title: ptsN mutant replicate 1

description: gene expression profile of ptsN mutant in M9 minimal medium, replicate 1.


title: TE fraction 59

status: Public on Sep 28 2010

type: genomic

city: Stanford

first: David

middle: Scott

last: Johnson

state: CA

address: 300 Pasteur Drive

department: Genetics

country: USA

institute: Stanford University

hyb_protocol: as per Illumina's instructions except reduced time to 6 hours

scan_protocol: iScan scanner

data_processing: Genotypes are inherently inaccurate in single cell microarray data due to biases introduced during multiple displacement amplification. Therefore  genotypes were not produced, and instead raw intensity data was used to build probabilistic models under the framework of the Parental Support   algorithm.

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: TE fraction

label_protocol: as per Illumina's instructions except reduced amplification time to 6 hours

extract_protocol: We thawed all fractions at 22°C, and then added Arcturus PicoPure Lysis Buffer (Molecular Devices, Sunnyvale, CA) to each of the biopsies. The tubes were incubated at 56°C for one hour, and then heat inactivated at 95°C for 10 minutes. DNA from the lysed biospsies was amplified using a commercial kit (GE Healthcare, Waukesha, WI) for multiple displacement amplification (MDA). MDA reactions were incubated at 30°C for 2.5 hours and then heat-inactivated at 65°C for five minutes.

tag: tissue

value: trophectoderm


title: 2513_p_2

type: RNA

city: Chiba

first: Shuhei

last: Noda

state: Chiba

address: Anagawa 4-9-1

department: Frontier research center

country: Japan

institute: National institute of radiological sciences

description: prior to treatment, radiotherapy alone

data_processing: global median normalization

molecule: total RNA

source_name: biopsy, prior to treatment, radiotherapy alone

tag: female, cervical cancer


title: 2032_p_1

source_name: biopsy, prior to treatment, carbon-ion radiotherapy


title: 176_p_1

description: prior to treatment, carbon-ion radiotherapy


title: 2029_p_1


title: 176_p_2


title: 2513_p_1

description: prior to treatment, radiotherapy alone


title: Annexin 1 treated cells, replicate 2

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

country: United Kingdom

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

description: Intensity values were obtained using the Affymetrix GeneChip Scanner 3000

hyb_protocol: According to Affymetrix Technical Manual (www.affymetrix.com). cRNA was fragmented prior to hybridization. Samples were incubates at 45C for 16 hours in an hybridization oven. After that, chips were washed and stained with streptavidin. After a washing step, chips were ready to be scanned.

data_processing: Data were normalized with RMA method using Bioconductor (affyPLM package).

label: Biotin

source_name: HEK293 cells

label_protocol: First, cDNA was obtained using the One-Cycle cDNA Synthesis kit. Then, the GeneChip Sample Cleanup Module was used to clean the samples. Finally, biotin-labeled cRNA was obtained using the GeneChip Labeling kit. All kits used were from Affymetrix.

growth_protocol: Cells were grown at 37C/5%CO2

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), according to manufacture's protocol

treatment_protocol: Cells were treated with 0.5uM Annexin 1 in PBS for 4 hours.

tag: HEK293 cells, transfected with ALX receptor (also called FPR2, formyl peptide receptor 2) in pGEX-4T-327 expresson vector and treated with Annexin 1.


title: 2775_p_2

description: prior to treatment, chemoradiotherapy

source_name: biopsy, prior to treatment, chemoradiotherapy


title: AC226 treated cells, replicate 1

scan_protocol: According to Affymetrix Technical Manual (www.affymetrix.com)

treatment_protocol: Cells were treated with  10uM Ac2-26 in PBS for 4 hours.

tag: HEK293 cells, transfected with ALX receptor (also called FPR2, formyl peptide receptor 2) in pGEX-4T-327 expresson vector and treated with the peptide Ac2-26.


title: Annexin 1 treated cells, replicate 1


title: CMV_2 Control sample, replicate 2

treatment_protocol: Cells were transfected with pGEX-4T-327 vector. Cells were treated with vehicle and used as controls for other treatments.

tag: HEK293 cells, transfected with empty vector, used as controls.


title: Patient tumor 33

status: Public on Sep 27 2010

city: Baltimore

first: Sheelu

last: Varghese

state: MD

address: 655 W Baltimore Street

department: surgery

institute: University of Maryland, Baltimore

description:
Patient tumor sample derived by surgical resection
cDNA derived from individual patient tumor total RNA samples hybridized against cDNA generated from human universal RNA

hyb_protocol: All tumor samples were hybridized against the common reference. Complementary DNA generated were fluorescently labeled with Cy5 (tumor samples) or Cy3 (reference). The human oligonucleotide array set (Hs-OperonV2-vW2) for ~22K genes were produced at the Advanced Technology Center (ATC) at the National Cancer Institute, Gaithersburg, MD were used. Microarray hybridization and washings were performed as described in the ATC protocol. http://arraytracker.nci.nih.gov/nciarrays.manual.october.2006.pdf

scan_protocol: Hybridized arrays were scanned with 10-µm resolution on a GenePix 4000A scanner (Axon Instruments). The resulting TIF images were extracted using GENEPIX PRO 3.0 software (Axon Instruments).

data_processing: The fluorescent intensity ratios were log2 transformed and normalized using Lowess smoother and then averaged expression ratios of each gene when it is represented more than once in a microarray platform. To identify genes with meaningful differences in expression data, we excluded any gene with missing expression data in more than 40% of the datasets and excluded genes based the 75th percentile of their log-expression values compared to reference across all arrays.

source_name: Peritoneal mesothelioma tumor

label_protocol: Total RNA (20µg) from patient tumor samples and Human Universal Reference  RNA, the reference sample for hybridization, were reverse transcribed using Reverse TranscriptaseIII.  All tumor samples were hybridized against the common reference. Complementary DNA generated were fluorescently labeled with Cy5 (tumor samples) or Cy3 (reference). The human oligonucleotide array set (Hs-OperonV2-vW2) for ~22K genes were produced at the Advanced Technology Center (ATC) at the National Cancer Institute, Gaithersburg, MD were used.

growth_protocol: Patient tumor samples were snap-frozen immediately after surgical resection

extract_protocol: Total RNA extracted using Trizol following manufacturer’s protocol

tag: disease state

value: mesothelioma

value: tumor

tag: gender

value: F

source_name: Human Universal RNA

tag: sample

value: Pooled total RNA


title: Patient tumor 35

value: M


title: Patient tumor 31


title: Patient tumor 34


title: Patient tumor 32


title: Patient tumor 36


title: ALXR_1 replicate 1

treatment_protocol: Cells were treated with vehicle and used as controls for other treatments.

tag: Cells were transfected with the annexin receptor ALXR (also called FPR2, formyl peptide receptor 2) in pGEX-4T-327 expression vector.


title: Patient tumor 37


title: Patient tumor 38


title: Patient tumor 41


title: Patient tumor 39


title: Patient tumor 40


title: Patient tumor 30


title: ALXR_2, replicate 2

tag: HEK293 cells, transfected with ALX receptor (also called FPR2, formyl peptide receptor 2) in pGEX-4T-327 expresson vector.


title: CMV_1 Control sample, replicate 1


title: 2773_p_1

description: prior to treatment, chemoradiotherapy


title: Patient tumor 29


title: Patient tumor 28


title: Patient tumor 18


title: Patient tumor 24


title: Patient tumor 20


title: Patient tumor 22


title: Patient tumor 17


title: Patient tumor 19


title: Patient tumor 25


title: Patient tumor 26


title: Patient tumor 16


title: 1591_p_2

description: prior to treatment, chemoradiotherapy


title: 1846_p_2

description: prior to treatment, chemoradiotherapy


title: Patient tumor 21


title: Patient tumor 15


title: 1591_p_1

description: prior to treatment, chemoradiotherapy


title: Patient tumor 13


title: Patient tumor 10


title: Patient tumor 12


title: 1995_p_1

description: prior to treatment, radiotherapy alone


title: Patient tumor 11


title: Patient tumor 14


title: Patient tumor 9


title: 2775_p_1

description: prior to treatment, chemoradiotherapy


title: 1846_p_1

description: prior to treatment, chemoradiotherapy


title: 1995_p_2

description: prior to treatment, radiotherapy alone


title: Patient tumor 8


title: Patient tumor 23


title: Ac226 treated cells, replicate 2

tag: HEK293 cells, transfected with ALX receptor (also called FPR2, formyl peptide receptor 2) in pGEX-4T-327 expresson vector and treated with Ac2-26 peptide


title: H5

city: Durham

first: Julia

middle: Ling-Yu

state: NC

address: CIEMAS Rm.2141, 101 Science Dr.

institute: Duke university

description: no additional information

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Expression Console (Affymetrix) was used to generate the RMA file. Cluster 3.0 was used for hierarhical clustering.

label: biotin

source_name: MCF7 cells

label_protocol: Affymetrix standard protocol

growth_protocol: MCF7 cells were serum starved for 24 hours followed by being exposed to control, lactic acidosis, glucose deprivation and hypoxia

extract_protocol: RNAs were extracted with miRVana kits from Ambion

treatment_protocol: MCF7 cells were treated with the conditions of control, 25mM lactic acidosis, 0 glucose and 1%oxygen for 4 hours

tag: stress

value: hypoxia


title: H4

description: no additional information


title: Elf5+/+ mammary gland, 16.5 days post coitus, sample 1

city: Darlinghurst

first: Renee

last: Rogers

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description:
16.5 WT 1
Biological replicate 1 of 3.

hyb_protocol: Microarray slides were immersed in 50 ml of hot Milli-Q water (80-95°C) and agitated gently for 5 mins prior to hybridisation.  The labelled cDNA was mixed with 0.64 μl of 25 mg/ml yeast tRNA, 4 μl of 2 mg/ml poly A and 20 μl of 1 mg/ml Cot1 DNA.  This mix was then dried under reduced pressure, and then dissolved in 16 μl of formamide and 6.25 x SSC.  The mixture was then heated to 100°C for 3 mins, transferred directly to ice before adding 0.5 μl of 10% SDS.  The solution was then applied to the centre of the cover slip and the array slide was lowered onto the cover slip.  The slide was then incubated at 42°C overnight in a humidified chamber.  The array slide was then immersed in a solution of 0.5 X SSC and 0.01% SDS until the coverslip detached from the slide.  After discarding the coverslip, the slide was washed in 0.5 X SSC and 0.1% SDS for 5 mins, and then 0.5 X SSC for 5 mins and then 0.2 X SSC for 3 mins.  The slide was then dried in a centrifuge at 750 rpm for 5 mins and stored in the dark prior to scanning.

scan_protocol: Microarray slides were scanned using an Agilent G2565BA DNA microarray scanner. Images were analysed with DigitalGENOME (Molecularware).

data_processing: LOWESS normalised. Prior to analysis, the following filtering steps were applied: 1) only genes with a mean reference (embryo) intensity equal to or above the average reference intensity (average for all the spots in the reference channel on that slide) in at least 6 of the 10 conditions were included;  and 2) the list of genes was also filtered on fold change, where genes must (in at least 1 of the 10 comparisons) have normalised data values that are greater or less than those in the other 9 conditions by a factor of 2 fold, i.e. the expression of the gene must change at one or more time points.  After these filters were applied, the number of genes on our list was a more manageable 2325. Genespring GX 7.3 (Agilent) software was used for all data processing.

label: Alexa 532

organism: Mus musculus

source_name: Total RNA from pooled whole mouse embryos e17.5

label_protocol: The purified cDNA was dried under reduced pressure, and then dissolved in 9 µL of 0.1 M NaHCO3 (pH 9.0). The mixture was added to a Cy dye aliquot (One Cy dye sachet (Amersham) is dissolved in 73 µL of anhydrous DMSO, and then 4.5 µL aliquots are distributed into sealable tubes. Each aliquot is dried under reduced pressure, sealed, and  then stored in a dessicator at –20°C), mixed, and then left to incubate at room temperature for 60 mins in the dark.  The labelled cDNA was mixed with 41 µL of Milli Q water, and then purified using a QIAquick PCR purification kit (Qiagen). The sample was eluted into a clean tube with 90 µL of Milli Q water. The purified labelled cDNA samples appear purple after being dried under reduced pressure.

