title: cartilage knee 08488_N

description: normal cartilage knee sample


title: cartilage knee 08200_OA

status: Public on Apr 01 2013

type: genomic

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

country: Spain

institute: INIBIC

description: osteoarthritic cartilage knee sample

hyb_protocol: bisulphite converted DNA using EZ DNA Methylation kit (Zimo Research) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan using standard recommended Illumina scanner setting

data_processing: Signal intensities were processed using methylumi and lumi R packages (R/Bioconductor). Methylumi R package with methylumIDAT function in order to obtain intensity signals, then transformed in a methyLumiM object, quantile color balance was adjusted and data were normalized using ssn procedure, obtaining as result M values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cartilage knee

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using a home-made CTAB and chloroform-based method after breaking up the cartilage.

tag: disease state

value: osteoarthritis

tag: age

value: >60 years

tag: Sex

value: male

tag: haplogroup

value: U

tag: tissue

value: knee cartilage


title: Phaeodactylum_White light_6h_rep1

type: RNA

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description: Phaeodactylum, Re-exposure to 6h white light after 48h dark treatment

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

molecule: total RNA

organism: Phaeodactylum tricornutum

label_protocol: Total RNA (150 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Cultures were grown in f/2 medium made with 0.2 μm-filtered and autoclaved local seawater supplemented with f/2 vitamins and inorganic nutrients, filter sterilized and added after autoclaving. The cultures were incubated at 15C under cool white fluorescent light at a scalar irradiance (EPAR) of ~100 µmol m-2 s-1 under continuous white light (CWL) conditions. The cells divided 1.5 times per day under these conditions. Cell division continued 6 h after light deprivation, after which it ceased.

extract_protocol: Diatom cultures were centrifuged at 4000 g for 10 min at 15°C. The supernatant was removed and the cell pellet was resuspended in 1 ml f/2 medium. The suspension was transferred to 2 ml tubes and centrifuged at 18000 g for 1 min at 4°C. Supernatants were removed and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: The cultures were dark-treated for 48 h (DT) before re-exposure to the previous light conditions for 0.5 h, 6 h or 24 h (WL 0.5, 6 and 24 h). Sampling of continuous white light (CWL) cultures and DT cultures were performed in addition to the sampling at the WL incubation times of 0.5 h, 6 h, and 24 h. Three biological replicas for each of the five treatments were harvested.

tag: clone

value: clone Pt 1 8.6 (CCMP632)


title: cartilage knee 08449_N

description: normal cartilage knee sample

value: normal

value: <50 years

value: female


title: cartilage knee 0825_N

description: normal cartilage knee sample

value: H


title: Phaeodactylum_White light_6h_rep2

source_name: Phaeodactylum, Re-exposure to 6h white light after 48h dark treatment


title: Validation patient #9 | Control Arm | Pre-treatment [Total Ig 1:200]

type: other

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

country: USA

institute: NCI

description: Sample name: 65

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.
The VALUEs represent the normalized ch1 signal for experiments that analyzed total Ig and IgG.  For the IgM experiments, the ch2 signal was normalized to determine levels of IgM antibodies.

molecule: other

source_name: Serum

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

extract_protocol: Serum was obtained from peripheral blood samples

treatment_protocol: Diluted 1:200

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: treatment

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Validation patient #8 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 46

value: PROSTVAC

value: Vaccine


title: cartilage knee 08260_OA

description: osteoarthritic cartilage knee sample

tag: disease state

tag: age

tag: Sex


title: Validation patient #6 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 33


title: Validation patient #5 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 29


title: Phaeodactylum_White light_0.5h_rep1

description: Phaeodactylum, Re-exposure to 0.5h white light after 48h dark treatment

tag: clone


title: Phaeodactylum_White light_0.5h_rep2

source_name: Phaeodactylum, Re-exposure to 0.5h white light after 48h dark treatment


title: Validation patient #4 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 21

tag: halabi predicted survival (months)


title: Phaeodactylum_Dark treated_48h_rep3

description: Phaeodactylum exposed to 48h darkness (no light)

source_name: Phaeodactylum, Dark treated, 48h


title: Phaeodactylum_White light_0.5h_rep3


title: cartilage knee 08493_OA

description: osteoarthritic cartilage knee sample

tag: haplogroup

value: J

tag: tissue


title: Phaeodactylum_Dark treated_48h_rep2


title: cartilage knee 08223_OA

description: osteoarthritic cartilage knee sample


title: cartilage knee 061198_N

description: normal cartilage knee sample

value: >50 years


title: cartilage knee 051337_N

description: normal cartilage knee sample


title: cartilage knee 07636_N

description: normal cartilage knee sample


title: cartilage knee 051255_N

description: normal cartilage knee sample


title: cartilage knee 08480_N

description: normal cartilage knee sample


title: cartilage knee 08454_N

description: normal cartilage knee sample


title: cartilage knee 08435_OA

description: osteoarthritic cartilage knee sample

value: osteoarthritis


title: Validation patient #3 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 13

tag: post-vaccination survival (months)

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

tag: treatment arm


title: Validation patient #7 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 41

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


title: Validation patient #2 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 9

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Phaeodactylum_White light_t0_rep3

description: Phaeodactylum exposed to continous white light, timepoint t0

source_name: Phaeodactylum, White light, t0


title: cartilage knee 08426_OA

description: osteoarthritic cartilage knee sample

value: >60 years


title: MFAP4 heart_rep8

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597.Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro6.1 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

organism: Mus musculus

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye. HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: 19 wk

tag: gender

value: male

tag: genetic background

value: heart

tag: genotype

tag: mouse id

source_name: Wt RNA pool heart

value: wt


title: Validation patient #1 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 1

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: MFAP4 heart_rep6

tag: age

tag: tissue


title: Phaeodactylum_Dark treated_48h_rep1

tag: clone

value: clone Pt 1 8.6 (CCMP632)


title: MFAP4 heart_rep7


title: cartilage knee 08288_OA

description: osteoarthritic cartilage knee sample

tag: disease state

tag: Sex

tag: haplogroup

value: knee cartilage


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

description: Sample name: 842

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.

treatment_protocol: Diluted 1:50

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


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

description: Sample name: 852

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


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

description: Sample name: 847

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: cartilage knee 08914_N

description: normal cartilage knee sample

value: normal

tag: age

tag: tissue


title: cartilage knee 08124_OA

description: osteoarthritic cartilage knee sample

tag: disease state

tag: Sex

value: H


title: Phaeodactylum_White light_t0_rep2

tag: clone


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

description: Sample name: 837

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)


title: cartilage knee 0853_N

description: normal cartilage knee sample

tag: haplogroup


title: Phaeodactylum_White light_t0_rep1


title: cartilage knee 08722_N

description: normal cartilage knee sample

value: female


title: cartilage knee 08478_OA

description: osteoarthritic cartilage knee sample


title: ZR75.1

city: Tokushima

first: Le

middle: Tan

last: Dat

state: Tokushima

address: 3-18-15, Kuramoto-cho

department: Genome center

country: Japan

institute: Tokushima university

description: US10053769_251485060524_S01_GE1_107_Sep09_1_3

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity in the range of 13-25 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's protocol. When the fragmentation reaction completed, 55 μl of 2x Agilent's GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 4x44K Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed one minute at room temperature with  Agilent's GE Wash Buffer 1 (addition of Triton X-102 at 0.005%) and one minute with 37°C GE Wash buffer 2 (pre-warmed overnight at 37°C), dried the array slides at room temperature about 10 seconds, then scanned immediately using Tecan scanner. The procedures were performed in the ozone - protection hood as recommendation by Agilent manufacturer.

