title: patient L90, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L90N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


title: Tumor 43

status: Public on Apr 01 2013

type: RNA

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Hybridization protocol Samples were hybidized onto beadchips according to microRNA expression profiling protocol from Illumina.

scan_protocol: Scan protocol Beadchips were scanned using Illumina iScan, standard protocol.

data_processing: The data were normalized using quantile normalization in Illumina GenomeStudio.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Tumor

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

extract_protocol: Total RNA was isolated from cell samples using TriZol reagent according to the manufacturer's protocol.

tag: tissue

value: Human Liver

tag: disease status

value: Tumor

tag: tumor stage


title: Validation patient #20 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

type: other

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

country: USA

institute: NCI

description: Sample name: 157

hyb_protocol: Arrays were blocked with BSA overnight, and serum (diluted 1:50) was incubated on the array for 3 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound Cy3 conjugated secondary antibody specific for human total immunoglobulin (IgM + IgG + IgA).  Signal from ch2 (635nm) was not analyzed since only one secondary antibody was used.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

data_processing:
First, median pixel intensity of each feature was background subtracted.  Second, signals for features that were saturated at the high photomultipler tube (PMT) setting were calculated by proportionally scaling the value from the low PMT setting according to a correction factor, which was calculated based on mid-intensity signals measured at the high and low PMT settings.  To account for slide-to-slide variations in array processing, microarray data were normalized by median centering based on a reference serum sample analyzed on each slide.  Additionally, a minimum signal of 150 was set as the floor.  Since array features were printed in duplicate and all samples were analyzed on two slides, pre-processing averaged normalized data from 4 technical replicates.  Final data are reported on a log 2 scale.
The VALUEs represent the normalized ch1 signal for experiments that analyzed total Ig and IgG.  For the IgM experiments, the ch2 signal was normalized to determine levels of IgM antibodies.

molecule: other

source_name: Serum

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a Cy3 conjugated anti-human total immunoglobulin (IgM+IgG+IgA) (Jackson 109-165-064).

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

value: Vaccine

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Tumor 44


title: patient L104, noncancerous liver tissue

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
Gene expression profile of surgically resected material.
L104N

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instructions using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data was normalized by robust multichip analysis (RMA) using R/Bioconductor.

source_name: surgically resected material, noncancerous liver

label_protocol: cRNA was prepared using the One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted from tissue specimens using the RNeasy kit (Qiagen, Hilden, Germany). Integrity of the obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).

treatment_protocol: Gene expression profiles of noncancerous liver tissues from 49 HCC patients were used.

tag: disease state

value: hepatocellular carcinoma (HCC)

value: noncancerous liver

tag: multicentric occurrence-free survival (days)

tag: event

value: no multicentric occurrence

tag: patient id


title: Validation patient #21 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 162

tag: halabi predicted survival (months)

value: Control


title: patient L84, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L84N

tag: tissue


title: Validation patient #18 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 147

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)


title: Validation patient #17 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 136

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Tumor 41

tag: disease status

tag: tumor stage


title: Tumor 40


title: Validation patient #16 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 127

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #19 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 152

tag: on-study psa

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient L96, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L96N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

value: multicentric occurrence

tag: patient id


title: Validation patient #22 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 170

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)


title: patient L77, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L77N

tag: tissue


title: patient L78, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L78N


title: Tumor 42

tag: disease status

tag: tumor stage


title: patient L64, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L64N


title: patient L80, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L80N


title: Validation patient #15 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 117

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


title: patient L70, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L70N


title: patient L57, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L57N


title: Tumor 38


title: Validation patient #13 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 101

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment


title: patient L76, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L76N

tag: disease state

tag: multicentric occurrence-free survival (days)


title: patient L47, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L47N

tag: event

tag: patient id


title: Tumor 36


title: Tumor 37


title: Validation patient #11 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 82

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Tumor 35

tag: tissue

tag: disease status

tag: tumor stage


title: patient L49, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L49N


title: Tumor 39


title: Validation patient #14 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 109

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #9 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 65

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Tumor 33


title: Tumor 34


title: Tumor 32


title: Validation patient #12 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 89

tag: treatment


title: patient L53, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L53N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


title: Validation patient #7 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 41

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient L31, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L31N

tag: tissue


title: patient L18, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L18N


title: Tumor 29

tag: disease status

tag: tumor stage


title: patient L42, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L42N


title: Validation patient #5 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 29

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #4 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 21

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Validation patient #6 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 33

tag: treatment


title: Tumor 30


title: Validation patient #3 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 13


title: patient L45, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L45N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


title: patient LC07, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
LC07N


title: Tumor 23


title: siRNA#2, replica 4

city: Taipei

first: Aliaksandr

middle: A

last: Yarmishyn

address: No. 201, Section 2, Shipai Road, Beitou District

institute: Taipei Veterans General Hospital

description: SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized using GenomeStudio software (v.2011.1.9.0).

source_name: SH-SY5Y cells_siRNA#2 targeting lncRNA BEHOT

label_protocol: biotin labeled cRNA was prepared using TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: SH-SY5Y cells were maintained in Ham’s F12 DMEM supplemented with 10% FBS in a humidified incubator at 370C with 5% CO2.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: siRNA duplexes and control ON-TARGETplus non-targeting pool (Dharmacon) were introduced into SH-SY5Y cells using Amaxa Nucleofector System (Lonza AG). Cells were plated onto laminin coated dishes and 24 hours later were induced to differentiate with 10 µM RA. 48 hours later cells were harvested for RNA analysis.