growth_protocol: Mice were mated, and the day of vaginal plug detection deemed 0.5 days post coitus (dpc).  Mice were humanely culled on the appropriate day of pregnancy and the abdominal mammary glands from two mice pooled.

extract_protocol: RNA was extracted from the mammary glands using the Rneasy maxi kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Mice were kept under regular 12hr light/dark cycles, and fed ad libitum.

tag: strain

tag: genotype

value: wildtype

value: whole body

tag: developmental stage

value: embryo

tag: age

value: 17.5 days post coitus

tag: sample type

value: reference

label: Alexa 635

source_name: Elf5 WT 16.5dpc

value: mammary gland

value: 16.5 days post coitus


title: Elf5+/- mammary gland, 14.5 days post coitus, sample 3

description:
14.5 HET 3
Biological replicate 3 of 3.

source_name: Elf5 HET 14.5dpc

tag: tissue

value: 14.5 days post coitus

tag: development stage


title: Elf5+/- mammary gland, 16.5 days post coitus, sample 3

description:
16.5 HET 3
Biological replicate 3 of 3.

source_name: Elf5 HET 16.5dpc


title: G2

description: no additional information

value: glucose deprivation


title: Elf5+/+ mammary gland, 16.5 days post coitus, sample 3

description:
16.5 WT 3
Biological replicate 3 of 3.


title: H3

description: no additional information


title: 2773_p_2

description: prior to treatment, chemoradiotherapy

tag: female, cervical cancer


title: Elf5+/+ mammary gland, 16.5 days post coitus, sample 2

description:
16.5 WT 2
Biological replicate 2 of 3.


title: Elf5+/- mammary gland, 16.5 days post coitus, sample 1

description:
16.5 HET 1
Biological replicate 1 of 3.

source_name: ELf5 HET 16.5dpc


title: Elf5+/- mammary gland, 14.5 days post coitus, sample 2

description:
14.5 HET 2
Biological replicate 2 of 3.


title: Elf5+/- mammary gland, 10.5 days post coitus, sample 2

description:
10.5 HET 2
Biological replicate 2 of 3.

source_name: Elf5 HET 10.5dpc

value: 10.5 days post coitus


title: Elf5+/- mammary gland, 14.5 days post coitus, sample 1

description:
14.5 HET 1
Biological replicate 1 of 3.

source_name: ELf5 HET 14.5dpc


title: G3

description: no additional information


title: H1

description: no additional information


title: Elf5+/- mammary gland, 16.5 days post coitus, sample 2

description:
16.5 HET 2
Biological replicate 2 of 3.


title: Elf5+/+ mammary gland, 14.5 days post coitus, sample 3

description:
14.5 WT 3
Biological replicate 3 of 3.

source_name: Elf5 WT 14.5dpc


title: Elf5+/+ mammary gland, 14.5 days post coitus, sample 2

description:
14.5 WT 2
Biological replicate 2 of 3.


title: G4

description: no additional information


title: Elf5+/+ mammary gland, 10.5 days post coitus, sample 3

description:
10.5 WT 3
Biological replicate 3 of 3.

source_name: Elf5 WT 10.5dpc


title: Elf5+/+ mammary gland, 10.5 days post coitus, sample 2

description:
10.5 WT 2
Biological replicate 2 of 3.


title: H2

description: no additional information


title: G5

description: no additional information


title: Elf5+/+ mammary gland, 14.5 days post coitus, sample 1

description:
14.5 WT 1
Biological replicate 1 of 3.


title: Elf5+/- mammary gland, 10.5 days post coitus, sample 1

description:
10.5 HET 1
Biological replicate 1 of 3.

source_name: ELf5 HET 10.5dpc


title: Elf5+/- mammary gland, 10.5 days post coitus, sample 3

description:
10.5 HET 3
Biological replicate 3 of 3.


title: Patient tumor 27


title: G1

description: no additional information


title: LA5

description: no additional information

value: lactic acidosis


title: Elf5+/- mammary gland, 8.5 days post coitus, sample 3

description:
8.5 HET 3
Biological replicate 3 of 3.

source_name: Elf5 HET 8.5dpc

value: 8.5 days post coitus


title: Elf5+/+ mammary gland, 8.5 days post coitus, sample 3

description:
8.5 WT 3
Biological replicate 3 of 3.

source_name: Elf5 WT 8.5dpc


title: Elf5+/+ mammary gland, 8.5 days post coitus, sample 1

description:
8.5 WT 1
Biological replicate 1 of 3.


title: Elf5+/- mammary gland, 8.5 days post coitus, sample 1

description:
8.5 HET 1
Biological replicate 1 of 3.

source_name: ELf5 HET 8.5dpc


title: Elf5+/- mammary gland, 8.5 days post coitus, sample 2

description:
8.5 HET 2
Biological replicate 2 of 3.


title: LA1

description: no additional information


title: LA4

description: no additional information


title: Patient tumor 7

value: mesothelioma

value: tumor


title: Elf5+/+ mammary gland, virgin, sample 1

description:
V WT 1
Biological replicate 1 of 3.

source_name: Elf5 WT V

value: virgin


title: C3

description: no additional information

value: control


title: LA2

description: no additional information


title: Elf5+/+ mammary gland, 8.5 days post coitus, sample 2

description:
8.5 WT 2
Biological replicate 2 of 3.


title: LA_24hr-3

description: gene expression data from MCF7 cells

growth_protocol: MCF7 cells were serum starved for 24 hours followed by being exposed to control media versus media containing 25mM lactic acidosis

treatment_protocol: MCF7 cells were treated with the control media and the media containing 25mM lactic acidosis for 1, 4, 12, 24 hours

tag: cell line

tag: treatment

value: media with 25mM lactic acid (24hr)


title: Elf5+/+ mammary gland, 10.5 days post coitus, sample 1

description:
10.5 WT 1
Biological replicate 1 of 3.

value: wildtype


title: LA3

description: no additional information


title: C5

description: no additional information


title: Elf5+/+ mammary gland, virgin, sample 3

description:
V WT 3
Biological replicate 3 of 3.

value: whole body


title: LA_24hr-2

description: gene expression data from MCF7 cells


title: C4

description: no additional information


title: Elf5+/- mammary gland, virgin, sample 2

description:
V HET 2
Biological replicate 2 of 3.

source_name: Elf5 HET V

value: embryo


title: LA_24hr-1

description: gene expression data from MCF7 cells


title: Patient tumor 6

source_name: Peritoneal mesothelioma tumor

tag: disease state

value: M

source_name: Human Universal RNA

value: Pooled total RNA


title: LA_12hr-3

description: gene expression data from MCF7 cells

source_name: MCF7 cells

value: media with 25mM lactic acid (12hr)


title: Elf5+/- mammary gland, virgin, sample 1

description:
V HET 1
Biological replicate 1 of 3.

source_name: Total RNA from pooled whole mouse embryos e17.5

value: 17.5 days post coitus

value: reference

source_name: ELf5 HET V

value: mammary gland


title: Elf5+/+ mammary gland, virgin, sample 2

description:
V WT 2
Biological replicate 2 of 3.


title: Patient tumor 3

tag: gender

value: F


title: Patient tumor 4

tag: sample


title: Patient tumor 5


title: Patient tumor 2


title: C1

description: no additional information


title: LA_12hr-2

description: gene expression data from MCF7 cells


title: Elf5+/- mammary gland, virgin, sample 3

description:
V HET 3
Biological replicate 3 of 3.


title: LA_4hr-3

description: gene expression data from MCF7 cells

value: media with 25mM lactic acid (4hr)


title: C2

description: no additional information


title: LA_12hr-1

description: gene expression data from MCF7 cells


title: LA_4hr-1

description: gene expression data from MCF7 cells


title: Patient tumor 1


title: LA_4hr-2

description: gene expression data from MCF7 cells


title: TKOMEF_Ctrl3

description: TXNIP-null MEF in control media

source_name: TXNIP-null MEF

value: TXNIP-null MEF


title: TKOMEF_LA1

description: TXNIP-null MEF in media of 10mM lactic acid

value: media with 10mM lactic acid


title: TKOMEF_Ctrl2

description: TXNIP-null MEF in control media


title: TKOMEF_LA3


title: TKOMEF_Ctrl1

description: TXNIP-null MEF in control media


title: TKOMEF_LA2


title: WTMEF_LA1

description: wildtype MEF in media with 10mM lactic acid

source_name: WTMEF

value: wildtype MEF


title: WTMEF_LA3


title: LA_1hr-1

description: gene expression data from MCF7 cells

value: media with 25mM lactic acid (1hr)


title: WTMEF_Ctrl3

description: wildtype MEF in control media

value: control


title: H2B K37A, replicate 3

city: Chapel Hill

first: Brian

last: Strahl

address: 120 Mason Farm Rd.   3060 Genetic Medicine, CB# 7260

department: Biochemistry and Biophysics

institute: University of North Carolina School of Medicine

description: YKG007 C

hyb_protocol: Standard Affymetrix protocol (briefly, 16 hours at 45˚C at 60 rpm in a GeneChip Hybridization Oven 640 on Yeast Genome 2.0 array).  The arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: Scanned with the GeneChip Scanner 3000 7G Plus Scanner with Autoloader.  Affymetrix GeneChip Command Console Software was used to operate the scanner and fluidics stations.

data_processing: Expression data was generated following scanning of the arrays with the Expression Console software from Affymetrix, where the RMA algorithm was used to generate the expression data.

organism: Saccharomyces cerevisiae

source_name: Acid-extracted histones from asynchronously grown yeast expressing H2B K37A mutation

label_protocol: Labeling was completed using MessageAmpTM II-Biotin Enhanced Kit (Ambion) according to manufacturer instructions

growth_protocol: Yeast cultures were grown in YPD simultaneously in triplicate to mid-exponential phase (OD600 = 1.0)

extract_protocol: RNA was isolated using the hot acidic phenol-chloroform method (Collart MA, Oliviero S (2001) Curr Protoc Mol Biol Chapter 13:Unit 13.12), followed by RNeasy Clean-up (QIAGEN).  RNA quality was determined using an Agilent Bioanalyzer.

tag: h2b status

value: K37A mutant

tag: genotype/variation

value: MATa (hta1-htb1)D::LEU2 (hta2-htb2)D::TRP1 leu2D1 ura3-52 lys2D1 lys2-128d his3D200 trp1D63 <pKG2 (HTA1-Flag-htb1 (K37A), HIS3)>


title: WTMEF_LA2


title: Wild-type H2B, replicate 1

description: YKG001 A

source_name: Acid-extracted histones from asynchronously grown yeast expressing wild-type H2B

value: wild type

value: MATa (hta1-htb1)D::LEU2 (hta2-htb2)D::TRP1 leu2D1 ura3-52 lys2D1 lys2-128d his3D200 trp1D63 <pZS145 (HTA1-Flag-HTB1, HIS3)>


title: LA_1hr-2

description: gene expression data from MCF7 cells


title: LA_1hr-3

description: gene expression data from MCF7 cells


title: H2B K37A, replicate 2

description: YKG007 B


title: Wild-type H2B, replicate 2

description: YKG001 B


title: WTMEF_Ctrl1

description: wildtype MEF in control media


title: H2B K37A, replicate 1

description: YKG007 A


title: Ctrl_24hr-3

description: gene expression data from MCF7 cells

value: control media (24hr)


title: Ctrl_24hr-1

description: gene expression data from MCF7 cells


title: Wild-type H2B, replicate 3

description: YKG001 C


title: Ctrl_24hr-2

description: gene expression data from MCF7 cells


title: Ctrl_12hr-3

description: gene expression data from MCF7 cells

value: control media (12hr)


title: Ctrl_12hr-2

description: gene expression data from MCF7 cells


title: Ctrl_4hr-3

description: gene expression data from MCF7 cells

value: control media (4hr)


title: Bone marrow_irradiated_Zn-yeast_6hr (Cy5) vs. Bone marrow_irradiated_methylcellulose_6hr (Cy3)

first: Kaori

last: Imadome

department: Research Center of Charged Particle Therapy

description: X-ray irradiated, methylcellulose (Cy3) vs. X-ray irradiated, Zn-yeast (Cy5).