scan_protocol: Dried microarray slides were scanned immediately on the Agilent DNA Microarray Scanner using one color scan setting for 4x44K array formats (Scan area: 61x21.6 mm; Scan resolution: 5μm; Dye channel: Green; Green PMT: 100%).

data_processing: Features of the scanned images were extract with Feature Extraction version 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid template: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The output files were processed for analysis of gene expression using GeneSpring version 11.5 and Microsoft Excel 2007.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Agilent's Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. cRNA was used for hybridization immediately without freezing and thawing.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit. DNase digestion were performed on-column. RNA was quantified using the NanoDrop-1000 Spectrophotometer and RNA quality was monitored using the Agilent 2100 Bioanalyzer (Agilent).

tag: cell line


title: cartilage knee 08802_OA

description: osteoarthritic cartilage knee sample


title: NCI-H1048

description: US10053769_251485046182_S01_GE1_107_Sep09_1_4


title: MFAP4 heart_rep3

tag: gender

tag: genetic background

tag: genotype

tag: mouse id


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

description: Sample name: 826

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: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

value: Pre-treatment


title: MFAP4 heart_rep4

tag: age

tag: tissue


title: cartilage knee 08137_N

description: normal cartilage knee sample

tag: disease state

tag: Sex


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

description: Sample name: 822

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: SBC-5_2

description: US10053769_251485060524_S01_GE1_107_Sep09_1_2

source_name: SBC-5 cells, duplicate sample 2

tag: cell line

value: SBC-5 cells


title: MFAP4 heart_rep1

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

tag: gender

tag: genetic background

tag: genotype

tag: mouse id

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562


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

description: Sample name: 816

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

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

value: Vaccine


title: MFAP4 heart_rep2

tag: age

tag: tissue


title: cartilage knee 08844_OA

description: osteoarthritic cartilage knee sample

tag: disease state

tag: Sex

tag: haplogroup

value: J


title: HCC1397

description: US10053769_251485060524_S01_GE1_107_Sep09_1_4


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

description: Sample name: 830

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

value: Control

tag: gleason score

tag: on-study psa

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


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

description: Sample name: 810

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

tag: treatment arm


title: SBC-5_1

description: US10053769_251485060524_S01_GE1_107_Sep09_1_1

source_name: SBC-5 cells, duplicate sample 1

tag: cell line


title: ACC-LC319/Bone2

description: US10053769_251485043161_S01_GE1_107_Sep09_1_4


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

description: Sample name: 802

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox


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

description: Sample name: 798

tag: age at enrollment (years)


title: siEGR4 (72 hr) _1

description: US10053769_251485060533_S01_GE1_107_Sep09_1_3

source_name: SBC-5 cells, siEGR4 (target), 72 hr after siRNA, duplicate sample 1

treatment_protocol: siRNA experiments (siEGFP; siEGR4), using Lipofectamin (Invitrogen), follwing the manufacturer's protocol.

value: siEGR4 (target)

tag: time

value: 72 hr


title: MFAP4 heart_rep5

tag: age

value: 19 wk

tag: gender

value: male

tag: genetic background

tag: tissue

tag: genotype

tag: mouse id


title: siEGFP (72 hr) _2

description: US10053769_251485060533_S01_GE1_107_Sep09_1_2

source_name: SBC-5 cells, siEGFP (control), 72 hr after siRNA, duplicate sample 2

tag: treatment

value: siEGFP (control)


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

description: Sample name: 793

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: gleason score

tag: on-study psa

tag: timepoint


title: GFP

city: Suita

first: Yusuke

last: Satoh

state: Osaka

address: 2-2, Yamada-Oka

department: Department of Hematology and Oncology

institute: Osaka University Graduate School of Medicine

description: Gene expression data from gene-transduced LSK Flt3- cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degrees on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: Gene-transduced LSK Flt3- cells, GFP control

label_protocol: Biotinylated cRNA were synthesized by the GeneChip 3' IVT Express Kit (Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA extraction was performed using a Trizol Reagent according to the manufacturer's protocol.

tag: strain

value: wild-type

tag: cell type

value: LSK Flt3- cells

tag: transduction

value: GFP


title: siEGR4 (72 hr) _2

description: US10053769_251485060533_S01_GE1_107_Sep09_1_4

source_name: SBC-5 cells, siEGR4 (target), 72 hr after siRNA, duplicate sample 2

tag: cell line


title: siEGFP (72 hr) _1

description: US10053769_251485060533_S01_GE1_107_Sep09_1_1

source_name: SBC-5 cells, siEGFP (control), 72 hr after siRNA, duplicate sample 1

tag: time


title: Satb1

source_name: Gene-transduced LSK Flt3- cells, Satb1


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

description: Sample name: 787

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: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: isotype-specific secondary antibody [fluorescently labeled]


title: siEGR4 (48 hr) _1

description: US10053769_251485060532_S01_GE1_107_Sep09_1_3

source_name: SBC-5 cells, siEGR4 (target), 48 hr after siRNA, duplicate sample 1

tag: treatment

value: 48 hr


title: siEGFP (48 hr) _2

description: US10053769_251485060532_S01_GE1_107_Sep09_1_2

source_name: SBC-5 cells, siEGFP (control), 48 hr after siRNA, duplicate sample 2


title: siEGFP (48 hr) _1

description: US10053769_251485060532_S01_GE1_107_Sep09_1_1

source_name: SBC-5 cells, siEGFP (control), 48 hr after siRNA, duplicate sample 1


title: Tumor_KO2

city: Miyazaki

first: Tsuyoshi

last: Fukushima

address: 5200 Kihara, Kiyotake

department: Pathology

institute: University of Miyazaki

description: Gene expression data from intestinal tumor of intestine-specific HAI-1 deficient Apc(Min/+) mice

hyb_protocol: Affymetrix standard procedure for Mouse Genome 430 2.0 array

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA normalization and log2 transformation). The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: tumor of the small intestine

label_protocol: Biotinylated cRNA were prepared using One-cycle target labeling kit according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All mice were housed in a pathogen-free barrier environment for the duration of the study. All mice had a C57BL/6 genetic background and were fed a semipurified AIN-76 diet under specific pathogen-free condition.

extract_protocol: Total RNAs were extracted with Trizol reagent and PureLink RNA Micro Kit (Invitrogen).

treatment_protocol: Mice with intestinal epithelial cell-specific deletion of the Spint1 gene (Spint1flox/flox/Vil-Cre) were generated by interbreeding mice carrying Spint1/LoxP homozygous alleles (Spint1flox/flox) with Cre transgenic mice under the control of the intestine-specific villin promoter. ApcMin/+ mice were then interbred with Spint1flox/flox/Vil-Cre mice, generating ApcMin/+ mice with intestine-specific deletion of the Spint1 gene (ApcMin/+/Spint1flox/flox/Vil-Cre).

