% DMSO GSS_161_16_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 5000uM GSS_161_18_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 5000uM GSS_161_21_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 1% DMSO GSS_161_19_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 500uM GSS_161_26_75-173

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1% DMSO GSS164_Overmann_Rat_II_07_75-180

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 1% DMSO GSS_161_28_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 5000uM GSS_161_15_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 500uM GSS_161_17_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 48hr 1% DMSO GSS_161_22_75-173

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 1000uM GSS164_Overmann_Rat_II_03_75-180

description: Time Course/Dose Response Study


title: Dioctyl Phthalate 24hr 250uM GSS164_Overmann_Rat_II_02_75-180

description: Time Course/Dose Response Study


title: C. tropicalis Opaque Block 7

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Mnorm value converted from log2 change by using 2^n of Mnorm Value, which yields the value in the PRE_VALUE column.

organism: Candida tropicalis

source_name: C. tropicalis opaque cells

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy5. Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: Cells grown overnight in liquid Spider media, diluted to 0.2 OD600, and grown to 1. Cells spun down and flash frozen in an ethanol/dry ice bath.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

tag: colony and cellular morphology

value: opaque state

source_name: Universal Reference

extract_protocol: RNA extracted using Ribopure Yeast Kit. RNA from 8 samples combined to comprise universal reference sample.

tag: reference

value: White and Opaque isolates of CAY1504 (white) and CAY2275 (opaque), RNA samples mixed


title: FaDu_HNSCC_cell_line_1

city: Toronto

first: Lusia

last: Sepiashvili

state: ONtario

address: 101 College street TMDT unit 9-807

department: Medical Biophysics

country: Canada

institute: UHN/OCI

description: Gene expression

hyb_protocol: Agilent Gene Expression Hybridization Kit G2534A was used according to manufacturer’s instructions.

scan_protocol: Standard Agilent scanning protocol (G2565C DNA Scanner)

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5 (Agilent)

source_name: cell line

label_protocol: 0.2 ug total RNA was used. Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used according to manufacturer’s instructions (labeling protocol version GE v5.7).

extract_protocol: RNA was extracted using the total RNA extraction kit (Norgen) according to manufacturer's instructions

tag: cell line

value: HNSCC cell line FaDu

tag: comparison to normal cells


title: UTSCC8_HNSCC_cell_line_2

description: Gene expression

value: HNSCC cell line UTSCC8


title: C. tropicalis Opaque Block 8


title: UTSCC42a_HNSCC_cell_line_3

description: Gene expression

value: HNSCC cell line UTSCC42a


title: NOE_normal_1

description: Gene expression

value: normal oral epithelial cell line


title: C. tropicalis Opaque Block 6


title: Acetaminophen 24hr 500uM GSS_161_14_75-173

description: Time Course/Dose Response Study


title: C. tropicalis Opaque Block 5


title: YPD ISP1-2

city: Pittsburgh

first: Xinghua

last: Lu

state: PA

address: 5607 Baum Blvd

department: Dept Biomedical Informatics

institute: University of Pittsburgh

description: Yeast grown in YPD, treated with ISP1 for 45 min

hyb_protocol: standarad Affymetrix protocol

scan_protocol: standarad Affymetrix protocol

data_processing: Bioconductor, affy package, RMA

organism: Saccharomyces cerevisiae

source_name: YPD ISP1-2

label_protocol: standarad Affymetrix protocol

growth_protocol: Yeast cells grown in YPD or synthetic complete (SC) medium.

extract_protocol: Phenol extraction

treatment_protocol: YPD ctrl, SC ctrl, YPD heat stress, YPD heat stress + ISP1, SC + myristate, SC+myristate + ISP1, YPD + ISP1

tag: treatment

value: YPD, treated with ISP1 for 45 min


title: YPD ISP1-1

source_name: YPD ISP1-1


title: YPD+Heat+ISP1-2

description: Yeast grown in YPD, treated with heat stress + ISP1 for 45 min


title: SC Myristate-2

description: Yeast grown in SC, treated with myristate for 45 min

source_name: SC Myristate-2

value: SC, treated with myristate for 45 min


title: SC+myristate+ISP1-1

description: Yeast grown in SC, treated with myristate + ISP1

value: SC, treated with myristate + ISP1


title: YPD ISP1-3

source_name: YPD ISP1-3


title: YPD+Heat+ISP1-1

value: YPD, treated with heat stress + ISP1 for 45 min


title: Acetaminophen 24hr 1% DMSO GSS_161_13_75-173

description: Time Course/Dose Response Study

value: DMSO

value: Male

value: Sprague Dawley


title: Acetaminophen 48hr 500uM GSS_161_11_75-173

description: Time Course/Dose Response Study

value: 48 hours


title: Acetaminophen 48hr 5000uM GSS_161_12_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 5000uM GSS_161_09_75-173

