title: Ras-overexpression - replicate 3

description: mouse ventral prostate


title: Ras-overexpression - replicate 2

status: Public on Apr 01 2013

type: RNA

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

description: mouse ventral prostate

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99C for 2 min. and then 45C for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse ventral prostate

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: the transformed cell lines are already stable prostate cancer cell lines, so growing transformed cells in DMEM medium with 10% FBS, while control PEC cells were cultured in prostate epithelial primary culture medium, change to normal DMEM medium with 10% FBS one night before harvest.

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

treatment_protocol: no special treatment to the cells before harvest, collected the cells when the confluence 85-90%

tag: strain

value: FVB

tag: transduction

value: transformed by ha-ras gene

tag: tissue

value: Primary prostate epithelial cell culture, oncogene-transduced


title: adenocarcinoma-279

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data normalized by quantile normalization with limma in R. Probes with present/absent call ≥ 0.05 assessed by Illumina Beadstudio software were treated as absent in analysis.

organism: Homo sapiens

source_name: adenocarcinoma

label_protocol: Biotin-NTP mix with T7 enzyme mix was used to make biotinylated cRNAs. The labeled cRNAs were purified, quantified, and checked again with Bioanalyzer.

extract_protocol:
Samples were extracted from human patients during surgical resection of lung tumors.
RNA was extracted with Trizol followed by DNAse I treatment and purification (RNeasy RNA purification kit, Qiagen). The purified RNA was quantified with Nanodrop and checked by Bioanalyzer for the quality.

tag: Sex

value: M


title: adenocarcinoma-24


title: E12.5_male_gonad_Cyp26b1 knockout_rep1and2

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

country: Japan

institute: National Institute of Genetics

description: Gene expression E12.5 mouse male gonad Cyp26b1 knockout

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
All gene list of E12.5-15.5 wild type and E12.5-14.5 Cyp26b1-targeted male gonad
The following normalization steps were applied: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median.
Averaged normalized signal intensities and flag calling for all genes of wild type and Cyp26b1-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).

source_name: embryonic male gonad

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Embryonic gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: gonad

value: male

tag: embryonic day

tag: genotype

tag: mouse line

value: MCH


title: adenocarcinoma-113

value: F


title: adenocarcinoma-139


title: E13.5_male_gonad_Cyp26b1 knockout_rep1and2

description: Gene expression E13.5 mouse male gonad Cyp26b1 knockout


title: E14.5_male_gonad_wild type_rep1and2

description: Gene expression E14.5 mouse male gonad wild type

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The following normalization steps were applied: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median.
Averaged normalized signal intensities and flag calling for all genes of wild type and Cyp26b1-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).

value: wild type


title: NeuT-overexpression - replicate 3

description: mouse ventral prostate

value: transformed by neuT gene


title: adenocarcinoma-428


title: adenocarcinoma-427


title: adenocarcinoma-452


title: adenocarcinoma-408


title: E13.5_male_gonad_wild type_rep1and2

description: Gene expression E13.5 mouse male gonad wild type


title: Src-overexpression - replicate 1

description: mouse ventral prostate

value: transformed by v-src gene


title: Myc overexpression - replicate 3

description: mouse ventral prostate

value: transformed by c-myc gene


title: E12.5_male_gonad_wild type_rep1and2

description: Gene expression E12.5 mouse male gonad wild type


title: NeuT-overexpression - replicate 1

description: mouse ventral prostate


title: adenocarcinoma-420


title: NeuT-overexpression - replicate 2

description: mouse ventral prostate


title: adenocarcinoma-513


title: adenocarcinoma-496


title: E14.5_male_gonad_Cyp26b1 knockout_Stra8 knockout_rep1and2

description: Gene expression E14.5 mouse male gonad Cyp26b1 knockout Stra8 knoctout

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The following normalization steps were applied: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median.
Averaged normalized signal intensities and flag calling for all genes of Cyp26b1- and Stra8-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).