tag: cell line

tag: cell type

value: neuroblastoma cells

tag: transfected with

value: siRNAs targeting lncRNA BEHOT

tag: time point

value: 48hrs after transfection


title: Tumor 24

tag: tissue

tag: disease status

tag: tumor stage


title: Tumor 22


title: Validation patient #1 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 1

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #2 | Control Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 9

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment


title: patient L08, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L08N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


title: patient L10, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L10N

tag: tissue


title: siRNA#2, replica 3

description: SAMPLE 11

tag: cell line

tag: cell type

tag: transfected with

tag: time point


title: siRNA#2, replica 1

description: SAMPLE 9


title: Tumor 21

tag: disease status

tag: tumor stage


title: siRNA#2, replica 2

description: SAMPLE 10


title: siRNA#1, replica 4

description: SAMPLE 8

source_name: SH-SY5Y cells_siRNA#1 targeting lncRNA BEHOT


title: siRNA#1, replica 3

description: SAMPLE 7


title: siRNA#1, replica 1

description: SAMPLE 5


title: Validation patient #115 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 842

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 3 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: Slides were scanned with a Genepix 4000A fluorescence scanner at two gain settings (typically 430 and 520) in order to increase dynamic range.  Signal from ch1 (532 nm) was analyzed to determine the level of bound DyLight 549 conjugated secondary antibody specific for human IgG.  Signal from ch2 (635nm) was analyzed to determine the level of bound DyLight 649 secondary antibody specific for human IgM.  Scanned images were analyzed with Genepix Pro (v6.0) to determine the fluorescence and background signal for each array component.

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti-human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgG

label: DyLight 649

value: IgM


title: Tumor 19


title: Validation patient #10 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 74

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #116 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 847


title: Tumor 17

tag: tissue


title: Tumor 18

tag: disease status


title: siRNA#1, replica 2

description: SAMPLE 6

tag: cell line

tag: cell type

tag: transfected with

tag: time point


title: Validation patient #114 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 837

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: Validation patient #117 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 852

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Tumor 16

tag: tumor stage


title: Validation patient #113 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 830

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment


title: Tumor 20

tag: tissue

tag: disease status


title: Validation patient #112 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 826


title: Tumor 15


title: Tumor 14


title: Control, replica 2

description: SAMPLE 2

source_name: SH-SY5Y cells_non-targeting siRNA control

tag: cell line

tag: cell type

tag: transfected with

value: non-targeting siRNA control

tag: time point


title: Control, replica 4

description: SAMPLE 4


title: Control, replica 3

description: SAMPLE 3


title: Validation patient #111 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 822

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: Control, replica 1

description: SAMPLE 1


title: Tumor 13

value: Human Liver


title: Validation patient #110 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 816

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #109 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 810

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #107 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 798

tag: on-study psa

tag: treatment


title: Validation patient #108 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 802


title: Tumor 11

tag: tissue

tag: disease status

value: Tumor

tag: tumor stage


title: Tumor 12


title: Tumor 10


title: 48 hr biofilm

city: Baltimore

first: NIKHIL

last: KUMAR

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

hyb_protocol: Slides were prehybridized in a 50 ml solution of 5X SSC, 0.1% SDS and 1% BSA for at least one hour at 42C, washed 10X in water and once in isopropanol, then dried by brief centrifugation. Labeled probes were re-suspended in hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 1 uL 0.1M DTT, 0.6 ug/uL salmon sperm DNA) and hybridized to the microarray slides in a 42C water bath for 16-20 h. Slides were washed twice in a low stringency buffer (2X SSC, 0.1% SDS) at 55C for 5 min, twice in a medium stringency buffer (0.1X SSC, 0.1% SDS) at room temperature for 5 min, twice in a high stringency buffer (0.1X SSC) at room temperature for 5 min, and finally in water for 2 min, and then dried by brief centrifugation.

scan_protocol: Scanned on GenePix 4000B.

data_processing: Iterative log-mean normalization and filtering using MIDAS.

label: Cy3, Cy5

organism: Streptococcus pneumoniae

source_name: planktonic control

label_protocol: Aliquots of 2 ug of the total RNAs were reverse transcribed into single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen), random hexamers (Invitrogen), 1X first strand buffer, 10 mM dithiothreitol (DTT), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP and 0.2 mM of aminoallyl-modified nucleotide (Invitrogen). The mixture was incubated overnight at 42C. Amine-modified cDNA was purified using QIAquick PCR purification kit (Qiagen), followed by chemical labeling with Cy3- or Cy5-NHS-ester fluorescent dyes (GE Healthcare).

growth_protocol: Bacterial strains were grown on tryptic soy blood agar plates at 37C in 5% CO2. For planktonic growth, Todd Hewitt Broth (THB) was inoculated with overnight plate cultures and grown to mid-logarithmic phase (OD620 = 0.5; ~1.0 X 108 CFU/mL) using normal culture conditions. Mature S. pneumoniae biofilms were grown under once-through flow conditions using a once-through biofilm line reactor, as previously described.

extract_protocol: Total RNA extracted using Rneasy Mini Kit, following manufacturer's instructions, with exception to bacterial lysis.

treatment_protocol: S. pneumoniae grown under biofilm conditions for 4, 12, 24, and 48 hours were collected, immediately suspended in RNAprotect and stored at -20C.

tag: time point

value: control

tag: sample type

value: planktonic

source_name: 48 hr biofilm

value: biofilm

value: 48 hr


title: Tumor 9


title: 24 hr biofilm

source_name: 24 hr biofilm

value: 24 hr


title: 4 hr biofilm

source_name: 4 hr biofilm

value: 4 hr


title: 12 hr biofilm

source_name: 12 hr biofilm

value: 12 hr


title: Validation patient #106 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 793

