title: 24_M4455_0_High

description:
R M4455 N=3 High
chip ID: 451215
_24_Cy3
PM

source_name: R M4455 N=3 High


title: 15 m. endometriosis_2

status: Public on Aug 27 2015

type: RNA

city: Basel

first: Damian

last: Roqueiro

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description: unique sample, no replicate

hyb_protocol: Hybridized to Affymetrix Human Genome U133 Plus 2.0 Arrays, according to Affymetrix protocol

scan_protocol: Used an HR3000 scanner. Data extraction was performed with the Affymetrix Gene-Chip Operating System V1.1, according to Affymetrix protocol

data_processing: Probe sets were mapped to unique Entrez Gene IDs using a custom Chip Description File (CDF HGU133plus2_Hs_ENTREZG in R package “hgu133plus2hsentrezg.db” version 14.1, March 2011). Expression data were normalized and background corrected with the Robust Multichip Average method using R/Bioconductor. Genes with low variability between different time points were discarded. Differentially expressed genes were found by using the limma package in R/Bioconductor. P-values were corrected for multiple-hypothesis testing with the Benjamini-Hochberg algorithm

label: biotin

molecule: total RNA

organism: Papio anubis

source_name: Induced endometriosis at 15 months

label_protocol: According to Affymetrix protocol

growth_protocol: Endometriosis was experimentally induced in four female baboons (Papio anubis) by intraperitoneal inoculation with menstrual endometrium on two consecutive menstrual cycles. Under laparoscopic guidance, approximately 1 g of menstrual tissue and fluid was deposited from the Pipelle at four sites: the pouch of Douglas, the uterine fundus, the cul de sac, and the ovaries. At the subsequent mense, the animals underwent a second laparoscopy and endometrial reseeding at the same ectopic sites.

extract_protocol: Eutopic endometria were homogenized in TRI-ZOL reagent (Invitrogen, Carlsbad, CA), and RNA was extracted. Total RNA was then subjected to DNase digestion to remove genomic DNA and was purified using the RNeasy Kit (Qiagen, Valencia, CA). RNA purity was confirmed by 260/280-nm absorbance ratios and analysis on an Agilent Bioanalyzer, following which cDNA was prepared according to the Affymetrix microarray preparation protocol (Affymetrix, Santa Clara, CA)

treatment_protocol: Eutopic endometrial tissues were harvested between days 9-11 postovulation and were snap frozen in liquid nitrogen for RNA extraction. Eutopic endometrium from the functionalis layer was consecutively harvested by endometriectomy from the same animals following experimental induction of endometriosis.

tag: Sex

value: female

tag: tissue

value: eutopic endometrium


title: UT_SCC59A

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: Gene expression data from cutaneous SCC cell lines

hyb_protocol: Each sample was hybridized to Human Genome Array U133 Plus 2.0 according to Affymetrix GeneChip Analysis Technical Manual.

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

data_processing: Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control hybridization process and in summarizing probe cell intensity data. After hybridization, quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA. Data were subjected to statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package Limma was used for performing the statistical analysis between the groups.

organism: Homo sapiens

source_name: Cutaneous squamous cell carcinoma 59A

label_protocol: Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis technical manual with specific protocols for using the GeneChip hybridization, wash and stain kit.

growth_protocol: NHEKs and cSCC cell lines were cultured and incubated at 37C.

extract_protocol: Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany)

treatment_protocol: NHEK and cSCC cell lines were serum starved for 24 hours and the cell lysates were harvested.

tag: cell line

value: Cutaneous SCC


title: UT_SCC111

source_name: Cutaneous squamous cell carcinoma 111


title: 4_M4294_6_Low

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

country: USA

institute: Oak Ridge National Lab

description:
M4294 N=1
chip ID: 451215
_4_Cy3
PM

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 6.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the Loess normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Saccharomyces cerevisiae

growth_protocol: Yeast Peptone Dextrose medium were used for general yeast growth, which was at a temperature between 30 °C and 35 °C. To establish a consistent growth rate, chemostats were utilized.

extract_protocol: RNA was extracted using a previously described method that involved resuspending previously frozen cells in TRIzol reagent (Invitrogen, CA) and lysis via a bead beating method [23]. Briefly, frozen cell pellets were resuspended into 3 mL TRIzol reagent. Cells were lysed by adding ~1.5 mL of cell pellet/TRIzol mixture to 2 mL screw top tubes containing 0.25 g glass beads (MoBio Laboratories, CA) and bead beating at three 20 second cycles at 6500 rpm for several aliquots. Bead beating was conducted in a Precellys-24 (Bertin Technologies, Montigny-le-Bretonneux, France) bead beater. RNA was treated with DNAse I (Ambion, TX), purified using an RNeasy mini kit (Qiagen, CA), and quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE). The quality of extracted RNA was determined with an Agilent BioAnalyzer. Purified RNA of high quality was used as the template to generate ds-cDNA using Invitrogen Superscript double-stranded synthesis kit according to the manufacturers protocols (Invitrogen, CA). ds-cDNA was labeled, hybridized and washed according to the NimbleGen protocols essentially as described previously  ( Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD: Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. BMC Genomics 2012, 13:336.)

treatment_protocol: Three 2L chemostat reactors with a base media of Yeast Nitrogen Base supplemented with synthetic complete amino acids (Sigma) were inoculated with either the 2-copy (M3201), 6- copy (M4294) or control strain (M4455). The reactor was controlled at 35 °C with continuous flushing of nitrogen/carbon dioxide (95:5).  After 3 exchanges of base media, a consistent growth rate of either 0.03 h-1 (low rate) or 0.3 h-1 (high rate) was achieved and a sample was taken for further analysis.  After sampling, 3 exchanges of base media were allowed for the strains to re-establish a steady state.  The chemostats were sampled again and this procedure was repeated for a total of 4 samples for the low growth reactor or 3 samples for the high growth reactor.