tag: tissue

value: tumor of the small intestine

tag: genotype

value: Apc (Min/+)/Spint1 (flox/flox)/Vil-Cre

tag: hai-1 expression

value: intestine-specific deletion

tag: tissue type

value: tumor


title: Tumor_Control2

description: Gene expression data from intestinal tumor of control  Apc(Min/+) mice

tag: strain

value: Apc (Min/+)/Spint1 (flox/flox)

value: expressed


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

description: Sample name: 781

source_name: Serum

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

value: PROSTVAC

tag: gleason score

tag: on-study psa

value: Vaccine

tag: timepoint

value: Pre-treatment

value: Total Ig


title: siEGR4 (48 hr) _2

description: US10053769_251485060532_S01_GE1_107_Sep09_1_4

source_name: SBC-5 cells, siEGR4 (target), 48 hr after siRNA, duplicate sample 2

tag: cell line

value: SBC-5 cells

value: siEGR4 (target)

tag: time


title: NHDF1- neo male

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young

institute: UCLA

hyb_protocol: Labeled cRNA was mixed with hybridization mix according to Affymetrix protocol and hybridized in Affymetrix GeneChip hybridization oven 645 at 45C for 16 hours with rotation at 60 rpm

scan_protocol: Scanning was performed on Affymetrix 7G scanner with target intensity 500

data_processing: Cel files were imported into Genespring and RMA normalized.  Probesets not expressed in at least 10% of samples were eliminated

source_name: wildtype fibroblasts

label_protocol: Labeling was performed with Ambion MESSAGEAMP PREMIER kit (cat#: 4383452)

growth_protocol: all grown in standard conditions: hESC/hiPSC (in KO serum replacer, hESC media), FBs (Dmem +10% FBS), NPCs (Dmem, N2, B27, Egf, Fgf)

extract_protocol: Cells were lysed, and run through Stratagene Total RNA isolation kit

tag: cell type

value: FBs

tag: genotype/variation

value: wildtype fibroblasts


title: Nontumor_KO2

description: Gene expression data from non-tumor intestinal tumor of intestine-specific HAI-1 deficient Apc(Min/+) mice

source_name: small intestinal mucosa

value: small intestinal mucosa

value: non-tumor


title: Tumor_KO1


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

description: Sample name: 776

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: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Tumor_Control1

tag: tissue

tag: genotype

tag: hai-1 expression

tag: tissue type


title: Nontumor_KO1

tag: strain


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

description: Sample name: 769

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: gleason score

tag: on-study psa

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: siEGR4 (24 hr) _2

description: US10053769_251485060525_S01_GE1_107_Sep09_1_4

source_name: SBC-5 cells, siEGR4 (target), 24 hr after siRNA, duplicate sample 2

tag: cell line

tag: time

value: 24 hr


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

description: Sample name: 762

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

tag: treatment arm

value: Control

tag: pre-vaccination igg titers for vaccinia

tag: timepoint


title: Nontumor_Control1

description: Gene expression data from non-tumor intestinal mucosa tissue of control  Apc(Min/+) mice

tag: tissue


title: Nontumor_Control2

tag: genotype


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

description: Sample name: 752

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: siEGR4 (24 hr) _1

description: US10053769_251485060525_S01_GE1_107_Sep09_1_3

source_name: SBC-5 cells, siEGR4 (target), 24 hr after siRNA, duplicate sample 1


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

description: Sample name: 738

tag: halabi predicted survival (months)


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

description: Sample name: 745

tag: post-vaccination survival (months)


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

description: Sample name: 729

tag: gleason score


title: siEGFP (24 hr) _1

description: US10053769_251485060525_S01_GE1_107_Sep09_1_1

source_name: SBC-5 cells, siEGFP (control), 24 hr after siRNA, duplicate sample 1

value: siEGFP (control)


title: 02_WT CD11b+

city: Tokyo

first: Jun

last: Kunisawa

address: 4-6-1 Shirokanedai, Minato-ku

institute: The University of Tokyo

hyb_protocol: After purification and fragmentation of aRNA, 12.5 ug of them was hybridized to GeneChip(R) Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: The array was incubated for 16 hr at 45°C, then automatically washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix). The Probe Array was scanned using a GeneChip Scanner 3000 7G.

data_processing: The scanned data  were processed with Affymetrix® Expression Console™ by MAS 5.0  algorithm .

source_name: CD11b+ IgA+ cells

label_protocol: RNA targets preparation for microarray expression analysis were performed according to the manufacturer's protocol using GeneChip(R) 3' IVT Express Kit (Affymetrix). One hundred nanograms of total RNA was converted into double-stranded cDNA template for transcription. In vitro transcription synthesized amplified RNA (aRNA) and incorporated a biotin-congugated nucleotide.

growth_protocol: Primary cells isolated from murine small intestine

extract_protocol: Rneasy kit

treatment_protocol: No treatment was applied

tag: background strain

value: Balb/c

tag: gender

value: female

tag: age

value: 9 wks

tag: cell type

value: CD11b+ IgA+

value: intestine


title: colorectal tumor_sporadic_biol repl5

city: Erlangen

first: Clemens

last: Neufert

address: Ulmenweg 18

department: First Department of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at MOE430A Affymetrix Mouse Expression 430A Array in the GeneChip Hybridization oven 640. Miroarrays were washed and stained according to manufacturer´s recommendations using Streptavidin Phycoerythrin for labeling of hybridized biotinylated cRNA.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: Data processing and analysis was performed with ArrayAssist software 5.0 (Stratagene). GC-RMA method was used for background transformation and normalization of expression levels. For enhanced significance analysis, microarrays were assigned to the 4 groups (CAC, CAC control epithelium, sporadic CRC, sporadic CRC control) according to the origin of the tissue. Baseline transformation (subtraction) was performed in respect to the expression levels of microarrays with control epthelium. Enhanced significance analysis was done with unpaired t-test including Benjamini-Hochberg false discovery rate p-value correction ['enhanced_significance_analysis.txt' available on Series records].

source_name: colorectal tumor_sporadic

label_protocol: Biotinylated cRNA were prepared from 5 ug total RNA according to standard protocols. First strand cDNA synthesis was performed with T7-oligo(dT) primer (Invitrogen),  reverse transcriptase Superscript II (Invitrogen) ans first strand buffer (Invitrogen). Second strand cDNA synthesis was done with E. coli DNA ligase (Invitrogen), E. coli DNA Polymerase I (Invitrogen) and second strand reaction buffer (Invitrogen). Biotinylated cRNA was synthesized with GeneChip IVT labeling kit (Affymetrix) according to the manufacturer´s instructions. All recommended cleanup-steps were done with GeneChip cleanup module (Affymetrix).