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

value: PROSTVAC

value: Vaccine

value: Pre-treatment


title: Tumor 8


title: Tumor 5


title: Validation patient #104 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 781

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: Validation patient #105 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 787

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #103 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 776

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Tumor 7


title: Tumor 4


title: Validation patient #101 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 762

value: Control

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Tumor 3


title: Tumor 1


title: Validation patient #99 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 745

tag: gleason score

tag: on-study psa


title: Validation patient #97 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 729

tag: treatment


title: Tumor 6

tag: tissue

tag: disease status


title: Validation patient #98 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 738


title: Validation patient #93 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 696


title: Validation patient #94 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 704


title: Validation patient #92 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 678


title: Validation patient #100 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 752


title: Validation patient #91 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 670


title: Validation patient #102 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 769


title: Tumor 2

data_processing: The data were normalised using quantile normalization in Illumina GenomeStudio.

tag: tumor stage


title: Validation patient #90 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 664


title: Validation patient #89 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 656


title: Validation patient #95 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 709


title: JJN3 PLKO hypoxia

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: JJN3 transfected with PLKO, hypoxic conditions.

hyb_protocol: Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0 Arrays. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The raw intensity signals were extracted from CEL files and normalized using the RMA package for Bioconductor and custom GeneAnnot-based Chip Definition Files version 2.2.0 in R software.

source_name: JJN3, control, hypoxia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Human myeloma cell line JJN3 was maintained in RPMI medium at 10% of fetal bovine serum (FBS) with 2nM of glutamine and antibiotics.

extract_protocol: Extraction of total RNA was performed using the RNeasy Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Anti-HIF-1 Lentivirus shRNA pool (Sigma Aldrich, Milan, Italy) was used for HIF-1 stable knock-out in JJN3, whereas the pLKO.1 lentiviral vector was the empty control vector. JJN3 permanent transfected with pLKO.1 or anti-HIF-1 shRNA pool were incubated in the presence or absence of hypoxic condition (1%O2, 5%CO2) or treated with the hypoxic mimetic drug CoCl2 at 100 _M or vehicle for 12-24 hours.

tag: cell line

tag: cell type

value: myeloma cells

tag: shRNA

value: empty pLKO vector

tag: condition

value: hypoxic


title: Validation patient #88 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 648

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

value: IgG

value: IgM


title: Validation patient #87 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 640

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: JJN3 anti-HIF normoxia

description: JJN3 treated with anti-HIF, normoxic conditions.

source_name: JJN3, anti-HIF-1, normoxia

value: normoxic


title: JJN3 PLKO normoxia

description: JJN3 transfected with PLKO, normoxic conditions.

source_name: JJN3, control, normoxia


title: JJN3 anti-HIF hypoxia

description: JJN3 treated with anti-HIF, hypoxic conditions.

source_name: JJN3, anti-HIF-1, hypoxia


title: Needle insertion 102HPI rep2

city: Leiden

first: Wouter

last: Veneman

state: Zuid-Holland

address: Einsteinweg 55

department: Institute Biology Leiden

country: Netherlands

institute: Leiden University

description:
252823310109_3u20b_S01_GE2_107_Sep09_1_2
Biological replicate 2 of 2

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28.5C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80C. Embryos were homogenized in 1 ml of TRIZOL Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37C with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were micro-injected into the yolk (2hpf) with (1) 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), (2)  mock-injected with PVP as a control, (3) Needle insertion as control, (4) Non-injected as a control. At 8 hpf (6 h post infection), 32 hpf (30 h post infection), 56 hpf (54 h post infection),  80 hpf (78 h post infection),  104 hpf (102 h post infection) or  128 hpf (126 h post infection) twenty embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

tag: reference

value: The CR (common reference) was a mixture of all RNA samples from this microarray study

tag: genotype/variation

value: Wildtype

tag: treatment group

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 102h post injection


title: PVP injection 102HPI rep2

description:
252823310099_3u20b_S01_GE2_107_Sep09_1_2
Biological replicate 2 of 2

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 102h post injection


title: Non-injected 102HPI rep2

description:
252823310101_3u20b_S01_GE2_107_Sep09_1_1
Biological replicate 2 of 2

value: non-injected control; RNA isolated at 104h post fertilization (=102hpi timepoint)


title: Validation patient #86 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 636

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment


title: Non-injected 78HPI

description:
252823310107_3u20b_S01_GE2_107_Sep09_1_4
Single sample

value: non-injected control; RNA isolated at 80h post fertilization (=78hpi timepoint)


title: Non-injected 102HPI rep1

description:
252823310105_3u20b_S01_GE2_107_Sep09_1_3
Biological replicate 1 of 2


title: Non-injected 126HPI

description:
252823310104_3u20b_S01_GE2_107_Sep09_1_4
Single sample

value: non-injected control; RNA isolated at 128h post fertilization (=126hpi timepoint)


title: Tumor 31

tag: tissue

value: Human Liver

tag: disease status

value: Tumor

tag: tumor stage


title: Validation patient #8 | Vaccine Arm | Pre-treatment [Total Ig 1:50]

description: Sample name: 46

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

value: PROSTVAC

value: Vaccine

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Validation patient #85 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 628

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint


title: Validation patient #83 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 612

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #84 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 620

value: Control

tag: post-vaccination igg titer for fowlpox


title: S. epi mcherry O-47 102HPI rep2

description:
252823310108_3u20b_S01_GE2_107_Sep09_1_1
Biological replicate 2 of 2

tag: reference

tag: genotype/variation

tag: treatment group

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 102h post injection


title: Validation patient #82 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 608