tag: strain

tag: pull

tag: growth rate

value: Low


title: Spontaneous_1

description: unique sample, no replicate

source_name: Spontaneous endometriosis


title: 2_M3201_2_Low

description:
M3201 N=3
chip ID: 451215
_2_Cy3
PM

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: 1_M3201_2_Low

description:
M3201 N=1
chip ID: 451215
_1_Cy3
PM

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: 21_M4455_0_High

description:
M4455 N=3 High
chip ID: 451215
_21_Cy3
PM

source_name: M4455 N=3 High

value: High


title: 15 m. endometriosis_1

description: unique sample, no replicate


title: UT_SCC7

source_name: Cutaneous squamous cell carcinoma 7


title: 16 m. endometriosis_1

description: unique sample, no replicate

source_name: Induced endometriosis at 16 months


title: 22_M4455_0_High

description:
R M4455 N=1 High
chip ID: 451215
_22_Cy3
PM

source_name: R M4455 N=1 High


title: UT_SCC118

source_name: Cutaneous squamous cell carcinoma 118


title: UT_SCC105

source_name: Cutaneous squamous cell carcinoma 105


title: 20_M4455_0_High

description:
M4455 N=2 High
chip ID: 451215
_20_Cy3
PM

source_name: M4455 N=2 High


title: 10 m. endometriosis_1

description: unique sample, no replicate

source_name: Induced endometriosis at 10 months


title: UT_SCC91

source_name: Cutaneous squamous cell carcinoma 91


title: UT_SCC12A

source_name: Cutaneous squamous cell carcinoma 12A


title: 7 m. endometriosis_1

description: unique sample, no replicate

source_name: Induced endometriosis at 7 months


title: 6 m. endometriosis_2

description: unique sample, no replicate

source_name: Induced endometriosis at 6 months


title: UT_SCC115_siRNA_rep2

description: Gene expression data from cutaneous SCC cells transfected with EphB2 siRNA

hyb_protocol: Samples were hybridized to GeneChip® Human Genome U219 16-array plate with specific protocols for using the GeneTitan® Hybridization, Wash and Stain Kit for 3’ IVT Array Plates.

scan_protocol: GeneTitan® Instrument was used to scan the arrays.

data_processing: Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control GeneTitan® hybridization process and in summarizing probe cell intensity data.  After hybridization quality was checked with AGCC and Expression ConsoleTM 1.1. The data were normalized to remove variation between samples caused by non-biological reasons. Normalization of the array was performed using GCRMA . Data were subjected for statistical analysis with Chipster (CSC-IT Center for Science, Ltd, Espoo, Finland). R package limma was used for performing the statistical testing between the groups.

source_name: UT_SCC115 transfected with EphB2 siRNA

label_protocol: Biotinylated cRNA were prepared according to One-cycle Target Labeling protocol for GeneChip® expression analysis techinical manual.

growth_protocol: cSCC cell lines were cultured at 37C to reach 60-70% confluency.

extract_protocol: 72 hours after transfections, RNAs were extracted according to the manufacturer's instruction and eluted in streile water ( Qiagen Rneasy kit, Qiagen GmbH, Hilden, Germany)

treatment_protocol: cSCC cell lines were transfected with control or EphB2 siRNA (75 nM) and incubated for 72 hours at 37C.

tag: protocol

value: EphB2 siRNA


title: 12 m. endometriosis_1

description: unique sample, no replicate

source_name: Induced endometriosis at 12 months


title: 6 m. endometriosis_1

description: unique sample, no replicate


title: UT_SCC115_siRNA_rep1


title: 18_M4294_6_High

description:
M4294 N=3 High
chip ID: 451215
_18_Cy3
PM

source_name: M4294 N=3 High


title: 17_M4294_6_High

description:
M4294 N=2 High
chip ID: 451215
_17_Cy3
PM

source_name: M4294 N=2 High


title: dcSSc_N15_12mo

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: SSc sample

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing: Images were quantified using Feature Extraction Software

source_name: Sample: Human Tissue Biopsy

label_protocol: 25ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: subject

value: lesional skin biopsy

tag: disease state

value: Diffuse Systemic Sclerosis

tag: treatment

value: Nilotinib

tag: time

value: 12 mo

source_name: Universal Human Reference

tag: sample type

value: Universal Human Reference


title: 14_M3201_2_High

description:
M3201 N=2 High
chip ID: 451215
_14_Cy3
PM

source_name: M3201 N=2 High


title: 13_M3201_2_High

description:
M3201 N=1 High
chip ID: 451215
_13_Cy3
PM

source_name: M3201 N=1 High


title: 16_M4294_6_High

description:
M4294 N=1 High
chip ID: 451215
_16_Cy3
PM

source_name: M4294 N=1 High


title: dcSSc_N11_12mo

description: SSc sample


title: 3 m. endometriosis_3

description: unique sample, no replicate

source_name: Induced endometriosis at 3 months


title: 15_M3201_2_High

description:
M3201 N=3 High
chip ID: 451215
_15_Cy3
PM

source_name: M3201 N=3 High


title: 3 m. endometriosis_1

description: unique sample, no replicate


title: UT_SCC59A_siRNA_rep2

source_name: UT_SCC59A transfected with EphB2 siRNA


title: dcSSc_N16_12mo

description: SSc sample


title: 3 m. endometriosis_2

description: unique sample, no replicate


title: dcSSc_N19_12mo

description: SSc sample


title: UT_SCC12A_siRNA_rep2

source_name: UT_SCC12A transfected with EphB2 siRNA


title: dcSSc_N5_12mo

description: SSc sample


title: dcSSc_N10_12mo

description: SSc sample


title: 1 m. endometriosis_2

description: unique sample, no replicate

source_name: Induced endometriosis at 1 month


title: UT_SCC59A_siRNA_rep1


title: UT_SCC12A_siRNA_rep1


title: UT_SCC115_control_rep2

description: Gene expression data from cutaneous SCC cells transfected with control siRNA