hyb_protocol: according to standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Dye biases between two signals, Red and Green, were corrected using Lowess normalization, subtracted background and converted to log10 of processed Red signal/processed Green signal.

source_name: bone marrow, X-ray irradiation, Zn-yeast administration, 6 hours

label_protocol: Agilent Low RNA Input Linear Amplification Kit

growth_protocol: The mice, received at 8 weeks of age, were housed five per cage and allowed free access to a commercial diet (MB-1, Funabashi Farm Co., Funabashi, Japan) and acidified water during the experimental period.  The animal rooms were maintained on a 12 h light-dark cycle, at an air temperature of 23 C, and a humidity of 55%.  The mice were 65-75 days old at the time of irradiation and weighed 24-29 g.

extract_protocol: ISOGEN (Wako pure chemical) + RNeasy (QIAGEN)

treatment_protocol: The zinc-containing yeast powder was suspended in a 0.5% methylcellulose solution. The suspension (0.3 ml of 8.5 mg/ml = 100 mg/kg) was administered i.p. to C3H mice immediately after 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after irradiation, the bone marrow was flushed from femora and was collected into centrifuge tubes.

value: male

value: 10 weeks

value: bone marrow

tag: irradiation

value: whole body irradiation

value: Zn-yeast

source_name: bone marrow, X-ray irradiation, methylcellulose administration, 6 hours

treatment_protocol: 0.3 ml of a 0.5% methylcellulose solution was administered i.p. to C3H mice immediately after 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after irradiation, the bone marrow was flushed from femora and was collected into centrifuge tubes.

value: methylcellulose


title: Bone marrow_irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_irradiated_Zn-yeast_6hr (Cy3)

description: X-ray irradiated, methylcellulose (Cy5) vs. X-ray irradiated, Zn-yeast (Cy3).


title: WTMEF_Ctrl2

description: wildtype MEF in control media


title: Ctrl_12hr-1

description: gene expression data from MCF7 cells


title: Bone marrow_non-irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_non-irradiated_Zn-yeast_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy5) vs.non-irradiated, Zn-yeast (Cy3).

source_name: bone marrow, non-irradiation, methylcellulose administration, 6 hours

treatment_protocol: 0.3 ml of a 0.5% methylcellulose solution was administered i.p. to C3H mice without 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after administration, the bone marrow was flushed from femora and was collected into centrifuge tubes.

source_name: bone marrow, non-irradiation, Zn-yeast administration, 6 hours

treatment_protocol: The zinc-containing yeast powder was suspended in a 0.5% methylcellulose solution. The suspension (0.3 ml of 8.5 mg/ml = 100 mg/kg) was administered i.p. to C3H mice without 7.5 Gy whole-body X-irradiation. Both femora were removed from mice 6 hours after administration, the bone marrow was flushed from femora and was collected into centrifuge tubes.


title: Ctrl_4hr-1

description: gene expression data from MCF7 cells


title: Bone marrow_non-irradiated_Zn-yeast_6hr (Cy5) vs. Bone marrow_non-irradiated_methylcellulose_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy3) vs.non-irradiated, Zn-yeast (Cy5).


title: Castration-recurrent; Biological replicate #3

type: SAGE

anchor: NlaIII

city: Vancouver

first: Marianne

middle: D.

last: Sadar

state: British Columbia

address: 675 W. 10th Ave

department: Genome Sciences Centre

country: Canada

institute: British Columbia Cancer Agency

description: LongSAGE libraries were constructed with 5ug of total RNA using the Invitrogen I-SAGE Long kit.

source_name: In vivo LNCaP Hollow Fibre model

growth_protocol: LNCaP cells were grown in hollow fibres in a mouse.

extract_protocol: Total RNA was isolated immediately from cells harvested from the in vivo Hollow Fibre model using TRIZOL Reagent following the manufacturer’s instructions. Genomic DNA was removed from RNA samples with DNaseI.

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13R at the castration-recurrent stage of hormonal progression of prostate cancer. Samples were retrieved 72 days following surgical castration of the mouse.

value: Stage in hormonal progression is castration-recurrent; Biological replicate #3

value: LNCaP

value: prostate cancer, castration-recurrent


title: Androgen-sensitive; Biological replicate #3

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13R at the androgen-sensitive stage of hormonal progression of prostate cancer. Samples were retrieved immediately following surgical castration of the mouse.

value: Stage in hormonal progression is androgen-sensitive; Biological replicate #3

value: prostate cancer, androgen-sensitive


title: Responsive to androgen-deprivation; Biological replicate #3

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13R at the responsive to androgen-deprivation stage of hormonal progression of prostate cancer. Samples were retrieved 10 days following surgical castration of the mouse.

value: Stage in hormonal progression is responsive to androgen-deprivation; Biological replicate #3

value: prostate cancer, responsive to androgen-deprivation


title: Bone marrow_non-irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_irradiated_methylcellulose_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy5) vs. X-ray irradiated, methylcellulose (Cy3).


title: Castration-recurrent; Biological replicate #2

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 15N at the castration-recurrent stage of hormonal progression of prostate cancer. Samples were retrieved 72 days following surgical castration of the mouse.

value: Stage in hormonal progression is castration-recurrent; Biological replicate #2


title: Androgen-sensitive; Biological replicate #1

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13N at the androgen-sensitive stage of hormonal progression of prostate cancer. Samples were retrieved immediately prior to castration of the mouse.

value: Stage in hormonal progression is androgen-sensitive; Biological replicate #1


title: Bone marrow_irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_non-irradiated_methylcellulose_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy3) vs. X-ray irradiated, methylcellulose (Cy5).


title: Responsive to androgen-deprivation; Biological replicate 2

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 15N at the responsive to androgen-deprivation stage of hormonal progression of prostate cancer. Samples were retrieved 10 days following surgical castration of the mouse.

value: Stage in hormonal progression is responsive to androgen-deprivation; Biological replicate #2


title: Androgen-sensitive; Biological replicate #2

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 15N at the androgen-sensitive stage of hormonal progression of prostate cancer. Samples were retrieved immediately prior to surgical castration of the mouse.

value: Stage in hormonal progression is androgen-sensitive; Biological replicate #2


title: Ctrl_4hr-2

description: gene expression data from MCF7 cells

value: control media (4hr)


title: Castration-recurrent; Biological replicate #1

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13N at the castration-recurrent stage of hormonal progression of prostate cancer. Samples were retrieved 72 days following surgical castration of the mouse.

value: Stage in hormonal progression is castration-recurrent; Biological replicate #1


title: Ctrl_1hr-2

description: gene expression data from MCF7 cells

value: control media (1hr)


title: Ctrl_1hr-1

description: gene expression data from MCF7 cells


title: Ctrl_1hr-3

description: gene expression data from MCF7 cells


title: Bone marrow_non-irradiated_methylcellulose_6hr (Cy5) vs. Bone marrow_irradiated_Zn-yeast_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy5) vs. X-ray irradiated, Zn-yeast (Cy3).

value: male

value: 10 weeks

value: bone marrow

value: whole body irradiation


title: Bone marrow_irradiated_Zn-yeast_6hr (Cy5) vs. Bone marrow_non-irradiated_methylcellulose_6hr (Cy3)

description: Non-irradiated, methylcellulose (Cy3) vs. X-ray irradiated, Zn-yeast (Cy5).

value: Zn-yeast

value: methylcellulose


title: Responsive to androgen-deprivation; Biological replicate #1

treatment_protocol: Fibres containing LNCaP cells were removed from mouse 13N at the responsive to androgen-deprivation stage of hormonal progression of prostate cancer. Samples were retrieved 10 days post surgical castration of the mouse.

value: Stage in hormonal progression is responsive to androgen-deprivation; Biological replicate #1

value: LNCaP


title: N-133 T414-S-NI vs. N-17 T26-S-NI

status: Public on Sep 26 2010

city: Stony Brook

first: Tianyi

last: Zhang

state: NY

address: 1500 Stony Brook Road

institute: Stony Brook University

hyb_protocol: Hybridized in microarray hybridization chamber as per manufacturer's recommendations.

scan_protocol: Scanned on Axon GenePix 4000B scanner.

data_processing: The data were normalized using print-tip loess (conducted with the LIMMA package in R). Rows with all GenePix flags less than -50 were removed. The missing values were imputed with the K-nearest neighbor method.

source_name: disease-unaffected ileum from control

label_protocol: Agilent Low RNA Input Linear Amplification Kit using 0.5 microgram total RNA.

extract_protocol: Trizol extraction of total RNA.

value: proximal ileal margin

tag: disease phenotype

value: no inflammatory bowel disease

value: reference (N-17)


title: N-48 T266-S-NI vs. N-17 T26-S-NI


title: N-35 T224-S-NI vs. N-17 T26-S-NI


title: N-53 T273-S-NI vs. N-17 T26-S-NI


title: N-69 T304-S-NI vs. N-17 T26-S-NI


title: N-98 T356-S-NI vs. N-17 T26-S-NI


title: N-93 T349-S-NI vs. N-17 T26-S-NI


title: N-54 T274-S-NI vs. N-17 T26-S-NI


title: N-42 T249-S-NI vs. N-17 T26-S-NI


title: N-73 T310-S-NI vs. N-17 T26-S-NI


title: N-49 T267-S-NI vs. N-17 T26-S-NI


title: N-46 T216-S-NI vs. N-17 T26-S-NI


title: N-52 T271-S-NI vs. N-17 T26-S-NI


title: N-50 T269-S-NI vs. N-17 T26-S-NI


title: N-55 T277-S-NI vs. N-17 T26-S-NI


title: N-41 T246-S-NI vs. N-17 T26-S-NI


title: N-33 T213-S-NI vs. N-17 T26-S-NI

description: This Sample represents two technical replicates.

data_processing: The data were normalized using print-tip loess (conducted with the LIMMA package in R). Rows with all GenePix flags less than -50 were removed. The missing values were imputed with the K-nearest neighbor method. Averages were taken for the two technical replicates.