title: E14.5_male_gonad_Cyp26b1 wild type_Stra8 wild type_rep1and2

description: Gene expression E14.5 mouse male gonad Cyp26b1 wild type Stra8 wild type


title: Myc overexpression - replicate 2

description: mouse ventral prostate


title: E14.5_male_gonad_Cyp26b1 knockout_Stra8 wild type_rep1and2

description: Gene expression E14.5 mouse male gonad Cyp26b1 knockout Stra8 wild type


title: adenocarcinoma-489


title: Myc overexpression - replicate 1

description: mouse ventral prostate


title: adenocarcinoma-494


title: adenocarcinoma-626


title: adenocarcinoma-476


title: adenocarcinoma-614


title: adenocarcinoma-621


title: PEC control - replicate 2

description: mouse ventral prostate

value: Primary prostate epithelial cell culture


title: PEC control - replicate 1

description: mouse ventral prostate


title: adenocarcinoma-483


title: MuRF1 +/- // MuRF2 -/-:  Biological replicate 4.

city: Chapel Hill

first: Monte

middle: Shaw

last: Willis

state: NC

address: 103 Mason Farm Road, MBRB 2340B

department: Pathology & Laboratory Medicine

institute: University of North Carolina

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner. Images were quantified using Genepix Pro (version 6.0).

data_processing: LOWESS normalized, background subtracted data obtained from processed Red signal/processed Green signal by Genepix Pro V 6.0. Data was subsequently downloaded and filtered for features present in less than 70% of arrays.

source_name: Total RNA from murine heart labeled with Cyanine-5 (red).

label_protocol: 50 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

extract_protocol: Total RNA extracted using Qiagen All-Prep kit following manufacturer's instructions

tag: Cardiac tissue

tag: untreated

source_name: Total RNA from pooled whole mouse neonates (day 1), labeled with Cyanine-3 (green).

tag: Strain

tag: Age

value: postnatal Day 1

tag: Tissue

value: whole pup


title: adenocarcinoma-629


title: MuRF1 +/- // MuRF2 -/-:  Biological replicate 3.


title: adenocarcinoma-611


title: adenocarcinoma-613


title: adenocarcinoma-9705


title: MuRF1 +/- // MuRF2 -/-:  Biological replicate 1.


title: MuRF1 +/- // MuRF2 -/-:  Biological replicate 2.


title: adenocarcinoma-9718


title: PEC control - replicate 3

description: mouse ventral prostate


title: AGO2 IP RNA vs Total RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Total RNA

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

extract_protocol: Total RNA was extracted from mouse adult testes using ISOGEN following manufacturer's instructions. AGO2 IP RNA or PIWIL1 IP RNA was extracted from mouse adult testes following below protocol. Mouse adult testes (approximately 50 mg) were homogenized in 1 mL of cell lysis buffer (20 mM Tris-HCl pH7.4, 2.5 mM MgCl2, 200 mM NaCl, 0.05 % NP40), and the cell lysate was cleared by centrifugation at 20000×g for 20 min at 4℃. After filtration with 0.45 μm filter of the cell lysate, 20 μL of Protein G-coupled beads (Dynal) bound with 5 μg of anti-PIWIL1 monoclonal antibody (2C12) or anti-AGO2 monoclonal antibody (3E7) was added to the cell lysate and mixed by rotation for 3 hours at 4℃. The beads were washed three times with 1mL of cell lysis buffer, and immunoprecipitated protein-RNA complex were eluted with 0.5% SDS solution. The eluted RNA included in immunoprecipitated complex was extracted with phenol / chloroform, and precipitated with ethanol and Ethachinmate (Nippon Gene).

tag: developmental stage

value: adult

value: testes

source_name: AGO2 IP RNA


title: MuRF1 +/+ // MuRF2 +/+:  Biological replicate 4.


title: PIWIL1 IP RNA vs Total RNA

source_name: PIWIL1 IP RNA


title: PBMC_9_30

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

description: 3 Year_TOL

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing:
Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish
probe group file: HuGene-1_1-st-v1.r4.pgf
meta-probeset file: HuGene-1_1-st-v1.r4.mps

label: SAPE

source_name: Recipient 9; 3 Year; Tolerant

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

tag: recipient

value: Peripheral Blood

tag: time-point

value: 3 Year

tag: induction

value: Alemtuzumab

tag: tolerance

value: Tolerant


title: adenocarcinoma-386

value: M


title: adenocarcinoma-378


title: adenocarcinoma-628


title: MuRF1 -/- // MuRF2 -/-:  Biological replicate 4.