source_name: UT_SCC115 transfected with control siRNA

value: control siRNA


title: dcSSc_N19base

description: SSc sample

value: baseline


title: Control_4

description: unique sample, no replicate

source_name: Disease free control


title: 1 m. endometriosis_1

description: unique sample, no replicate


title: Control_3

description: unique sample, no replicate


title: dcSSc_N16base

description: SSc sample


title: dcSSc_N15base

description: SSc sample


title: UT_SCC59A_control_rep2

source_name: UT_SCC59A transfected with control siRNA


title: dcSSc_N11base

description: SSc sample


title: Control_2

description: unique sample, no replicate


title: 19_M4455_0_High

description:
M4455 N=1 High
chip ID: 451215
_19_Cy3
PM

source_name: M4455 N=1 High


title: chloroform fraction of M. sylvestris/infected

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

description:
SAMPLE 3
Test

hyb_protocol: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php

scan_protocol: For the normalization was conducted using the housekeeping gene:GAPDH

data_processing:
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
[non-normalized_data.txt] SAMPLE report non-normalized data (raw Ct_Target).
[fold-change.txt] SAMPLE test target gene signal normalized to housekeeping gene (2^-ΔCttest)/SAMPLEcontrol target gene signal normalized to HKG (2^-ΔCtcontrol)

label: SYBR Green

source_name: epithelial cells

label_protocol: PCR assays were performed using the PCR assay panel following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by step II (DNase I treatment).

treatment_protocol: PCR assays were performed using a extract and fractions of M. Silvestres for a 24h treatment period

value: gingival tissue

tag: cell type

value: monocyte

tag: infection

value: A. actinomycetemcomitans

value: M. sylvestris extract, chloroform fraction

tag: treatment time

value: 1 day


title: aqueous fraction of M. sylvestris/ infected

description:
SAMPLE 4
Test

value: M. sylvestris extract, aqueous fraction


title: extract of M. sylvestris/ infected

description:
SAMPLE 2
Test

value: M. sylvestris extract


title: dcSSc_N10base

description: SSc sample


title: allograft kidney 476

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

description: transplanted kidney control replicate from mouse 476

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.1 ST ArrayArray. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Robubst Multiarray Average (RMA) algorithm with quantile normalization method.

organism: Mus musculus

source_name: Donor kidney from a  BALB/c mouse latently infected with MCMV

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

growth_protocol: BALB/c and C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor, ME).  MCMV (Smith strain) was purchased from the American Type Culture Collection (Manassas, VA), and propagated in mice by harvesting salivary glands 14 days post-infection.  Virus stocks were titered on confluent monolayers of murine embryo fibroblasts.  To establish latency, three to four-week old female BALB/c mice were infected i.p. with 5 x 105 pfu of MCMV (Smith strain)  and housed for 3-6 months in the Northwestern University Center for Comparative Medicine.

extract_protocol: Frozen tissue collected at 48 hr post-transplant was immediately transferred to tubes containing TriZol and 5 mm stainless steel beads (Qiagen), and the tissue was disrupted by mechanical shaking in a TissueLyser (Qiagen) at room temperature for 5 min.  RNAs were purified with PureLink RNA Minikits (Ambion), using on-column DNAse treatment as directed by the manufacturer.  RNA was quantified on a nanodrop spectrophotometer, and quality was assessed on an Agilent 2100 bioanalyzer.

treatment_protocol: Donor kidneys from latently infected BALB/c mice were transplanted into recipient C57BL/6 mice as previously described (Zhang et al., 1995), except that recipients were bi-laterally nephrectomized at the time of the transplant.  The pararenal glands were left intact.  The contralateral donor kidney was frozen in liquid nitrogen at the time of the transplant for use as a matching, Day 0 latent control.  Transplanted kidneys were frozen in liquid nitrogen at the time of sacrifice.

value: Allograft Kidney

tag: age

value: 48 hours post transplant

value: BALB/c


title: dcSSc_N5base

description: SSc sample

value: lesional skin biopsy


title: UT_SCC59A_control_rep1

value: Cutaneous SCC


title: non-treated (infected)

description:
SAMPLE 1
Control

value: non-treated


title: UT_SCC12A_control_rep2

source_name: UT_SCC12A transfected with control siRNA


title: Validation patient #117 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200

status: Public on Aug 26 2015

type: protein

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

institute: NCI

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.

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.

molecule: protein

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 1:200

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: Control

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: timepoint

value: Pre-treatment

tag: molecule

value: Total Ig


title: Validation patient #116 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200

value: PROSTVAC

tag: treatment

value: Vaccine


title: Validation patient #115 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Control_1

description: unique sample, no replicate

tag: Sex

value: female

tag: tissue

value: eutopic endometrium


title: control kidney 475

description: matching kidney control replicate from mouse 475

value: Control Kidney

tag: strain


title: control kidney 476

description: matching kidney control replicate from mouse 476

tag: age


title: UT_SCC12A_control_rep1

tag: cell line

tag: protocol

value: control siRNA


title: Validation patient #114 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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


title: allograft kidney 475

description: transplanted kidney control replicate from mouse 475


title: Validation patient #113 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: SPHD_rep2

type: genomic

city: Paris

first: Angela

last: Taddei

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: ChIP anti-Sir3 in S.cerevisiae cells from the dense fraction of 7 days YPD cultures