description: Time Course/Dose Response Study

value: 24 hours


title: C. tropicalis White Block 4

source_name: C. tropicalis white cells

value: white state


title: SC Myristate-1

source_name: SC Myristate-1


title: Acetaminophen 24hr 500uM GSS_161_08_75-173

description: Time Course/Dose Response Study

value: Acetaminophen


title: SC+myristate+ISP1-2

description: Yeast grown in SC, treated with myristate + ISP2

value: SC, treated with myristate + ISP2


title: YPD Heat-2

description: Yeast grown in YPD, subject to heat stress for 45 min

source_name: YPD Heat-2

value: YPD, subject to heat stress for 45 min


title: C. tropicalis White Block 2

source_name: Universal reference

value: White and Opaque isolates of CAY1504 (white) and CAY2275 (opaque), RNA samples mixed


title: YPD Heat-3

source_name: YPD Heat-3


title: C. tropicalis White Block 3


title: SC+myristate+ISP1-3

description: Yeast grown in SC, treated with myristate + ISP3

value: SC, treated with myristate + ISP3


title: YPD Heat-1

source_name: YPD Heat-1


title: C. tropicalis White Block 1


title: YPD+Heat+ISP1-3


title: SC ctrl-3

description: Yeast cells grow in synthetic complete medium (0.17 % yeast nitrogen base (US Biological), 0.5 % ammonium sulfate, 2 mM sodium hydroxide, and 0.07 % synthetic complete supplement was used, SCD is SC containing 2 % dextrose. )

source_name: SC ctrl-3


title: SC ctrl-2

source_name: SC ctrl-2

value: synthetic complete medium (0.17 % yeast nitrogen base (US Biological), 0.5 % ammonium sulfate, 2 mM sodium hydroxide, and 0.07 % synthetic complete supplement was used, SCD is SC containing 2 % dextrose. )


title: Acetaminophen 48hr 1% DMSO GSS_161_10_75-173

description: Time Course/Dose Response Study


title: Acetaminophen 24hr 1% DMSO GSS_161_07_75-173

description: Time Course/Dose Response Study


title: SC ctrl-1

source_name: SC ctrl-1


title: Acetaminophen 48hr 5000uM GSS_161_06_75-173

description: Time Course/Dose Response Study

source_name: Primary Rat Hepatocytes


title: YPD ctrl-2

description: yeast cells grow in normal YPD medium

source_name: YPD ctrl-2

value: normal YPD medium


title: Acetaminophen 48hr 1% DMSO GSS_161_04_75-173

description: Time Course/Dose Response Study


title: hepatic inflammatory cells_adipose tissue derived stem cell treatment_No.10

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

institute: Kanazawa University

description: SAMPLE 16

hyb_protocol: The 1.65 microgram of cRNA was fragmented and hybiridized to Whole Mouse Genome 4x44K Array (Agilent) oligo DNA chip using hybridization buffer (Agilent Gene Expression Hybridization Kit) at 60 celcius degree for 17 hours.

scan_protocol: Scanned on an Agilent G2505B scanner. Agilent Feature Extraction Software (version 10.5.1.1) was used for image quantification, background subtraction, and normalization.

data_processing: background subtracted and normalized

organism: Mus musculus

label_protocol: cRNA was amplified and labaled with Cy3 fluorescence using Low QuickAmp Labeling Kit (Agilent Techologies, Santa Clara, CA).

extract_protocol: RNA was extracted from the enriched fraction of tumor-infiltrating inflammatory cells using MicroRNA isolation kit (Stratagene). Total RNA from blood was isolated using Mouse RiboPure-Blood RNA Isolation Kit (Ambion) in accordance with the manufacturer's protocol.

treatment_protocol:
Adipose tussue derived stem cells obtained from inguinal adipose tissue of GFP-transgenic mice were obtained by collagenase digestion and expanded in culture until use.
Liver cirrhosis murine model was established feeding C57Bl/6 female mice with atherogenic high-fat diet for 40 weeks. The mice were injected with 1x10^5 GFP-ADSCs twice every two weeks via the subcapusle of the spleen. After two weeks of the last injection, the liver and intrahepatic inflammatory cells were obtained.