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

value: IgG

value: IgM


title: Validation patient #81 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 600

tag: halabi predicted survival (months)


title: Non-injected 54HPI

description:
252823310108_3u20b_S01_GE2_107_Sep09_1_2
Single sample

value: The CR (common reference) was a mixture of all RNA samples from this microarray study

value: non-injected control; RNA isolated at 56h post fertilization (=54hpi timepoint)


title: Patient A00588 (repl 4)

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: The microarray slides were pre-hybridized for 2 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. Hybridization was done with an Advalytix SlideBooster. The slides were washed twice with SSC-0.2% SDS, once with 0.1X SSC-0.2% SDS and 3 times with 0.1X SSC. A final wash with isopropanol was performed and slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

source_name: Tumor Vasculature

label_protocol: The generated antisense (a)RNA was amplified and labeled with either Cy3 or Cy5 monofunctional dye (Amersham Pharmacia Biotech, Piscataway, NJ, USA) using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Austin, TX, USA) according to he manufacturer’s instructions. RNA purity (A260/280 ratio) and Amino Allyl incorporation levels (A289/260 ratio) were determined using the Bio-analyzer (Agilent Technologies, Mississauga, ON, Canada). In general, good quality aRNA appeared as a broad peak, ranging from 200 to 2000 bases in length.

extract_protocol:
Ten (10) frozen human tumor and the matching adjacent non-tumor tissues from patients diagnosed with invasive ductal carcinoma were obtained from the Ontario Tumor Bank (OTB; Toronto, ON, Canada). Specimens were selected using the following criteria: 1) gender (female), 2) histology (infiltrating ductal carcinoma, IDC), 3) availability of normal adjacent breast tissue, 4) high degree of vascularity, 5) availability of clinical patient data, and 6) patient age (between 35 and 65 years). Frozen tissue samples were embedded in OCT, cut (at -21°C) into 8 µm serial sections using a cryotome (Leica CM1900, Richmond Hill, ON, Canada), mounted on Superfrost Plus microscope slides (Fisher Scientific, Ottawa, ON, Canada), and kept at -80°C until used. Blood vessels in the normal and tumor tissue sections were stained with fluorescein-labeled Ulex Europeaus Agglutinin I lectin (UEA1; Vector Laboratories, Burlington, ON, Canada) as described previously [48]. UEA1-labeled blood vessels were dissected using a PixCell II-LCM instrument (Molecular Devices, Sunnyvale, CA, USA) with a 7.5 μm laser spot size, 0.75-0.90 ms laser pulse, and a 25-30 mV laser beam power. Approximately 500-700 laser shots (microvessel cells) were captured per high-sensitivity (HS) cap (CapSure HS LCM Caps; Molecular Devices, Sunnyvale, CA, USA).
Two to three caps containing a total of 1,000-1,500 shots were collected per tissue sample, lysed in 100 μL of RNA lysis buffer containing 0.7 μL of β-mercaptoethanol (Stratagene, La Jolla, CA, USA) and used for RNA isolation, amplification, and labeling prior to microarray analyses. Total endothelial RNA was extracted (PicoPure RNA Isolation Kit; Molecular Devices, Sunnyvale, CA, USA) according to the manufacturer’s instructions, and further amplified using the HS RNA Amplification Kit (Arcturus, Mountain View, CA, USA) according to the manufacturer’s instructions.

tag: tissue

value: Tumor Vasculature

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

value: Not fully determined

tag: tmn pathological staging

value: T3 | N0 (ITC) | MX

source_name: Normal Microvasculature

value: Normal Microvasculature


title: Patient A00588 (repl 3)


title: Patient A00588 (repl 2)


title: Patient A00588 (repl 1)


title: Validation patient #79 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 584

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Patient A00554 (repl 1)

value: T2 | N2, NOS | MX


title: Validation patient #78 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 577

tag: post-vaccination igg titer for fowlpox

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Patient A00554 (repl 2)


title: Validation patient #77 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 571

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #80 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 592

tag: on-study psa

tag: treatment


title: Needle insertion 78HPI

description:
252823310106_3u20b_S01_GE2_107_Sep09_1_4
Single sample

tag: reference

tag: genotype/variation

value: Wildtype

tag: treatment group

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 78h post injection


title: Needle insertion 102HPI rep1

description:
252823310103_3u20b_S01_GE2_107_Sep09_1_4
Biological replicate 1 of 2

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 102h post injection


title: Validation patient #76 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 563

tag: halabi predicted survival (months)

value: PROSTVAC

value: Vaccine


title: Non-injected 6HPI

description:
252823310100_3u20b_S01_GE2_107_Sep09_1_1
Single sample

value: non-injected control; RNA isolated at 8h post fertilization (=6hpi timepoint)


title: Needle insertion 126HPI

description:
252823310102_3u20b_S01_GE2_107_Sep09_1_1
Single sample

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 126h post injection


title: Needle insertion 6HPI

description:
252823310099_3u20b_S01_GE2_107_Sep09_1_3
Single sample

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 6h post injection


title: Needle insertion 30HPI

description:
252823310107_3u20b_S01_GE2_107_Sep09_1_1
Single sample

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 30h post injection


title: Patient A00342 (repl 5)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging

value: T2 | N1, NOS | MX


title: Patient A00342 (repl 4)


title: PVP injection 102HPI rep1

description:
252823310104_3u20b_S01_GE2_107_Sep09_1_2
Biological replicate 1 of 2

value: The CR (common reference) was a mixture of all RNA samples from this microarray study

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 102h post injection


title: Patient A00342 (repl 3)

value: Tumor Vasculature


title: Validation patient #74 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 546