growth_protocol: Colitis-associated tumorigenesis was performed by intraperitoneal injection of Azoxymethane (10mg/kg) into C57BL/6J wildtype mice followed by 3 cycles of Dextran Sodium Sulfate (DSS) in drinking water. Each DSS-cycle was composed of DSS (2.5% (w/v) in drinking water for 7 days, followed by a recovery phase with regular drinking water for 14 days. Sporadic tumors were from C57BL/6J-ApcMin/+/J mice. All tumors were obtained from the from the lower 6th of the large intestine and they had the same size covering between ¼ and up to ½ of the colonic circumferenc as evaluated by mini-endoscopy.

extract_protocol: For RNA-purification, tumors and purified distal colon epithelium were placed in RNeasy lysis buffer (Qiagen), disrupted and homogenized using a master mill (Qiagen) before being processed by using the RNeasy Mini kit (Qiagen) according to the manufacturer´s recommendations.

treatment_protocol: For epithelial purification, distal colonic specimens were incubated in prewarmed HBSS supplemented with EDTA (2mM), EGTA (1mM), DTT, and FCS (1%) with gentle agitation at 37°C for 20min. To avoid bias caused by the 20min incuabtion, all tumors were treated exact the same.

tag: strain

value: male

tag: tissue origin

value: the lower 6th of the large intestine

value: Apcmin/+ tumors from the distal colorectum

tag: animals per sample

tag: experimental block


title: hiPSC IMR9.4 p9

source_name: wildtype hiPSCs

value: hiPSC

tag: genotype/variation

value: wildtype hiPSCs


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

description: Sample name: 709

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

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: on-study psa

tag: treatment

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


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

description: Sample name: 704

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

value: PROSTVAC

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

value: Vaccine


title: 01_JK1(WT-)

hyb_protocol: cRNA (15 µg) was fragmented at 94°C in the presence of a fragmentation buffer (Affymetrix). Fifteen micrograms of the cRNA was hybridized to Affymetrix GeneChip® Mouse Genome 430 2.0 Array (Affymetrix).

source_name: CD11b- IgA+ cells

label_protocol: Isolated total RNA were amplified and labeled as described in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). First, total RNA (1 µg) was converted into double-stranded cDNA using the One-Cycle cDNA Synthesis Kit (Affymetrix). Double-stranded cDNA was purified by using a GeneChip Sample Cleanup Module (Affymetrix). In vitro transcription reactions were performed using a GeneChip IVT Labeling Kit, which includes T7 RNA polymerase and Biotin-labeled ribonucleotides. Biotin-labeled cRNA was purified using a GeneChip Sample Cleanup Module. The concentration of cRNA was calculated from light absorbance at 260 nm using a UV spectrophotometer.

tag: background strain

tag: gender

tag: age

tag: cell type

value: CD11b- IgA+

tag: tissue


title: colorectal tumor_sporadic_biol repl4

tag: strain

tag: tissue origin

tag: animals per sample

tag: experimental block


title: colorectal control epithelium_sporadic_biol repl3

description: sporCRC contr3

source_name: colorectal control epithelium_sporadic

value: tumor-free distal colon epithelium


title: SNDISH15, biological rep2

city: Richmond

first: Myrna

last: Serrano

state: VA

address: 1101 East Marshall St

institute: Virginia Commonwealth University

description:
SNDISH15_2
Gene expression data from SND1 knockdown 2.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0002.

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

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and RMA as the normalization method.

source_name: SND1 knockdown 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit, P/N 702646 Rev. 8, Affymetrix).

growth_protocol: Steady-state proliferating cells.

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

treatment_protocol: No treatment was done.

tag: cell line

value: human hepatocellular carcinoma

tag: shRNA


title: 02_JK2(WT+)

value: Balb/c


title: SBC-5 (0)_2

description: US10053769_251485060524_S01_GE1_107_Sep09_1_2

source_name: SBC-5 cells, at 0 hr (= 24 hr after passaged), no treatment, duplicate sample 2

value: SBC-5 cells

tag: treatment

value: no treatment

tag: time

value: 0 hr


title: SNDISH15, biological rep1

description:
SNDISH15_1
Gene expression data from SND1 knockdown 2.


title: SNDISH12, biological rep3

description:
SNDISH12_3
Gene expression data from SND1 knockdown 1.

source_name: SND1 knockdown 1


title: colorectal control epithelium_sporadic_biol repl2

description: sporCRC contr2


title: SNDISH15, biological rep3

description:
SNDISH15_3
Gene expression data from SND1 knockdown 2.


title: siEGFP (24 hr) _2

description: US10053769_251485060525_S01_GE1_107_Sep09_1_2

source_name: SBC-5 cells, siEGFP (control), 24 hr after siRNA, duplicate sample 2

value: siEGFP (control)

value: 24 hr


title: 01_WT CD11b-

value: female

value: 9 wks

value: intestine


title: hiPSC 3975.2 p9

value: hiPSC

tag: genotype/variation

value: wildtype hiPSCs


title: SBC-5 (0)_1

description: US10053769_251485060524_S01_GE1_107_Sep09_1_1

source_name: SBC-5 cells, at 0 hr (= 24 hr after passaged), no treatment, duplicate sample 1


title: gm015588_p7_p2_npc

source_name: neural progenitor cell

value: NPC

value: NPCs derived from A-T patient


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

description: Sample name: 696

source_name: Serum

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: on-study psa

value: Vaccine

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: hiPSC 3975.4 p6

tag: cell type


title: colorectal tumor_sporadic_biol repl3

tag: strain

tag: gender

value: male

tag: tissue origin

value: the lower 6th of the large intestine

tag: tissue

value: Apcmin/+ tumors from the distal colorectum

tag: animals per sample

tag: experimental block


title: SNDISH12, biological rep2

description:
SNDISH12_2
Gene expression data from SND1 knockdown 1.

tag: cell line

value: human hepatocellular carcinoma

tag: shRNA


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

description: Sample name: 678

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: age at enrollment (years)

tag: gleason score

tag: treatment


title: colorectal tumor_sporadic_biol repl2


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

description: Sample name: 664

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: on-study psa

tag: timepoint


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

description: Sample name: 670

tag: isotype-specific secondary antibody [fluorescently labeled]


title: colorectal control epithelium_sporadic_biol repl1

description: sporCRC contr1

tag: strain

tag: gender

tag: tissue

value: tumor-free distal colon epithelium

tag: animals per sample


title: SNDISH12, biological rep1

description:
SNDISH12_1
Gene expression data from SND1 knockdown 1.

tag: cell line

tag: cell type

tag: shRNA


title: gm01588_p7_hipsc

source_name: induced pluripotent stem cells

tag: genotype/variation

value: hiPSC derived from AT patient


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

description: Sample name: 648

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: age at enrollment (years)

tag: gleason score


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

description: Sample name: 656

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: treatment


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

description: Sample name: 640

tag: on-study psa

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: ag04405_p5_p2_npc


title: QGY, biological rep2

description:
QGY_2
Gene expression data from control clone.

source_name: control clone

tag: cell line


title: colorectal tumor_sporadic_biol repl1

tag: strain

tag: gender

tag: tissue origin

tag: tissue

tag: animals per sample

tag: experimental block


title: colorectal tumor_colitis-associated_biol repl4

source_name: colorectal tumor_colitis-associated

value: distal colitis-associated tumors


title: colorectal tumor_colitis-associated_biol repl3


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

description: Sample name: 636

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: age at enrollment (years)


title: ag04405_p5_hipsc

tag: cell type

tag: genotype/variation


title: QGY, biological rep1

description:
QGY_1
Gene expression data from control clone.


