title: Ly6D−CLPs 1

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Labs

country: Canada

institute: BC Cancer Agency

hyb_protocol: Hybridization was carried out on the Affymetrix Mouse GeneChip ST 2.0.

scan_protocol: Agilent Bioanalyzer 2100, RNA amplification, and microarray services were performed by Sick Kids®, The Centre for Applied Genomics.

data_processing: All data analysis was performed with FlexArray 1.6.3 (Genome Quebec). Data were normalized using Affymetriz Power Tools (APT).

source_name: bone marrow

treatment_protocol: Total RNA from highly purified sorted progenitors was extracted using Trizol (Invitrogen).

tag: tissue

value: bone marrow

tag: cell markers

tag: developmental stage

value: adult


title: Ly6D+CLPs 1

status: Public on Feb 17 2016

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Agilent Bioanalyzer 2100, RNA amplification, and microarray services were performed by Sick Kids®, The Centre for Applied Genomics.

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

tag: strain


title: D283Med Control, Biological Replicate 3

city: São Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: São Paulo

address: Rua do Matão, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description:
D3
Gene expression data from D283Med Control, Biological Replicate 3.

hyb_protocol: 3.5 μg of fragmented and labeled ss-DNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed processed by Affymetrix® Expression Console Software (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

organism: Homo sapiens

source_name: Cell culture of D283Med control

label_protocol: 5.5 μg of ss-cDNA were fragmented and labeled with WT Labeling Kit (Biotin-based labelling) following manufacturer's instructions.

growth_protocol: Medulloblastoma cell lines (Daoy, USP-13-Med and D283Med) were maintained in standard cell culture conditions (37ºC and 5% CO2). Media was replaced every 3 days and cells were subcultivated when 80% of confluency was reached.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Medulloblastoma cell lines (Daoy, USP-13-Med and D283Med) had OCT4A overexpression by retrovirus infection.

tag: cell line

tag: cell type

value: medulloblastoma cell line

tag: overexpression

value: control

tag: cell culture confluency


title: Ly6D−CLPs 2


title: D283Med OCT4A, Biological Replicate 1

description:
DO1
Gene expression data from D283Med OCT4A, Biological Replicate 1.

source_name: Cell culture of D283Med OCT4A


title: Ly6D+CLPs 2


title: LMPP+s 3


title: s60_tetraploid_progeny3_rep1

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Samples were hybridised to slides using a NimbleGen hybridization system

scan_protocol: The slide was scanned using an Axon GenePix® 4000A scanner, after which resulting images were imported into NimbleScan software for grid alignment and expression data analyses

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Medicago sativa

source_name: tetraploid progeny, S60 plant, leaf

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit

growth_protocol: The parents and the selected 2x and 4x progeny plants were cloned by cuttings and were reared in a screen house in natural conditions, with complete randomization.

extract_protocol: About three trifoliate leaves per sample were finely ground in liquid nitrogen and total RNA was further purified with the Qiagen RNeasy minikit

tag: parental/progeny

value: tetraploid progeny

tag: genotype


title: USP-13-Med Control, Clone 1

description:
P131
Gene expression data from USP-13-Med Control, Clone 1.

source_name: Cell culture of USP-13-Med control


title: USP-13-Med Control, Clone 2

description:
P132
Gene expression data from USP-13-Med Control, Clone 2.


title: USP-13-Med Control, Clone 3

description:
P133
Gene expression data from USP-13-Med Control, Clone 3.


title: Rat_myelinating_cultures_untreated_10days_CTR_T2_rep1

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

hyb_protocol: The processed RNAs were hybridized to Affymetrix GeneChip® Rat Gene 1.0 ST Arrays using the manufacturer's protocols for using the Fluidics Station 450.

scan_protocol: The hybridized arrays were scanned on the Gene Array Scanner 3000-7G.

data_processing: The data analysis was carried out in Partek Genomics Suite (version 6.5) software. The probeset-level data were normalised using the GCRMA normalisation method and summarised to the transcript cluster level using the One-Step Tukey's Biweight method.

organism: Rattus norvegicus

source_name: Rat neurosphere-derived astrocytes

label_protocol: The total RNAs were processed and labelled with biotin using the Ambion® WT Expression Kit following the Affymetrix GeneChip® WT Terminal Labeling and Hybridization protocol.

growth_protocol:
Neurospheres were generated from striata of P1 Sprague-Dawley rats by resuspending enzymatically dissociated cells in 20ml neurosphere media [DMEM/F12 (1:1, DMEM containing 4,500 mg/L glucose), supplemented with 0.105 % NaHCO3, 2 mM glutamine, 5,000 IU/ml penicillin, 5µg/ml streptomycin, 5.0mM HEPES, 0.0001% bovine serum albumin (all from Invitrogen), 25 µg/ml insulin, 100 µg/ml apotransferrin, 60uM putrescine, 20nM progesterone, and 30nM sodium selenite (all from Sigma)] and plating them into a 75 cm3 tissue culture flask. The culture was supplemented with 20ng/ml mouse submaxillary gland epidermal growth factor (R&D Systems) and maintained at 37ºC in a humidified atmosphere of 7% CO2/93% air. Every 2-3 days, 5 ml NSM and 4 µl EGF were added to the flask. Neurosphere-derived astrocytes (NsAs) were obtained by triturating neurospheres and plating them onto Poly-L lysine (PLL, 13ug/ml, Sigma) -coated coverslips (13 mm diameter, VWR International, Leicestershire, UK) in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine (Sigma) until they formed a confluent monolayer.
NsAs conditioned media was obtained from confluent NsAs monolayers grown in DM without insulin in the presence or absence of 100ng/ml FGF9, medium changed every other day and stored at -80°C until further use. These supernatants were then used to treat myelinating cultures (3:1 vol/vol supernatant/fresh DM without insulin) from 18-28 DIV in the presence or absence of a neutralizing antibody specific for human FGF9 (Abcam, 10 μg/ml).
Myelinating spinal cord cultures were derived from E15.5 Sprague-Dawley (SD) embryos. Spinal cords were dissected out, cleared of meninges, minced with a scalpel blade and enzymatically dissociated with 2.5% trypsin (Invitrogen) and 1.33% collagenase (ICN Pharmaceuticals, UK). Enzymatic activity was stopped by adding 1 ml of a solution containing 0.52 mg/ml soybean trypsin inhibitor, 3.0 mg/ml bovine serum albumin, and 0.04 mg/ml DNase (Sigma). The tissue was then triturated, centrifuged and resuspended in plating medium (PM, 50% DMEM, 25% horse serum, 25% HBSS) and 150,000 cells per 100 µl plated on cover slips coated with a confluent monolayer of NsAs. Coverslips were placed in 35-mm Petri dishes (3 per dish) and left in the incubator to attach for 2 hours, after which 300 µl of PM and 500 µl of differentiation medium (DM) [DMEM (4,500 mg/ml glucose), 10 ng/ml biotin, 0.5% hormone mixture (1 mg/ml apotransferrin, 20 mM Putrescine, 4 μM progesterone, and 6 μM selenium; formulation based on Bottenstein and Sato, 197940), 50 nM hydrocortisone, and 0.1 μg/ml insulin (all reagents from Sigma) ] were added. Cultures were fed every 2 days by removing 500 µl of media and replacing it with fresh DM media, after 12 days insulin was removed from the DM used to feed the cultures. The effect of recombinant human FGF9 and other soluble factors (all obtained from R&D Systems) on these in vitro myelinating cultures was investigated by adding them to the culture media from day 18 (i.e., when myelination has just begun) to day 28 in vitro.

extract_protocol: RNA was extracted from myelinating cultures grown in the presence or absence of FGF9 (100 ng/ml) for 24h and 10 days using the Qiagen RNeasy Micro kit according to the manufacturer's instructions. RNA quality and integrity were checked using the Agilent Bioanalyzer 6000 Nano LabChip platform.

treatment_protocol: The in vitro myelinating cultures were either untreated or treated with human FGF9 (100ng/ml). Samples were collected at 24 hours and 10 days from the untreated and treated myelinating cultures.

value: Sprague Dawley

value: myelinating culture

tag: treatment

value: untreated

tag: time point


title: Rat_myelinating_cultures_treated_with_FGF9_24hr_FGF_T1_rep2

value: fibroblast growth factor 9 (FGF9)


title: USP-13-Med OCT4A, Clone 2

description:
P13O2
Gene expression data from USP-13-Med OCT4A, Clone 2.

source_name: Cell culture of USP-13-Med OCT4A


title: D283Med Control, Biological Replicate 2

description:
D2
Gene expression data from D283Med Control, Biological Replicate 2.


title: Rat_myelinating_cultures_untreated_24hr_CTR_T1_rep1


title: Rat_myelinating_cultures_treated_with_FGF9_24hr_FGF_T1_rep1


title: Rat_myelinating_cultures_untreated_24hr_CTR_T1_rep2


title: D283Med Control, Biological Replicate 1

description:
D1
Gene expression data from D283Med Control, Biological Replicate 1.


title: Rat_myelinating_cultures_treated_with_FGF9_10days_FGF_T2_rep1


title: Daoy Control, Clone 3

description:
DAOY 3
Gene expression data from Daoy Control, Clone 3.

source_name: Cell culture of Daoy control

value: Daoy


title: Daoy OCT4A, Clone 1

description:
OCT 1
Gene expression data from Daoy OCT4A, Clone 1.

source_name: Cell culture of Daoy OCT4A


title: Daoy OCT4A, Clone 2

description:
OCT 2
Gene expression data from Daoy OCT4A, Clone 2.


title: LMPP-s 2


title: Daoy Control, Clone 2

description:
DAOY 2
Gene expression data from Daoy Control, Clone 2.