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Pre-treatment

value: IgG

value: IgM


title: PVP injection 126HPI

description:
252823310105_3u20b_S01_GE2_107_Sep09_1_1
Single sample

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 126h post injection


title: Non-injected 30HPI

description:
252823310101_3u20b_S01_GE2_107_Sep09_1_4
Single sample

value: Wildtype

value: non-injected control; RNA isolated at 32h post fertilization (=30hpi timepoint)


title: Validation patient #75 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 554

value: Control

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Patient A00342 (repl 1)

value: Normal Microvasculature


title: Patient A00342 (repl 6)


title: PVP injection 78HPI

description:
252823310101_3u20b_S01_GE2_107_Sep09_1_3
Single sample

tag: reference

tag: genotype/variation

tag: treatment group

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 78h post injection


title: Validation patient #73 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 537

tag: halabi predicted survival (months)

tag: on-study psa

tag: treatment


title: Validation patient #71 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 518

value: PROSTVAC

value: Vaccine


title: Patient A00342 (repl 2)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Needle insertion 54HPI

description:
252823310109_3u20b_S01_GE2_107_Sep09_1_4
Single sample

value: with needle insertion into the yolk at 2 hpf; RNA isolated at 54h post injection


title: PVP injection 54HPI

description:
252823310100_3u20b_S01_GE2_107_Sep09_1_2
Single sample

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 54h post injection


title: Validation patient #72 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 525

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Patient A00319 (repl 6)

value: T2 | N1, NOS | M1


title: Patient A00319 (repl 5)


title: Patient A00319 (repl 4)


title: Validation patient #70 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 510

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: PVP injection 6HPI

description:
252823310108_3u20b_S01_GE2_107_Sep09_1_3
Single sample

tag: reference

value: The CR (common reference) was a mixture of all RNA samples from this microarray study

tag: genotype/variation

tag: treatment group

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 6h post injection


title: Patient A00319 (repl 2)

tag: tissue

tag: patient age

value: Tumor Vasculature


title: Validation patient #69 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 498

tag: halabi predicted survival (months)

tag: on-study psa

tag: treatment

value: Pre-treatment


title: Patient A00319 (repl 3)

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Validation patient #68 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 489

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: IgG


title: Patient A00319 (repl 1)


title: Validation patient #67 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 482

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgM


title: Validation patient #66 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 474


title: PVP injection 30HPI

description:
252823310098_3u20b_S01_GE2_107_Sep09_1_2
Single sample

tag: reference

tag: genotype/variation

tag: treatment group

value: injected with PVP into the yolk at 2 hpf; RNA isolated at 30h post injection


title: S. epi mcherry O-47 102HPI rep1

description:
252823310102_3u20b_S01_GE2_107_Sep09_1_3
Biological replicate 1 of 2

value: Wildtype

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 102h post injection


title: Validation patient #65 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 467

tag: halabi predicted survival (months)

tag: on-study psa

tag: treatment


title: S. epi mcherry O-47 126HPI

description:
252823310103_3u20b_S01_GE2_107_Sep09_1_3
Single sample

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 126h post injection


title: S. epi mcherry O-47 78HPI

description:
252823310109_3u20b_S01_GE2_107_Sep09_1_3
Single sample

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 78h post injection


title: Validation patient #64 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 459


title: Patient A00310 (repl 4)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging

value: T1c | N0, NOS | MX

value: Normal Microvasculature


title: Validation patient #61 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 439

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Vaccine


title: Validation patient #60 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 432

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: S. epi mcherry O-47 54HPI

description:
252823310106_3u20b_S01_GE2_107_Sep09_1_2
Single sample

tag: reference

tag: genotype/variation

tag: treatment group

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 54h post injection


title: S. epi mcherry O-47 30HPI

description:
252823310099_3u20b_S01_GE2_107_Sep09_1_4
Single sample

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 30h post injection


title: Validation patient #58 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 420

tag: halabi predicted survival (months)

tag: on-study psa

tag: treatment


title: Validation patient #59 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 424


title: S. epi mcherry O-47 6HPI

description:
252823310098_3u20b_S01_GE2_107_Sep09_1_3
Single sample

value: The CR (common reference) was a mixture of all RNA samples from this microarray study

value: injected with S. epidermidis into the yolk at 2 hpf; RNA isolated at 6h post injection


title: Validation patient #54 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 398

value: Control


title: Patient A00310 (repl 1)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging

value: Tumor Vasculature


title: Validation patient #57 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 412

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Pre-treatment

value: IgG


title: Validation patient #56 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 407

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgM


title: Validation patient #53 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 390

tag: halabi predicted survival (months)

tag: on-study psa


title: Patient A00289 (repl 5)

tag: tissue

value: T1c | N1, NOS | MX


title: Patient A00289 (repl 4)

tag: patient age


title: Patient A00289 (repl 6)

tag: tumor size (cm)


title: Patient A00310 (repl 2)

tag: hormonal status (er/pr/her2)


title: Patient A00278 (repl 6)

tag: tmn pathological staging

value: T2 | N0, NOS | M0


title: Patient A00289 (repl 2)


title: Patient A00289 (repl 3)


title: 14d_control_rep3

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

description: Gene expression after 14 day exposure to vehicle control (0.0014% ethanol)

hyb_protocol: 600 ng of purified Cy3-labeled cRNA was hybridized to the custom 8x15,000 G. holbrooki microarray using Gene Expression hybridization kit (Agilent, Santa Clara, USA). In brief, Cy3 was incubated with blocking agent and fragmentation buffer at 60 oC for 30 minutes. Hybridization buffer was then added to the sample and 40 μL of the sample was added to the gasket. The microarray slide was then incubated with the gasket for 17 hours at 65 C while spinning at 10 rpm. The slide was then washed and dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scannerusing one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted Processed Signal intensities.