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Enrichment scores for each replicate were computed by applying a z-score transformation to raw Cy5/Cy3 ratio using R scale function

molecule: genomic DNA

label_protocol: 4/5 of the immunoprecipitated DNA and 3/5 of the DNA from the whole cell extract were amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol: For stationnary phase cells, cells were precultured overnight in YPD, and cultures were inoculated at the density of 0.2 OD, for 7 days at 30 °C with shaking (225rpm). The dense fraction was isolated by density gradient fractionnation in Percoll (Sigma Aldrich)

extract_protocol: A total of 20 660nm O.D equivalent of cells were fixed in 20 mL with 0.9 % formaldehyde for 15 min at 30°C, quenched with 0.125 M glycine and washed twice in cold TBS 1x pH 7.6. Pellets were suspended in 1mL TBS 1X, centrifuged and frozen in liquid nitrogen for -80°C storage. All following steps were done at 4°C unless indicated. Pellets were re-suspended in 500 µL of lysis buffer (0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA pH 8, 16.7 mM Tris pH8, 167 mM NaCl, 0.5 % BSA, 0.02 g.L-1 tRNA and 2.5 µL of protease inhibitor from SIGMA P1860) and mechanically lysed by three cycles of 30 s with 710-1.180 µm glass beads followed by two cycles of 30 s with 500 µm zirconium/silica beads (Biospec Products) using a Fastprep instrument (MP Biomedicals). Each bead beating cycle was followed by 5 min incubation on ice. The chromatin was fragmented to a mean size of 500 bp by sonication in the Bioruptor XL (Diagenode) for 14 min at high power with 30 s on / 30 s off and centrifuged 5 min at 13 000 rpm. 10 µL were kept to be used as Input DNA. Cleared lysate was incubated overnight with 1 µL of polyclonal antibody anti-Sir3 (Agro-bio). 50 µL of magnetic beads protein A (NEB) were added to the mixture and incubated for 4h at 4°C. Magnetic beads were washed sequentially with lysis buffer, twice with RIPA buffer (0.1% SDS, 10mM Tris pH7.6, 1mM EDTA pH8, 0,1% sodium deoxycholate and 1% TritonX-100), twice with RIPA buffer supplemented with 300 mM NaCl, twice in LiCl buffer (250 mM LiCl, 0.5% NP40, 0.5 % sodium deoxycholate), with TE 0.2% TritonX-100 and with TE. Input were diluted 10x with elution buffer (50mM Tris, 10mM EDTA pH8, 1%SDS) and beads were re-suspended in 100 µL elution buffer. A reversal cross-linking was performed by heating samples overnight at 65°C. Proteins were digested with proteinase K in presence of glycogen and the remaining DNA was purified on QIAquick PCR purification columns. Finally, samples were treated with 29 µg.mL-1 RNAse A 30 min at 37°C.

source_name: Whole cell extract


title: expo_rep2

description: ChIP anti-Sir3 in exponentially growing S.cerevisiae cells

source_name: ChIP anti-Sir3_Fermentation_rep2

growth_protocol: For exponentially growing cells, cells were precultured overnight in YPD, and grown from 0.2 to 1 O.D in rich medium (YPD) at 30°C.


title: control kidney 511

description: matching kidney control replicate from mouse 511

source_name: Donor kidney from a mouse latently infected with MCMV


title: Validation patient #111 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: allograft kidney 511

description: transplanted kidney control replicate from mouse 511


title: Validation patient #110 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200

tag: on-study psa

tag: timepoint

tag: molecule


title: Validation patient #106 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200

tag: treatment


title: Validation patient #103 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #109 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #104 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #105 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #102 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #101 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: expo_rep1

source_name: ChIP anti-Sir3_Fermentation_rep1

tag: strain


title: Validation patient #98 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #94 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #91 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #99 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #100 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #97 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #95 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #92 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #93 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #90 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #108 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: SPHD_rep1


title: Validation patient #86 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #85 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #89 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #87 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #79 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #81 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #84 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #83 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #77 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #78 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #73 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #82 | Vaccine Arm | Post-treatment | Day 28 | Validation Total Ig 1-200


title: Validation patient #71 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #70 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #74 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #75 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #76 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #88 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #80 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #112 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #72 | Control Arm | Post-treatment | Day168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #68 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #64 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #65 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #66 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #67 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #61 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #59 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #58 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #69 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #57 | Vaccine Arm | Post-treatment | Day 112 | Validation Total Ig 1-200


title: genomic DNA from colorectal cancer sample #181 (CIMP low)

city: Toronto

first: Daniel

last: De Carvalho

state: ON

address: 101 College St

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Cultured primary cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: cimp

value: low

tag: disease state

value: Colorectal Cancer (CRC)


title: genomic DNA from colorectal cancer sample #73 (non-CIMP)

value: non-CIMP


title: UT_SCC115_control_rep1

tag: cell line

tag: protocol


title: Validation patient #60 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)


title: Validation patient #56 | Vaccine Arm | Post-treatment | Day 112 | Validation Total Ig 1-200

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

tag: treatment arm


title: Validation patient #53 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #54 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Validation patient #50 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200

tag: gleason score

tag: on-study psa


title: Validation patient #48 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200

tag: timepoint

tag: molecule


title: Validation patient #47 | Vaccine Arm | Post-treatment | Day 28 | Validation Total Ig 1-200

tag: treatment


title: genomic DNA from colorectal cancer sample #92 (CIMP high)

tag: cimp

value: High


title: Validation patient #44 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #49 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #46 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #43 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #45 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #42 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #52 | Control Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #41 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #51 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #38 | Control Arm | Post-treatment | Day 28 | Validation Total Ig 1-200


title: Validation patient #37 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #39 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #40 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #33 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #34 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #35 | Control Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #28 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #32 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #31 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #30 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #36 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #29 | Vaccine Arm | Post-treatment | Day168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #26 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #27 | Vaccine Arm | Post-treatment | Day 112 | Validation Total Ig 1-200


title: Validation patient #24 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #25 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #21 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #23 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #20 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #17 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #18 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #16 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #15 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #13 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #12 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #8 | Vaccine Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #10 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #7 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #107 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #11 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #9 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #22 | Control Arm | Post-treatment | Day168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #3 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #116 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

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).