title: LMPP-s 3


title: LMPP-s 1


title: Daoy Control, Clone 1

description:
DAOY 1
Gene expression data from Daoy Control, Clone 1.


title: LMPP+s 2


title: LMPP+s 1


title: Human Peripheral Blood monocytes [Sample_80]

status: Public on Feb 16 2016

city: New Haven

first: Rakesh

last: Verma

state: CT

address: 333 Cedar St.

department: Yale Cancer Center

country: USA

institute: Yale University

hyb_protocol: Samples were hybridized with GeneChip® Human Transcriptome Array 2.0 (Affymetrix) and scanned at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data on coding genes were analyzed using Genespring GX 12.5 platform. Data were imported via exon expression workflow employing RMA16 (normalization) for analyzing the coding genes using the specific annotation support file for human transcriptome array 2.0 (as  provided by Genespring GX).

source_name: aPD1+aCTLA4-post (T2)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix) at the Yale Center for Genome Anlaysis (YCGA) Microarray Core Facility.

growth_protocol: Not Applicable

extract_protocol: RNA was isolated from sorted peripheral blood monocytes using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: gender

value: M

tag: individual

value: T

tag: agent

value: Combo

value: post

value: Peripheral Blood monocytes


title: Rat_myelinating_cultures_untreated_10days_CTR_T2_rep2


title: Human Peripheral Blood monocytes [Sample_73]

source_name: aPD1+aCTLA4-pre (Q1)

value: Q

value: pre


title: Human Peripheral Blood monocytes [Sample_79]

source_name: aPD1+aCTLA4-pre (T1)


title: Human Peripheral Blood monocytes [Sample_77]

source_name: aPD1+aCTLA4-pre (S1)

value: F

value: S


title: Rat_myelinating_cultures_treated_with_FGF9_10days_FGF_T2_rep2


title: Human Peripheral Blood monocytes [Sample_76]

source_name: aPD1+aCTLA4-post sequential therapy sample (R2)

value: R

value: Seq

value: post sequential therapy sample


title: Human Peripheral Blood monocytes [Sample_75]

source_name: aPD1+aCTLA4-pre sequential therapy sample (R1)

value: pre sequential therapy sample


title: Human Peripheral Blood monocytes [Sample_74]

source_name: aPD1+aCTLA4-post (Q2)


title: Human Peripheral Blood monocytes [Sample_70]

description: Inadequate RNA sample for aPD1+aCTLA4-pre (O1)

source_name: aPD1+aCTLA4-post (O2)

value: O


title: Human Peripheral Blood monocytes [Sample_59]

source_name: aPD1-pre (J1)

value: J


title: Human Peripheral Blood monocytes [Sample_56]

source_name: aCTLA4-post (H2)

value: H


title: Human Peripheral Blood monocytes [Sample_62]

source_name: aCTLA4-post (K2)

value: K


title: Human Peripheral Blood monocytes [Sample_57]

source_name: aPD1+aCTLA4-pre (I1)

value: I


title: Human Peripheral Blood monocytes [Sample_78]

source_name: aPD1+aCTLA4-post (S2)


title: Human Peripheral Blood monocytes [Sample_71]

source_name: aPD1-pre (P1)

value: M

value: P


title: Human Peripheral Blood monocytes [Sample_72]

source_name: aPD1-post (P2)

value: post


title: Human Peripheral Blood monocytes [Sample_64]

source_name: aPD1+aCTLA4-post sequential therapy sample (L2)

value: L

value: Peripheral Blood monocytes


title: Human Peripheral Blood monocytes [Sample_68]

source_name: aCTLA4-post (N2)

value: N


title: Human Peripheral Blood monocytes [Sample_65]

source_name: aPD1-pre (M1)

value: pre


title: Human Peripheral Blood monocytes [Sample_63]

source_name: aPD1+aCTLA4-pre sequential therapy sample (L1)


title: Human Peripheral Blood monocytes [Sample_67]

source_name: aCTLA4-pre (N1)


title: Human Peripheral Blood monocytes [Sample_61]

source_name: aCTLA4-pre (K1)


title: Human Peripheral Blood monocytes [Sample_60]

source_name: aPD1-post (J2)


title: USP-13-Med OCT4A, Clone 3

description:
P13O3
Gene expression data from USP-13-Med OCT4A, Clone 3.

source_name: Cell culture of USP-13-Med OCT4A

value: medulloblastoma cell line


title: Human Peripheral Blood monocytes [Sample_58]

source_name: aPD1+aCTLA4-post (I2)

value: F

value: Combo


title: Human Peripheral Blood monocytes [Sample_53]

source_name: aPD1-pre (G1)

value: G


title: Human Peripheral Blood monocytes [Sample_66]

source_name: aPD1-post (M2)


title: Human Peripheral Blood monocytes [Sample_55]

source_name: aCTLA4-pre (H1)


title: Human Peripheral Blood monocytes [Sample_54]

source_name: aPD1-post (G2)


title: Human Peripheral Blood monocytes [Sample_51]

source_name: aPD1+aCTLA4-pre sequential therapy sample (F1)

value: Seq

value: pre sequential therapy sample


title: Human Peripheral Blood monocytes [Sample_52]

source_name: aPD1+aCTLA4-post sequential therapy sample (F2)

value: post sequential therapy sample


title: Human Peripheral Blood monocytes [Sample_50]

source_name: aCTLA4-post (E2)

value: E


title: Human Peripheral Blood monocytes [Sample_49]

source_name: aCTLA4-pre (E1)


title: Human Peripheral Blood monocytes [Sample_46]

source_name: aPD1+aCTLA4-post (C2)

value: C


city: RTP

first: Pierre

middle: Robert

last: Bushel

state: NC

department: Biostatistics and Computational Biology Branch

institute: NIEHS

description:
Average Baseline Group for Level Control vs. Overdose Subject 6: APAP
23187

hyb_protocol: For each two-color comparison, 750 ng of each Cy3 and Cy5 cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hrs in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning.

scan_protocol: Gene expression pixel intensities were extracted by scanning the microarrays with an Agilent Scanner (Agilent Technologies, Wilmington, DE).

data_processing:
The raw pixel intensity gene expression data were loaded into the Rosetta Resolver database (build 5.1.0.1.23, Rosetta Inpharmatics; Agilent Technologies, Palo Alto, CA) and error weighted ratio values computed from the normalized and background-subtracted pixel intensity values as described in Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, et al. Functional discovery via a compendium of expression profiles. Cell 2000; 102(1): 109-126.
Log base 10 ratio data (Overdose patients: average of baseline group [APAP sham -72hr day 0 human blood] to patient; Baseline group: Reference to APAP sham -72hr day 0 human blood).

label_protocol: Human universal reference (Stratagene, La Jolla, CA) and patients' RNA samples were amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit and labeled with the Cy3 and Cy5 cytofluors respectively according to manufacturer’s protocol.

extract_protocol: Blood was collected by using PAXgene vacutainer tubes (PreAnalytiX; Qiagen) and RNA was isolated as described by the manufacturer.

tag: reference composition

value: Average Baseline control

value: Whole Blood

source_name: Overdose Subject 6: APAP

value: APAP Overdose Subject 6


title: Human Peripheral Blood monocytes [Sample_44]

source_name: aCTLA4-post (B2)

value: B

value: post


title: Human Peripheral Blood monocytes [Sample_48]

source_name: aPD1-post (D2)

value: D

value: Peripheral Blood monocytes


description:
Stratagene Human Universal Reference vs. APAP sham 2 -72hr day 0 human blood
23181

source_name: Stratagene human universal reference

value: 10 human cell lines

source_name: APAP sham 2 -72hr day 0 human blood

value: Baseline control


description:
Average Baseline Group for Level Control vs. Overdose Subject 4: APAP
23189

source_name: average of baseline group [APAP sham -72hr day 0 human blood]

source_name: Overdose Subject 4: APAP

value: APAP Overdose Subject 4


description:
Average Baseline Group for Level Control vs. Overdose Subject 2: APAP
23185

source_name: Overdose Subject 2: APAP

value: APAP Overdose Subject 2


title: Human Peripheral Blood monocytes [Sample_47]

source_name: aPD1-pre (D1)

value: F

value: pre


description:
Stratagene Human Universal Reference vs. APAP sham 3 -72hr day 0 human blood
23192

source_name: APAP sham 3 -72hr day 0 human blood


description:
Average Baseline Group for Level Control vs. Overdose Subject 5: APAP
23186

source_name: Overdose Subject 5: APAP

value: APAP Overdose Subject 5


title: Subject5_Day_7

data_processing: The log base 2 pixel intensity values from the Cy3 and Cy5 channels were background subtracted, corrected for dye bias and normalized across arrays via systematic variation normalization (SVN) as described in Chou JW, Paules RS, Bushel PR. Systematic variation normalization in microarray data to get gene expression comparison unbiased. Journal of bioinformatics and computational biology 2005; 3(2): 225-241.  Then the data was corrected for batch effects using an empirical Bayes model with the classification of the subjects and before or after dosing as covariates and parametric estimation of priors such as decribed in Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8(1): 118-127.

label_protocol: 500 ng of total RNA (universal reference and subject samples) was amplified, labeled (with cytofluor reversal) using the Agilent Low RNA Input Fluorescent Linear Amplification Kit, according to manufacturer’s protocol.

extract_protocol: Each day peripheral blood (7.5 mls) was drawn into PAXgene™ blood RNA collection tubes (3 tubes @ 2.5 mls). Samples were mixed and RNA was isolated according to the manufacturer’s protocol, including the optional on-column DNase digestion. RNA quality was assessed with an Agilent Bioanalyzer™ and only samples with intact 18S and 28S ribosomal RNA peaks were used for microarray analysis.