value: female

tag: treated with

value: adipose tissue-derived stem cells

tag: tissue

value: hepatic inflammatory cells


title: YPD ctrl-1

description: yeast cells grow in normal YPD medium

source_name: YPD ctrl-1


title: hepatic inflammatory cells_PBS treatment_No.14

description: SAMPLE 12

value: PBS


title: YPD ctrl-3

description: yeast cells grow in normal YPD medium

source_name: YPD ctrl-3


title: Acetaminophen 48hr 500uM GSS_161_05_75-173

description: Time Course/Dose Response Study


title: hepatic inflammatory cells_adipose tissue derived stem cell treatment_No.9

description: SAMPLE 15


title: hepatic inflammatory cells_adipose tissue derived stem cell treatment_No.8

description: SAMPLE 14


title: Acetaminophen 24hr 5000uM GSS_161_03_75-173

description: Time Course/Dose Response Study


title: hepatic inflammatory cells_PBS treatment_No.11

description: SAMPLE 9


title: liver_adipose tissue derived stem cell treatment_No.9

description: SAMPLE 7

value: liver


title: hepatic inflammatory cells_PBS treatment_No.12

description: SAMPLE 10


title: Acetaminophen 24hr 1% DMSO GSS_161_01_75-173

description: Time Course/Dose Response Study

value: DMSO

value: Male


title: hepatic inflammatory cells_PBS treatment_No.13

description: SAMPLE 11


title: Acetaminophen 24hr 500uM GSS_161_02_75-173

description: Time Course/Dose Response Study

value: Sprague Dawley


title: liver_adipose tissue derived stem cell treatment_No.7

description: SAMPLE 5


title: CLF1 CD4 T cells H3K9ac

type: genomic

city: Xi'an

first: ke

last: wang

state: Shaanxi

address: Yanta west road 276#

department: First Affiliated Hospital of Medical College

institute: Xi'an Jiaotong University

description: ChIP-chip CD4 T cells H3K9ac

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and 6 µg labeled DNA was diluted in 5 µl of water and hybridized in 18 ul of buffer containing 50% 2Xbuffer, 20% Hybridization Component A, 2% Alignment Oligo . Arrays were hybridized in Maui hybridization stations for 16 h at 42C, and then washed in wash buffer follow the  manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.3 ChIP data extraction.

molecule: genomic DNA

source_name: H3K9ac ChIP DNA from CLF1 CD4 T cells

label_protocol: 1 µg amplified ChIP DNA and iput DNA was directly labeled by ROCHE Nimblegen labeling kit with klenow enzyme and random priming with Cy5 and Cye respectively. (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Specimens directly from patients, not cultured in vitro

extract_protocol: Histone proteins were cross-linked to genomic DNA from isolating 2x10E6 CD4 T cells with 1% formaldehyde (final concentration) for 10 min at 37C; glycine (0.125 M) was then added for 5 min at 37C to stop the reaction. After being washed twice with 10 ml of ice-cold 1×PBS, the CD4 T cells were resuspended with 600 μl lysis buffer (10 mM Tris-HCl pH 8.0; NaCl 100 mM; EDTA 1 mM pH 8.0; Na-deoxycholate 0.1% and protease inhibitors) and incubated on ice for 30 min. Then the CD4 T cells suspension was sonicated for 4 min total time (9 s “on” and 30 s “off”) to reduce DNA lengths to between 200 and 1,000 bp. The lysate was then divided into three fractions. The first lysate was gently rotating incubated with 10 μl acetyl-histone H3 (Lys9) antibody (Cell Signaling Technology, Boston, USA) [Acetyl-histone H3 (Lys9) antibody: #9671,Cell Signaling Technology, Boston, USA] for 2 h at 4C. The second lysate was used as negative control. Third lysate was used for input control. To collect the immunoprecipitated complexes, 30 μl of ChIP-grade protein G agarose beads (Cell Signaling Technology, Boston, USA) [ChIP-grade protein G agarose beads: #9007,Cell Signaling Technology, Boston, USA] were added and gently rotating incubated at 4C overnight. Agrarose beads were separated from solution by a brief 1 minute centrifugation in 3000 rpm at 4C. Then the beads were sequentially washed in low salt, high salt, LiCl salt, and TE buffers. The histone/DNA complexes were eluted by elution buffers, and formaldehyde crosslinks were reversed by heating the samples at 65℃ for 6 h. Samples were treated with RNase for 20 min at 37C and then proteinase K for 1 h at 45C. DNA was extracted by the phenol/chloroform method, ethanol-precipitated, and resuspended in water.