organism: Gambusia holbrooki

source_name: 14-day exposure, control

label_protocol: For amplification and labelling, the Quick Amp Labeling kit (Agilent, Santa Clara, USA) was utilized with adjustments made for a half reaction, one color (Cy3) protocol. In brief, T7 primers were annealed to 1000 ng RNA with the addition of RNA spike-in controls (One color RNA spike-in mix; Agilent, Santa Clara, USA) and were incubated at 65 oC for 10 minutes. cDNA synthesis using MMLV-RT was conducted at 40 oC for 2 hours followed by 65 oC for 15 minutes. cDNA was reverse-transcribed into cRNA using a T7 RNA polymerase with the addition of Cy3 to the reaction for incorporation into the samples. in vitro transcription proceded at 40 oC for 2 hours. Labeled cRNA was purified using the RNeasy kit (QIAGEN, Hilden, Germany) and eluted in nuclease-free water. The cRNA concentration and specific activity (pmol Cy3 per µg cRNA) was determined using the Nanodrop (ThermoScientific, Waltham, USA).

extract_protocol: RNA was isolated from frozen liver samples using TRIzol reagent (Invitrogen, Grand Island, USA) following the manufacturer’s protocol. In brief, livers were homogenized in 1 mL TRIzol and after a 5 min incubation at room temperature, 200 µL chloroform was added and the upper aqueous layer containing the RNA was separated from the organic layer via high-speed centrifugation. The RNA was precipitated out of the aqueous layer using isopropanol and washed twice with ethanol. The quality and quantity of the RNA was determined using the Nanodrop (ThermoScientific, Waltham, USA) as well as the 2100 BioAnalyzer (Agilent, Santa Clara, USA).

treatment_protocol: G. holbrooki from laboratory stocks were transferred to aerated 7L glass tanks and exposed via semi-static renewal (60% water change daily) to either the vehicle control (ethanol, 0.0014% final concentration) or 1  μg/L of the potent androgen receptor (AR) agonist TB (17β-hydroxyestra-4,9,11-trien-3-one) (Steraloids, Newport, USA). Four tanks per treatment were utilized and two G. holbrooki were sampled from each tank in both treatment groups after 14 days of exposure. Mosquitofish were anesthetized using Tricaine-S (Western Chemical, Ferndale, USA) and sacrificed via spinal transection. Livers were removed, snap-frozen in liquid nitrogen, and stored at -80 oC until RNA isolation.

value: liver

tag: gender

value: female


title: Validation patient #52 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 386

source_name: Serum

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment


title: Patient A00278 (repl 4)


title: 14d_control_rep2


title: 14d_TB_rep4

description: Gene expression after 14 day exposure to TB (1 ug/L)

source_name: 14-day exposure, TB


title: Validation patient #51 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 380

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: 14d_TB_rep3


title: Patient A00289 (repl 1)


title: 14d_TB_rep2


title: Validation patient #50 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 375

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #49 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 372

tag: halabi predicted survival (months)

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Patient A00310 (repl 3)

tag: tissue

tag: patient age

value: T1c | N0, NOS | MX


title: 14d_TB_rep1


title: Validation patient #47 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 365

tag: on-study psa


title: 14d_control_rep1


title: White cells (RBY717) in SCD Replicate 1

city: Providence

first: Richard

middle: J

last: Bennett

state: RI

address: 171 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

description: Biological replicate 1 of 2. White cells, SCD, harvested after 12h.

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

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

data_processing: Data normalized using Goulphar. Mnorm log2 values were averaged for each spot.

organism: Candida albicans

source_name: C. albicans wildtype white a/a from SC5314

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy3 (reference) or Cy5 (experimental). Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: CAY2903 and RBY717 were grown in LP and SCD for 12 hours and in SOR for 16 hours at 25°C.  Cells spun down and flash frozen in liquid nitrogen.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

tag: strain

tag: phenotype

value: white

tag: growth conditions

value: SCD,  25°C, 12h

source_name: Universal reference

tag: sample type

value: mixture of ch1 samples including opaque and white cells in LP, SOR and SCD as reference


title: Validation patient #46 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 357

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

value: PROSTVAC

tag: treatment

value: Vaccine


title: White cells (RBY717) in SCD Replicate 2

description: Biological replicate 2 of 2. White cells, SCD, harvested after 12h.


title: Patient A00278 (repl 2)

value: Normal Microvasculature

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Validation patient #45 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 342

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #44 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 334

tag: halabi predicted survival (months)

tag: on-study psa

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Patient A00026 (repl 6)

tag: tissue

tag: patient age

value: T2 | N1 mic | M0


title: Patient A00278 (repl 1)


title: Patient A00278 (repl 3)


title: Opaque cells (CAY2903) in SCD Replicate 2

description: Biological replicate 2 of 2. Opaque cells, SCD, harvested after 12h.

source_name: C. albicans opaque cells with Act1-Wor1 overexpression a/a

tag: strain

tag: phenotype

value: opaque

tag: growth conditions

tag: sample type


title: Validation patient #43 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 326

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment


title: Validation patient #48 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 368

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Patient A00026 (repl 5)

value: Tumor Vasculature

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Validation patient #41 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 298

tag: halabi predicted survival (months)

value: Control

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: timepoint

value: Pre-treatment


title: Validation patient #42 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 312

tag: isotype-specific, secondary antibody [fluorescently labeled]

value: IgG

value: IgM


title: Opaque cells (CAY2903) in SCD Replicate 1

description: Biological replicate 1 of 2. Opaque cells, SCD, harvested after 12h.