value: IgG

label: DyLight 649

value: IgM


title: Validation patient #1 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #4 | Control Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #117 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #115 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #19 | Vaccine Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #114 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #14 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #111 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #110 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #109 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #113 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #112 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #2 | Control Arm | Post-treatment | Day 168/EARLY WD | Validation Total Ig 1-200


title: Validation patient #5 | Control Arm | Post-treatment | Day 56 | Validation Total Ig 1-200


title: Validation patient #6 | Vaccine Arm | Post-treatment | Day 84 | Validation Total Ig 1-200


title: Validation patient #106 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #105 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #104 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #101 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #102 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #103 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #99 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #94 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #98 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #97 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #100 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #95 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #91 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #93 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #89 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #92 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #87 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #90 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #86 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #107 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #108 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #88 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #85 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #81 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #82 |  Vaccine Arm  | Post-treatment | Day 28 | Validation IgM 1-50


title: Validation patient #80 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #78 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #79 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #76 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #77 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #75 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #74 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #72 |  Control Arm  | Post-treatment | Day168/EARLY WD | Validation IgM 1-50


title: Validation patient #66 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #70 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #65 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #84 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #71 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #68 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #69 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #60 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #67 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #83 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #61 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #58 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #54 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #57 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgM 1-50


title: Validation patient #53 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #56 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgM 1-50


title: Validation patient #52 |  Control Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #49 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #50 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #73 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #48 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #51 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #45 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #47 |  Vaccine Arm  | Post-treatment | Day 28 | Validation IgM 1-50


title: Validation patient #46 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #59 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #42 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #64 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #41 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #40 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #37 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #39 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #36 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #38 |  Control Arm  | Post-treatment | Day 28 | Validation IgM 1-50


title: Validation patient #31 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: WT0395 ToxS L33S vs toxSL33Sdelta rpoE rep3

city: Hanover

first: Salvador

last: Almagro-Moreno

address: 112 Vail Building

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

description: Biological replicate 3 of 4, SAM118 vs SAM292

hyb_protocol: 25% formamide 42 degrees O/N

scan_protocol: Scanned at 550 and 650 nm at 70-90% laser power using a GMS418 Scanner. Image saved as tif and imported into Scanalyze (Michael Eisen ver. 2.50, Stanford University)

data_processing: Data was background subtracted and filtered to exclude values below 200 in both channels and lowess normalized using BRB array Tools software.  Probes absent in more than 50% of samples were excluded from further analysis.

organism: Vibrio cholerae O395

source_name: Cultured cells

label_protocol: Reverse transcription using aadUTP followed by coupling to Alexa555 or Alexa647

growth_protocol: Sychronized samples in LB pH6.5/30C, final OD600 0.5

extract_protocol: Standard RNA extraction byTRIZOL, DNASE treatment

tag: genotype/variation

value: toxS L33S

value: toxS L33S delta rpoE


title: Validation patient #34 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #32 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: WT0395 ToxS L33S vs toxSL33Sdelta rpoE rep4

description: Biological replicate 4 of 4, SAM118 vs SAM292


title: Validation patient #30 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

value: Control


title: Validation patient #28 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50

value: Pre-treatment


title: Validation patient #33 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: WT0395 ToxS L33S vs toxSL33Sdelta rpoE rep1

description: Biological replicate 1 of 4, SAM118 vs SAM292


title: Validation patient #44 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #29 |  Vaccine Arm  | Post-treatment | Day168/EARLY WD | Validation IgM 1-50


title: Validation patient #43 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #26 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #25 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #27 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgM 1-50


title: Validation patient #24 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #23 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #35 |  Control Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: WT0395 ToxS L33S vs toxSL33Sdelta rpoE rep2

description: Biological replicate 2 of 4, SAM118 vs SAM292


title: Validation patient #22 |  Control Arm  | Post-treatment | Day168/EARLY WD | Validation IgM 1-50


title: Validation patient #21 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: mir-998 mutant, biological rep1

city: Chicago

first: Mary

last: Truscott

state: IL

address: 900 S Ashland Ave, room 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

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

data_processing: The total 6 affymetrix (Drosophila 2)*.CEL files were background corrected, normalized using R-Bioconductor package “affy” (http://www.bioconductor.org/packages/2.0/bioc/html/affy.html) and annotation package drosophila2.db (http://www.bioconductor.org/packages/release/data/annotation/html/drosophila2.db.html). Quality of microarray experiment was verified by Bioconductor package “arrayQualityMetrics” (http://www.bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html) (Kauffmann 2009).

organism: Drosophila melanogaster

source_name: mir-998 mutant

growth_protocol: Flies were cultured on standard medium at 25 degrees C

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

tag: tissue

value: larval eye discs

tag: genotype

tag: age

value: wandering third instar larvae


title: Validation patient #19 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

value: PROSTVAC

value: Vaccine


title: mir-998 mutant, biological rep3


title: Validation patient #20 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

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

tag: treatment arm


title: wild-type (w1118), biological rep3

source_name: wild-type (w1118)


title: Validation patient #17 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #18 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Validation patient #15 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50

tag: gleason score

tag: on-study psa


title: Validation patient #14 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50

tag: timepoint

tag: molecule


title: Validation patient #16 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50

tag: treatment


title: Validation patient #12 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: wild-type (w1118), biological rep2


title: Validation patient #11 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #7 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #8 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: mir-998 mutant, biological rep2


title: Validation patient #6 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #5 |  Control Arm  | Post-treatment | Day 56 | Validation IgM 1-50


title: Validation patient #10 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #4 |  Control Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #3 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #2 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #116 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

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.  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 Cy3-conjugated anti-human total immunoglobulin (IgM+IgG+IgA) (Jackson Immuno, 109-165-064).

value: Total Ig


title: Validation patient #117 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #13 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50


title: Validation patient #9 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgM 1-50


title: Validation patient #115 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Validation patient #110 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #111 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Vector Nutlin 3A

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from Nutlin-treated, vector-transfected MCF7 cells

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

source_name: RNA from Nutlin-treated, vector-transfected MCF7 cells

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol.