treatment_protocol: Individuals given placebos were classified as within the Placebo group.  Responders:  Individuals with a 2-fold increase in serum ALT from their respective baseline value and greater than 2x the upper limit of normal (as defined by historical data from the UNC hospital: females = 30 IU/L; males = 40 IU/L) in response to acetaminophen.  Non-responders: Individuals receiving acetaminophen but not meeting the “Responder” criteria.  The baseline for normal was defined as the mean of the daily ALT measurements obtained in the 3 days before the start of acetaminophen dosing (the acclimation period).

value: Male

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

tag: age

tag: response

value: Responder

value: Acetaminophen

tag: time

value: Day 7


title: Subject5_Day_3

tag: tissue

value: Whole Blood

value: C

value: Day 3


title: Human Peripheral Blood monocytes [Sample_42]

source_name: aPD1-post (A2)

value: M

value: A

value: post


title: Subject5_Day_5

value: 10 human cell lines

value: Day 5


title: Subject5_Day_4

value: Day 4


title: Human Peripheral Blood monocytes [Sample_43]

source_name: aCTLA4-pre (B1)

value: B

value: Peripheral Blood monocytes


title: Subject5_Day_6

value: Day 6


title: Subject5_Day_1

value: Day 1


title: Subject5_Day_8

value: Male

value: Day 8


title: Subject71_Day_8

value: Non-responder

value: Acetaminophen


title: Subject5_Day_2

value: Whole Blood

value: Responder

value: Day 2


title: Subject71_Day_7

value: C

value: Day 7


title: Human Peripheral Blood monocytes [Sample_45]

source_name: aPD1+aCTLA4-pre (C1)

value: M

value: Combo

value: pre


title: Human Peripheral Blood monocytes [Sample_41]

source_name: aPD1-pre (A1)

value: A


title: Subject71_Day_6

value: 10 human cell lines


title: Subject71_Day_3

value: Day 3


title: Subject71_Day_2


title: Subject71_Day_1


title: Subject69_Day_7

value: Female

value: AA


title: Subject71_Day_5

value: Male

value: Day 5


title: Subject69_Day_8

value: Non-responder

value: Day 8


title: Subject71_Day_4

value: Whole Blood

value: Acetaminophen

value: Day 4


title: Subject69_Day_4


title: Subject69_Day_6

value: Day 6


title: Subject65_Day_8


title: Subject69_Day_1

value: Day 1


title: Subject65_Day_7

value: Day 7


description:
Stratagene Human Universal Reference vs. APAP sham 1 -72hr day 0 human blood
23180

source_name: APAP sham 1 -72hr day 0 human blood

value: Baseline control


title: Subject65_Day_4


title: Subject65_Day_3


title: Subject59_Day_6

value: Placebo


title: Subject65_Day_1


title: Subject59_Day_4


title: Subject59_Day_5


title: Subject65_Day_2

value: Day 2


title: Subject65_Day_6

value: 10 human cell lines


title: Subject69_Day_2


title: Subject59_Day_7


title: Subject59_Day_2


title: Subject65_Day_5


title: Subject69_Day_5


title: Subject69_Day_3

value: Day 3


title: Subject59_Day_8


title: Subject59_Day_1


title: Subject58_Day_7

value: Female

value: H


title: Subject59_Day_3

value: Male

value: AA


title: Subject58_Day_3

value: Non-responder


title: Subject58_Day_1


title: Subject58_Day_8

value: Day 8


title: Subject58_Day_2

value: Whole Blood


title: Subject58_Day_4

value: Acetaminophen


title: Subject58_Day_5

value: Day 5


title: Subject55_Day_5

value: C


title: Subject55_Day_4

value: Day 4


title: Subject55_Day_1

value: Day 1


title: Subject58a_Day_6

value: Day 6


title: Subject55_Day_6

value: Placebo


title: Subject50_Day_2

value: Day 2


title: Subject55_Day_2

value: 10 human cell lines


title: Subject50_Day_8


title: Subject55_Day_7

value: Day 7


title: Subject48_Day_8


title: Subject55_Day_3

value: Female

value: Day 3


title: Subject50_Day_1

value: Male


title: Subject55_Day_8


title: Subject50_Day_6

value: AA


title: Subject50_Day_7

value: Non-responder


title: Subject50_Day_3


title: Subject50_Day_4


title: Subject50_Day_5


description:
Average Baseline Group for Level Control vs. Overdose Subject 3: APAP
23188

value: Average Baseline control

source_name: Overdose Subject 3: APAP

value: APAP Overdose Subject 3


title: Subject48_Day_5

value: Whole Blood

value: Acetaminophen


title: Subject48_Day_4


title: Subject48_Day_7


title: Subject48_Day_1


title: Subject48_Day_6


title: Subject48_Day_3


title: Subject46_Day_8

value: C

value: Responder

value: Day 8


title: Subject46_Day_7


title: Subject46_Day_6

value: Day 6


title: Subject46_Day_5

value: Day 5


title: Subject48_Day_2

value: Day 2


title: Subject43_Day_8

value: 10 human cell lines

value: H


title: Subject46_Day_4

value: Female

value: Day 4


title: Subject43_Day_3

value: Male

value: Day 3


title: Subject43_Day_4


title: Subject43_Day_7

value: Day 7


title: Subject43_Day_2


title: Subject42_Day_4

value: Non-responder


title: Subject42_Day_3


title: Subject46_Day_2


title: Subject42_Day_5


title: Subject46_Day_1

value: Day 1


title: Subject42_Day_8

value: Whole Blood


title: Subject43_Day_5

value: Acetaminophen


title: Subject43_Day_6


title: Subject42_Day_1


title: Subject46a_Day_3

value: C


title: Subject43_Day_1

value: Responder


title: Subject36_Day_8

value: Placebo

value: Day 8


title: Subject42_Day_6

value: Day 6


title: Subject42_Day_7


title: Subject42_Day_2

value: Day 2


title: Subject36_Day_5

value: 10 human cell lines

value: Day 5


title: Subject36_Day_7

value: Female

value: H


title: Subject36_Day_3


title: Subject36_Day_4

value: Day 4


title: Subject36_Day_2


title: Subject34_Day_8

value: Male


title: Subject36_Day_1


title: Subject36_Day_6


title: Subject34_Day_7

value: Day 7


title: Subject34_Day_5

value: Non-responder


title: Subject34_Day_3

value: Day 3


title: Subject34_Day_4

value: Whole Blood


title: Subject32_Day_4

value: Acetaminophen


title: Subject32_Day_7


title: Subject34_Day_2


title: Subject34_Day_6


title: Subject32_Day_5


title: Subject32_Day_3


title: Subject32_Day_2


title: Subject34_Day_1

value: Day 1


title: Subject32_Day_1


title: Subject31_Day_7


title: Subject31_Day_2


title: Subject31_Day_1


title: Subject31_Day_8


title: Subject31_Day_4


title: Subject30_Day_4


title: Subject30_Day_8


title: Subject30_Day_6


title: Subject31_Day_5


title: Subject32_Day_6


title: Subject30_Day_7


title: Subject32_Day_8


title: Subject30_Day_2


title: Subject31_Day_3


title: Subject31_Day_6


title: Subject30_Day_1


title: Subject30_Day_5


title: Subject30_Day_3


title: Subject29_Day_8


title: Subject29_Day_7


title: Subject28_Day_3

value: C

value: Responder


title: Subject29_Day_1


title: Subject29_Day_5


title: Subject27_Day_2


title: Subject28_Day_2


title: Subject29_Day_6


title: Subject29_Day_4


title: Subject27_Day_7


title: Subject27_Day_5


title: Subject28_Day_7


title: Subject28_Day_4


title: Subject28_Day_6


title: Subject29_Day_2


title: Subject28_Day_5


title: Subject28_Day_1


title: Subject27_Day_4


title: Subject28_Day_8

value: Day 8


title: Subject26_Day_6

value: Day 6


title: Subject29_Day_3


title: Subject27_Day_8


title: Subject26_Day_5


title: Subject26_Day_7


title: Subject27_Day_3


title: Subject27_Day_1


title: Subject27_Day_6


title: Subject26_Day_4


title: Subject26_Day_3


title: Subject26_Day_8


title: Subject26_Day_2

value: Day 2


title: Subject26_Day_1

value: 10 human cell lines


title: Subject25_Day_2

value: Placebo


title: Subject25_Day_5

value: Day 5


title: Subject25_Day_7


title: Subject25_Day_4


title: Subject25_Day_3


title: Subject24_Day_8


title: Subject24_Day_7


title: Subject25_Day_6


title: Subject9_Day_7


title: Subject25_Day_8


title: Subject25_Day_1


title: Subject24_Day_4


title: Subject24_Day_6


title: Subject24_Day_3


title: Subject9_Day_2


title: Subject24_Day_1


title: Subject9_Day_8


title: Subject24_Day_2


title: Subject24_Day_5


title: Subject9_Day_3


title: Subject8_Day_8

value: Female

value: H


title: Subject9_Day_4

value: Male

value: Day 4


title: Subject8_Day_7

value: Non-responder

value: Day 7


title: Subject9_Day_5

value: Whole Blood


title: Subject9_Day_1


title: Subject9_Day_6


title: Subject8_Day_6

value: Acetaminophen


title: Subject8_Day_4


title: Subject8_Day_5


title: Subject8_Day_3

value: Day 3


title: Subject7_Day_5

value: C


title: Subject8_Day_1

value: Day 1


title: Subject7_Day_1


title: Subject7_Day_6


title: Subject7_Day_7


title: Subject7_Day_4


title: Subject4_Day_8

value: Day 8


title: Subject7_Day_8


title: Subject7_Day_2


title: Subject4_Day_7


title: Subject7_Day_3


title: Subject4_Day_4


title: Subject4_Day_2


title: Subject4_Day_5


title: Subject70_Day8


title: Subject4_Day_1


title: N2 Array31_Cy5

city: Utrecht

first: Basten

last: Snoek

address: Padualaan

department: Mol. Plant. Physiology

country: Netherlands

institute: Utrecht University

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis’-protocol from Agilent

scan_protocol: Agilent Feature Extraction Software

data_processing: For normalization the Limma package was used with for Agilent array recommended settings. No background correction was performed. For within-array normalization, the LOESS method was used and for between-array normalization, the quantile method was used

organism: Caenorhabditis elegans

growth_protocol: Synchronized developmental stage L4 worms, grown as previously described Brenner 1974 on nematode growth medium (NGM) agar plates seeded with Escherichia coli strain OP50 at 20 °C.