treatment_protocol: CD4 T cells were MACs sorted from peripheral blood mononuclear cells

tag: cell type

value: CD4 T cells

tag: diagnosis

value: chronic hepatitis B related liver failure

value: peripheral blood

tag: chip antibody

source_name: Input  DNA from CLF1 CD4 T cells

value: None,Input DNA


title: hepatic inflammatory cells_adipose tissue derived stem cell treatment_No.7

description: SAMPLE 13

tag: strain

tag: gender


title: liver_adipose tissue derived stem cell treatment_No.10

description: SAMPLE 8


title: CLF2 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CLF2 CD4 T cells

source_name: Input  DNA from CLF2 CD4 T cells


title: CLF3 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CLF3 CD4 T cells

source_name: Input DNA from CLF3 CD4 T cells


title: CHB-A3 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-A3 CD4 T cells

value: chronic hepatitis B in active stage

source_name: Input  DNA from CHB-A3 CD4 T cells


title: HEP_C HSF1_ChIP_promoter

city: Gliwice

first: Joanna

last: Polanska

address: Akademicka 16

department: Automatic Control

country: Poland

institute: Silesian University of Technology

description:
HSF1 binding sites in control hepatocytes; biological rep 1-3, promoter array
AB1: ChIP
AB0: Ctrl

hyb_protocol: Fragmented and labeled DNA (7.5 ug per sample) in Hybridization Cocktail in a total volume 200 ul was hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000

data_processing: Data was quantile normalized with the use of dCHIP software and Mm_PromPR_v02-1_NCBIv36.NR.bpmap file. 5th percentile was used for background substraction (PM-only). The further analysis was done in Matlab environment, the subsets of probes related to the regions defined by gene Accession Number were analyzed individually. The statistical tests for signal enhancement within the region and nonuniformity of the signal AB1-AB0 difference distribution were performed. Linked results file includes log2 MBEI signal.

source_name: HSF1 ChIP DNA from untreated hepatocytes [AB1 replicates]

label_protocol: Samples (7.5 ug amplified double-stranded DNA) were enzymatically fragmented and labeled  using the WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

extract_protocol:
Hepatocytes were isolated by collagenase type IA perfusion of the liver and resuspended  in DMEM medium supplemented with 10% fetal bovine serum, 0.004% gentamycin and 1uM insulin
Untreated cells or cells immediatelly after heat shock treatment were fixed by adding of formaldehyde to a final concentration of 1% and incubated at room temperature for 10 minutes. Next 2.5 M glycine was added (1/20 volume) for 5 minutes. Cells were washed with ice-cold PBS and lysed following the manufacturer’s protocol. To obtain recommended shared DNA size fragments (between 200-1000 bp), chromatin from heat shocked samples had to be sonicated using two times more pulses than chromatin from control samples. ChIP on chip analyses were done according to the Affymetrix protocol   (http://media.affymetrix.com/support/downloads/manuals/chromatin_immun_ChIP.pdf), with one modification: in the second round of immunoprecipitated DNA amplification, 2 mM magnesium chloride was applied instead of the recommended 0.75 mM.

treatment_protocol: untreated

value: FVB/N

value: male

tag: age

value: hepatocytes

tag: antibody

value: HSF1 rabbit polyclonal (SPA-901, Stressgen), 15ug for 5x107 cells

source_name: mock IP from control hepatocytes [AB0 replicates]


title: SC Myristate-3

source_name: SC Myristate-3

value: SC, treated with myristate for 45 min


title: UCC2003 pNZ44  versus UCC2003 pNZ44SerR dye swap

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).  Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 pNZ44-SerR/pNZ44 ratios from a duplicate array experiment.  Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 pNZ44

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 pNZ44-SerR and Bifidobacterium breve UCC2003 pNZ44 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany).The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: genotype/variation

source_name: Bifidobacterium breve UCC2003 pNZ44-serR


title: UCC2003 pNZ44  versus UCC2003 pNZ44SerR

description: gene expression array


title: liver_adipose tissue derived stem cell treatment_No.8

description: SAMPLE 6

value: female

value: adipose tissue-derived stem cells


title: liver_PBS treatment_No.12

description: SAMPLE 2

source_name: liver_PBS treatment

value: PBS


title: SC_43 HSF1_ChIP_promoter

description:
HSF1 binding sites in spermatocytes heat shocked at 43°C; biological rep 1-3, promoter array
AB1: ChIP
AB0: Ctrl

source_name: HSF1 ChIP DNA from spermatocytes heat shocked at 43°C [AB1 replicates]

extract_protocol:
Spermatocytes were isolated by unit gravity sedimentation of spermatogenic cells (obtained after collagenase type IA/trypsin/DNase I digestion of decapsulated testes) in 1-3% w/v linear BSA gradient. Finally cells were suspended in RPMI medium supplemented with 10% fetal bovine serum, 0.004% gentamycin and 6mM sodium lactate
Untreated cells or cells immediatelly after heat shock treatment were fixed by adding of formaldehyde to a final concentration of 1% and incubated at room temperature for 10 minutes. Next 2.5 M glycine was added (1/20 volume) for 5 minutes. Cells were washed with ice-cold PBS and lysed following the manufacturer’s protocol. To obtain recommended shared DNA size fragments (between 200-1000 bp), chromatin from heat shocked samples had to be sonicated using two times more pulses than chromatin from control samples. ChIP on chip analyses were done according to the Affymetrix protocol   (http://media.affymetrix.com/support/downloads/manuals/chromatin_immun_ChIP.pdf), with one modification: in the second round of immunoprecipitated DNA amplification, 2 mM magnesium chloride was applied instead of the recommended 0.75 mM.