title: N-37 T236-S-NI vs. N-17 T26-S-NI


title: N-38 T240-S-NI vs. N-17 T26-S-NI


title: N-34 T217-S-NI vs. N-17 T26-S-NI


title: N-13 T14-S-NI vs. N-17 T26-S-NI


title: N-15 T23-S-NI vs. N-17 T26-S-NI


title: N-19 T30-S-NI vs. N-17 T26-S-NI


title: CD-928 T458-S-NI vs. N-17 T26-S-NI

source_name: disease-unaffected ileum from Crohn's disease patient

value: illeal Crohn's disease


title: CD-223 T489-S-NI vs. N-17 T26-S-NI


title: CD-924 T450-S-NI vs. N-17 T26-S-NI


title: CD-957 T501-S-NI vs. N-17 T26-S-NI


title: CD-917 T425-S-NI vs. N-17 T26-S-NI


title: CD-939 T477-S-NI vs. N-17 T26-S-NI


title: CD-936 T471-S-NI vs. N-17 T26-S-NI


title: CD-923 T439-S-NI vs. N-17 T26-S-NI


title: N-75 T312-S-NI vs. N-17 T26-S-NI


title: CD-919 T432-S-NI vs. N-17 T26-S-NI


title: CD-794 T323-S-NI vs. N-17 T26-S-NI


title: CD-349 T230-S-NI vs. N-17 T26-S-NI


title: CD-888 T370-S-NI vs. N-17 T26-S-NI


title: CD-829 T327-S-NI vs. N-17 T26-S-NI


title: CD-379 T101-S-NI vs. N-17 T26-S-NI


title: CD-714 T214-S-NI vs. N-17 T26-S-NI


title: CD-918 T430-S-NI vs. N-17 T26-S-NI


title: CD-884 T366-S-NI vs. N-17 T26-S-NI


title: CD-846 T358-S-NI vs. N-17 T26-S-NI


title: CD-757 T276-S-NI vs. N-17 T26-S-NI


title: CD-336 T94-S-NI vs. N-17 T26-S-NI


title: CD-404 T100-S-NI vs. N-17 T26-S-NI


title: CD-451 T115-S-NI vs. N-17 T26-S-NI


title: CD-529 T163-S-NI vs. N-17 T26-S-NI


title: CD-216 T91-S-NI vs. N-17 T26-S-NI


title: CD-323 T176-S-NI vs. N-17 T26-S-NI


title: CD-196 T27-S-NI vs. N-17 T26-S-NI


title: CD-557 T194-S-NI vs. N-17 T26-S-NI


title: CD-382 T93-S-NI vs. N-17 T26-S-NI


title: CD-178 T4-S-NI vs. N-17 T26-S-NI


title: CD-155 T37-S-NI vs. N-17 T26-S-NI


title: CD-650 T229-S-NI vs. N-17 T26-S-NI


title: CD-233 T95-S-NI vs. N-17 T26-S-NI


title: CD-710 T454-S-NI vs. N-17 T26-S-NI


title: CD-563 T191-S-NI vs. N-17 T26-S-NI


title: CD-133 T5-S-NI vs. N-17 T26-S-NI


title: CD-401 T97-S-NI vs. N-17 T26-S-NI


title: CD-256 T67-S-NI vs. N-17 T26-S-NI


title: CD-340 T108-S-NI vs. N-17 T26-S-NI


title: CD-312 T78-S-NI vs. N-17 T26-S-NI


title: CD-185 T9-S-NI vs. N-17 T26-S-NI


title: CD-19 14892 NI vs. N-17 T26-S-NI


title: CD-22 14892 NI vs. N-17 T26-S-NI


title: UC250 T238-S-II vs. N-17 T26-S-NI

source_name: disease-unaffected ileum from ulcerative colitis patient

value: ulcerative colitis


title: CD-15  14881 NI vs. N-17 T26-S-NI


title: UC386 T455-S-NI vs. N-17 T26-S-NI


title: UC394 T465-S-NI vs. N-17 T26-S-NI


title: UC380 T459-S-NI vs. N-17 T26-S-NI


title: UC201 T285-S-NI vs. N-17 T26-S-NI


title: UC306 T288-S-NI vs. N-17 T26-S-NI


title: UC107 T294-S-NI vs. N-17 T26-S-NI


title: UC238 T297-S-NI vs. N-17 T26-S-NI


title: N-39 T244-S-NI vs. N-17 T26-S-NI


title: UC335 T329-S-NI vs. N-17 T26-S-NI


title: UC348 T345-S-NI vs. N-17 T26-S-NI


title: UC396 T478-S-NI vs. N-17 T26-S-NI


title: UC379 T442-S-NI vs. N-17 T26-S-NI


title: CD-493 T142-S-NI vs. N-17 T26-S-NI


title: UC199 T222-S-NI vs. N-17 T26-S-NI


title: UC297 T272-S-NI vs. N-17 T26-S-NI


title: CD-275 T70-S-NI vs. N-17 T26-S-NI


title: UC384 T452-S-NI vs. N-17 T26-S-NI


title: UC175 T325-S-NI vs. N-17 T26-S-NI


title: CD-235 T58-S-NI vs. N-17 T26-S-NI


title: UC385 T453-S-NI vs. N-17 T26-S-NI


title: UC221 T221-S-NI vs. N-17 T26-S-NI


title: UC177 T221-S-NI vs. N-17 T26-S-NI


title: UC309 T284-S-NI vs. N-17 T26-S-NI


title: UC256 T245-S-II vs. N-17 T26-S-NI


title: UC89 T74-S-NI vs. N-17 T26-S-NI


title: UC153 T119-S-NI vs. N-17 T26-S-NI


title: UC167 T227-S-Ni vs. N-17 T26-S-NI


title: UC59 T56-S-NI vs. N-17 T26-S-NI


title: UC7 T110-S-NI vs. N-17 T26-S-NI


title: CD-124 T1-S-NI vs. N-17 T26-S-NI


title: UC165 T150-S-NI vs. N-17 T26-S-NI


title: GM17198 (650K)

status: Public on Sep 25 2010

city: Rochester

first: Liewei

last: Wang

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

description: Genomic DNA extracted from lymphoblastoid cell line was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: Samples are applied to each BeadChip. The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50mers (covalently linked to one of over 500,000 bead types) during hybridization. One bead type corresponds to each allele per SNP locus.  Unhybridized and non-specifically hybridized DNA is washed away. The chip undergoes staining and extension in capillary flow-through chambers. Singlebase extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates detectable labels on the BeadChip and determines the genotype call for the sample.

scan_protocol: The Illumina BeadArray Reader scans the BeadChip, using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores.

data_processing: Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using HumanHap650Y v3.0 Whole-Genome Genotyping Kit  (Illumina).

source_name: lymphoblastoid cell line GM17198

label_protocol: 750 ng of high quality DNA samples are denatured and neutralized, and then are isothermally amplified in an overnight step.  The amplified product is fragmented by a controlled enzymatic process that does not require gel electrophoresis. The process uses end-point fragmentation to avoid overfragmenting the sample.  After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4ºC, and resuspended in a hybridization buffer.

extract_protocol: Genomic DNA was purchased from the Coriell Cell Repository (Camden, NJ), which was extracted from the cell cultures in the Repositories

tag: ethnic group

value: AA African-American

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17165 (650K)

source_name: lymphoblastoid cell line GM17165


title: GM17106 (650K)

source_name: lymphoblastoid cell line GM17106


title: GM17166 (650K)

source_name: lymphoblastoid cell line GM17166


title: GM17185 (650K)

source_name: lymphoblastoid cell line GM17185


title: GM17196 (650K)

source_name: lymphoblastoid cell line GM17196


title: GM17164 (650K)

source_name: lymphoblastoid cell line GM17164


title: GM17184 (650K)

source_name: lymphoblastoid cell line GM17184


title: GM17161 (650K)

source_name: lymphoblastoid cell line GM17161


title: GM17180 (650K)

source_name: lymphoblastoid cell line GM17180


title: GM17188 (650K)

source_name: lymphoblastoid cell line GM17188


title: GM17197 (650K)

source_name: lymphoblastoid cell line GM17197


title: GM17200 (650K)

source_name: lymphoblastoid cell line GM17200


title: GM17183 (650K)

source_name: lymphoblastoid cell line GM17183


title: GM17182 (650K)

source_name: lymphoblastoid cell line GM17182


title: GM17181 (650K)

source_name: lymphoblastoid cell line GM17181


title: GM17194 (650K)

source_name: lymphoblastoid cell line GM17194


title: GM17190 (650K)

source_name: lymphoblastoid cell line GM17190


title: GM17186 (650K)

source_name: lymphoblastoid cell line GM17186


title: GM17187 (650K)

source_name: lymphoblastoid cell line GM17187


title: GM17195 (650K)

source_name: lymphoblastoid cell line GM17195


title: GM17192 (650K)

source_name: lymphoblastoid cell line GM17192


title: GM17162 (650K)

source_name: lymphoblastoid cell line GM17162


title: GM17177 (650K)

source_name: lymphoblastoid cell line GM17177


title: GM17179 (650K)

source_name: lymphoblastoid cell line GM17179


title: GM17178 (650K)

source_name: lymphoblastoid cell line GM17178


title: GM17191 (650K)

source_name: lymphoblastoid cell line GM17191


title: GM17193 (650K)

source_name: lymphoblastoid cell line GM17193


title: GM17176 (650K)

source_name: lymphoblastoid cell line GM17176


title: GM17174 (650K)

source_name: lymphoblastoid cell line GM17174


title: GM17199 (650K)

source_name: lymphoblastoid cell line GM17199


title: GM17163 (650K)

source_name: lymphoblastoid cell line GM17163


title: GM17168 (650K)

source_name: lymphoblastoid cell line GM17168


title: GM17173 (650K)

source_name: lymphoblastoid cell line GM17173


title: GM17167 (650K)

source_name: lymphoblastoid cell line GM17167


title: GM17157 (650K)

source_name: lymphoblastoid cell line GM17157


title: GM17160 (650K)

source_name: lymphoblastoid cell line GM17160


title: GM17154 (650K)

source_name: lymphoblastoid cell line GM17154


title: GM17148 (650K)

source_name: lymphoblastoid cell line GM17148


title: GM17171 (650K)

source_name: lymphoblastoid cell line GM17171


title: GM17189 (650K)

source_name: lymphoblastoid cell line GM17189


title: GM17150 (650K)

source_name: lymphoblastoid cell line GM17150


title: GM17147 (650K)

source_name: lymphoblastoid cell line GM17147


title: GM17146 (650K)

source_name: lymphoblastoid cell line GM17146


title: GM17143 (650K)

source_name: lymphoblastoid cell line GM17143


title: GM17172 (650K)

source_name: lymphoblastoid cell line GM17172


title: GM17156 (650K)

source_name: lymphoblastoid cell line GM17156


title: GM17170 (650K)

source_name: lymphoblastoid cell line GM17170


title: GM17159 (650K)

source_name: lymphoblastoid cell line GM17159


title: GM17149 (650K)

source_name: lymphoblastoid cell line GM17149


title: GM17175 (650K)

source_name: lymphoblastoid cell line GM17175


title: GM17140 (650K)

source_name: lymphoblastoid cell line GM17140


title: GM17155 (650K)

source_name: lymphoblastoid cell line GM17155


title: GM17141 (650K)

source_name: lymphoblastoid cell line GM17141


title: GM17142 (650K)

source_name: lymphoblastoid cell line GM17142


title: GM17139 (650K)

source_name: lymphoblastoid cell line GM17139


title: GM17158 (650K)

source_name: lymphoblastoid cell line GM17158


title: GM17145 (650K)

source_name: lymphoblastoid cell line GM17145


title: GM17144 (650K)

source_name: lymphoblastoid cell line GM17144


title: GM17135 (650K)

source_name: lymphoblastoid cell line GM17135


title: GM17132 (650K)

source_name: lymphoblastoid cell line GM17132


title: GM17134 (650K)

source_name: lymphoblastoid cell line GM17134


title: GM17138 (650K)

source_name: lymphoblastoid cell line GM17138


title: GM17131 (650K)

source_name: lymphoblastoid cell line GM17131


title: GM17137 (650K)

source_name: lymphoblastoid cell line GM17137


title: GM17125 (650K)

source_name: lymphoblastoid cell line GM17125


title: GM17121 (650K)

source_name: lymphoblastoid cell line GM17121


title: GM17128 (650K)

source_name: lymphoblastoid cell line GM17128


title: GM17124 (650K)

source_name: lymphoblastoid cell line GM17124


title: GM17136 (650K)

source_name: lymphoblastoid cell line GM17136


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 213179463_95724

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

description:
Liver toxicants vs. non-toxicants based on overall necrosis score
MAQC_Distribution_Status: MAQC_V -- Validation

hyb_protocol: The biotin-labeled cRNA was fragmented and hybridized to the Rat Genome 230 2.0 Array (Affymetrix, Inc.) for 17 hours, prior to washing and scanning.

scan_protocol: Data were extracted from scanned images using the Affymetrix Scanner and GeneChip Operating Software (Affymetrix, Inc.).

data_processing: Affymetrix MAS5

organism: Rattus norvegicus

source_name: Liver

label_protocol: 1 μg of total RNA from the left liver lobe of each individual rat was labeled using the GeneChip One-Cycle Target Labeling kit (Affymetrix, Inc., Santa Clara, CA, USA) following the manufacturer’s protocol.

growth_protocol: F344/N male rats grow to 10-12 weeks old before exposed to one of eight hepatotoxicants

extract_protocol: Total RNA was isolated from the flash frozen portion of the left lateral liver lobe using RNeasy Midi columns (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol.

treatment_protocol: Rats were exposed for 6, 24 or 48 hours to a low, medium or high dose of one of eight hepatotoxicants. All animals were fasted for 12-18 hours prior to exposure.