tag: strain

tag: phenotype

tag: growth conditions

tag: sample type


title: White cells (RBY717) in SOR Replicate 1

description: Biological replicate 1 of 2. White cells, SOR, harvested after 16h.

value: Sorbitol,  25°C, 16h


title: Validation patient #40 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 287

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: treatment


title: Opaque cells (CAY2903) in SOR Replicate 4

description: Biological replicate 4 of 4. Opaque cells, SOR, harvested after 16h.


title: Validation patient #38 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 276

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Opaque cells (CAY2903) in SOR Replicate 3

description: Biological replicate 3 of 4. Opaque cells, SOR, harvested after 16h.


title: White cells (RBY717) in SOR Replicate 2

description: Biological replicate 2 of 2. White cells, SOR, harvested after 16h.


title: Validation patient #36 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 267

tag: halabi predicted survival (months)


title: Patient A00026 (repl 3)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Opaque cells (CAY2903) in SOR Replicate 1

description: Biological replicate 1 of 4. Opaque cells, SOR, harvested after 16h.


title: White cells (RBY717) in LP Replicate 2

description: Biological replicate 2 of 2. White cells, LP, harvested after 12h.

value: Low phospahte, 25°C, 12h


title: Validation patient #35 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 257

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: White cells (RBY717) in LP Replicate 1

description: Biological replicate 1 of 2. White cells, LP, harvested after 12h.

tag: strain

tag: phenotype

tag: growth conditions

tag: sample type


title: Patient A00026 (repl 4)


title: Opaque cells (CAY2903) in LP Replicate 4

description: Biological replicate 4 of 4. Opaque cells, LP, harvested after 12h.


title: 14d_control_rep4

value: liver

tag: gender

value: female


title: Validation patient #34 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 252

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: treatment


title: Validation patient #33 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 247

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Opaque cells (CAY2903) in SOR Replicate 2

description: Biological replicate 2 of 4. Opaque cells, SOR, harvested after 16h.


title: Validation patient #32 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 240

tag: gleason score

tag: on-study psa


title: Validation patient #39 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 279

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #31 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 233


title: Validation patient #37 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 271


title: Opaque cells (CAY2903) in LP Replicate 1

description: Biological replicate 1 of 4. Opaque cells, LP, harvested after 12h.

tag: strain

tag: phenotype


title: Validation patient #27 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 202


title: Validation patient #28 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 210


title: Opaque cells (CAY2903) in LP Replicate 2

description: Biological replicate 2 of 4. Opaque cells, LP, harvested after 12h.

tag: growth conditions

tag: sample type


title: Opaque cells (CAY2903) in LP Replicate 3

description: Biological replicate 3 of 4. Opaque cells, LP, harvested after 12h.


title: Validation patient #29 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 218

tag: halabi predicted survival (months)


title: Patient A00026 (repl 1)

tag: tissue

tag: patient age

tag: tumor size (cm)

tag: hormonal status (er/pr/her2)

tag: tmn pathological staging


title: Validation patient #26 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 197

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: treatment


title: Patient A00278 (repl 5)

value: T2 | N0, NOS | M0


title: Patient A00026 (repl 2)


title: Validation patient #24 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 184

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #22 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 170

tag: halabi predicted survival (months)


title: Validation patient #23 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 177


title: Validation patient #30 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 221


title: Validation patient #18 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 147


title: Validation patient #14 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 109


title: Validation patient #15 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 117


title: Validation patient #16 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 127


title: Validation patient #13 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 101


title: Validation patient #12 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 89


title: Validation patient #20 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 157


title: Validation patient #17 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 136


title: Validation patient #9 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 65


title: Validation patient #11 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 82


title: Validation patient #8 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 46


title: Validation patient #10 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 74


title: Validation patient #25 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 192


title: Validation patient #7 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 41


title: Validation patient #5 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 29


title: Validation patient #1 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 1


title: Validation patient #6 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 33


title: Validation patient #4 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 21


title: Validation patient #19 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 152


title: Validation patient #21 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 162


title: Validation patient #2 | Control Arm | Pre-treatment [IgM 1:50]

description: Sample name: 9


title: Validation patient #3 | Vaccine Arm | Pre-treatment [IgM 1:50]

description: Sample name: 13


title: Validation patient #116 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 847

label: DyLight 549

label_protocol: After serum was incubated on the array, bound anti-glycan antibodies were labeled for 2 hours with a combination of DyLight549 conjugated anti human IgG (Jackson 109-505-008) and DyLight 649 conjugated anti-human IgM  (Jackson Immuno, 109-495-043).


title: Validation patient #114 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 837


title: Validation patient #115 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 842


title: Validation patient #112 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 826


title: Validation patient #113 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 830


title: Validation patient #117 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 852


title: Validation patient #110 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 816


title: Validation patient #111 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 822


title: Validation patient #108 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 802


title: Validation patient #107 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 798


title: Validation patient #109 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 810


title: Training patient #19 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Z1

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:200) was incubated on the array for 3 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

treatment_protocol: Diluted 1:200

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

value: Pre-vaccination

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Training patient #13 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Y1

tag: treatment


title: Training patient #10 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: X1

tag: post-vaccination igg titer for fowlpox


title: Training patient #7 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: W1

tag: age at enrollment (years)


title: Training patient #4 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: V1


title: Validation patient #104 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 781

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #102 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 769

tag: halabi predicted survival (months)

tag: on-study psa

value: Vaccine

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #25 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: U2

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #105 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 787

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: treatment


title: Training patient #22 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: T2

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #101 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 762

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #15 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: R2

tag: halabi predicted survival (months)

tag: on-study psa

tag: gleason #

tag: ellispot

tag: timepoint


title: Training patient #9 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Q2