extract_protocol: RNA extraction was done using RNEasy Micro Kit (Qiagen)

tag: developmental stage


title: Subject70_Day7


title: wn046 Array30_Cy5

label_protocol: Two-Color Microarray-Based Gene Expression Analysis’-protocol from Agilent


title: Subject8_Day_2


title: Subject4_Day_3


title: Subject4_Day_6

value: Day 6


title: Mock Array34_Cy5

value: control


title: Mock Array32_Cy5


title: Mock Array36_Cy5


title: wn075 Array39_Cy5


title: Mock Array38_Cy5


title: Subject70_Day5

value: 10 human cell lines


title: Mock Array35_Cy5


title: Mock Array27_Cy5


title: wn098 Array29_Cy5


title: Subject70_Day4

value: Placebo


title: Mock Array37_Cy5


title: Mock Array25_Cy5


title: Subject70_Day2


title: wn041 Array28_Cy5


title: CB4856 Array33_Cy5


title: Subject70_Day3


title: wn134 Array26_Cy5


title: wn057 Array24_Cy5


title: Subject70_Day6


title: Subject70_Day1


title: wn159 Array23_Cy5


title: Mock Array22_Cy5


title: wn113 Array21_Cy5


title: Subject68_Day7

value: AA


title: Subject68_Day8


title: Subject68_Day2


title: Subject68_Day5


title: Subject68_Day6


title: Subject68_Day3


title: Subject68_Day4


title: Subject60_Day_6


title: Mock Array13_Cy5


title: wn129 Array19_Cy5


title: Subject68_Day1


title: Subject60_Day_5

value: Day 5


title: wn146 Array14_Cy5


title: Mock Array18_Cy5


title: wn058 Array16_Cy5


title: N2 Array20_Cy5


title: wn185 Array17_Cy5


title: Subject60_Day_8

value: H


title: Subject60_Day_3

value: Male


title: Subject60_Day_7


title: wn161 Array11_Cy5


title: Subject60_Day_2

value: Day 2


title: Mock Array15_Cy5


title: wn048 Array10_Cy5


title: Mock Array09_Cy5


title: Mock Array12_Cy5


title: wn071 Array08_Cy5


title: Subject60_Day_1


title: Subject57_Day_7

value: Responder


title: Subject56_Day_8


title: Subject57_Day_6


title: wn038 Array06_Cy5


title: Subject57_Day_2


title: Mock Array39_Cy3


title: Mock Array01_Cy5


title: Subject56_Day_7

value: Day 7


title: Mock Array04_Cy5


title: CB4856 Array07_Cy5


title: Subject57_Day_3

value: Whole Blood


title: wn142 Array37_Cy3


title: wn098 Array02_Cy5


title: wn109 Array36_Cy3


title: wn020 Array05_Cy5


title: Subject56_Day_6

value: Acetaminophen


title: Subject57_Day_4

value: Day 4


title: Subject57_Day_5

value: C


title: Subject57_Day_1

value: Day 1


title: wn135 Array38_Cy3


title: Subject56_Day_5


title: Mock Array03_Cy5


title: wn106 Array35_Cy3


title: Mock Array33_Cy3


title: wn076 Array34_Cy3


title: Subject60_Day_4


title: CB4856 Array32_Cy3


title: Subject56_Day_2


title: Subject56_Day_3

value: Day 3


title: Subject57_Day_8

value: Day 8


title: Subject56_Day_1


title: Subject54_Day_8

value: Non-responder


title: Subject54_Day_5

value: 10 human cell lines


title: Mock Array28_Cy3

value: control


title: Subject54_Day_6

value: AA

value: Day 6


title: Mock Array24_Cy3


title: Mock Array31_Cy3


title: Mock Array29_Cy3


title: Subject54_Day_4


title: Subject53_Day_8

value: Female

value: H


title: Subject54_Day_7

value: Male


title: Subject54_Day_3


title: Subject54_Day_2

value: Day 2


title: Subject54_Day_1


title: Subject53_Day_7

value: Responder

value: Day 7


title: Mock Array26_Cy3


title: wn152 Array22_Cy3


title: wn177 Array21_Cy3


title: wn176 Array20_Cy3


title: Mock Array30_Cy3


title: Subject53_Day_6

value: Whole Blood

value: Acetaminophen


title: Subject53_Day_5

value: Day 5


title: Mock Array17_Cy3


title: wn140 Array25_Cy3


title: Mock Array19_Cy3


title: Subject53_Day_4

value: Day 4


title: wn158 Array18_Cy3


title: Subject53_Day_3

value: Day 3


title: Subject52_Day_8

value: Placebo

value: Day 8


title: Subject52_Day_7

value: 10 human cell lines


title: Subject52_Day_5


title: wn034 Array15_Cy3


title: wn128 Array13_Cy3


title: Subject53_Day_1

value: Day 1


title: N2 Array12_Cy3


title: wn162 Array14_Cy3


title: Subject52_Day_6


title: Subject52_Day_1


title: wn021 Array07_Cy3


title: Subject52_Day_3


title: wn186 Array27_Cy3


title: wn072 Array11_Cy3


title: Mock Array16_Cy3

value: control


title: Subject52_Day_2


title: wn174 Array09_Cy3


title: Mock Array06_Cy3


title: wn153 Array10_Cy3


title: Subject47_Day_8

value: AA

value: Non-responder


title: Subject53_Day_2

value: Female

value: H


title: Subject52_Day_4


title: Mock Array08_Cy3


title: Mock Array05_Cy3


title: wn110 Array04_Cy3


title: Subject47_Day_7

value: Male


title: Subject56_Day_4

value: C

value: Responder


title: Subject47_Day_4

value: Whole Blood


title: wn124 Array02_Cy3


title: Subject47_Day_6

value: Acetaminophen

value: Day 6


title: Subject47_Day_2

value: Day 2


title: Subject47_Day_3

value: Day 3


title: Subject45_Day_7

value: Day 7


title: wn116 Array03_Cy3


title: Subject47_Day_1


title: Mock Array23_Cy3


title: Subject45_Day_4

value: Day 4


title: Subject45_Day_6

value: 10 human cell lines


title: Subject45_Day_3


title: wn190 Array01_Cy3


title: Subject45_Day_5

value: Day 5


title: Subject45_Day_8

value: Day 8


title: Subject45b_Day_2


title: Subject45_Day_1

value: Day 1


title: Subject44_Day_8

value: AA

value: Non-responder


title: Subject44_Day_6

value: Female


title: Subject44_Day_4


title: Subject44_Day_7


title: Subject44_Day_5


title: 99-091N_LN CRPC metastasis [CGH]

type: genomic

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
99-091N CRPC lymph node metastasis
99-091N_LN

hyb_protocol: Cy3 and Cy5 probes were combined and hybridized to Agilent 2x400K SurePrint G3 CGH Microarrays and washed following the manufacturer’s specifications.

scan_protocol: Fluorescent array images were collected using the Agilent DNA microarray scanner G2505C and Agilent Feature Extraction software.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to grid and extract the data using the CGH_107_Sep09 protocol with default settings. Feature Extraction Grid_GenomicBuild was hg18:NCBI36:Mar2006. Control probes were removed, duplicate probes averaged, and log2 ratios defined as gProcessedSignal/rProcessedSignal.

molecule: genomic DNA

source_name: A pool of reference normal male DNA

label_protocol: One microgram of high molecular weight genomic DNA from each sample was labeled by random priming using the Agilent Genomic DNA Enzymatic Labeling Kit (Cy3-dUTP.)  A pool of reference normal male DNA (Promega, Part No. G1471) was labeled with Cy5-dUTP following manufacturer's suggest protocols

value: male

extract_protocol:
Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.
Genomic DNA was isolated from OCT sections of localized and metastatic tissues with ≥50% tumor content, 1mm punches from frozen bone metastases as well as patient-matched normal tissues using the Qiagen QiaAmp DNA Micro kit incorporating RNAse-treatment. DNA quality was assessed by agarose gel electrophoresis.