value: left lateral liver lobe

tag: strain

tag: age

value: 10-12 weeks

tag: compound

value: Diquat Dibromide

tag: hybdate

tag: route

tag: vehicle

value: PBS

tag: control

value: Y

tag: dose

value: 0 mg/kg

tag: time of exposure

value: 6 hours

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution

value: NIEHS/Cogenics


title: GM17133 (650K)

source_name: lymphoblastoid cell line GM17133

tag: ethnic group

tag: cell line (coriell id)


title: GM17122 (650K)

source_name: lymphoblastoid cell line GM17122

tag: wei id

tag: cell type


title: GM17119 (650K)

source_name: lymphoblastoid cell line GM17119


title: GM17127 (650K)

source_name: lymphoblastoid cell line GM17127


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 213179464_95640

tag: tissue

tag: strain

tag: gender

value: male

tag: age

value: 24 hours


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707354_91773

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 48 hours


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707355_91702

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17120 (650K)

source_name: lymphoblastoid cell line GM17120


title: GM17126 (650K)

source_name: lymphoblastoid cell line GM17126


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707353_91697

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17123 (650K)

source_name: lymphoblastoid cell line GM17123

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 212707347_91777

tag: tissue

tag: strain

tag: gender

tag: age


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 212707348_95717

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17116 (650K)

source_name: lymphoblastoid cell line GM17116


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 212707346_95716

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707352_91775

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 212707345_91851


title: GM17115 (650K)

source_name: lymphoblastoid cell line GM17115

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 212707344_95740

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17117 (650K)

source_name: lymphoblastoid cell line GM17117


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707351_91685

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 212707341_95661

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 212707342_95736

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547233_91711

value: N

value: 25 mg/kg


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547235_91730


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547232_91729

value: 20 mg/kg


title: GM17110 (650K)

source_name: lymphoblastoid cell line GM17110

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17113 (650K)

source_name: lymphoblastoid cell line GM17113


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547231_91885

tag: tissue

tag: strain

tag: gender

tag: age


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547230_91882

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17114 (650K)

source_name: lymphoblastoid cell line GM17114


title: GM17111 (650K)

source_name: lymphoblastoid cell line GM17111


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547208_90972

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547226_91863

value: 10 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17112 (650K)

source_name: lymphoblastoid cell line GM17112

tag: ethnic group

value: AA African-American

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547228_91848

tag: tissue

tag: strain

tag: gender

tag: age


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547188_93883

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 212707343_95714

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547203_91778

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Galactosamine; 400 mg/kg; 48 hours; 212519586_95751

value: Galactosamine

value: 400 mg/kg


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547229_91847

value: left lateral liver lobe

value: 10-12 weeks


title: liver; Galactosamine; 400 mg/kg; 48 hours; 212519583_95727

value: PBS


title: GM17118 (650K)

source_name: lymphoblastoid cell line GM17118

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17108 (650K)

source_name: lymphoblastoid cell line GM17108


title: GM17129 (650K)

source_name: lymphoblastoid cell line GM17129


title: liver; Galactosamine; 0 mg/kg; 48 hours; 212519572_91811

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age

value: Y

value: 0 mg/kg


title: liver; Galactosamine; 0 mg/kg; 48 hours; 212519571_91701

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: NIEHS/Cogenics


title: liver; Galactosamine; 100 mg/kg; 48 hours; 212519579_91747

value: male

tag: control

tag: dose

value: 100 mg/kg

tag: time of exposure

tag: necrosis score


title: liver; Galactosamine; 100 mg/kg; 24 hours; 212519566_91687

value: 24 hours

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Galactosamine; 400 mg/kg; 48 hours; 212519585_95764

value: N

value: 48 hours


title: GM17103 (650K)

source_name: lymphoblastoid cell line GM17103

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: liver; Galactosamine; 400 mg/kg; 24 hours; 212519568_91690

tag: tissue

tag: strain

tag: gender

tag: age


title: liver; Galactosamine; 400 mg/kg; 6 hours; 212519554_95633

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 6 hours


title: GM17130 (650K)

source_name: lymphoblastoid cell line GM17130


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547213_91683

value: Diquat Dibromide

tag: control

tag: dose

value: 25 mg/kg

tag: time of exposure

tag: necrosis score


title: liver; Galactosamine; 100 mg/kg; 6 hours; 212519547_91792

value: Galactosamine

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Galactosamine; 0 mg/kg; 24 hours; 212519556_95693


title: liver; Galactosamine; 100 mg/kg; 24 hours; 212519565_91688


title: liver; Galactosamine; 25 mg/kg; 6 hours; 212519544_95652


title: GM17107 (650K)

source_name: lymphoblastoid cell line GM17107

tag: ethnic group

value: AA African-American

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17109 (650K)

source_name: lymphoblastoid cell line GM17109


title: GM17104 (650K)

source_name: lymphoblastoid cell line GM17104


title: liver; Galactosamine; 0 mg/kg; 6 hours; 212519540_91719

tag: tissue

value: left lateral liver lobe

tag: strain

tag: gender

tag: age


title: liver; Galactosamine; 25 mg/kg; 6 hours; 212519543_95638

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Galactosamine; 0 mg/kg; 6 hours; 212519539_91715

value: PBS

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Thioacetamide; 15 mg/kg; 48 hours; 212350814_90975

value: Thioacetamide

value: Gavage

value: Corn Oil

value: 15 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Thioacetamide; 0 mg/kg; 6 hours; 212350852_91801

value: male

value: Y

value: 0 mg/kg

value: NIEHS/Cogenics


title: liver; Thioacetamide; 0 mg/kg; 48 hours; 212350860_91780

value: 48 hours


title: liver; Thioacetamide; 0 mg/kg; 24 hours; 212350853_91742

value: 24 hours


title: liver; Thioacetamide; 50 mg/kg; 48 hours; 212350819_91067

value: N

value: 50 mg/kg


title: liver; Thioacetamide; 150 mg/kg; 48 hours; 212350823_91054

value: 150 mg/kg


title: liver; Thioacetamide; 150 mg/kg; 24 hours; 212350618_90963


title: liver; Diquat Dibromide; 20 mg/kg; 48 hours; 212547227_91866

value: Diquat Dibromide

value: 20 mg/kg


title: liver; Thioacetamide; 50 mg/kg; 24 hours; 212350615_90996

value: left lateral liver lobe

value: 10-12 weeks


title: liver; Thioacetamide; 15 mg/kg; 24 hours; 212350612_93839

value: Thioacetamide


title: liver; Thioacetamide; 50 mg/kg; 6 hours; 212350561_90813

value: Gavage

value: 6 hours


title: liver; Thioacetamide; 50 mg/kg; 24 hours; 212350613_90961

value: Corn Oil


title: liver; Thioacetamide; 15 mg/kg; 6 hours; 212350556_90852

value: male

value: 15 mg/kg


title: liver; Thioacetamide; 15 mg/kg; 6 hours; 212350557_90821


title: liver; Monocrotaline; 50 mg/kg; 48 hours; 212333199_90890

value: Monocrotaline


title: liver; Monocrotaline; 50 mg/kg; 48 hours; 212333197_90925

value: NIEHS/Cogenics


title: liver; Thioacetamide; 0 mg/kg; 48 hours; 212350859_91815

value: Y

value: 0 mg/kg

value: 48 hours


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547183_93686

value: PBS

value: N


title: liver; Monocrotaline; 10 mg/kg; 48 hours; 212333195_90926

value: 10 mg/kg


title: liver; Monocrotaline; 50 mg/kg; 48 hours; 212333196_90909

value: 50 mg/kg


title: liver; Monocrotaline; 50 mg/kg; 48 hours; 212333198_90888

value: left lateral liver lobe


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547190_93824

value: 10-12 weeks

value: Diquat Dibromide

value: 25 mg/kg


title: liver; Thioacetamide; 50 mg/kg; 6 hours; 212350562_90863

value: Thioacetamide

value: Gavage

value: 6 hours


title: liver; Monocrotaline; 10 mg/kg; 48 hours; 212333194_90849

value: male

value: Corn Oil


title: liver; Monocrotaline; 10 mg/kg; 48 hours; 212333192_90873

value: Monocrotaline

value: NIEHS/Cogenics


title: liver; Monocrotaline; 10 mg/kg; 48 hours; 212333193_90823


title: liver; Monocrotaline; 0 mg/kg; 48 hours; 212333190_90826

value: Y

value: 0 mg/kg


title: liver; Monocrotaline; 30 mg/kg; 24 hours; 212333187_90835

value: 30 mg/kg

value: 24 hours


title: GM17105 (650K)

source_name: lymphoblastoid cell line GM17105

tag: ethnic group

value: AA African-American

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: liver; Monocrotaline; 0 mg/kg; 48 hours; 212333188_90841

tag: tissue

value: left lateral liver lobe

tag: strain

tag: gender

tag: age

value: 48 hours


title: liver; Monocrotaline; 0 mg/kg; 48 hours; 212333189_90825

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17102 (650K)

source_name: lymphoblastoid cell line GM17102


title: liver; Monocrotaline; 30 mg/kg; 24 hours; 212333184_90870

tag: control

value: N

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Monocrotaline; 0 mg/kg; 48 hours; 212333191_90874

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Thioacetamide; 150 mg/kg; 6 hours; 212350565_93884