treatment_protocol: cells were heat shocked at 43°C for 5, 10 or 20 minutes, than pooled together, and used for chromatin immunoprecipitation as one sample.

value: spermatocytes

source_name: mock IP from spermatocytes heat shocked at 43°C [AB0 replicates]


title: liver_PBS treatment_No.14

description: SAMPLE 4

value: liver


title: HEP_43 HSF1_ChIP_promoter

description:
HSF1 binding sites in hepatocytes heat shocked at 43°C; biological rep 1-3, promoter array
AB1: ChIP
AB0: Ctrl

source_name: HSF1 ChIP DNA from hepatocytes heat shocked at 43°C [AB1 replicates]

source_name: mock IP from hepatocytes heat shocked at 43°C [AB0 replicates]


title: liver_PBS treatment_No.13

description: SAMPLE 3


title: CHB-A2 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-A2 CD4 T cells

source_name: Input  DNA from CHB-A2 CD4 T cells


title: SC_C HSF1_ChIP_promoter

description:
HSF1 binding sites in control spermatocytes; biological rep 1-3, promoter array
AB1: ChIP
AB0: Ctrl

source_name: HSF1 ChIP DNA from untreated spermatocytes [AB1 replicates]

source_name: mock IP from control spermatocytes [AB0 replicates]


title: SC_38 HSF1_ChIP_promoter

description:
HSF1 binding sites in spermatocytes heat shocked at 38°C; biological rep 1-3, promoter array
AB1: ChIP
AB0: Ctrl

source_name: HSF1 ChIP DNA from spermatocytes heat shocked at 38°C [AB1 replicates]

treatment_protocol: cells were heat shocked at 38°C for 5, 10 or 20 minutes, than pooled together, and used for chromatin immunoprecipitation as one sample.

source_name: mock IP from spermatocytes heat shocked at 38°C [AB0 replicates]


title: NC2 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from NC2 CD4 T cells

growth_protocol: Specimens directly from normal controls, not cultured in vitro

value: normal control

source_name: Input  DNA from NC2 CD4 T cells


title: CHB-A1 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-A1 CD4 T cells

source_name: Input  DNA from CHB-A1 CD4 T cells


title: CHB-T1 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-T1 CD4 T cells

value: chronic hepatitis B in tolerance stage

source_name: Input DNA from CHB-T1 CD4 T cells


title: GATA3KO_2

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: Sorted Gata3 deficient Tregs

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

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

data_processing: Robust Multi-array Average (RMA) analysis.

source_name: Spleen and lymph nodes

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

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

value: GATA3 KO

value: Tregs


title: GATA3KO_3

description: Sorted Gata3 deficient Tregs


title: OGA S L1 8WG16 #2

status: Public on Aug 27 2012

first: Michael

last: Krause

address: 5 Center Drive

department: LMB/NIDDK

institute: NIH

hyb_protocol: ChIP and input DNAs were amplified by whole-genome amplification (WGA) using the GenomePlex WGA Kit (Sigma). The resulting amplified DNAs were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.  Amplified DNAs were fragmented and labeled using the DNA Terminal Labeling Kit (Affymetrix), and then hybridized to Affymetrix C. elegans GeneChip Tiling 1.0 arrays at 45o C overnight.

scan_protocol: Arrays were washed and scanned, and the resulting CEL files were analyzed using Affymetrix TAS software

data_processing: Thresholds were selected, and the resulting BED files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals). To determine genes most strongly linked to O-GlcNAc associated (RL-2 reactive) chromatin regions, the input-normalized ChIP signal intensity for each probe from mutants unable to O-GlcNAcylate protein substrates (ogt-1(ok430)) was subtracted from that of mutants that are unable to remove GlcNAc from substrates (oga-1(ok1207)).  A value at, or above, 2.2 was used to threshold resulting data in order to determine O-GlcNAc peaks.  Bioinformatic analysis (GenPathway) was used to identify genes associated with RL2 peaks above threshold and located within 2 kb of the transcriptional start site (genome version, WS195).  Application of these criteria resulted in the identification of 828 genes associated with O-GlcNAc-positive chromatin.