tag: patient

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: LN

tag: age (yrs)

tag: psa ng/ml

tag: androgen deprivation therapy (adt)

value: L=LHRH agonist; O=orchiectomy:L

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,Ni,K

tag: chemotherapy

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject44_Day_1

tag: individual

value: Whole Blood

tag: gender

tag: treatment

value: Acetaminophen


title: Subject44_Day_2

tag: reference composition

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: Day 2


title: Subject44_Day_3

tag: age

tag: response

value: Day 3


title: Subject41_Day_8

value: 10 human cell lines

tag: tissue

value: Male

value: H

value: Responder

tag: time


title: Subject41_Day_7

value: Day 7


title: 99-091P_LN CRPC metastasis [CGH]

description:
99-091P CRPC lymph node metastasis
99-091P_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: patient


title: Subject47_Day_5

value: AA

value: Non-responder

value: Day 5


title: 99-091J_LN CRPC metastasis [CGH]

description:
99-091J CRPC lymph node metastasis
99-091J_LN

extract_protocol: reference normal male DNA (Promega, Part No. G1471)

value: male

tag: tumor type

value: CRPC metastasis

value: LN


title: 99-091C_LIVER CRPC metastasis [CGH]

description:
99-091C CRPC liver metastasis
99-091C_LIVER

tag: tumor site

value: LIVER

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,Ni,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 99-091K_LN CRPC metastasis [CGH]

description:
99-091K CRPC lymph node metastasis
99-091K_LN

tag: age (yrs)


title: 99-069I_CAP CRPC primary/localized tumor [CGH]

description:
99-069I CRPC bladder_neck primary/localized tumor
99-069I_CAP

value: CRPC primary/localized

tag: psa ng/ml

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 99-069F_LUNG CRPC metastasis [CGH]

description:
99-069F CRPC lung metastasis
99-069F_LUNG

value: LUNG

tag: androgen deprivation therapy (adt)


title: Subject41_Day_4

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

value: Responder

value: Acetaminophen

value: Day 4


title: 99-069G1_PERITONEUM CRPC metastasis [CGH]

description:
99-069G1 CRPC peritoneum metastasis
99-069G1_PERITONEUM

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: PERITONEUM

tag: secondary ar pathway antagonism (arpa)


title: Subject41_Day_3

value: Day 3


title: 99-091I_LN CRPC metastasis [CGH]

description:
99-091I CRPC lymph node metastasis
99-091I_LN

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,Ni,K

tag: chemotherapy

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 99-064N_LN CRPC metastasis [CGH]

description:
99-064N CRPC lymph node metastasis
99-064N_LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F


title: Subject41_Day_6

value: 10 human cell lines

tag: individual

value: Day 6


title: 99-091L_LN CRPC metastasis [CGH]

description:
99-091L CRPC lymph node metastasis
99-091L_LN

tag: gender


title: 99-090A2_LIVER CRPC metastasis [CGH]

description:
99-090A2 CRPC liver metastasis
99-090A2_LIVER

value: LIVER

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 98-372K2_CAP CRPC primary/localized tumor [CGH]

description:
98-372K2 CRPC bladder_neck primary/localized tumor
98-372K2_CAP

value: CRPC primary/localized

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D


title: Subject40_Day_8

value: Whole Blood

value: Female

value: H

value: Non-responder

tag: treatment

value: Acetaminophen

value: Day 8


title: 98-362B1_LN CRPC metastasis [CGH]

description:
98-362B1 CRPC lymph node metastasis
98-362B1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:NA

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:NA


title: Subject41_Day_1

tag: reference composition

value: 10 human cell lines

value: Male

value: Responder

value: Day 1


title: 98-328J_LN CRPC metastasis [CGH]

description:
98-328J CRPC lymph node metastasis
98-328J_LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:C,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject40_Day_7

value: Whole Blood

value: Female

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: H

value: Day 7


title: 97-201J_LN CRPC metastasis [CGH]

description:
97-201J CRPC lymph node metastasis
97-201J_LN

value: male

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,D,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 99-064O_LN CRPC metastasis [CGH]

description:
99-064O CRPC lymph node metastasis
99-064O_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F


title: Subject41_Day_5

value: 10 human cell lines

value: Male

tag: age

value: Responder

value: Acetaminophen

value: Day 5


title: Subject40_Day_6

value: Whole Blood

tag: response

value: Non-responder

value: Day 6


title: Subject40_Day_5

tag: tissue

value: Female

value: H


title: 98-328O_LIVER CRPC metastasis [CGH]

description:
98-328O CRPC liver metastasis
98-328O_LIVER

value: male

value: LIVER

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:C,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject41_Day_2

tag: time

value: Day 2


title: Subject40_Day_4

value: Day 4


title: 98-372L_LN CRPC metastasis [CGH]

description:
98-372L CRPC lymph node metastasis
98-372L_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: patient

value: CRPC metastasis

value: LN

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 97-201M_LN CRPC metastasis [CGH]

description:
97-201M CRPC lymph node metastasis
97-201M_LN

tag: tumor type

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,D,K


title: Subject40_Day_2

value: 10 human cell lines

value: Whole Blood

value: Non-responder

value: Acetaminophen


title: 98-328K_PERITONEUM CRPC metastasis [CGH]

description:
98-328K CRPC peritoneum metastasis
98-328K_PERITONEUM

value: male

tag: tumor site

value: PERITONEUM


title: 97-201K_LN CRPC metastasis [CGH]

description:
97-201K CRPC lymph node metastasis
97-201K_LN

tag: age (yrs)


title: Subject39_Day_8

value: Female

value: AA

value: Day 8


title: Subject39_Day_7

value: Day 7


title: Subject40_Day_1

value: H

value: Day 1


title: Subject40_Day_3

value: Day 3


title: 97-159H2_LIVER CRPC metastasis [CGH]

description:
97-159H2 CRPC liver metastasis
97-159H2_LIVER

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LIVER

tag: psa ng/ml

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,D


title: Subject39_Day_6

value: 10 human cell lines

value: Whole Blood

value: Day 6


title: Subject39_Day_4

value: Non-responder

value: Acetaminophen

value: Day 4


title: 12-005K1_LUNG CRPC metastasis [CGH]

description:
12-005K1 CRPC lung metastasis
12-005K1_LUNG

value: male

value: LUNG

tag: androgen deprivation therapy (adt)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,Ni,5ARI,K,A

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: 98-328H_APPENDIX CRPC metastasis [CGH]

description:
98-328H CRPC appendix metastasis
98-328H_APPENDIX

value: APPENDIX

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:C,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject39_Day_3

value: Female

value: AA

value: Day 3


title: 12-021H4_LIVER CRPC metastasis [CGH]

description:
12-021H4 CRPC liver metastasis
12-021H4_LIVER

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LIVER

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,A

tag: chemotherapy


title: Subject39_Day_5

value: 10 human cell lines

tag: individual

value: Whole Blood

value: Non-responder

value: Acetaminophen

value: Day 5


title: Subject39_Day_2

tag: gender

value: Day 2


title: 11-028L1_LUNG CRPC metastasis [CGH]

description:
11-028L1 CRPC lung metastasis
11-028L1_LUNG

value: male

value: LUNG

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:C


title: 12-011I7_LN CRPC metastasis [CGH]

description:
12-011I7 CRPC lymph node metastasis
12-011I7_LN

value: LN

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Subject39_Day_1

value: Female

value: AA

tag: treatment

value: Day 1


title: 97-201I_CAP CRPC primary/localized tumor [CGH]

description:
97-201I CRPC prostate primary/localized tumor
97-201I_CAP

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC primary/localized

value: PROSTATE

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,D,K


title: 97-201H_CAP CRPC primary/localized tumor [CGH]

description:
97-201H CRPC bladder primary/localized tumor
97-201H_CAP

value: BLADDER


title: 12-011D26_CAP CRPC primary/localized tumor [CGH]

description:
12-011D26 CRPC prostate primary/localized tumor
12-011D26_CAP

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,A


title: 12-011J1_CAP CRPC primary/localized tumor [CGH]

description:
12-011J1 CRPC bladder primary/localized tumor
12-011J1_CAP

value: male


title: 11-028G3_ADRENAL CRPC metastasis [CGH]

description:
11-028G3 CRPC adrenal metastasis
11-028G3_ADRENAL

value: CRPC metastasis

value: ADRENAL


title: 12-005I2_LIVER CRPC metastasis [CGH]

description:
12-005I2 CRPC liver metastasis
12-005I2_LIVER

value: LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,Ni,5ARI,K,A

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: 10-013F1_LN CRPC metastasis [CGH]

description:
10-013F1 CRPC lymph node metastasis
10-013F1_LN

value: LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:C,M


title: Subject37_Day_5

tag: reference composition

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

value: Non-responder

value: Acetaminophen

value: Day 5


title: Subject35_Day_8

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: Placebo

value: Day 8


title: Subject37_Day_3

tag: age

value: Day 3


title: 08-020N2_LN CRPC metastasis [CGH]

description:
08-020N2 CRPC lymph node metastasis
08-020N2_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: 10-039E3_LUNG CRPC metastasis [CGH]

description:
10-039E3 CRPC lung metastasis
10-039E3_LUNG

value: LUNG

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject37_Day_4

value: 10 human cell lines

value: Whole Blood

value: Male

tag: response

value: Day 4


title: Subject37_Day_8

tag: tissue

value: H

value: Non-responder

value: Acetaminophen


title: 09-006F1_RENAL CRPC metastasis [CGH]

description:
09-006F1 CRPC renal metastasis
09-006F1_RENAL

value: RENAL

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 10-013G1_RETROPERITONEAL CRPC metastasis [CGH]

description:
10-013G1 CRPC retroperitoneal metastasis
10-013G1_RETROPERITONEAL

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: RETROPERITONEAL

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:C,M


title: Subject35_Day_6

value: 10 human cell lines

value: Placebo

tag: time

value: Day 6


title: Subject37_Day_6

value: Whole Blood

value: Male


title: Subject37_Day_1

value: H

value: Non-responder

value: Day 1


title: Subject35_Day_7

value: Day 7


title: 10-013J2_LN CRPC metastasis [CGH]

description:
10-013J2 CRPC lymph node metastasis
10-013J2_LN

tag: patient

value: LN


title: 08-093J1_LN CRPC metastasis [CGH]