value: Thioacetamide

value: 150 mg/kg


title: liver; Monocrotaline; 30 mg/kg; 24 hours; 212333185_90848

value: Gavage


title: liver; Monocrotaline; 50 mg/kg; 24 hours; 212333183_90815

value: male

value: 50 mg/kg


title: liver; Monocrotaline; 30 mg/kg; 24 hours; 212333186_90845

value: Monocrotaline

value: Corn Oil


title: liver; Monocrotaline; 50 mg/kg; 24 hours; 212333180_91072

value: NIEHS/Cogenics


title: liver; Monocrotaline; 50 mg/kg; 24 hours; 212333182_91045


title: liver; Monocrotaline; 50 mg/kg; 24 hours; 212333181_91074


title: liver; Monocrotaline; 10 mg/kg; 24 hours; 212333179_90860

value: 10 mg/kg


title: liver; Monocrotaline; 10 mg/kg; 24 hours; 212333178_90865


title: liver; Monocrotaline; 0 mg/kg; 24 hours; 212333174_90830

value: Y

value: 0 mg/kg


title: liver; Monocrotaline; 10 mg/kg; 24 hours; 212333177_90859

value: 24 hours


title: liver; Monocrotaline; 300 mg/kg; 6 hours; 212333169_91092

value: 300 mg/kg

value: 6 hours


title: liver; Monocrotaline; 300 mg/kg; 6 hours; 212333168_91040

value: left lateral liver lobe


title: liver; Monocrotaline; 0 mg/kg; 24 hours; 212333175_90844

value: 10-12 weeks


title: liver; Monocrotaline; 50 mg/kg; 6 hours; 212333164_91093

value: N


title: liver; Monocrotaline; 0 mg/kg; 24 hours; 212333172_90839


title: liver; Monocrotaline; 300 mg/kg; 6 hours; 212333170_90923


title: liver; Monocrotaline; 50 mg/kg; 6 hours; 212333165_91055


title: liver; Monocrotaline; 300 mg/kg; 6 hours; 212333171_90838


title: liver; Monocrotaline; 10 mg/kg; 24 hours; 212333176_90898


title: liver; Monocrotaline; 50 mg/kg; 6 hours; 212333167_91098


title: liver; Monocrotaline; 0 mg/kg; 6 hours; 212333159_90562


title: liver; Monocrotaline; 10 mg/kg; 6 hours; 212333160_90509


title: liver; Monocrotaline; 10 mg/kg; 6 hours; 212333162_90512


title: liver; Monocrotaline; 0 mg/kg; 24 hours; 212333173_90869


title: liver; Monocrotaline; 10 mg/kg; 6 hours; 212333163_90962


title: liver; Monocrotaline; 50 mg/kg; 6 hours; 212333166_91042


title: liver; Monocrotaline; 10 mg/kg; 6 hours; 212333161_90527


title: liver; Monocrotaline; 0 mg/kg; 6 hours; 212333157_90606


title: liver; Monocrotaline; 0 mg/kg; 6 hours; 212333158_90585


title: liver; Monocrotaline; 0 mg/kg; 6 hours; 212333156_90594


title: liver; N-Nitrosomorpholine; 300 mg/kg; 48 hours; 212304991_90638

value: N-Nitrosomorpholine

value: 48 hours


title: liver; N-Nitrosomorpholine; 50 mg/kg; 48 hours; 212304988_90600

value: Gavage


title: liver; N-Nitrosomorpholine; 50 mg/kg; 24 hours; 212304971_90595

value: male


title: liver; N-Nitrosomorpholine; 10 mg/kg; 24 hours; 212304965_90643


title: liver; N-Nitrosomorpholine; 0 mg/kg; 24 hours; 212304963_90743


title: liver; N-Nitrosomorpholine; 300 mg/kg; 48 hours; 212304990_90597


title: liver; N-Nitrosomorpholine; 0 mg/kg; 48 hours; 212304978_90647


title: liver; N-Nitrosomorpholine; 10 mg/kg; 24 hours; 212304966_90603


title: liver; N-Nitrosomorpholine; 50 mg/kg; 6 hours; 212304953_90737

value: 50 mg/kg


title: liver; N-Nitrosomorpholine; 10 mg/kg; 6 hours; 212304950_90759


title: liver; N-Nitrosomorpholine; 50 mg/kg; 6 hours; 212304954_90782


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 6 hours; 212276303_90766

value: 1, 4-Dichlorobenzene

value: 150 mg/kg


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 48 hours; 212276292_90696

value: Corn Oil

value: NIEHS/Cogenics


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 48 hours; 212276280_90709

value: Y


title: liver; N-Nitrosomorpholine; 10 mg/kg; 6 hours; 212304949_90751

value: 10 mg/kg


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 6 hours; 212276301_90784

value: 15 mg/kg


title: liver; N-Nitrosomorpholine; 300 mg/kg; 24 hours; 212304974_90648

value: 300 mg/kg

value: 24 hours


title: liver; N-Nitrosomorpholine; 10 mg/kg; 6 hours; 212304952_90769

value: left lateral liver lobe

value: 6 hours


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 48 hours; 212276290_90697

value: 10-12 weeks

value: N


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 48 hours; 212276291_90671

value: 48 hours


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 48 hours; 212276284_90702

value: Gavage


title: liver; N-Nitrosomorpholine; 50 mg/kg; 6 hours; 212304955_90746

value: male

value: N-Nitrosomorpholine


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 24 hours; 212276268_90723

value: 1, 4-Dichlorobenzene


title: liver; 1, 4-Dichlorobenzene; 15 mg/kg; 6 hours; 212276299_90753


title: liver; N-Nitrosomorpholine; 0 mg/kg; 24 hours; 212304962_90770

value: 0 mg/kg


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 48 hours; 212276278_90681

value: Corn Oil


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 24 hours; 212276265_90718

value: NIEHS/Cogenics


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 24 hours; 212276277_90678


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 48 hours; 212276281_90721

value: Y


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 24 hours; 211981980_33305

value: 1, 2-Dichlorobenzene


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 6 hours; 212276261_33332


title: liver; 1, 4-Dichlorobenzene; 150 mg/kg; 6 hours; 212276256_33318

value: 150 mg/kg


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 48 hours; 210759912_55262

value: 15 mg/kg


title: liver; 1, 4-Dichlorobenzene; 1500 mg/kg; 6 hours; 212276258_90665


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 24 hours; 210759905_72020

value: 24 hours


title: liver; 1, 4-Dichlorobenzene; 0 mg/kg; 24 hours; 212276264_90663

value: left lateral liver lobe


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 24 hours; 210759901_72005


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 48 hours; 210759908_55267


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 24 hours; 210759891_55280


title: liver; 1, 2-Dichlorobenzene; 15 mg/kg; 24 hours; 210759894_72199


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 6 hours; 210759889_33289

value: 6 hours


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 48 hours; 210759917_55240

value: 10-12 weeks


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 24 hours; 210759898_72185

value: N


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 24 hours; 210759890_55272


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 24 hours; 210759903_72002


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 6 hours; 210759883_33284


title: liver; 1, 2-Dichlorobenzene; 1500 mg/kg; 6 hours; 210759887_33304


title: liver; 1, 2-Dichlorobenzene; 150 mg/kg; 6 hours; 210759884_33301


title: liver; Bromobenzene; 250 mg/kg; 48 hours; 210556328_33476

value: Bromobenzene

value: 250 mg/kg

value: 48 hours


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 6 hours; 210759874_33307

value: male

value: Gavage


title: liver; Bromobenzene; 75 mg/kg; 48 hours; 210556324_33458

value: 75 mg/kg


title: liver; Bromobenzene; 250 mg/kg; 48 hours; 210556327_33460

value: Corn Oil


title: liver; Bromobenzene; 75 mg/kg; 48 hours; 210556321_33496

value: NIEHS/Cogenics


title: liver; Bromobenzene; 0 mg/kg; 48 hours; 210556316_30613

value: Y

value: 0 mg/kg


title: liver; Bromobenzene; 75 mg/kg; 48 hours; 210556323_33501


title: liver; Bromobenzene; 25 mg/kg; 48 hours; 210556317_30642

value: 25 mg/kg


title: liver; Bromobenzene; 250 mg/kg; 48 hours; 210556326_33484


title: liver; Bromobenzene; 25 mg/kg; 48 hours; 210556319_33445


title: liver; Bromobenzene; 75 mg/kg; 48 hours; 210556322_33477


title: liver; Bromobenzene; 0 mg/kg; 48 hours; 210556313_30614


title: liver; Bromobenzene; 250 mg/kg; 48 hours; 210556325_33465


title: liver; Bromobenzene; 0 mg/kg; 48 hours; 210556314_30664


title: liver; Bromobenzene; 250 mg/kg; 24 hours; 210556310_33473


title: liver; Bromobenzene; 25 mg/kg; 48 hours; 210556320_33502


title: liver; Bromobenzene; 75 mg/kg; 24 hours; 210556308_33466


title: liver; Bromobenzene; 0 mg/kg; 48 hours; 210556315_30639


title: liver; Bromobenzene; 25 mg/kg; 24 hours; 210556302_50600


title: liver; Bromobenzene; 75 mg/kg; 24 hours; 210556305_33500


title: liver; Bromobenzene; 75 mg/kg; 24 hours; 210556307_33486


title: liver; Bromobenzene; 25 mg/kg; 24 hours; 210556303_50602


title: liver; Bromobenzene; 25 mg/kg; 24 hours; 210556301_50639


title: liver; Bromobenzene; 0 mg/kg; 24 hours; 210556300_30665


title: liver; Bromobenzene; 25 mg/kg; 24 hours; 210556304_33485


title: liver; Bromobenzene; 250 mg/kg; 24 hours; 210556312_30612


title: liver; Bromobenzene; 75 mg/kg; 24 hours; 210556306_33469


title: liver; Bromobenzene; 250 mg/kg; 24 hours; 210556311_30617


title: liver; Bromobenzene; 250 mg/kg; 24 hours; 210556309_33482


title: liver; Bromobenzene; 250 mg/kg; 6 hours; 210556295_50613


title: liver; Bromobenzene; 250 mg/kg; 6 hours; 210556293_50601


title: liver; Bromobenzene; 250 mg/kg; 6 hours; 210556294_50593


title: liver; Bromobenzene; 0 mg/kg; 24 hours; 210556297_30656


title: liver; Bromobenzene; 0 mg/kg; 24 hours; 210556299_30630


title: liver; Bromobenzene; 0 mg/kg; 24 hours; 210556298_30606


title: liver; Bromobenzene; 250 mg/kg; 6 hours; 210556296_30619


title: liver; Bromobenzene; 75 mg/kg; 6 hours; 210556292_50590


title: liver; Bromobenzene; 25 mg/kg; 6 hours; 210556287_30641


title: liver; Bromobenzene; 25 mg/kg; 6 hours; 210556288_30667


title: liver; Bromobenzene; 75 mg/kg; 6 hours; 210556290_30658


title: liver; Bromobenzene; 75 mg/kg; 6 hours; 210556289_30633


title: liver; Bromobenzene; 25 mg/kg; 6 hours; 210556285_88525


title: liver; Bromobenzene; 0 mg/kg; 6 hours; 210556284_30607


title: liver; Bromobenzene; 75 mg/kg; 6 hours; 210556291_30659


title: liver; Bromobenzene; 25 mg/kg; 6 hours; 210556286_30626


title: liver; Bromobenzene; 0 mg/kg; 6 hours; 210556283_30663


title: liver; Bromobenzene; 0 mg/kg; 6 hours; 210556281_30666


title: liver; Bromobenzene; 0 mg/kg; 6 hours; 210556282_30609


title: liver; 1, 2-Dichlorobenzene; 0 mg/kg; 48 hours; 210759909_55266

value: 1, 2-Dichlorobenzene


title: liver; Diquat Dibromide; 0 mg/kg; 48 hours; 212707350_91684

description:
Liver toxicants vs. non-toxicants based on overall necrosis score
MAQC_Distribution_Status: MAQC_T -- Training

value: Diquat Dibromide

value: PBS


title: liver; Galactosamine; 400 mg/kg; 6 hours; 213482571_95602

value: left lateral liver lobe

value: Galactosamine

value: 400 mg/kg

value: 6 hours


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547238_91738

value: 10-12 weeks

value: N


title: liver; Bromobenzene; 25 mg/kg; 48 hours; 210556318_33451

value: male

value: Bromobenzene

value: 48 hours


title: liver; Diquat Dibromide; 0 mg/kg; 24 hours; 212707349_91788

value: 24 hours


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547237_91736

value: NIEHS/Cogenics


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547236_91727


title: liver; Diquat Dibromide; 25 mg/kg; 48 hours; 212547234_91712


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547224_91881

value: 10 mg/kg


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547223_91728


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547225_91855


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547221_91731


title: liver; Diquat Dibromide; 10 mg/kg; 48 hours; 212547222_91732


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547220_91714

value: 5 mg/kg


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547219_91707


title: GM17293 (550K)

data_processing: Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using HumanHap550 v3.0 Whole-Genome Genotyping Kit (Illumina).

source_name: lymphoblastoid cell line GM17293

tag: ethnic group

value: CA Caucasian-American

tag: cell line (coriell id)

tag: wei id

tag: cell type

value: EBV-transformed lymphoblastoid cells


title: GM17807 (550K)

source_name: lymphoblastoid cell line GM17807

value: HCA Han Chinese-American


title: GM17281 (550K)

source_name: lymphoblastoid cell line GM17281


title: GM17850 (550K)

source_name: lymphoblastoid cell line GM17850


title: GM17295 (550K)

source_name: lymphoblastoid cell line GM17295


title: GM17283 (550K)

source_name: lymphoblastoid cell line GM17283


title: GM17279 (550K)

source_name: lymphoblastoid cell line GM17279


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547218_91779

tag: tissue

tag: strain

tag: gender

tag: age

value: Diquat Dibromide

value: PBS


title: GM17805 (550K)

source_name: lymphoblastoid cell line GM17805


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547217_91768

value: left lateral liver lobe

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17277 (550K)

source_name: lymphoblastoid cell line GM17277


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547215_91819

source_name: Liver

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17847 (550K)

source_name: lymphoblastoid cell line GM17847


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547214_91686

value: 25 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17852 (550K)

source_name: lymphoblastoid cell line GM17852

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17838 (550K)

source_name: lymphoblastoid cell line GM17838


title: GM17840 (550K)

source_name: lymphoblastoid cell line GM17840


title: GM17842 (550K)

source_name: lymphoblastoid cell line GM17842


title: GM17844 (550K)

source_name: lymphoblastoid cell line GM17844


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547212_90993

tag: tissue

tag: strain

tag: gender

tag: age


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547211_90959

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: GM17827 (550K)

source_name: lymphoblastoid cell line GM17827


title: GM17843 (550K)

source_name: lymphoblastoid cell line GM17843


title: GM17846 (550K)

source_name: lymphoblastoid cell line GM17846


title: GM17839 (550K)