title: LNCaP_enzalutamide 1 x 10E-5 M plus DHT 100 nM_rep3

city: Santiago

first: Ivan

middle: Esteban

last: Alfaro

address: Zañartu 1482

department: Molecular Innovation and Drug Discovery

country: Chile

institute: Fundacion Ciencia y Vida

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G using GeneChip Operating Software to generate raw and averaged image files (.DAT and .CEL).

data_processing:
Affymetrix MAS 5.0 algorithm was used as the scaling (value set to 500) and summarization method. We used a One-way ANOVA (ANalysis Of VAriance) model to test for differentially expressed genes between the groups. For each pair of treatments, a two-sample t-test is also carried out. P-values are corrected to control the false discovery rate (FDR) using the Benjamini & Hochberg method and probes with values less than 0.05 are considered statistically significant [differentially_expressed.txt].
The logRatio is the difference in the means of the two groups being compared [logRatio_data.txt]. The means are calculated from the values produced by the MAS5 algorithm, which are in the log2 space

label_protocol: Biotinylated cRNA were prepared using a modified MessageAmp procedure (Life Technologies, Inc.) from 1 ug total RNA.

growth_protocol: LNCaP cells were grown in RPMI 1640 supplemented with 5% hormone depleted FBS at 37°C in 5% CO2 incubator

extract_protocol: E.Z.N.A.™ Total RNA kit (Omega Bio-Tek) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: LNCaP cells were treated with vehicle (DMSO), DHT (100 nM), enzalutamide (1 or 10 µM) or DHT (100 nM) plus enzalutamide (1 or 10 µM) for 16 hours before RNA extraction.

value: LNCaP

value: left supraclavicular lymph node metastatic prostate carcinoma cells

tag: treated with

value: 10 µM enzalutamide plus DHT 100 nM for 16hrs


title: QGY, biological rep3

description:
QGY_3
Gene expression data from control clone.


title: LNCaP_enzalutamide 1 x 10E-5 M plus DHT 100 nM_rep1


title: LNCaP_enzalutamide 1 x 10E-5 M plus DHT 100 nM_rep2


title: Negative control shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from 3T3-L1 adipocytes treated with negative control shRNA and 10µM isoproterenol for 3 hrs

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 3T3-L1 preadipocytes were cultured in low (1g/l) glucose DMEM medium containing 10% fetal calf serum (FCS) and 1% penicillin/streptomycin (P/S) and differentiated into mature white adipocytes two days post confluency by the addition of 1 µg/ml insulin, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), 0.25 µM dexamethasone and 1/1000 volume ABP (50 mg/ml L-ascorbate, 1 mM biotin, 17 mM pantothenate) in high (4.5 g/l) glucose DMEM containing 10% FCS and 1% P/S

extract_protocol: RNeasy Mini Kit (Quiagen)

treatment_protocol: Mature adipocytes 9 days after induction of differentiation were transduced with adenoviruses carrying shRNA against TBLR1 or a control sequence at a multiplicity of infection (MOI) of 500. After 3 days, cells were preincubated in Krebs-Ringer buffer for 2 hrs, then cells were stimulated with 10 µM isoproterenol for 3 hrs.

value: 3T3-L1 adipocytes

tag: vector

value: Control shRNA

tag: treatment

value: 10µM isoproterenol, 3 hrs


title: TBLR1 specific shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 3

description: Gene expression data from 3T3-L1 adipocytes treated with TBLR1 specific shRNA and 10µM isoproterenol for 3 hrs

value: TBLR1 shRNA


title: LNCaP_enzalutamide 1 x 10E-6 M plus DHT 100 nM_rep2

value: 1 µM enzalutamide plus DHT 100 nM for 16hrs


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

description: Sample name: 620

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: TBLR1 specific shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 2


title: colorectal control epithelium_colitis-associated_biol repl1

description: CAC contr1

tag: strain

tag: gender

value: male

tag: tissue

tag: animals per sample

tag: experimental block


title: colorectal control epithelium_colitis-associated_biol repl2

description: CAC contr2


title: colorectal tumor_colitis-associated_biol repl1

tag: tissue origin

value: the lower 6th of the large intestine


title: TBLR1 specific shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 1

tag: cell type


title: LNCaP_enzalutamide 1 x 10E-6 M plus DHT 100 nM_rep1

tag: cell line

tag: treated with


title: LNCaP_enzalutamide 1 x 10E-6 M plus DHT 100 nM_rep3


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

description: Sample name: 612

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

value: PROSTVAC

tag: age at enrollment (years)

tag: treatment

value: Vaccine


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

description: Sample name: 628

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: timepoint


title: LNCaP_enzalutamide 1 x 10E-5 M plus vehicle_rep2

value: 10 µM enzalutamide plus vehicle for 16hrs


title: colorectal tumor_colitis-associated_biol repl2

tag: strain

tag: gender

tag: tissue

tag: animals per sample

tag: experimental block


title: Negative control shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 1

tag: cell type

tag: vector


title: LNCaP_enzalutamide 1 x 10E-5 M plus vehicle_rep3

tag: cell line

tag: treated with


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

description: Sample name: 600

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

tag: age at enrollment (years)

tag: isotype-specific secondary antibody [fluorescently labeled]


title: TBLR1 specific shRNA transduced cells, not treated with isoproterenol, replicate 3

description: Gene expression data from 3T3-L1 adipocytes treated with TBLR1 specific shRNA

tag: treatment


title: TBLR1 specific shRNA transduced cells, not treated with isoproterenol, replicate 2


title: Negative control shRNA transduced cells, treated with 10µM isoproterenol for 3 hrs, replicate 2


title: LNCaP_enzalutamide 1 x 10E-5 M plus vehicle_rep1


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

description: Sample name: 592

value: Control

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: timepoint


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

description: Sample name: 571


title: LNCaP_enzalutamide 1 x 10E-6 M plus vehicle_rep3

tag: cell type

value: 1 µM enzalutamide plus vehicle for 16hrs


title: LNCaP_enzalutamide 1 x 10E-6 M plus vehicle_rep2

value: LNCaP


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

description: Sample name: 584


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

description: Sample name: 577


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

description: Sample name: 608


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

description: Sample name: 563


title: Negative control shRNA transduced cells, not treated with isoproterenol, replicate 3

description: Gene expression data from 3T3-L1 adipocytes treated with negative control shRNA

tag: vector


title: Negative control shRNA transduced cells, not treated with isoproterenol, replicate 2


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

description: Sample name: 554


title: TBLR1 specific shRNA transduced cells, not treated with isoproterenol, replicate 1