description:
08-093J1 CRPC lymph node metastasis
08-093J1_LN

value: male

tag: tumor type

value: L=LHRH agonist; O=orchiectomy:L

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: Subject37_Day_7

value: Acetaminophen


title: 08-020D1_CAP CRPC primary/localized tumor [CGH]

description:
08-020D1 CRPC prostate primary/localized tumor
08-020D1_CAP

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC primary/localized

tag: tumor site

value: PROSTATE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: 07-050XX1_BONE CRPC metastasis [CGH]

description:
07-050XX1 CRPC bone metastasis
07-050XX1_BONE

value: CRPC metastasis

value: BONE

tag: age (yrs)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,E


title: Subject35_Day_5

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

value: Placebo

value: Day 5


title: Subject37_Day_2

value: Non-responder

value: Day 2


title: Subject35_Day_4

value: Day 4


title: 08-037F1_LIVER CRPC metastasis [CGH]

description:
08-037F1 CRPC liver metastasis
08-037F1_LIVER

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LIVER

tag: psa ng/ml

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,5ARI,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: 07-062F2_LUNG CRPC metastasis [CGH]

description:
07-062F2 CRPC lung metastasis
07-062F2_LUNG

value: CRPC metastasis

value: LUNG

tag: androgen deprivation therapy (adt)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K


title: 06-134H1_LN CRPC metastasis [CGH]

description:
06-134H1 CRPC lymph node metastasis
06-134H1_LN

value: LN

value: L=LHRH agonist; O=orchiectomy:O

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D


title: Subject33_Day_8

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

value: Acetaminophen

value: Day 8


title: Subject35_Day_3

value: Placebo

value: Day 3


title: Subject35_Day_2

value: Day 2


title: 07-042H2_LN CRPC metastasis [CGH]

description:
07-042H2 CRPC lymph node metastasis
07-042H2_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,K,D

tag: chemotherapy

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject33_Day_7

tag: individual

value: Non-responder

value: Day 7


title: 07-044KK5_BONE CRPC metastasis [CGH]

description:
07-044KK5 CRPC bone metastasis
07-044KK5_BONE

tag: gender

value: CRPC metastasis

value: BONE

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,5ARI,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: Subject35_Day_1

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

tag: treatment

value: Day 1


title: Subject33_Day_6

tag: reference composition

value: Acetaminophen

value: Day 6


title: 08-006H1_LN CRPC metastasis [CGH]

description:
08-006H1 CRPC lymph node metastasis
08-006H1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LN

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D


title: Subject33_Day_5

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: Non-responder

value: Day 5


title: 06-127H3_LN CRPC metastasis [CGH]

description:
06-127H3 CRPC lymph node metastasis
06-127H3_LN

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: 06-081J1_LN CRPC metastasis [CGH]

description:
06-081J1 CRPC lymph node metastasis
06-081J1_LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: 06-081K2_LN CRPC metastasis [CGH]

description:
06-081K2 CRPC lymph node metastasis
06-081K2_LN


title: Subject33_Day_4

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

tag: age

value: Day 4


title: Subject33_Day_2

tag: response

value: Acetaminophen

value: Day 2


title: Subject23_Day_8

tag: tissue

value: C

value: Responder

value: Day 8


title: 06-081F2_LN CRPC metastasis [CGH]

description:
06-081F2 CRPC lymph node metastasis
06-081F2_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LN


title: Subject33_Day_3

value: Non-responder

tag: time

value: Day 3


title: 07-050EE1_BONE CRPC metastasis [CGH]

description:
07-050EE1 CRPC bone metastasis
07-050EE1_BONE

tag: patient

value: CRPC metastasis

value: BONE

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,E


title: 06-081H5_LN CRPC metastasis [CGH]

description:
06-081H5 CRPC lymph node metastasis
06-081H5_LN

tag: tumor type

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: Subject33_Day_1

value: 10 human cell lines

value: Whole Blood

value: Male

value: H

value: Acetaminophen

value: Day 1


title: Subject23_Day_5

value: C

value: Responder

value: Day 5


title: 06-081E2_LIVER CRPC metastasis [CGH]

description:
06-081E2 CRPC liver metastasis
06-081E2_LIVER

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: tumor site

value: LIVER


title: 06-047QQ1_BONE CRPC metastasis [CGH]

description:
06-047QQ1 CRPC bone metastasis
06-047QQ1_BONE

value: CRPC metastasis

value: BONE

tag: age (yrs)

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject23_Day_6

value: 10 human cell lines

value: Day 6


title: Subject23_Day_4

value: Whole Blood

value: Male

value: Day 4


title: Subject23_Day_2

value: Acetaminophen

value: Day 2


title: Subject23_Day_3

value: C

value: Responder

value: Day 3


title: 06-047H1_LN CRPC metastasis [CGH]

description:
06-047H1 CRPC lymph node metastasis
06-047H1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LN

tag: psa ng/ml


title: 06-081D3_CAP CRPC primary/localized tumor [CGH]

description:
06-081D3 CRPC prostate primary/localized tumor
06-081D3_CAP

value: CRPC primary/localized

value: PROSTATE

tag: androgen deprivation therapy (adt)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: Subject23_Day_7

value: 10 human cell lines

value: Day 7


title: Subject23_Day_1

value: Whole Blood

value: Day 1


title: 05-217F1_LN CRPC metastasis [CGH]

description:
05-217F1 CRPC lymph node metastasis
05-217F1_LN

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L

tag: secondary ar pathway antagonism (arpa)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 05-217N1_LN CRPC metastasis [CGH]

description:
05-217N1 CRPC lymph node metastasis
05-217N1_LN

tag: chemotherapy


title: Subject22_Day_8

tag: individual

value: Female

value: H

value: Non-responder

value: Acetaminophen

value: Day 8


title: Subject22_Day_6

tag: gender

value: Day 6


title: Subject22_Day_7

tag: treatment


title: 05-214G1_LN CRPC metastasis [CGH]

description:
05-214G1 CRPC lymph node metastasis
05-214G1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C


title: 05-214BB2_BONE CRPC metastasis [CGH]

description:
05-214BB2 CRPC bone metastasis
05-214BB2_BONE

value: BONE


title: 05-217L3_LUNG CRPC metastasis [CGH]

description:
05-217L3 CRPC lung metastasis
05-217L3_LUNG

value: LUNG


title: 05-187J3_LN CRPC metastasis [CGH]

description:
05-187J3 CRPC lymph node metastasis
05-187J3_LN

value: CRPC metastasis

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: Subject22_Day_4

tag: reference composition

value: 10 human cell lines

value: Whole Blood

value: Day 4


title: 05-187I1_CAP CRPC primary/localized tumor [CGH]

description:
05-187I1 CRPC prostate primary/localized tumor
05-187I1_CAP

value: CRPC primary/localized

value: PROSTATE

value: L=LHRH agonist; O=orchiectomy:L


title: 05-214E1_LN CRPC metastasis [CGH]

description:
05-214E1 CRPC lymph node metastasis
05-214E1_LN


title: 05-165M1_LN CRPC metastasis [CGH]

description:
05-165M1 CRPC lymph node metastasis
05-165M1_LN

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject22_Day_5

value: Female

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: H

value: Non-responder

value: Acetaminophen

value: Day 5


title: Subject22_Day_3

tag: age

value: Day 3


title: 05-165O_ADRENAL CRPC metastasis [CGH]

description:
05-165O CRPC adrenal metastasis
05-165O_ADRENAL

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: ADRENAL


title: 05-148E3_LIVER CRPC metastasis [CGH]

description:
05-148E3 CRPC liver metastasis
05-148E3_LIVER

value: CRPC metastasis

value: LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,5ARI

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: 06-081I1_LUNG CRPC metastasis [CGH]

description:
06-081I1 CRPC lung metastasis
06-081I1_LUNG

value: LUNG

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: 05-165K5_LUNG CRPC metastasis [CGH]

description:
05-165K5 CRPC lung metastasis
05-165K5_LUNG

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: 05-144R1_CAP CRPC primary/localized tumor [CGH]

description:
05-144R1 CRPC prostate primary/localized tumor
05-144R1_CAP

value: CRPC primary/localized

value: PROSTATE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Subject20_Day_8

value: 10 human cell lines

value: Whole Blood

value: Female

value: C

tag: response

value: Responder

value: Acetaminophen

value: Day 8


title: 05-144Z1_LN CRPC metastasis [CGH]

description:
05-144Z1 CRPC lymph node metastasis
05-144Z1_LN

value: male

tag: tissue

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN


title: Subject20_Day_7

tag: time

value: Day 7


title: Subject20_Day_5

value: Day 5


title: Subject22_Day_2

value: H

value: Non-responder

value: Day 2


title: Subject22_Day_1

value: Day 1


title: Subject20_Day_4

value: 10 human cell lines

value: Day 4


title: 05-144M1_LN CRPC metastasis [CGH]

description:
05-144M1 CRPC lymph node metastasis
05-144M1_LN

tag: patient

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Subject20_Day_1

value: Whole Blood

value: Female

value: C

value: Responder

value: Acetaminophen


title: 05-144I1_LN CRPC metastasis [CGH]

description:
05-144I1 CRPC lymph node metastasis
05-144I1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: tumor type

value: CRPC metastasis

value: LN


title: Subject20_Day_2


title: Subject20_Day_6

value: Day 6


title: 05-144HH1_BONE CRPC metastasis [CGH]

description:
05-144HH1 CRPC bone metastasis
05-144HH1_BONE

tag: tumor site

value: BONE


title: Subject19_Day_7

value: H

value: Non-responder

value: Day 7


title: 05-144H1_LN CRPC metastasis [CGH]

description:
05-144H1 CRPC lymph node metastasis
05-144H1_LN

tag: age (yrs)

value: L=LHRH agonist; O=orchiectomy:L


title: 05-144EE1_BONE CRPC metastasis [CGH]

description:
05-144EE1 CRPC bone metastasis
05-144EE1_BONE

tag: psa ng/ml

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K


title: 05-187E1_LIVER CRPC metastasis [CGH]

description:
05-187E1 CRPC liver metastasis
05-187E1_LIVER

value: LIVER

tag: androgen deprivation therapy (adt)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: Subject19_Day_4

value: 10 human cell lines

value: Whole Blood

value: Female

value: Day 4


title: Subject19_Day_2

value: Acetaminophen

value: Day 2


title: 05-123E2_LN CRPC metastasis [CGH]

description:
05-123E2 CRPC lymph node metastasis
05-123E2_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN

tag: secondary ar pathway antagonism (arpa)