source_name: lymphoblastoid cell line GM17839


title: GM17845 (550K)

source_name: lymphoblastoid cell line GM17845


title: liver; Diquat Dibromide; 5 mg/kg; 48 hours; 212547216_91814

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17841 (550K)

source_name: lymphoblastoid cell line GM17841


title: GM17837 (550K)

source_name: lymphoblastoid cell line GM17837


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547210_90992

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17828 (550K)

source_name: lymphoblastoid cell line GM17828

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17835 (550K)

source_name: lymphoblastoid cell line GM17835


title: GM17833 (550K)

source_name: lymphoblastoid cell line GM17833


title: GM17831 (550K)

source_name: lymphoblastoid cell line GM17831


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547206_91798

source_name: Liver

tag: tissue

tag: strain

tag: gender

tag: age

value: 20 mg/kg


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547204_91784

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547198_95679

tag: control

value: N

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547207_91013

value: male

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547199_95631


title: liver; Diquat Dibromide; 25 mg/kg; 24 hours; 212547209_91027


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547202_95677


title: liver; Diquat Dibromide; 20 mg/kg; 24 hours; 212547205_91781


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547195_95666


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547197_95659


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547194_90991


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547196_95731


title: liver; Diquat Dibromide; 10 mg/kg; 24 hours; 212547200_95658


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547192_91836


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547193_90966


title: GM17826 (550K)

source_name: lymphoblastoid cell line GM17826

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17824 (550K)

source_name: lymphoblastoid cell line GM17824


title: GM17825 (550K)

source_name: lymphoblastoid cell line GM17825


title: liver; Diquat Dibromide; 5 mg/kg; 24 hours; 212547191_91783

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17818 (550K)

source_name: lymphoblastoid cell line GM17818


title: GM17816 (550K)

source_name: lymphoblastoid cell line GM17816


title: GM17817 (550K)

source_name: lymphoblastoid cell line GM17817


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547189_93886

tag: compound

tag: hybdate

tag: route

tag: vehicle

value: 6 hours


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547187_93838

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547185_93734

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: liver; Diquat Dibromide; 25 mg/kg; 6 hours; 212547186_93828


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547184_93719


title: GM17823 (550K)

source_name: lymphoblastoid cell line GM17823

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: GM17815 (550K)

source_name: lymphoblastoid cell line GM17815


title: GM17814 (550K)

source_name: lymphoblastoid cell line GM17814


title: GM17292 (550K)

source_name: lymphoblastoid cell line GM17292


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547180_93731

tag: tissue

tag: strain

tag: gender

tag: age


title: GM17811 (550K)

source_name: lymphoblastoid cell line GM17811


title: GM17810 (550K)

source_name: lymphoblastoid cell line GM17810


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547181_93732

tag: compound

tag: hybdate

tag: route

tag: vehicle


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547179_91812

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17812 (550K)

source_name: lymphoblastoid cell line GM17812


title: GM17291 (550K)

source_name: lymphoblastoid cell line GM17291


title: GM17813 (550K)

source_name: lymphoblastoid cell line GM17813


title: GM17808 (550K)

source_name: lymphoblastoid cell line GM17808


title: GM17806 (550K)

source_name: lymphoblastoid cell line GM17806


title: GM17290 (550K)

source_name: lymphoblastoid cell line GM17290


title: GM17294 (550K)

source_name: lymphoblastoid cell line GM17294


title: GM17296 (550K)

source_name: lymphoblastoid cell line GM17296


title: GM17809 (550K)

source_name: lymphoblastoid cell line GM17809


title: GM17288 (550K)

source_name: lymphoblastoid cell line GM17288


title: liver; Diquat Dibromide; 20 mg/kg; 6 hours; 212547182_93711

source_name: Liver

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17285 (550K)

source_name: lymphoblastoid cell line GM17285

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: KN13

city: Pittsburgh

first: Haiwen

state: PA

address: 3343 Forbes Ave

department: Genomics and Proteomics Core Laboratories

institute: University of Pittsburgh

description: both infected with SHIV and colonized with Pneumocystis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetix GeneChip Scanner 3000 with 7G Upgrade.

data_processing: The data is read by Matlab bioinformatics Tool box from the CEL files. PM only signal is exported. The probe intensities in each probe set is averaged. Using our in-house softwares AutoEA and caGEDA, the data is Quantile95 normalized

organism: Macaca fascicularis

label_protocol: Biotinylated cRNA was prepared using the One-Cycle cDNA Synthesis and IVT Labeling Kits (Affymetrix) according to manufacturer's protocol.

extract_protocol: RNA was extracted from lung tissue by pulverizing liquid Nitrogen-frozen tissue and then processing  pulverized samples in the Qiagen Rneasy Mini Kit.

treatment_protocol: Ten cynomolgus macaques (Macaca fasicularis) were infected with simian/human immunodeficiency virus (SHIV89.6) and co-housed with other immunocompromised macaques to increase environmental exposure to Pneumocystis (Pc) organisms, so that natural colonization of the lungs could take place as immunosuppression developed.  Analyses were performed on RNA extracted from whole lung tissue based on macaques that became colonized with Pc (n=6) versus those that remained non-colonized (n=4).  IACUC # 0810330A-3

tag: tissue

value: lung


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547178_90924

tag: strain

tag: gender

tag: age

tag: compound


title: GM17287 (550K)

source_name: lymphoblastoid cell line GM17287


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547177_90920

tag: hybdate

tag: route

tag: vehicle

tag: control


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547176_90918

tag: dose

tag: time of exposure

tag: necrosis score

tag: necrosis class


title: KN08

description: infected with SHIV but it did not become colonized with Pneumocystis


title: KN12


title: KN07


title: KN14

description: neither infected with SHIV nor was it colonized with Pneumocystis


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547175_90902

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: GM17289 (550K)

source_name: lymphoblastoid cell line GM17289

tag: ethnic group

tag: cell line (coriell id)

tag: wei id

tag: cell type


title: KN11

tag: tissue


title: KN04


title: KN06


title: KN03


title: GM17286 (550K)

source_name: lymphoblastoid cell line GM17286


title: Rdp1_clr4D_3

city: Basel

first: Katrina

last: Woolcock

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: hybridization was performed for 16h at 45°C and 60rpm in an Affymetrix hybridization oven; washing steps were done in an Affymetrix Fluidics station with the Affymetrix protocol FS450_0002

scan_protocol: GeneChips were scanned with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing:
oligo-level data was rma background corrected, quantile normalized and log2 transformed using Bioconductor packages tilingArray and preprocessCore on R version 2.9
expr_M_CorV2.wig
wiggle file showing the results of all the above contrasts. Normalization of the tiling array data: All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected, quantile normalised and log2 transformed on the oligo level using the following command: expr <- log2(normalize.quantiles(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE))))). Contrasts were computed on the oligo level by subtracting respective columns of expression. Reannotation of the Affymetrix S. pombe Tiling 1.0FR Array: The sequences of the 1174792 perfect match oligos were extracted from the BPMAP file Sp20b_M_v04.bpmap (www.affymetrix.com) using the readBpmap function from the affxparser package. Alignment to the S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) was performed by the software bowtie (version 0.9.9.1) allowing for up to 100 matches per oligo. Correcting a bias caused by variable fragment size between GATC restriction sites: While inspecting oligo level contrasts in a genome browser we noticed enrichment breakpoints coinciding with GATC restriction sites. Therefore we speculated that during sample preparation, certain fragment sizes might be depleted or enriched. Plotting the fragment sizes between two GATC restriction sites against the average enrichment in the corresponding fragment confirmed this observation on a genome-wide scale. We speculated that this resulted from small differences in the sample preparation process, probably during the step of size selection. In addition to fragment size-dependent mean enrichment/depletion, we noticed discontinuity of the contrast variability coinciding with GATC restriction sites. We plotted the fragment sizes between two GATC restriction sites against the standard deviation of the enrichment in the corresponding fragment and observed discontinuities on a genome-wide level. Both observed effects are highly unlikely to be of biological origin because they are tightly correlated to the fragment size between GATC restriction sites. Therefore, we designed a software that would at least partially reverse the bias and correct the initial data. For every contrast independently, the corrector walks through all the fragments (between GATCs) and adjusts the mean and the standard deviation of all the oligos that are located within the fragment. The adjustment is fragment size-dependent and the extent of correction is determined from the lowess fit of the corresponding contrast. In more detail, for a given fragment size, the value of the lowess smoother is evaluated and compared to the average level of the given contrast. Therefore the corrector does not modulate the overall mean or the variability of the contrasts.

organism: Schizosaccharomyces pombe

label_protocol: DNA was fragmented and labeled with the GeneChip Whole Transcript Double-Stranded DNA Terminal Labelling Kit (Affymetrix)

growth_protocol: Strains grown at 30 degress in YES medium to OD600=0.4

extract_protocol: Genomic DNA isolated using Dneasy Blood and Tissue Kit (Qiagen)

treatment_protocol: Harvested cells were spheroplasted to remove cell wall

tag: strain

tag: expression

value: Dam only


title: GM17282 (550K)

source_name: lymphoblastoid cell line GM17282


title: Rdp1_clr4D_2


title: GM17280 (550K)

source_name: lymphoblastoid cell line GM17280


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547174_90914

tag: gender

tag: age

tag: compound

tag: hybdate

tag: route

value: NIEHS/Cogenics


title: KN01


title: Dcr1_clr4D_3


title: KN02


title: GM17278 (550K)

source_name: lymphoblastoid cell line GM17278


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547172_90916

tag: vehicle

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: Arb1_clr4D_2

description: Not used in publication due to poor reproducibility, likely resulting from non-functionality of Dam-Arb1 fusion protein


title: Dcr1_clr4D_2


title: Arb1_clr4D_1


title: GM17276 (550K)

source_name: lymphoblastoid cell line GM17276

tag: ethnic group


title: Rdp1_wt_3


title: Arb1_clr4D_3


title: Dcr1_clr4D_1


title: GM17284 (550K)

source_name: lymphoblastoid cell line GM17284

tag: cell line (coriell id)


title: liver; Diquat Dibromide; 10 mg/kg; 6 hours; 212547173_90944

value: 10 mg/kg

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)

tag: institution


title: Arb1_wt_3

tag: strain

tag: expression


title: Dcr1_wt_3


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547169_90892

tag: tissue

tag: gender

tag: age

value: 5 mg/kg


title: Rdp1_wt_2


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547171_90934

tag: compound

tag: hybdate

tag: route


title: Arb1_wt_2


title: GM17274 (550K)

source_name: lymphoblastoid cell line GM17274

value: CA Caucasian-American

tag: wei id

tag: cell type


title: Dcr1_wt_2


title: Rdp1_wt_1


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547168_95712

tag: vehicle

tag: control

tag: dose

tag: time of exposure

tag: necrosis score


title: Swi6_dcr1D_2


title: Swi6_dcr1D_1


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547170_90897

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)


title: liver; Galactosamine; 400 mg/kg; 48 hours; 212519584_95636

tag: strain

value: Galactosamine

value: 400 mg/kg

value: 48 hours

tag: institution


title: Dcr1_wt_1

tag: expression


title: Swi6_wt_3_clr4D_as_ctrl


title: liver; Galactosamine; 100 mg/kg; 48 hours; 212519582_91698

tag: tissue

tag: gender

tag: age

value: PBS

value: 100 mg/kg


title: Rdp1_clr4D_1


title: GM17275 (550K)

source_name: lymphoblastoid cell line GM17275

tag: ethnic group

tag: cell line (coriell id)

value: EBV-transformed lymphoblastoid cells


title: liver; Galactosamine; 100 mg/kg; 48 hours; 212519581_91699

value: left lateral liver lobe

tag: compound

tag: hybdate

tag: route


title: liver; Diquat Dibromide; 5 mg/kg; 6 hours; 212547167_95711

value: 10-12 weeks

value: Diquat Dibromide

tag: vehicle

tag: control

tag: dose


title: Swi6_clr4D_3


title: GM17272 (550K)