source_name: ChIP

label_protocol: Genomic DNA regions of interest were isolated using an antibody against one of the following epitopes: the unmodified and Ser-5-P-modified heptad repeat (YSPTSPS) and of the C-terminal domain (CTD) of RNA PolII (8WG16 MMS-126R, Covance and abBently Ser-5-P; Zhang et al 2005); the Ser-2-phosphorylated and non-modified heptad repeat of the CTD domain (ab5095, Abcam); the Ser-2-P modfied CTD heptad repeat (abBentley Ser-2-P; Kim et al, 2010); O-linked N-acetylglucosamine modified peptides (RL2; ab2739, Abcam), HGAC85-derived O-linked N-acetylglucosamine {Turner et al., 1990, #40278} (MA1-076, Thermo Scientific), and Ser/Thr-O-linked N-acetylglucosamine (CTD 110.6; MMS-248R, Covance)

growth_protocol: Embryos were isolated from wild type and mutant gravid adults by bleach treatment and shaken gently with good aeration in sterile buffer to hatch and collected 48 hours later.  For feeding, the starved animals were plated on NGM with E. coli (OP50) and allowed to feed for 3 hours prior to collection.

extract_protocol: C. elegans larvae were disrupted and fixed by brief sonication in 1% formaldehyde followed by incubation for 20 min. at room temperature. After washing, lysates were sonicated again to shear the DNA to an average length of 300-500 bp.  Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.

treatment_protocol: Starved and fed L1 animals were wild type or one of two mutant strains: loss of the O-GlcNAc transferase ogt-1(ok430) and loss of the O-GlcNAcase oga-1(ok1207)

tag: genotype

value: oga-1(ok1207) mutant

tag: Stage

tag: condition

value: Starved

tag: anitbody

value: PolII:RNA PolII CTD non-P and Ser-2-P (ab8WG16; Covance MMS-126R)

source_name: Wild type input chromatin

value: Wild type


title: NC3 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from NC3 CD4 T cells

value: CD4 T cells

value: peripheral blood

source_name: Input DNA from NC3 CD4 T cells

value: None,Input DNA


title: OGA F L1 8WG16

value: Fed 3 hrs


title: liver_PBS treatment_No.11

description: SAMPLE 1

source_name: liver_PBS treatment

value: female


title: OGT F L1 8WG16

value: ogt-1(ok430) mutant


title: N2 S L1 8WG16 #2

value: Wild Type


title: OGA F L1 8WG16 #2


title: N2 F L1 8WG16


title: NC1 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from NC1 CD4 T cells

source_name: Input DNA from NC1 CD4 T cells


title: OGT S L1 8WG16


title: CHB-T3 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-T3 CD4 T cells

source_name: Input  DNA from CHB-T3 CD4 T cells


title: GATA3KO_1

description: Sorted Gata3 deficient Tregs


title: CHB-T2 CD4 T cells H3K9ac

description: ChIP-chip CD4 T cells H3K9ac

source_name: H3K9ac ChIP DNA from CHB-T2 CD4 T cells

source_name: Input  DNA from CHB-T2 CD4 T cells


title: WT_3

description: Sorted Gata3 sufficient Tregs

value: WT


title: WT_2

description: Sorted Gata3 sufficient Tregs


title: OGT S L1 Bentley Ser5P

value: Pol II:RNA PollII CTD Ser-5-P (Bentley)


title: OGT F L1 Bentley Ser5P


title: N2 F L1 Bentley Ser5P


title: N2 S L1 Bentley Ser5P


title: OGA F L1 Bentley Ser5P


title: OGA S L1 Bentley Ser5P


title: N2 S L1 Bentley Ser2P

value: Pol II:RNA PollII CTD Ser-2-P (Bentley)


title: OGA S L1 Bentley Ser2P


title: N2 F L1 Bentley Ser2P


title: OGT F L1 Bentley Ser2P


title: OGA S L1 5095 #2

value: Pol II:RNA PolII CTD Ser-2-P (ab5095, Abcam)


title: WT_1

description: Sorted Gata3 sufficient Tregs


title: OGT S L1 Bentley Ser2P


title: N2 S L1 5095 #2


title: OGA F L1 5095 #2


title: Max-null ES cells (Nam+)(Dox+)

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: Gene expression data of Nam- and Dox-treated Max-null ES cells.

hyb_protocol: Labeled samples were hybridized to the microarrays according to the manufacturer's protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was performed as described elsewhere (Irizarry et al. Nucleic Acids Res. e15, 2003).

data_processing: The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res. e15, 2003) via the R/Bioconductor affy 2.13.1 package using default analysis settings.

source_name: Max-non-expressing ES cells with Nam

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

growth_protocol: ES cells were cultured under conventional ES culture conditions with LIF and serum.

extract_protocol: Total RNAs were prepared using TRIzol reagent from Invitrogen (15596-026).

treatment_protocol: Nam (4mM) and doxycycline were added.