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject19_Day_3

value: H

value: Non-responder

value: Day 3


title: 05-092I1_LN CRPC metastasis [CGH]

description:
05-092I1 CRPC lymph node metastasis
05-092I1_LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

tag: chemotherapy

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:C


title: 05-123D1_CAP CRPC primary/localized tumor [CGH]

description:
05-123D1 CRPC prostate primary/localized tumor
05-123D1_CAP

value: CRPC primary/localized

value: PROSTATE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D


title: Subject19_Day_1

value: 10 human cell lines

tag: individual

value: Whole Blood

value: Female

value: Day 1


title: 05-011G4_LUNG CRPC metastasis [CGH]

description:
05-011G4 CRPC lung metastasis
05-011G4_LUNG

tag: gender

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LUNG


title: 05-092E7_LIVER CRPC metastasis [CGH]

description:
05-092E7 CRPC liver metastasis
05-092E7_LIVER

value: CRPC metastasis

value: LIVER


title: 05-144U1_ADRENAL CRPC metastasis [CGH]

description:
05-144U1 CRPC adrenal metastasis
05-144U1_ADRENAL

value: ADRENAL

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 05-144E1_LIVER CRPC metastasis [CGH]

description:
05-144E1 CRPC liver metastasis
05-144E1_LIVER

value: L=LHRH agonist; O=orchiectomy:L


title: 05-144W1_SPLEEN CRPC metastasis [CGH]

description:
05-144W1 CRPC spleen metastasis
05-144W1_SPLEEN

value: SPLEEN


title: Subject19_Day_5

value: H

value: Non-responder

tag: treatment

value: Acetaminophen

value: Day 5


title: Subject19_Day_6

tag: reference composition

value: 10 human cell lines

value: Whole Blood

value: Day 6


title: 05-092D1_CAP CRPC primary/localized tumor [CGH]

description:
05-092D1 CRPC bladder primary/localized tumor
05-092D1_CAP

value: male

value: CRPC primary/localized

value: BLADDER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:C


title: 04-112I1_LN CRPC metastasis [CGH]

description:
04-112I1 CRPC lymph node metastasis
04-112I1_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,Ni,K,D


title: 05-011D2_LN CRPC metastasis [CGH]

description:
05-011D2 CRPC lymph node metastasis
05-011D2_LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D


title: 04-112N1_CAP CRPC primary/localized tumor [CGH]

description:
04-112N1 CRPC bladder primary/localized tumor
04-112N1_CAP

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 04-112H3_LN CRPC metastasis [CGH]

description:
04-112H3 CRPC lymph node metastasis
04-112H3_LN


title: 04-149J1_CAP CRPC primary/localized tumor [CGH]

description:
04-149J1 CRPC prostate primary/localized tumor
04-149J1_CAP

value: PROSTATE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,5ARI

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M


title: 04-149E2_LN CRPC metastasis [CGH]

description:
04-149E2 CRPC lymph node metastasis
04-149E2_LN


title: 05-116F_LUNG CRPC metastasis [CGH]

description:
05-116F CRPC lung metastasis
05-116F_LUNG

value: LUNG

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 04-112M1_LN CRPC metastasis [CGH]

description:
04-112M1 CRPC lymph node metastasis
04-112M1_LN

value: male


title: 04-112G3_LN CRPC metastasis [CGH]

description:
04-112G3 CRPC lymph node metastasis
04-112G3_LN


title: Subject20_Day_3

value: 10 human cell lines

value: Whole Blood

value: Female

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: C

value: Responder

value: Acetaminophen

value: Day 3


title: 04-101J1_LN CRPC metastasis [CGH]

description:
04-101J1 CRPC lymph node metastasis
04-101J1_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B


title: Subject19_Day_8

value: H

tag: age

value: Non-responder

value: Day 8


title: 04-101H1_PERITONEAL CRPC metastasis [CGH]

description:
04-101H1 CRPC peritoneal metastasis
04-101H1_PERITONEAL

value: PERITONEAL

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Subject17_Day_7

value: 10 human cell lines

value: Male

tag: response

value: Day 7


title: 04-101F2_CAP CRPC primary/localized tumor [CGH]

description:
04-101F2 CRPC prostate primary/localized tumor
04-101F2_CAP

value: male

tag: tissue

value: CRPC primary/localized

value: PROSTATE


title: Subject17_Day_8

value: Whole Blood

value: C

value: Acetaminophen

tag: time


title: Subject16_Day_4

value: Female

value: Responder

value: Day 4


title: Subject17_Day_4


title: Subject16_Day_7


title: Subject17_Day_5

value: Day 5


title: Subject16_Day_5


title: Subject16_Day_8


title: Subject17_Day_6

value: Non-responder

value: Day 6


title: Subject16_Day_3

value: Day 3


title: Subject16_Day_6


title: Subject16_Day_1

value: Day 1


title: Subject17_Day_1

value: 10 human cell lines


title: Subject16_Day_2

value: Day 2


title: Subject17_Day_2

value: Male


title: Subject17_Day_3


title: Subject15_Day_8

value: Day 8


title: 04-101L3_LN CRPC metastasis [CGH]

description:
04-101L3 CRPC lymph node metastasis
04-101L3_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: patient

value: CRPC metastasis

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: Subject15_Day_7

value: Whole Blood

value: C

value: Acetaminophen

value: Day 7


title: Subject15_Day_6

value: Non-responder

value: Day 6


title: 04-050O2_CAP CRPC primary/localized tumor [CGH]

description:
04-050O2 CRPC prostate primary/localized tumor
04-050O2_CAP

tag: tumor type

value: CRPC primary/localized

value: PROSTATE

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K


title: Subject15_Day_5

value: 10 human cell lines

value: Male

value: Day 5


title: Subject15_Day_3

value: Day 3


title: Subject15_Day_1

value: Day 1


title: Subject15_Day_4

value: Day 4


title: 03-192D2_LN CRPC metastasis [CGH]

description:
03-192D2 CRPC lymph node metastasis
03-192D2_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

tag: tumor site

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E


title: Subject14_Day_8

value: Whole Blood

value: Female

value: A

value: Non-responder

value: Acetaminophen

value: Day 8


title: 04-050V1_LN CRPC metastasis [CGH]

description:
04-050V1 CRPC lymph node metastasis
04-050V1_LN

tag: age (yrs)

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 03-192C2_LN CRPC metastasis [CGH]

description:
03-192C2 CRPC lymph node metastasis
03-192C2_LN

tag: psa ng/ml


title: 04-050W1_LN CRPC metastasis [CGH]

description:
04-050W1 CRPC lymph node metastasis
04-050W1_LN

tag: androgen deprivation therapy (adt)


title: 03-192B2_LUNG CRPC metastasis [CGH]

description:
03-192B2 CRPC lung metastasis
03-192B2_LUNG

value: LUNG

tag: secondary ar pathway antagonism (arpa)


title: 03-192E3_SPLEEN CRPC metastasis [CGH]

description:
03-192E3 CRPC spleen metastasis
03-192E3_SPLEEN

value: male

value: SPLEEN

tag: chemotherapy


title: 04-050L1_LN CRPC metastasis [CGH]

description:
04-050L1 CRPC lymph node metastasis
04-050L1_LN

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis


title: 04-050G2_LN CRPC metastasis [CGH]

description:
04-050G2 CRPC lymph node metastasis
04-050G2_LN

value: LN


title: 03-139M9_RETROPERITONEAL CRPC metastasis [CGH]

description:
03-139M9 CRPC retroperitoneal metastasis
03-139M9_RETROPERITONEAL

value: RETROPERITONEAL

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject14_Day_4

value: 10 human cell lines

tag: individual

value: Whole Blood

value: Female

value: A

value: Day 4


title: Subject14_Day_5

tag: gender

value: Non-responder

value: Acetaminophen

value: Day 5


title: Subject14_Day_6

tag: treatment

value: Day 6


title: 04-050N1_CAP CRPC primary/localized tumor [CGH]

description:
04-050N1 CRPC prostate primary/localized tumor
04-050N1_CAP

value: male

value: CRPC primary/localized

value: PROSTATE

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 03-139E3_RETROPERITONEAL CRPC metastasis [CGH]

description:
03-139E3 CRPC retroperitoneal metastasis
03-139E3_RETROPERITONEAL

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: RETROPERITONEAL

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,K,D


title: Subject14_Day_7

tag: reference composition

value: 10 human cell lines

value: Whole Blood

value: Female

value: A

value: Day 7


title: 03-082OO_BONE CRPC metastasis [CGH]

description:
03-082OO CRPC bone metastasis
03-082OO_BONE

value: BONE

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 03-130L_RETROPERITONEAL CRPC metastasis [CGH]

description:
03-130L CRPC retroperitoneal metastasis
03-130L_RETROPERITONEAL

value: male

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:N


title: 03-192A1_LIVER CRPC metastasis [CGH]