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

description: Sample name: 546


title: Negative control shRNA transduced cells, not treated with isoproterenol, replicate 1


title: LNCaP_DHT 100 nM_rep2

source_name: LNCaP_DHT 100 nM

tag: cell line

value: left supraclavicular lymph node metastatic prostate carcinoma cells

value: 100 nM DHT for 16hrs


title: LNCaP_enzalutamide 1 x 10E-6 M plus vehicle_rep1

tag: treated with


title: LNCaP_DHT 100 nM_rep3


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

description: Sample name: 525

tag: halabi predicted survival (months)


title: AK12_PMH_48hr_10µM_Csa_2

city: Maastricht

first: Anke

last: Van Summeren

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

description:
SAMPLE 5
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO

hyb_protocol: The targets were hybridized according to the manufacturer's recommended procedures on high-density oligonucleotide GeneChips (Affymetrix Mouse Genome 430 2.0 GeneChip arrays).

scan_protocol: The GeneChips were washed and stained using a fluidics station by Affymetrix and scanned in an Affymetrix GeneArray scanner.

data_processing: First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were technically deviating.   The CustomCDF annotation (Affymetrix mouse4302) (Version 11.0.1, ENTREZG) from BrainArray Microarray  were used.  The Affymetrix .CEL files were imported in R 2.11.0 using the affy library in BioConductor. All probes were reannotated using the BrainArray customCDF files (EntrezGene, version 11.0.1), followed by a RMA normalization step. Prior to the statistical analysis all probesets (excluding  positive and negative controls spotted in the array) had to pass a detection filter criteria [Present/Marginal >= 2 out of 3 biological replicates per condition, control or treated with CsA], resulting in a total of 10,848 reporters.

label: Biotin

source_name: PMH_48hour_10µM_cyclosporin A

label_protocol: cRNA targets were prepared according to the Affymetrix protocol.

growth_protocol: Cells from three independent biological replicates with viability > 80 were used and cultured on collagen gel-precoated six-well plates at a density of 6.5 105 cells/ml. Cells were allowed to attach for 2 to 4 h at 37°C in a humidified chamber with 95:5% air/CO2 in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, 0.5 U/ml insulin, 7 ng/ml glucagon, and 2% penicillin/streptomycin (5000 U/ml penicillin; 5000 μm/ml streptomycin). After attachment, medium containing unattached cells and debris was removed by washing, and the cultures were overlaid with a second collagen layer to form a collagen-collagen sandwich culture. Primary cultures of mouse hepatocytes were cultured at 37°C in a humidified chamber with 95:5% air/CO2 in serum-free culture medium supplemented with 0.5 U/ml insulin, 7 ng/ml glucagon, 7.5 μg/ml hydrocortisone, and 2% penicillin/streptomycin (5000 U/ml penicillin; 5000 μm/ml streptomycin). Cells from three independent biological experiments (each from a different animal) were harvested at 48 h after isolation for gene expression analysis.

extract_protocol: Total RNA was isolated after  48 hours of incubation with cyclosporin A or DMSO. Total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer's instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.

treatment_protocol: The primairy mouse hepatocytes were exposed as to 10 μM cyclosporine A or 0.5 % DMSO as a vehicle control for 48 hours.

tag: strain

tag: gender

value: primary hepatocytes


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

description: Sample name: 537

tag: post-vaccination survival (months)

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

tag: treatment arm


title: AK12_PMH_48hr_10µM_Csa_3

description:
SAMPLE 6
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO


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

description: Sample name: 518

tag: age at enrollment (years)

tag: treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Non-tumor 21

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

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

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

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

source_name: Non-tumor

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

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

tag: tissue

value: Human Liver

tag: disease status

value: Non-tumor

tag: tumor stage

value: N


title: Non-tumor 20


title: AK41_PMH_48hr_0.5%_DMSO_3

description:
SAMPLE 3
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO


title: LNCaP_vehicle_rep2

value: vehicle (DMSO) for 16hrs


title: LNCaP_DHT 100 nM_rep1


title: LNCaP_vehicle_rep3


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

description: Sample name: 510

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: timepoint

value: Pre-treatment


title: AK9_PMH_48hr_0.5%_DMSO_1

description:
SAMPLE 1
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO

tag: strain

tag: cell type


title: Non-tumor 19


title: AK25_PMH_48hr_0.5%_DMSO_2

description:
SAMPLE 2
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO

tag: gender


title: Human lymphocytes gamma 3

city: Stanford

first: Leng

last: Han

address: 265 Campus Dr

institute: Stanford University

hyb_protocol: Hybridization were followed standard Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640

scan_protocol: GeneChips were scanned using theAffymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method.

source_name: Human lymphocytes-3 for 5 Gy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Extraction of lymphocyte total RNA from whole blood sample was performed according to the manufacturer's instructions.

treatment_protocol: γ-Irradiation (5 Gy)

value: Lymphocyte

value: 5 Gy gamma


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

description: Sample name: 498

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

value: Total Ig


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

description: Sample name: 489

tag: treatment arm

tag: age at enrollment (years)

tag: treatment


title: AK12_PMH_48hr_10µM_Csa_1

description:
SAMPLE 4
Gene expression data from Primary mouse hepatocytes exposed to 10µM Cyclosporin A or 0.5 % DMSO

value: male


title: MS+DOI_MD3

city: Mumbai

first: Madhurima

last: Benekareddy

state: Maharashtra

address: 1, Homibhabha Road, Colaba

department: Department of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description: Microarrays were scanned on an Agilent scanner (G2565AA) at 100% laser power, 30% PMT. Data extraction was carried out with Agilent Feature Extraction software (version 9.1), and normalization was done using linear per array algorithm according to the manufacturer’s protocol.

hyb_protocol: The labeled aRNA samples were hybridized on to a Custom Rat Array 8X15K (AMADID: 21617). 600 ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled RNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution. Laser detection of Cyanine 3 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing:
Feature extracted data was analyzed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data
1. Transformation: Set measurements less than 0.01 to 0.01,
2. Per Chip: Normalize to 50th percentile,
3. Per Gene: Normalize to Specific Samples (Control).
Differentially regulated Genes were filtered with cutoff of > 1.5 for Up regulation and < 0.66 for Down Regulation were obtained. The p-value cutoff used was 0.05.

organism: Rattus norvegicus

source_name: prefrontal cortex, MS group, DOI

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442).  Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. aRNA was generated by in vitro transcription and the dyes Cy3 CTP(Agilent) were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled aRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: 30mg of tissue was used for RNA isolation by   using Qiagen Rneasy Minikit (Cat No: 74106) as per the manufacturer’s instructions . The RNA was eluted in 30 µl of RNase free water (Ambion, AM9939). RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). RNA was stored at −80 °C until use.

tag: tissue

value: brain

tag: brain region

value: prefrontal cortex

tag: group

value: MS

value: DOI


title: MS+DOI_MD4


title: Human lymphocytes gamma 2

source_name: Human lymphocytes-2 for 5 Gy


title: Non-tumor 18

tag: disease status

tag: tumor stage


title: Transgenic harboring a CaMsrB2 overexpression system under 2 days water withdrawal (replicate 2)

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression system under 2 days water withdrawal (replicate 2)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Wild type and transgenic rice (Oryza sativa L. cv. ILMI) plants were grown under the conditions specified. Sterilized seeds were germinated in Murashige-Skoog (MS) solid medium in a growth chamber in the dark at 28°C for three days followed by in the light at 28°C for one day, transplanted into soil, and grown in a glasshouse (16 h light/8 h dark cycle) at 28-30°C. Each plant was grown in a pot (4x4x5 cm3; six plants per pot) filled with rice nursery soil (Bio-media, Kyeongju, Korea) for 6-week-old after germination. For drought stress, water was removed from the pots of 6-week-old plants, which is treated by water withholding for two days.

extract_protocol: Total and polysomal RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: genotype

value: Transgenic harboring a CaMsrB2 overexpression and Bar selection system

tag: phenotype

value: Drought-resistent

tag: cultivar

value: ILMI

value: under 2 days water withdrawal


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

description: Sample name: 482

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.