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #106 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 793

tag: age at enrollment (years)

tag: treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #99 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 745

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm


title: Validation patient #98 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 738

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #100 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 752

tag: halabi predicted survival (months)

tag: on-study psa


title: Training patient #1 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: O2

tag: gleason #

tag: ellispot

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #97 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 729

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Validation patient #103 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 776

tag: treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #94 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 704

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)


title: Validation patient #93 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 696

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #95 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 709

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #32 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: N1

tag: halabi predicted survival (months)

tag: on-study psa

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #21 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: M1

tag: gleason #

tag: ellispot

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #92 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 678

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #16 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: K1

tag: halabi predicted survival (months)

tag: on-study psa


title: Validation patient #90 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 664

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #91 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 670


title: Training patient #31 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: H1

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #28 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: G1

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #23 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: F1

tag: age at enrollment (years)

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Validation patient #88 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 648

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: on-study psa

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #8 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: P2

tag: gleason #

tag: ellispot

tag: tregs


title: Validation patient #87 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 640

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #89 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 656

tag: timepoint


title: Validation patient #86 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 636


title: Training patient #20 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: E1

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #30 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Ee1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #27 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Dd1

tag: on-study psa

tag: gleason #


title: Validation patient #85 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 628

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #14 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: D1

tag: ellispot

tag: tregs

tag: timepoint


title: Validation patient #84 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 620

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #12 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: C1

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #26 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Bb1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: gleason #

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Validation patient #82 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 608

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #29 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Cc1

tag: ellispot

tag: tregs

tag: timepoint


title: Training patient #5 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: B1

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #24 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: Aa1

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #2 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: I1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa


title: Validation patient #81 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 600

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: treatment


title: Validation patient #80 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 592

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #79 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 584

tag: timepoint


title: Validation patient #78 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 577


title: Validation patient #77 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 571


title: Training patient #19 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Z1

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #76 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 563

tag: halabi predicted survival (months)

tag: age at enrollment (years)

tag: on-study psa


title: Validation patient #83 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 612

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Training patient #13 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Y1

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #74 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 546

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #4 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: V1

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #10 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: X1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: post-vaccination igg titer for fowlpox


title: Training patient #25 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: U2

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #22 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: T2


title: Training patient #7 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: W1


title: Training patient #15 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: R2


title: Validation patient #73 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 537

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #72 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 525

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #71 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 518


title: Validation patient #69 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 498


title: Validation patient #68 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 489


title: Training patient #9 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Q2

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Training patient #8 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: P2

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: post-vaccination igg titer for fowlpox


title: Validation patient #67 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 482

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: treatment


title: Validation patient #70 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 510

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: timepoint

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #66 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 474


title: Training patient #21 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: M1

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #1 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: O2

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #65 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 467

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #3 | Vaccine Arm | Day 0 [Total Ig 1:200]

description: Sample name: A1

tag: gleason #

tag: ellispot

tag: timepoint


title: Training patient #16 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: K1

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)


title: Validation patient #75 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 554

tag: halabi predicted survival (months)

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #31 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: H1

tag: on-study psa

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #61 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 439

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #2 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: I1

tag: gleason #

tag: ellispot

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: timepoint


title: Training patient #28 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: G1

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa


title: Validation patient #60 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 432

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #23 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: F1

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #20 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: E1

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #30 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Ee1

tag: gleason #

tag: ellispot


title: Validation patient #59 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 424

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #57 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 412

tag: halabi predicted survival (months)

tag: age at enrollment (years)

tag: timepoint


title: Validation patient #56 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 407

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: on-study psa


title: Validation patient #58 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 420

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #27 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Dd1

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Training patient #32 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: N1

tag: gleason #

tag: ellispot

tag: post-vaccination igg titer for fowlpox

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #54 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 398

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: age at enrollment (years)


title: Training patient #14 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: D1

tag: on-study psa

tag: tregs

tag: timepoint


title: Training patient #29 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Cc1

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #53 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 390

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #64 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 459

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #5 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: B1

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #12 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: C1

tag: age at enrollment (years)

tag: on-study psa


title: Validation patient #52 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 386

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: timepoint


title: Validation patient #50 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 375

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Training patient #26 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Bb1

tag: tregs

tag: survival status at last follow-up (1 = alive, 0 = deceased)

tag: overall survival (mos)

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #51 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 380

tag: halabi predicted survival (months)

tag: treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Training patient #24 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: Aa1

tag: age at enrollment (years)

tag: gleason #

tag: ellispot

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Training patient #3 | Vaccine Arm | Day 0 [Total Ig 1:50]

description: Sample name: A1

tag: on-study psa

tag: timepoint


title: Validation patient #48 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 368

tag: post-vaccination survival (months)

tag: survival status at last follow-up (1 = alive, 0 = dead)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #49 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 372

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox


title: Validation patient #47 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 365

tag: treatment

tag: isotype-specific, secondary antibody [fluorescently labeled]


title: Validation patient #46 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 357

tag: age at enrollment (years)


title: Validation patient #45 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 342


title: Validation patient #44 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 334


title: Validation patient #43 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 326


title: Validation patient #42 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 312


title: Validation patient #40 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 287


title: Validation patient #41 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 298


title: Validation patient #38 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 276


title: Validation patient #35 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 257


title: Validation patient #37 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 271


title: Validation patient #36 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 267


title: Validation patient #34 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 252


title: Validation patient #33 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 247


title: Validation patient #31 | Vaccine Arm | Pre-treatment [IgG 1:50]

description: Sample name: 233


title: Validation patient #30 | Control Arm | Pre-treatment [IgG 1:50]

description: Sample name: 221