growth_protocol: Human breast adenocarcinoma cells MCF7 stably expressing shRNA to p53 from the pSUPER vector, designated as “MCF7-p53i”, or carrying pSUPER vector as a control (“MCF7-vec”) were cultured in RPMI-1640 medium supplemented with 10% heat inactivated FBS and 50 U/ml of penicillin, 50 µg/ml of streptomycin (Invitrogen, Carlsbad, CA)

extract_protocol: Rneasy, Qiagen

treatment_protocol: MCF7-vector or MCF7-p53i cells were treated with Nutlin-3 at 10 μM or DMSO 0.1% for 45 h followed by an additional 3 h with or without flagellin (500 ng/ml)

tag: cell line


title: Validation patient #112 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Vector Nutlin SB203580 3

description: Gene expression from SB203580+Nutlin-treated, vector-transfected MCF7 cells

source_name: RNA from SB203580+Nutlin-treated, vector-transfected MCF7 cells


title: wild-type (w1118), biological rep1

tag: tissue


title: Validation patient #109 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Vector Nutlin Flagellin SB203580 3

description: Gene expression from Flagellin+SB203580+Nutlin-treated, vector-transfected MCF7 cells

source_name: RNA from Flagellin+SB203580+Nutlin-treated, vector-transfected MCF7 cells


title: Vector Nutlin Flagellin 3A

description: Gene expression from Flagellin+Nutlin-treated, vector-transfected MCF7 cells

source_name: RNA from Flagellin+Nutlin-treated, vector-transfected MCF7 cells


title: Vector Nutlin Flagellin 2A


title: Vector Nutlin Flagellin SB203580 1


title: Vector Nutlin SB203580 2


title: Vector Nutlin Flagellin SB203580 2


title: Validation patient #1 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgM 1-50

treatment_protocol: Diluted 1:50


title: Validation patient #108 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #107 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Vector Nutlin Flagellin 1A


title: Vector Nutlin SB203580 1


title: Vector Nutlin 2A


title: Validation patient #114 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #104 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #113 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #106 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #105 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #103 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #101 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #102 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #100 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #98 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #99 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #91 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #95 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #94 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #92 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #97 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #90 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #93 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: p53i Nutlin Flagellin 3

description: Gene expression from Flagellin+Nutlin-treated, p53 shRNA-transfected MCF7 cells

source_name: RNA from Flagellin+Nutlin-treated, p53 shRNA-transfected MCF7 cells


title: Validation patient #89 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: p53i Nutlin 3

description: Gene expression from Nutlin-treated, p53 shRNA-transfected MCF7 cells

source_name: RNA from Nutlin-treated, p53 shRNA-transfected MCF7 cells


title: Validation patient #88 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #87 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: p53i DMSO Flagellin 3

description: Gene expression from Flagellin-treated, p53 shRNA-transfected MCF7

source_name: RNA from Flagellin-treated, p53 shRNA-transfected MCF7


title: Vector Nutlin Flagellin 3


title: Validation patient #86 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: p53i DMSO 3

description: Gene expression from vehicle-treated, p53 shRNA-transfected MCF7 cells

source_name: RNA from vehicle-treated, p53 shRNA-transfected MCF7 cells


title: Vector Nutlin 3


title: Validation patient #85 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

source_name: Serum


title: p53i Nutlin 2


title: Validation patient #83 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Vector Nutlin 1A


title: Validation patient #84 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Vector DMSO 3

description: Gene expression from vehicle-treated, vector-transfected MCF7 cells

source_name: RNA from vehicle-treated, vector-transfected MCF7 cells


title: Vector Flagellin 3

description: Gene expression from Flagellin-treated, vector-transfected MCF7 cells

source_name: RNA from Flagellin-treated, vector-transfected MCF7 cells


title: p53i DMSO Flagellin 2


title: Validation patient #82 |  Vaccine Arm  | Post-treatment | Day 28 | Total Ig 1-50


title: Validation patient #80 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #79 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #76 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #78 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #77 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #81 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #74 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #73 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #75 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: p53i DMSO 2


title: Validation patient #72 |  Control Arm  | Post-treatment | Day168/EARLY WD | Total Ig 1-50


title: Validation patient #71 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #69 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #70 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Vector Flagellin 2


title: Vector Nutlin 2


title: p53i Nutlin Flagellin 1


title: Validation patient #68 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: p53i Nutlin Flagellin 2


title: Validation patient #67 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #66 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Vector DMSO 2


title: p53i DMSO Flagellin 1


title: Vector Nutlin Flagellin 2


title: Validation patient #65 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #64 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #61 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: p53i DMSO 1


title: Validation patient #60 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #59 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: p53i Nutlin 1


title: Validation patient #58 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Vector Nutlin Flagellin 1


title: Vector Nutlin 1


title: Validation patient #57 |  Vaccine Arm  | Post-treatment | Day 112 | Total Ig 1-50


title: Training patient #13 |  Vaccine Arm  | Day 82 | Training Total Ig 1-200

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.

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: Post-vaccination

value: total Ig


title: Training patient #19 |  Vaccine Arm  | Day 83 | Training Total Ig 1-200

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox


title: Validation patient #56 |  Vaccine Arm  | Post-treatment | Day 112 | Total Ig 1-50

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: age at enrollment (years)

tag: gleason score


title: Training patient #7 |  Vaccine Arm  | Day 87 | Training Total Ig 1-200

tag: on-study psa

tag: gleason #

tag: treatment

tag: timepoint

tag: molecule


title: Validation patient #54 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #53 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Validation patient #50 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50


title: Validation patient #52 |  Control Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Validation patient #47 |  Vaccine Arm  | Post-treatment | Day 28 | Total Ig 1-50


title: Validation patient #48 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50


title: Validation patient #46 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Training patient #4 |  Vaccine Arm  | Day 81 | Training Total Ig 1-200

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 #25 |  Vaccine Arm  | Day 90 | Training Total Ig 1-200

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: post-vaccination igg titer for fowlpox


title: Training patient #22 |  Vaccine Arm  | Day 88 | Training Total Ig 1-200


title: Training patient #15 |  Vaccine Arm  | Day 82 | Training Total Ig 1-200


title: Validation patient #44 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

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: Vector DMSO 1

tag: cell line


title: Validation patient #51 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

tag: timepoint


title: Training patient #9 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: tregs

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

tag: overall survival (mos)

tag: molecule


title: Validation patient #41 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: post-vaccination igg titer for fowlpox


title: Validation patient #42 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

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

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #40 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)


title: Training patient #1 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

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 #39 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: gleason score

tag: treatment

tag: timepoint


title: Training patient #32 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: tregs