description:
03-192A1 CRPC liver metastasis
03-192A1_LIVER

value: LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E


title: 03-130M4_LIVER CRPC metastasis [CGH]

description:
03-130M4 CRPC liver metastasis
03-130M4_LIVER

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis


title: Subject14_Day_3

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: Non-responder

value: Acetaminophen

value: Day 3


title: 03-081L_LN CRPC metastasis [CGH]

description:
03-081L CRPC lymph node metastasis
03-081L_LN

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 03-027P2_LIVER CRPC metastasis [CGH]

description:
03-027P2 CRPC liver metastasis
03-027P2_LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject14_Day_1

value: 10 human cell lines

value: Whole Blood

value: Female

value: A

tag: age

value: Day 1


title: Subject14_Day_2

tag: response

value: Day 2


title: 03-082K2_LN CRPC metastasis [CGH]

description:
03-082K2 CRPC lymph node metastasis
03-082K2_LN

value: male

tag: tissue

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: Subject15_Day_2

value: Male

value: C

value: Non-responder

value: Acetaminophen

tag: time


title: Subject10_Day_6

value: H

value: Responder

value: Day 6


title: 02-142II_BONE CRPC metastasis [CGH]

description:
02-142II CRPC bone metastasis
02-142II_BONE

tag: patient

value: CRPC metastasis

value: BONE

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: Subject10_Day_7

value: 10 human cell lines

value: Whole Blood

value: Female

value: Day 7


title: Subject10_Day_4

value: Day 4


title: Subject10_Day_5

value: Day 5


title: 02-083E1_LN CRPC metastasis [CGH]

description:
02-083E1 CRPC lymph node metastasis
02-083E1_LN

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: tumor type

value: LN

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 02-065P3_CAP CRPC primary/localized tumor [CGH]

description:
02-065P3 CRPC prostate primary/localized tumor
02-065P3_CAP

value: CRPC primary/localized

tag: tumor site

value: PROSTATE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: 03-027M1_LUNG CRPC metastasis [CGH]

description:
03-027M1 CRPC lung metastasis
03-027M1_LUNG

value: CRPC metastasis

value: LUNG

tag: age (yrs)

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K


title: Subject10_Day_3

value: 10 human cell lines

value: Whole Blood

value: Female

value: H

value: Responder

value: Acetaminophen

value: Day 3


title: Subject10_Day_8

value: Day 8


title: Subject10_Day_2

value: Day 2


title: Subject6_Day_7

value: Male

value: C/H

value: Non-responder

value: Day 7


title: 01-181AA_BONE CRPC metastasis [CGH]

description:
01-181AA CRPC bone metastasis
01-181AA_BONE

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: BONE

tag: psa ng/ml

value: L=LHRH agonist; O=orchiectomy:NA

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:NA

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:NA


title: Subject10_Day_1

value: 10 human cell lines

value: Whole Blood

value: Female

value: Day 1


title: Subject6_Day_6

value: Acetaminophen

value: Day 6


title: 02-065N1_SKIN CRPC metastasis [CGH]

description:
02-065N1 CRPC skin metastasis
02-065N1_SKIN

value: CRPC metastasis

value: SKIN

tag: androgen deprivation therapy (adt)

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject6_Day_5

value: Male

value: C/H

value: Non-responder

value: Day 5


title: 02-065W2_SCROTUM CRPC metastasis [CGH]

description:
02-065W2 CRPC scrotum metastasis
02-065W2_SCROTUM

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: SCROTUM

tag: secondary ar pathway antagonism (arpa)


title: Subject6_Day_4

value: 10 human cell lines

value: Whole Blood

value: Day 4


title: 03-163S4_LIVER CRPC metastasis [CGH]

description:
03-163S4 CRPC liver metastasis
03-163S4_LIVER

value: LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B

tag: chemotherapy


title: Subject6_Day_3

tag: individual

value: Acetaminophen

value: Day 3


title: 01-120A1_LIVER CRPC metastasis [CGH]

description:
01-120A1 CRPC liver metastasis
01-120A1_LIVER

tag: gender

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,M


title: 02-065M3_LN CRPC metastasis [CGH]

description:
02-065M3 CRPC lymph node metastasis
02-065M3_LN

value: LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D


title: Subject6_Day_1

value: Male

value: C/H

value: Non-responder

tag: treatment

value: Day 1


title: Foxo1(-/-)/VEGF(+)-3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: ES cell-derived endothelial cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: For the induction of ECs, ES cells were seeded on OP9 stromal cell layer and cultured in alpha-MEM supplemented with 10% FCS and 0.05 mM 2-mercaptoethanol for 6.5 days.

extract_protocol: Total RNA samples were extracted from cells using RNeasy Plus Mini Kit (QIAGEN #74134).

treatment_protocol: For VEGF stimulation, recombinant murine VEGF-A (10 ng/ml) was added in the medium during the last two days (4.5–6.5 days).

tag: genotype

value: VEGF treated

tag: cell type

value: ES cell-derived endothelial cells


title: 01-095C6_LIVER CRPC metastasis [CGH]

description:
01-095C6 CRPC liver metastasis
01-095C6_LIVER

value: male

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: LIVER

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,E,M


title: 01-120C1_LN CRPC metastasis [CGH]

description:
01-120C1 CRPC lymph node metastasis
01-120C1_LN

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L


title: 01-095N1_LN CRPC metastasis [CGH]

description:
01-095N1 CRPC lymph node metastasis
01-095N1_LN


title: Foxo1(-/-)/VEGF(+)-2


title: Foxo1(-/-)/VEGF(+)-1


title: 00-090T3_LN CRPC metastasis [CGH]

description:
00-090T3 CRPC lymph node metastasis
00-090T3_LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,E


title: 00-140N1_LN CRPC metastasis

description: 00-140N1 CRPC lymph node metastasis

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.1.1.1 were used to grid and extract the data using the GE2-v5_10_Apr08 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Eight-micron thick sections from soft tissue CRPC frozen metastases in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.

tag: batch

value: LN


title: 00-140N1_LN CRPC metastasis [CGH]

description:
00-140N1 CRPC lymph node metastasis
00-140N1_LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M


title: 01-087MM_BONE CRPC metastasis [CGH]

description:
01-087MM CRPC bone metastasis
01-087MM_BONE

value: BONE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: 00-140K3_CAP CRPC primary/localized tumor

description: 00-140K3 CRPC bladder primary/localized tumor

value: male

extract_protocol: Eight-micron thick sections from CRPC localized tumors in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: CRPC primary/localized

value: BLADDER


title: Foxo1(+/+)/VEGF(+)-2

value: wild-type

value: VEGF treated

value: ES cell-derived endothelial cells


title: 00-090G2_LUNG CRPC metastasis [CGH]

description:
00-090G2 CRPC lung metastasis
00-090G2_LUNG

value: A pool of reference normal male DNA (Promega, Part No. G1471)

value: CRPC metastasis

value: LUNG

value: L=LHRH agonist; O=orchiectomy:L


title: 00-140G1_LIVER CRPC metastasis [CGH]

description:
00-140G1 CRPC liver metastasis
00-140G1_LIVER

value: LIVER


title: 00-140J9_LN CRPC metastasis [CGH]

description:
00-140J9 CRPC lymph node metastasis
00-140J9_LN

value: LN


title: Foxo1(+/+)/VEGF(+)-3


title: 00-090B2_LN CRPC metastasis [CGH]

description:
00-090B2 CRPC lymph node metastasis
00-090B2_LN

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,C,E


title: 00-140FF_BONE CRPC metastasis [CGH]

description:
00-140FF CRPC bone metastasis
00-140FF_BONE

value: BONE

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:B,K

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M


title: 00-029J2_LN CRPC metastasis [CGH]

description:
00-029J2 CRPC lymph node metastasis
00-029J2_LN

value: male

value: L=LHRH agonist; O=orchiectomy:O

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:N


title: 00-140H1_LUNG CRPC metastasis

description: 00-140H1 CRPC lung metastasis

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

value: Samples were obtained from patients who died of metastatic CRPC and who signed written informed consent for a rapid autopsy performed within 6 hours of death, under the aegis of the Prostate Cancer Donor Program at the University of Washington. The Institutional Review Boards of the University of Washington and of the Fred Hutchinson Cancer Research Center approved this study. Visceral metastases were identified at the gross level, bone biopsies were obtained according to a template from 20 different sites and metastases identified at a histological level.


title: Subject6_Day_8

tag: reference composition

value: 10 human cell lines

value: Whole Blood

value: Male

tag: ethnicity (c= caucasian, h=hispanic, aa=african american, a=asian)

value: C/H

tag: age

tag: response

value: Non-responder

value: Acetaminophen

value: Day 8


title: 01-087QQ1_BONE CRPC metastasis [CGH]

description:
01-087QQ1 CRPC bone metastasis
01-087QQ1_BONE

tag: tissue

value: A pool of reference normal male DNA (Promega, Part No. G1471)

tag: patient

tag: tumor type

value: CRPC metastasis

value: L=LHRH agonist; O=orchiectomy:L

value: 5ARI=5-alphareductase antagonist; A=abiraterone; B=bicalutamide; D=DES; F=flutamide; K=ketoconazole; Ni=nilutamide; N=none:F,B,K,D

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:D,M


title: 00-010K_LIVER CRPC metastasis [CGH]

description:
00-010K CRPC liver metastasis
00-010K_LIVER

value: male

tag: tumor site

value: LIVER

tag: age (yrs)

tag: psa ng/ml

value: D=docetaxel; C=carboplatin; E=estramustine; M=mitoxantrone; N=none:M