value: male

value: embryonic stem (ES) cells

value: nicotinamide (Nam)

tag: max expression

value: no


title: N2 F L1 5095 #2


title: Max-null ES cells (Nam+)(Dox-)

description: Gene expression data of Nam-treated, Dox-untreated Max-null ES cells.

source_name: Max-expressing ES cells with Nam

treatment_protocol: Nam (4mM) was added, but doxycycline was not added.

value: yes


title: N2 F L1 5095

value: Wild type


title: OGA F L1 Bentley Ser2P

value: oga-1(ok1207) mutant


title: OGT S L1 5095 #2

value: Starved


title: OGT F L1 5095 #2


title: OGT F L1 HCAC85

value: HCAC85:O-GlcNAc (MA1-076, Thermo Scientific (prev Affinity BioReagents))


title: OGA F L1 5095

value: Fed 3 hrs


title: OGA F L1 HCAC85


title: N2 F L1 HCAC85


title: OGT F L1 5095


title: N2 F L1 8WG16 #2

value: PolII:RNA PolII CTD non-P and Ser-2-P (ab8WG16; Covance MMS-126R)


title: PN11-0204

city: Nijmegen

first: Rolph

last: Pfundt

address: Geert Grooteplein Zuid 6

department: Genetics

country: Netherlands

institute: RUNMC

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.0 and Copy Number Analyzer for Affymetrix GeneChip mapping (CNAGT 2.0) software. The inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAG2.0. Regions of homozygosity (LCSH/LOH) were determined with a likelihood based algorithm implemented in CNAG2.0.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: peripheral (EDTA) blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: No culture but direct isolation from peripheral blood

extract_protocol: Genomic DNA was isloated with a Chemagen/Hamilton magnetic bead DNA isolation robot

value: female


title: H1P76

city: Bad Nauheim

first: Jason

last: Lai

state: Hessen

address: Ludwigstrasse 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute For Heart and Lung Research

description: Biological replicate 3

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Separate colors are background-subtracted followed by quantile normalization.

label: Cy3 and Cy5

source_name: human ESC

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: human embyronic stem cell line

tag: cell line

tag: molecule type

value: Bisulfite converted DNA


title: iPCH358Col11

description: biological replicate 3

data_processing: Background-subtracted followed by quantile normalization. Impute insignificant detection value (detection_pval>0.05) to minimum detectable value

source_name: Induced Pluripotent Cancer Cell

value: induced pluripotent cancer cell

value: iPCH358 Col11


title: piPCH358Col3

description: biological replicate 3

source_name: Differentiated Induced Pluripotent Cancer Cell

value: post induced pluripotent cancer cell


title: H1P99C

description: Biological replicate 3

value: male


title: H460P22B

description: biological replicate 3

source_name: Lung Large Cell Carcinoma

value: lung large cell carcinoma


title: Secondary Lung, biological replicate 1

city: Worcester

first: Susan

middle: L

last: Swain

state: MA

address: 55 Lake Avenue North

department: Pathology

institute: University of Massachusetts Medical School

description: Gene expression data from secondary HNT CD4 T cell effectors from the lung on day 7 post influenza infection

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on M430.2 GeneChip Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

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

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

label: Biotin

source_name: Secondary HNT CD4 T cell effectors from the lung on day 7 post influenza infection

growth_protocol: Congenic Thy1.1 donor naïve or memory CD4 T cells were adoptively transferred to naïve Thy1.2 BALB/c mice in 200uL PBS.  Mice were subsequently infected with 0.1 LD50 A/PR8/34 influenza A virus.

extract_protocol: Total RNA was extracted from cells with RNeasy Mini Kit from QIAGEN and amplified (MessageAmp a RNA; Ambion) according to manufacturers instructions.

treatment_protocol: On day 7 post infection, donor CD4 T cells were re-isolated from adoptive hosts by enrichment with CD4 magnetic beads (Milteny) followed by facs sorting for Thy1.1 and CFSE-divided populations.

value: Balb/c

value: In vivo primed HNT TCR Tg CD4 T cell

tag: infection

value: influenza A

tag: source tissue

value: lung


title: Secondary dLN, biological replicate 2

description: Gene expression data from secondary HNT CD4 T cell effectors from the dLN on day 7 post influenza infection

source_name: Secondary HNT CD4 T cell effectors from the dLN on day 7 post influenza infection

tag: cell type

value: dLN


title: H358P13B

description: biological replicate 3

source_name: Lung Adenocarcinoma Cell Line

value: lung adenocarcinoma


title: IMR90P6B

description: biological replicate 3

source_name: Human Fetal Lung Fibroblast

value: fetal lung fibroblast

value: IMR90 P6


title: Secondary Spleen, biological replicate 1

description: Gene expression data from secondary HNT CD4 T cell effectors from the spleen on day 7 post influenza infection