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).

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

value: Vaccine

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: LNCaP_vehicle_rep1

tag: cell line

value: LNCaP

tag: cell type

value: left supraclavicular lymph node metastatic prostate carcinoma cells

tag: treated with


title: MS+DOI_MD2

tag: tissue

tag: brain region

tag: treatment


title: Non-tumor 16

value: Human Liver

tag: disease status

value: Non-tumor

tag: tumor stage

value: N


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

description: Sample name: 474

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

tag: age at enrollment (years)

value: Pre-treatment

value: Total Ig


title: MS+DOI_MD1

value: brain

tag: group


title: Transgenic harboring a CaMsrB2 overexpression system under 2 days water withdrawal (replicate 1)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression system under 2 days water withdrawal (replicate 1)

tag: genotype

tag: phenotype

tag: cultivar


title: Non-tumor 15


title: Human lymphocytes gamma 1

source_name: Human lymphocytes-1 for 5 Gy

value: Lymphocyte

value: 5 Gy gamma


title: Human lymphocytes control 2

source_name: Human lymphocytes-2 for 0 Gy

value: control


title: Transgenic harboring a CaMsrB2 overexpression system before water withdrawal (replicate 2)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression system before water withdrawal (replicate 2)

value: Transgenic harboring a CaMsrB2 overexpression and Bar selection system

value: before water withdrawal


title: Human lymphocytes control 1

source_name: Human lymphocytes-1 for 0 Gy


title: Non-tumor 17


title: Tumor 72

source_name: Tumor

value: Tumor


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

description: Sample name: 467

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


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

description: Sample name: 459

tag: treatment


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

description: Sample name: 439

tag: halabi predicted survival (months)


title: Transgenic harboring a CaMsrB2 overexpression system before water withdrawal (replicate 3)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression system before water withdrawal (replicate 3)

value: Drought-resistent

value: ILMI


title: Human lymphocytes control 3

source_name: Human lymphocytes-3 for 0 Gy

tag: cell type


title: Tumor 71

tag: tissue

tag: disease status

tag: tumor stage


title: Tumor 69


title: Tumor 68


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

description: Sample name: 424

tag: post-vaccination survival (months)

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

tag: treatment arm

value: PROSTVAC

tag: age at enrollment (years)

value: Vaccine


title: Transgenic harboring a CaMsrB2 overexpression system before water withdrawal (replicate 1)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression system before water withdrawal (replicate 1)

tag: genotype

tag: phenotype

tag: cultivar


title: Transgenic harboring a CaMsrB2 overexpression and Bar selection system under 2 days water withdrawal (replicate 2)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression and Bar selection system under 2 days water withdrawal (replicate 2)

value: under 2 days water withdrawal


title: Tumor 70

value: Human Liver


title: Transgenic harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 3)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 3)


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

description: Sample name: 420

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: gleason score


title: K562 p42-ER_vehicle control treated_biological rep3

city: Singapore

first: Daniel

middle: G

last: Tenen

address: 14 Medical Drive, #12-01

department: Cancer Science Institute of Singapore

country: Singapore

institute: National University of Singapore

description:
K562 p42-C/EBPa-ER VC 3
Gene expression data following control treatment of the inducible C/EBPa-ER protein with vehicle control.

hyb_protocol: A total of 2.5µg of labelled cDNA, along with GeneChip Hybridization Control reagents (Affymetrix), was injected into an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. The chips were incubated for 18 hours at 45oC and rotated at 60rpm to allow hybridization. The chips were then washed and stained using the GeneChip Hybridization Wash and Stain Kit (Affymetrix) using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS 3000 with the GeneChip Operating software version 1.4.0.036.

data_processing: CEL files were normalized using the BRB-Array's RMA preprocessing function. Prediction Analysis of Microarrays (PAM, Stanford University) was used to identify probe sets which represent genes differentially expressed between two conditions.

source_name: K562 p42-C/EBPa-ER, vehicle control treated, 6 hours

label_protocol: Briefly, for each sample, 200ng of total RNA in a volume of 5µl was amplified using the Applause WT Amp ST, RNA Amplification System (NuGen, San Carlos, CA) and labelled with the Encore Biotin Module, Post–Amplification System (NuGen).

growth_protocol: K562 cells stably expressing p42-C/EBPa-ER were maintained in phenol red-free RPMI medium supplemented with 10% charcoal-stripped FBS.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini kit according to the manufacturer's instructions.

treatment_protocol: Induction of nuclear localization of C/EBPa-ER fusion protein was achieved by addition of 1 uM beta-estradiol as indicated into the culture medium. Vehicle control-treated cells were treated with 1uM ethanol.

tag: cell line

value: K562 cells stably transfected with p42 C/EBPa-ER

tag: treatment

value: ethanol vehicle control

tag: treatment duration

value: 6 hours


title: K562 p42-ER_vehicle control treated_biological rep4

description:
K562 p42-C/EBPa-ER VC 4
Gene expression data following control treatment of the inducible C/EBPa-ER protein with vehicle control.


title: Transgenic harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 1)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 1)


title: Transgenic harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 2)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression and Bar selection system before water withdrawal (replicate 2)


title: Wild type under 2 days water withdrawal (replicate2)

description: Wild type Oryza sativa L. cv. ILMI under 2 days water withdrawal (replicate2)

value: Wild-type

value: normal


title: Transgenic harboring a CaMsrB2 overexpression and Bar selection system under 2 days water withdrawal (replicate 1)

description: Transgenic Oryza sativa L. cv. ILMI harboring a CaMsrB2 overexpression and Bar selection system under 2 days water withdrawal (replicate 1)


title: Tumor 66

tag: tissue


title: K562 p42-ER_vehicle control treated_biological rep2

description:
K562 p42-C/EBPa-ER VC 2
Gene expression data following control treatment of the inducible C/EBPa-ER protein with vehicle control.


title: K562 p42-ER_estradiol treated_biological rep3

description:
K562 p42-C/EBPa-ER E2 3
Gene expression data following translocation of the inducible C/EBPa-ER protein into the nucleus with beta-estradiol.

source_name: K562 p42-C/EBPa-ER, estradiol treated, 6 hours

value: beta-estradiol


title: K562 p42-ER_estradiol treated_biological rep1

description:
K562 p42-C/EBPa-ER E2 1
Gene expression data following translocation of the inducible C/EBPa-ER protein into the nucleus with beta-estradiol.