source_name: lymphoblastoid cell line GM17272

tag: wei id

tag: cell type


title: liver; Diquat Dibromide; 0 mg/kg; 6 hours; 212547148_91823

value: male

value: Y

value: 0 mg/kg

tag: time of exposure

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)


title: GM17273 (550K)

source_name: lymphoblastoid cell line GM17273


title: Arb1_wt_1

tag: strain

tag: expression

value: Dam only


title: Swi6_clr4D_2


title: GM17268 (550K)

source_name: lymphoblastoid cell line GM17268

tag: ethnic group


title: Swi6_wt_3


title: liver; Galactosamine; 100 mg/kg; 48 hours; 212519580_91724

tag: tissue

tag: gender

tag: age

value: N

tag: institution

value: NIEHS/Cogenics


title: Swi6_wt_2_clr4D_as_ctrl


title: GM17267 (550K)

source_name: lymphoblastoid cell line GM17267

tag: cell line (coriell id)


title: Swi6_wt_2


title: Swi6_wt_1_clr4D_as_ctrl


title: GM17270 (550K)

source_name: lymphoblastoid cell line GM17270


title: Swi6_clr4D_1


title: GM17269 (550K)

source_name: lymphoblastoid cell line GM17269


title: Swi6_wt_1


title: liver; Galactosamine; 25 mg/kg; 48 hours; 212519578_91721

source_name: Liver

tag: compound

tag: hybdate

tag: route

tag: vehicle

tag: control

value: 25 mg/kg


title: liver; Galactosamine; 25 mg/kg; 48 hours; 212519577_91695

tag: dose

tag: time of exposure

tag: necrosis score


title: GM17271 (550K)

source_name: lymphoblastoid cell line GM17271

value: CA Caucasian-American

tag: wei id

tag: cell type


title: liver; Galactosamine; 25 mg/kg; 48 hours; 212519575_91722

tag: strain

value: Galactosamine

tag: necrosis class

tag: necrosis level (linkon)

tag: necrosis level (ekl)


title: liver; Galactosamine; 25 mg/kg; 48 hours; 212519576_91713

tag: tissue

tag: gender

tag: age


title: GM17265 (550K)

source_name: lymphoblastoid cell line GM17265

tag: ethnic group

tag: cell line (coriell id)


title: liver; Galactosamine; 0 mg/kg; 48 hours; 212519574_91770

tag: compound

tag: hybdate

tag: route

tag: institution


title: GM17264 (550K)

source_name: lymphoblastoid cell line GM17264


title: GM17266 (550K)

source_name: lymphoblastoid cell line GM17266


title: liver; Galactosamine; 0 mg/kg; 48 hours; 212519573_91769

tag: vehicle

tag: control

tag: dose

tag: time of exposure


title: liver; Galactosamine; 400 mg/kg; 24 hours; 212519570_91692

tag: strain

value: 400 mg/kg

value: 24 hours

tag: necrosis score


title: liver; Galactosamine; 400 mg/kg; 24 hours; 212519569_91706

value: PBS

tag: necrosis class

tag: necrosis level (linkon)


title: GM17261 (550K)

source_name: lymphoblastoid cell line GM17261

tag: wei id

tag: cell type


title: GM17263 (550K)

source_name: lymphoblastoid cell line GM17263


title: GM17262 (550K)

source_name: lymphoblastoid cell line GM17262


title: GM17240 (550K)

source_name: lymphoblastoid cell line GM17240


title: GM17797 (550K)

source_name: lymphoblastoid cell line GM17797

value: HCA Han Chinese-American


title: GM17798 (550K)

source_name: lymphoblastoid cell line GM17798

value: EBV-transformed lymphoblastoid cells


title: GM17747 (550K)

source_name: lymphoblastoid cell line GM17747


title: liver; Galactosamine; 400 mg/kg; 24 hours; 212519567_91704

tag: tissue

value: left lateral liver lobe

tag: gender

tag: age

tag: necrosis level (ekl)


title: GM17746 (550K)

source_name: lymphoblastoid cell line GM17746

tag: ethnic group

tag: cell line (coriell id)


title: liver; Galactosamine; 100 mg/kg; 24 hours; 212519564_91691

value: 10-12 weeks

tag: compound

tag: hybdate

tag: route

value: 100 mg/kg

tag: institution


title: GM17214 (550K)

source_name: lymphoblastoid cell line GM17214


title: GM17206 (550K)

source_name: lymphoblastoid cell line GM17206


title: GM17803 (550K)

source_name: lymphoblastoid cell line GM17803


title: liver; Galactosamine; 100 mg/kg; 24 hours; 212519563_91694

value: male

tag: vehicle

tag: control

tag: dose

tag: time of exposure


title: GM17802 (550K)

source_name: lymphoblastoid cell line GM17802


title: GM17846 (510S)

data_processing: Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using Infinium HumanExon510S-2 DNA Analysis Kit (Illumina).

source_name: lymphoblastoid cell line GM17846


title: GM17800 (550K)

source_name: lymphoblastoid cell line GM17800


title: liver; Galactosamine; 25 mg/kg; 24 hours; 212519562_91705

source_name: Liver

tag: strain

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: GM17845 (510S)

source_name: lymphoblastoid cell line GM17845

tag: wei id

tag: cell type


title: GM17842 (510S)

source_name: lymphoblastoid cell line GM17842


title: GM17840 (510S)

source_name: lymphoblastoid cell line GM17840


title: GM17843 (510S)

source_name: lymphoblastoid cell line GM17843


title: GM17799 (550K)

source_name: lymphoblastoid cell line GM17799


title: GM17801 (550K)

source_name: lymphoblastoid cell line GM17801


title: GM17844 (510S)

source_name: lymphoblastoid cell line GM17844


title: GM17847 (510S)

source_name: lymphoblastoid cell line GM17847


title: GM17804 (550K)

source_name: lymphoblastoid cell line GM17804


title: GM17796 (550K)

source_name: lymphoblastoid cell line GM17796


title: GM17841 (510S)

source_name: lymphoblastoid cell line GM17841


title: liver; Galactosamine; 25 mg/kg; 24 hours; 212519561_91734

tag: tissue

tag: gender

tag: age

tag: necrosis level (ekl)


title: GM17850 (510S)

source_name: lymphoblastoid cell line GM17850

tag: ethnic group

tag: cell line (coriell id)


title: liver; Galactosamine; 25 mg/kg; 24 hours; 212519560_95663

tag: compound

tag: hybdate

tag: route

tag: institution


title: GM17839 (510S)

source_name: lymphoblastoid cell line GM17839


title: liver; Galactosamine; 25 mg/kg; 24 hours; 212519559_95689

tag: vehicle

tag: control

tag: dose

tag: time of exposure


title: GM17795 (550K)

source_name: lymphoblastoid cell line GM17795


title: GM17793 (550K)

source_name: lymphoblastoid cell line GM17793


title: GM17852 (510S)

source_name: lymphoblastoid cell line GM17852


title: GM17838 (510S)

source_name: lymphoblastoid cell line GM17838


title: liver; Galactosamine; 0 mg/kg; 24 hours; 212519558_95642

source_name: Liver

tag: strain

value: Y

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: GM17792 (550K)

source_name: lymphoblastoid cell line GM17792

tag: wei id

tag: cell type


title: liver; Galactosamine; 0 mg/kg; 24 hours; 212519557_95634

tag: tissue

tag: gender

tag: age

value: 0 mg/kg

tag: necrosis level (ekl)


title: GM17835 (510S)

source_name: lymphoblastoid cell line GM17835

tag: ethnic group

tag: cell line (coriell id)


title: GM17794 (550K)

source_name: lymphoblastoid cell line GM17794


title: liver; Galactosamine; 0 mg/kg; 24 hours; 212519555_95657

tag: compound

tag: hybdate

tag: route

tag: institution


title: GM17837 (510S)

source_name: lymphoblastoid cell line GM17837


title: GM17833 (510S)

source_name: lymphoblastoid cell line GM17833


title: GM17791 (550K)

source_name: lymphoblastoid cell line GM17791


title: liver; Galactosamine; 400 mg/kg; 6 hours; 212519552_95670

tag: vehicle

tag: control

tag: dose

tag: time of exposure

value: 6 hours


title: liver; Galactosamine; 400 mg/kg; 6 hours; 212519551_95644

tag: strain

value: N

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: GM17790 (550K)

source_name: lymphoblastoid cell line GM17790

tag: wei id

tag: cell type


title: GM17789 (550K)

source_name: lymphoblastoid cell line GM17789


title: GM17831 (510S)

source_name: lymphoblastoid cell line GM17831


title: GM17826 (510S)

source_name: lymphoblastoid cell line GM17826


title: GM17815 (510S)

source_name: lymphoblastoid cell line GM17815


title: GM17825 (510S)

source_name: lymphoblastoid cell line GM17825


title: liver; Galactosamine; 100 mg/kg; 6 hours; 212519550_95755

tag: tissue

tag: gender

tag: age

tag: necrosis level (ekl)

value: NIEHS/Cogenics


title: GM17818 (510S)

source_name: lymphoblastoid cell line GM17818

tag: ethnic group

tag: cell line (coriell id)


title: liver; Galactosamine; 100 mg/kg; 6 hours; 212519549_91787

tag: compound

tag: hybdate

tag: route

tag: institution


title: GM17823 (510S)

source_name: lymphoblastoid cell line GM17823


title: GM17812 (510S)

source_name: lymphoblastoid cell line GM17812


title: GM17785 (550K)

source_name: lymphoblastoid cell line GM17785


title: GM17813 (510S)

source_name: lymphoblastoid cell line GM17813


title: GM17817 (510S)

source_name: lymphoblastoid cell line GM17817


title: GM17814 (510S)

source_name: lymphoblastoid cell line GM17814


title: GM17810 (510S)

source_name: lymphoblastoid cell line GM17810


title: GM17827 (510S)

source_name: lymphoblastoid cell line GM17827


title: liver; Galactosamine; 100 mg/kg; 6 hours; 212519548_91793

source_name: Liver

tag: vehicle

tag: control

tag: dose

tag: time of exposure


title: GM17807 (510S)

source_name: lymphoblastoid cell line GM17807


title: liver; Galactosamine; 25 mg/kg; 6 hours; 212519546_95723

tag: strain

value: 25 mg/kg

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: GM17809 (510S)

source_name: lymphoblastoid cell line GM17809

tag: wei id

tag: cell type


title: GM17811 (510S)

source_name: lymphoblastoid cell line GM17811


title: liver; Galactosamine; 25 mg/kg; 6 hours; 212519545_95653

tag: tissue

tag: gender

tag: age

tag: necrosis level (ekl)


title: GM17779 (550K)

source_name: lymphoblastoid cell line GM17779

tag: ethnic group

tag: cell line (coriell id)


title: GM17808 (510S)

source_name: lymphoblastoid cell line GM17808


title: liver; Galactosamine; 0 mg/kg; 6 hours; 212519542_95686

tag: compound

tag: hybdate

tag: route

tag: institution


title: GM17806 (510S)

source_name: lymphoblastoid cell line GM17806


title: GM17783 (550K)

source_name: lymphoblastoid cell line GM17783


title: liver; Galactosamine; 0 mg/kg; 6 hours; 212519541_91716

tag: vehicle

tag: control

tag: dose

tag: time of exposure


title: GM17824 (510S)

source_name: lymphoblastoid cell line GM17824


title: GM17804 (510S)

source_name: lymphoblastoid cell line GM17804


title: GM17776 (550K)

source_name: lymphoblastoid cell line GM17776


title: GM17816 (510S)

source_name: lymphoblastoid cell line GM17816


title: GM17775 (550K)

source_name: lymphoblastoid cell line GM17775


title: liver; Thioacetamide; 0 mg/kg; 48 hours; 212350857_91799

tag: strain

value: Thioacetamide

value: Gavage

value: Corn Oil

value: 48 hours

tag: necrosis score

tag: necrosis class

tag: necrosis level (linkon)


title: liver; Thioacetamide; 0 mg/kg; 48 hours; 212350858_91800

tag: tissue

tag: gender


title: GM17801 (510S)

source_name: lymphoblastoid cell line GM17801

tag: wei id

tag: cell type