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

tag: overall survival (mos)


title: Validation patient #49 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #38 |  Control Arm  | Post-treatment | Day 28 | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: on-study psa


title: Training patient #10 |  Vaccine Arm  | Day 79 | Training Total Ig 1-200

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #21 |  Vaccine Arm  | Day 89 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: tregs

tag: timepoint


title: Validation patient #37 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: gleason score


title: Validation patient #35 |  Control Arm  | Post-treatment | Day 56 | Total Ig 1-50

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

tag: post-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #45 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #34 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: age at enrollment (years)

tag: on-study psa


title: Validation patient #32 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Training patient #16 |  Vaccine Arm  | Day 26 | Training Total Ig 1-200

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 #8 |  Vaccine Arm  | Day 86 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: tregs

tag: treatment

tag: timepoint


title: Validation patient #31 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: gleason score


title: Validation patient #33 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: molecule


title: Training patient #2 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

tag: on-study psa

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


title: Validation patient #30 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: treatment


title: Validation patient #29 |  Vaccine Arm  | Post-treatment | Day168/EARLY WD | Total Ig 1-50

tag: timepoint


title: Validation patient #27 |  Vaccine Arm  | Post-treatment | Day 112 | Total Ig 1-50

tag: halabi predicted survival (months)


title: Validation patient #26 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: post-vaccination survival (months)


title: Training patient #31 |  Vaccine Arm  | Day 82 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for fowlpox


title: Training patient #28 |  Vaccine Arm  | Day 83 | Training Total Ig 1-200

tag: post-vaccination igg titer for fowlpox


title: Validation patient #28 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

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 #36 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: molecule


title: Training patient #30 |  Vaccine Arm  | Day 34 | Training Total Ig 1-200

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: treatment


title: Training patient #23 |  Vaccine Arm  | Day 83 | Training Total Ig 1-200

tag: halabi predicted survival (months)

tag: gleason #

tag: ellispot

tag: timepoint


title: Validation patient #25 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox


title: Validation patient #23 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #24 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Training patient #20 |  Vaccine Arm  | Day 81 | Training Total Ig 1-200

tag: tregs

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #21 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: treatment


title: Validation patient #22 |  Control Arm  | Post-treatment | Day168/EARLY WD | Total Ig 1-50

tag: timepoint


title: Validation patient #20 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: post-vaccination survival (months)


title: Validation patient #19 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

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


title: Training patient #27 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #18 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #16 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: on-study psa


title: Training patient #29 |  Vaccine Arm  | Day 83 | Training Total Ig 1-200

tag: tregs

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #17 |  Control Arm  | Post-treatment | Day 84 | Total Ig 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

tag: timepoint


title: Validation patient #14 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: post-vaccination igg titer for fowlpox


title: Training patient #12 |  Vaccine Arm  | Day 80 | Training Total Ig 1-200

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #15 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score


title: Training patient #26 |  Vaccine Arm  | Day 57 | Training Total Ig 1-200

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 fowlpox


title: Validation patient #12 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 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

tag: molecule


title: Validation patient #5 |  Control Arm  | Post-treatment | Day 56 | Total Ig 1-50

tag: post-vaccination igg titer for fowlpox

tag: timepoint


title: Validation patient #8 |  Vaccine Arm  | Post-treatment | Day 56 | Total Ig 1-50

tag: treatment arm


title: Validation patient #6 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #10 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: post-vaccination igg titers for vaccinia


title: Validation patient #4 |  Control Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: age at enrollment (years)


title: Validation patient #1 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: gleason score


title: Training patient #5 |  Vaccine Arm  | Day 84 | Training Total Ig 1-200

tag: on-study psa

tag: gleason #

tag: ellispot

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Training patient #24 |  Vaccine Arm  | Day 95 | Training Total Ig 1-200

tag: halabi predicted survival (months)

tag: tregs

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox


title: Training patient #3 |  Vaccine Arm  | Day 85 | Training Total Ig 1-200

tag: post-vaccination igg titer for fowlpox

tag: treatment

tag: molecule


title: Training patient #19 |  Vaccine Arm  | Day 83 | Total Ig 1-50

tag: timepoint


title: Training patient #14 |  Vaccine Arm  | Day 82 | Training Total Ig 1-200


title: Validation patient #117 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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).

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: Training patient #7 |  Vaccine Arm  | Day 87 | Total Ig 1-50

tag: age at enrollment (years)

tag: on-study psa

tag: gleason #

tag: ellispot


title: Training patient #4 |  Vaccine Arm  | Day 81 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: tregs

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #114 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination igg titer for fowlpox

tag: gleason score


title: Validation patient #112 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: treatment

tag: molecule


title: Validation patient #113 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: timepoint


title: Validation patient #2 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

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

tag: treatment arm


title: Validation patient #9 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Training patient #10 |  Vaccine Arm  | Day 79 | Total Ig 1-50

tag: age at enrollment (years)

tag: on-study psa

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #11 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: halabi predicted survival (months)


title: Validation patient #13 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50


title: Training patient #22 |  Vaccine Arm  | Day 88 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #116 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: treatment

tag: molecule


title: Validation patient #110 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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


title: Validation patient #111 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: age at enrollment (years)

tag: on-study psa


title: Training patient #9 |  Vaccine Arm  | Day 85 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: gleason #

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox


title: Training patient #13 |  Vaccine Arm  | Day 82 | Total Ig 1-50

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Validation patient #108 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: treatment

tag: molecule


title: Validation patient #105 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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


title: Validation patient #3 |  Vaccine Arm  | Post-treatment | Day 84 | Total Ig 1-50

tag: halabi predicted survival (months)

tag: age at enrollment (years)

tag: on-study psa


title: Training patient #25 |  Vaccine Arm  | Day 90 | Total Ig 1-50

tag: gleason #

tag: ellispot

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox


title: Validation patient #115 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: post-vaccination igg titer for fowlpox


title: Validation patient #106 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: gleason score

tag: treatment


title: Validation patient #107 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