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

city: Frederick

first: Christopher

last: Campbell

address: 376 Boyles Street

description: Sample name: 432

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

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

source_name: Serum

extract_protocol: Serum was obtained from peripheral blood samples

tag: halabi predicted survival (months)

tag: on-study psa

tag: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: K562 p42-ER_vehicle control treated_biological rep1

description:
K562 p42-C/EBPa-ER VC 1
Gene expression data following control treatment of the inducible C/EBPa-ER protein with vehicle control.


title: K562 p42-ER_estradiol treated_biological rep4

description:
K562 p42-C/EBPa-ER E2 4
Gene expression data following translocation of the inducible C/EBPa-ER protein into the nucleus with beta-estradiol.


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

description: Sample name: 412

tag: post-vaccination survival (months)

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

tag: treatment arm


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

description: Sample name: 407

tag: age at enrollment (years)


title: Tumor 65

tag: disease status

tag: tumor stage


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

description: Sample name: 398

value: Control

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Tumor 64


title: K562 p42-ER_estradiol treated_biological rep2

description:
K562 p42-C/EBPa-ER E2 2
Gene expression data following translocation of the inducible C/EBPa-ER protein into the nucleus with beta-estradiol.


title: Wild type under 2 days water withdrawal (replicate1)

description: Wild type Oryza sativa L. cv. ILMI under 2 days water withdrawal (replicate1)

tag: genotype

tag: phenotype

tag: cultivar


title: Tumor 63


title: Tumor 67


title: Tumor 62


title: Tumor 61


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

description: Sample name: 390

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: treatment


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

description: Sample name: 375

tag: halabi predicted survival (months)

tag: on-study psa


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

description: Sample name: 380

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


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

description: Sample name: 386

tag: post-vaccination survival (months)

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


title: Wild type before water withdrawal (replicate 2)

description: Wild type Oryza sativa L. cv. ILMI before water withdrawal (replicate 2)

value: before water withdrawal


title: patient L165, noncancerous liver tissue

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

description:
Gene expression profile of surgically resected material.
L165N

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

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

source_name: surgically resected material, noncancerous liver

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

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

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

tag: disease state

value: hepatocellular carcinoma (HCC)

tag: tissue

value: noncancerous liver

tag: multicentric occurrence-free survival (days)

tag: event

value: no multicentric occurrence

tag: patient id


title: Wild type before water withdrawal (replicate 1)

description: Wild type Oryza sativa L. cv. ILMI before water withdrawal (replicate 1)

tag: genotype

value: ILMI


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

institute: NCI

description: Sample name: 372

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)


title: Tumor 59

tag: disease status

value: Tumor

tag: tumor stage


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

description: Sample name: 368

tag: halabi predicted survival (months)

value: PROSTVAC

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: treatment

value: Vaccine


title: patient L157, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L157N

tag: disease state


title: Wild type before water withdrawal (replicate 3)

description: Wild type Oryza sativa L. cv. ILMI before water withdrawal (replicate 3)

tag: phenotype

tag: cultivar


title: patient L163, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L163N

tag: tissue

tag: multicentric occurrence-free survival (days)

tag: event


title: Tumor 60

value: Human Liver


title: Non-tumor 13

value: Non-tumor

value: N


title: Non-tumor 14


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

description: Sample name: 365

tag: post-vaccination survival (months)

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

tag: treatment arm

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


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

description: Sample name: 357

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)


title: Non-tumor 12

tag: disease status

tag: tumor stage


title: patient L154, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L154N

tag: patient id


title: 252800411248-8

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: A549 pmiR-210 48h vs A549 pmiR-67 48h

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: LimmaGUI differential expression analysis with lowess intra-slide normalization and quantile inter-slide normalization.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen

tag: cell line

tag: amount in (µg)

tag: origin

value: Lung


title: 252800411248-5

description: A549 pmiR-67 24h vs A549 pmiR-210 24h


title: Non-tumor 10

tag: tissue


title: Non-tumor 11


title: 252800411248-7

description: A549 pmiR-67 48h vs A549 pmiR-210 48h


title: patient L71, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L71N

tag: disease state

tag: multicentric occurrence-free survival (days)

value: multicentric occurrence


title: Non-tumor 9


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

description: Sample name: 326

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

tag: post-vaccination igg titer for fowlpox

tag: gleason score

tag: on-study psa

tag: treatment


title: patient L155, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L155N

tag: event


title: patient L108, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L108N


title: patient L144, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L144N


title: patient L150, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L150N


title: patient L143, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L143N


title: patient L147, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L147N


title: Non-tumor 8


title: patient L141, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L141N


title: patient L140, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L140N


title: patient L137, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L137N


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

description: Sample name: 342

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: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


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

description: Sample name: 334


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

description: Sample name: 298


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

description: Sample name: 312


title: Non-tumor 7

tag: tissue

tag: disease status

tag: tumor stage


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

description: Sample name: 287

tag: halabi predicted survival (months)


title: Non-tumor 5


title: Non-tumor 6


title: Non-tumor 3


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

description: Sample name: 276

tag: post-vaccination survival (months)


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

description: Sample name: 279

tag: post-vaccination igg titer for fowlpox


title: Non-tumor 4


title: Non-tumor 2


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

description: Sample name: 267

tag: gleason score


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

description: Sample name: 271

tag: on-study psa


title: Non-tumor 1


title: Tumor 58


title: Tumor 57


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

description: Sample name: 257

tag: treatment


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

description: Sample name: 252


title: Tumor 56


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

description: Sample name: 240


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

description: Sample name: 247


title: Tumor 55


title: Tumor 54


title: patient L127, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L127N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


title: patient L110, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L110N


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

description: Sample name: 233

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

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: patient L130, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L130N

tag: tissue


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

description: Sample name: 221

tag: age at enrollment (years)

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Tumor 53

tag: disease status

tag: tumor stage


title: patient L111, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L111N


title: 252800411248-6

description: A549 pmiR-210 24h vs A549 pmiR-67 24h

tag: cell line

tag: amount in (µg)

tag: origin


title: patient L107, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L107N

tag: disease state


title: patient L109, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L109N

tag: multicentric occurrence-free survival (days)


title: patient L134, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L134N

tag: event


title: patient L121, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L121N

tag: patient id


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

description: Sample name: 218

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

tag: on-study psa

tag: treatment


title: patient L123, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L123N

tag: tissue


title: patient L128, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L128N


title: patient L126, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L126N


title: patient L120, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L120N


title: patient L122, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L122N


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

description: Sample name: 210

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Tumor 52

tag: disease status

tag: tumor stage


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

description: Sample name: 202


title: Tumor 51


title: patient L105, noncancerous liver tissue

description:
Gene expression profile of surgically resected material.
L105N

tag: disease state

tag: multicentric occurrence-free survival (days)

tag: event

tag: patient id


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

description: Sample name: 192

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


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

description: Sample name: 184

tag: gleason score

tag: on-study psa

tag: treatment


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

description: Sample name: 197

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Tumor 50

tag: tissue


title: Tumor 47

tag: disease status


title: Tumor 48

tag: tumor stage


title: Tumor 49


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

description: Sample name: 177

tag: age at enrollment (years)

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Tumor 46


title: Tumor 45