source_name: Secondary HNT CD4 T cell effectors from the spleen on day 7 post influenza infection

value: spleen


title: IMR90P6B

description: biological replicate 3

value: female


title: H1P106B

description: Biological replicate 2

value: human embyronic stem cell line


title: Primary Lung, biological replicate 3

description: Gene expression data from primary HNT CD4 T cell effectors from the lung on day 7 post influenza infection

source_name: Primary HNT CD4 T cell effectors from the lung on day 7 post influenza infection

value: Naïve HNT TCR Tg CD4 T cell


title: Secondary Lung, biological replicate 2


title: iPCH460Col9

description: biological replicate 3

value: induced pluripotent cancer cell

value: iPCH460 Col9


title: Primary Lung, biological replicate 2


title: Secondary dLN, biological replicate 1


title: IMR90P6A

description: Biological replicate 1

value: Bisulfite converted DNA


title: H358P14

description: biological replicate 2

value: male


title: iPCH460Col5

description: biological replicate 2

value: iPCH460 Col5


title: Secondary Spleen, biological replicate 2

value: Balb/c


title: iPSIMR90Col1

description: biological replicate 2

source_name: Induced Pluripotent Stem Cell

value: Induced Pluripotent stem cell


title: H1P99B

description: Biological replicate 2


title: piPCH358Col1

description: biological replicate 2

value: post induced pluripotent cancer cell


title: H460P21

description: biological replicate 2

value: lung large cell carcinoma


title: iPSIMR90Col9

description: biological replicate 3


title: Primary Lung, biological replicate 1

value: influenza A

value: lung


title: piPCH358Col1

description: biological replicate 2


title: H460P21B

description: biological replicate 3


title: iPSIMR90Col9

description: biological replicate 3


title: piPCH358Col11

description: biological replicate 1


title: iPSIMR90Col10

description: Biological replicate 1


title: iPCH460Col12

description: biological replicate 1

value: iPCH460 Col12


title: iPCH358Col3

description: Biological replicate 1

value: iPCH358 Col3


title: Primary dLN, biological replicate 2

description: Gene expression data from primary HNT CD4 T cell effectors from the dLN on day 7 post influenza infection

source_name: Primary HNT CD4 T cell effectors from the dLN on day 7 post influenza infection

value: dLN


title: Primary dLN, biological replicate 1


title: H460P21A

description: biological replicate 1


title: Primary dLN, biological replicate 3


title: IMR90P6A

description: Biological replicate 1

value: fetal lung fibroblast

value: IMR90 P6

value: female


title: H1P99A

description: Biological replicate 1

value: human embyronic stem cell line


title: Primary Spleen, biological replicate 2

description: Gene expression data from primary HNT CD4 T cell effectors from the spleen on day 7 post influenza infection

source_name: Primary HNT CD4 T cell effectors from the spleen on day 7 post influenza infection

value: Naïve HNT TCR Tg CD4 T cell

value: spleen


title: iPCH358Col1

description: biological replicate 2

value: induced pluripotent cancer cell

value: iPCH358 Col1

value: male


title: Primary Spleen, biological replicate 1

value: Balb/c


title: H358P14B

description: biological replicate 3

value: lung adenocarcinoma

value: Bisulfite converted DNA


title: IMR90P5

description: biological replicate 2


title: iPCH460Col9

description: biological replicate 3

value: iPCH460 Col9


title: Primary Spleen, biological replicate 3

value: influenza A


title: iPCH358Col3

description: Biological replicate 1


title: H358P14A

description: biological replicate 1


title: H358P13A

description: biological replicate 1


title: H460P22A

description: biological replicate 1

value: lung large cell carcinoma


title: iPCH358Col11

description: biological replicate 3

value: iPCH358 Col11


title: piPCH460Col5

description: biological replicate 3

value: post induced pluripotent cancer cell


title: piPCH358Col11

description: biological replicate 1


title: iPCH358Col1

description: biological replicate 2


title: iPSIMR90Col10

description: Biological replicate 1

value: Induced Pluripotent stem cell


title: H1P106A

description: Biological replicate 1


title: genomic DNA from fresh cord blood sample 2 (BeadChip)

city: Cambridge

first: Thomas

middle: A

last: Down

address: Tennis Court Road

department: WT/CRUK Gurdon Institute

institute: University of Cambridge

description: normal cord blood spot sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio softwarre

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from dried blood spot samples using the GenSolve kit as per manufacturers instructures.  DNA was extracted from other samples using the Qiagen DNeasy kit.

tag: sample id

tag: sample type

value: cord blood

tag: tissue

value: blood