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

tag: molecule


title: Validation patient #101 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #103 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia

tag: timepoint


title: Validation patient #99 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: age at enrollment (years)


title: Validation patient #102 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: on-study psa


title: Validation patient #100 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Training patient #32 |  Vaccine Arm  | Day 85 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for vaccinia


title: Training patient #1 |  Vaccine Arm  | Day 85 | Total Ig 1-50

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

tag: overall survival (mos)

tag: pre-vaccination igg titer for fowlpox

tag: post-vaccination igg titer for fowlpox


title: Training patient #8 |  Vaccine Arm  | Day 86 | Total Ig 1-50

tag: treatment

tag: molecule


title: Validation patient #104 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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: gleason score


title: Training patient #15 |  Vaccine Arm  | Day 82 | Total Ig 1-50

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: on-study psa

tag: timepoint


title: Training patient #21 |  Vaccine Arm  | Day 89 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #98 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia


title: Validation patient #94 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: post-vaccination igg titer for fowlpox


title: Validation patient #93 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment


title: Training patient #16 |  Vaccine Arm  | Day 26 | Total Ig 1-50

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

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #92 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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: gleason score


title: Validation patient #89 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: age at enrollment (years)

tag: on-study psa

tag: timepoint


title: Validation patient #90 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia


title: Training patient #31 |  Vaccine Arm  | Day 82 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Training patient #2 |  Vaccine Arm  | Day 85 | Total Ig 1-50

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

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: treatment


title: Validation patient #87 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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: molecule


title: Validation patient #88 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: timepoint


title: Training patient #28 |  Vaccine Arm  | Day 83 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #86 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #91 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment


title: Validation patient #109 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination survival (months)


title: Validation patient #97 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

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


title: Validation patient #95 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm


title: Training patient #30 |  Vaccine Arm  | Day 34 | Total Ig 1-50

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

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Training patient #20 |  Vaccine Arm  | Day 81 | Total Ig 1-50

tag: age at enrollment (years)

tag: halabi predicted survival (months)

tag: molecule


title: Validation patient #85 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: gleason score

tag: on-study psa

tag: timepoint


title: Validation patient #80 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia


title: Validation patient #78 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination igg titer for fowlpox


title: Validation patient #83 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment


title: Validation patient #82 |  Vaccine Arm  | Post-treatment | Day 28 | Validation IgG 1-50

tag: post-vaccination survival (months)


title: Validation patient #81 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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


title: Training patient #14 |  Vaccine Arm  | Day 82 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #79 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm


title: Validation patient #76 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: age at enrollment (years)


title: Validation patient #77 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)


title: Training patient #23 |  Vaccine Arm  | Day 83 | Total Ig 1-50

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

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Validation patient #75 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score

tag: on-study psa

tag: timepoint


title: Validation patient #72 |  Control Arm  | Post-treatment | Day168/EARLY WD | Validation IgG 1-50

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Training patient #29 |  Vaccine Arm  | Day 83 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

tag: pre-vaccination igg titer for vaccinia


title: Training patient #12 |  Vaccine Arm  | Day 80 | Total Ig 1-50

tag: age at enrollment (years)

tag: halabi predicted survival (months)

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

tag: overall survival (mos)


title: Training patient #26 |  Vaccine Arm  | Day 57 | Total Ig 1-50

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Training patient #27 |  Vaccine Arm  | Day 85 | Total Ig 1-50

tag: on-study psa


title: Training patient #5 |  Vaccine Arm  | Day 84 | Total Ig 1-50

tag: timepoint


title: Validation patient #84 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #71 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

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

tag: post-vaccination igg titer for fowlpox

tag: treatment


title: Validation patient #68 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: age at enrollment (years)


title: Validation patient #69 |  Control Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: halabi predicted survival (months)


title: Validation patient #74 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #67 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Training patient #24 |  Vaccine Arm  | Day 95 | Total Ig 1-50

tag: gleason #

tag: ellispot

tag: tregs

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

tag: pre-vaccination igg titer for vaccinia


title: Training patient #3 |  Vaccine Arm  | Day 85 | Total Ig 1-50

tag: on-study psa

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox

tag: molecule


title: Training patient #19 |  Vaccine Arm  | Day 83 | Training IgM 1-50

tag: timepoint


title: Training patient #13 |  Vaccine Arm  | Day 82 | Training IgM 1-50


title: Validation patient #60 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #7 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Total Ig 1-50

tag: halabi predicted 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


title: Validation patient #59 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #58 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50


title: Validation patient #65 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #73 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #61 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50


title: Validation patient #64 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50


title: Validation patient #57 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgG 1-50


title: Training patient #10 |  Vaccine Arm  | Day 79 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: tregs

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

tag: pre-vaccination igg titer for vaccinia


title: Validation patient #70 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: on-study psa

tag: molecule


title: Validation patient #56 |  Vaccine Arm  | Post-treatment | Day 112 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: timepoint


title: Validation patient #53 |  Control Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #52 |  Control Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination igg titers for vaccinia

tag: gleason score


title: Validation patient #66 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: halabi predicted survival (months)

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


title: Validation patient #51 |  Vaccine Arm  | Post-treatment | Day 84 | Validation IgG 1-50

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Validation patient #50 |  Vaccine Arm  | Post-treatment | Day 168/EARLY WD | Validation IgG 1-50

tag: treatment


title: Training patient #25 |  Vaccine Arm  | Day 90 | Training IgM 1-50

tag: gleason #

tag: ellispot

tag: overall survival (mos)

tag: post-vaccination igg titer for vaccinia

tag: pre-vaccination igg titer for fowlpox


title: Training patient #4 |  Vaccine Arm  | Day 81 | Training IgM 1-50

tag: on-study psa

tag: tregs

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

tag: pre-vaccination igg titer for vaccinia

tag: molecule


title: Validation patient #48 |  Vaccine Arm  | Post-treatment | Day 56 | Validation IgG 1-50

tag: post-vaccination survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: timepoint