title: adenocarcinoma-9747


title: F3-II3

type: genomic

city: Nijmegen

first: Ingrid

last: Vogelaar

address: Geert Grooteplein Zuid 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Centre

description: germline sample patient with two MLH1 variants

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from two times 250 ng genomic DNA ((Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix) using an Affymetrix scanner 3000.

data_processing: Genotyping information obtained using Affymetrix Genotyping Concole software (v2.1)

molecule: genomic DNA

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from two times 250 ng genomic DNA (Genome-Wide Human SNP Nsp/Sty 6.0 User Guide manual 702504 Rev.1, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

value: Blood

value: carrier of MLH1 variants


title: MuRF1 -/- // MuRF2 +/-:  Biological replicate 4.


title: Patient 31, Atheroma plaque

city: Lyon

first: Catherine

last: Cerutti

address: 8 avenue Rockefeller

country: France

institute: Université Lyon 1 & Hôpital Nord-Ouest

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_83

hyb_protocol: cRNAs were hybridized for 16 hours at 45oC on GeneChip® Human Gene 1.0 ST arrays using the GeneChip® Hybridization Oven 640 (Affymetrix).

scan_protocol: The GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned using the GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: The data were analyzed with Expression Console v1.1 software using the default RMA summarization method.

source_name: Carotid atheroma plaque obtained from endarterectomy

label_protocol: Biotinylated cRNAs were prepared by IGBMC Microarray and Sequencing Platform according to the standard Affymetrix protocol from 1 ug total RNA.

tag: patient

tag: disease state

value: hypertension

value: Atheroma plaque


title: Patient 32, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_85

tag: tissue


title: Patient 32, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_84

source_name: Macroscopically intact carotid tissue adjacent to the atheroma plaque

value: Macroscopically intact tissue


title: adenocarcinoma-375

tag: Sex

value: F


title: adenocarcinoma-356


title: MuRF1 +/+ // MuRF2 +/+:  Biological replicate 3.


title: adenocarcinoma-289


title: MuRF1 -/- // MuRF2 -/-:  Biological replicate 3.


title: adenocarcinoma-9843


title: adenocarcinoma-9801


title: Patient 31, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_82


title: F3-II2


title: adenocarcinoma-9739


title: F2-II3


title: F1-II2


title: adenocarcinoma-535


title: adenocarcinoma-525


title: Patient 29, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_79


title: adenocarcinoma-9897


title: Patient 29, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_78


title: adenocarcinoma-520


title: adenocarcinoma-9908


title: Patient 30, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_80


title: adenocarcinoma-355


title: adenocarcinoma-9864


title: MuRF1 -/- // MuRF2 +/-:  Biological replicate 1.


title: MuRF1 -/- // MuRF2 -/-:  Biological replicate 2.


title: MuRF1 -/- // MuRF2 +/-:  Biological replicate 3.


title: adenocarcinoma-9896


title: MuRF1 +/+ // MuRF2 +/+:  Biological replicate 2.


title: MuRF1 -/- // MuRF2 +/-:  Biological replicate 2.


title: MuRF1 +/+ // MuRF2 +/+:  Biological replicate 1.


title: Patient 30, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_81


title: adenocarcinoma-9875


title: adenocarcinoma-516


title: adenocarcinoma-506


title: Patient 28, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_77


title: MuRF1 -/- // MuRF2 -/-:  Biological replicate 1.


title: adenocarcinoma-607


title: adenocarcinoma-9853


title: adenocarcinoma-593


title: Cebpaf/f -4-hydroxytamoxifen replicate 2

city: Denver

first: Xiaopeng

last: Qi

state: CO

address: 1400 Jackson Street,

institute: National Jewish health

description: Cebpa f/f basophils without 4-hydrotamoxifen treatment

hyb_protocol: Fragmented cDNA was hybridized at 42˚C overnight using the HybBag mixing system with 1× OneArray Hybridization Buffer (Phalanx Biotech, Belmont, CA, USA), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics Axon 4100A scanner, and measured using GenePixPro Software

data_processing: Statistical analysis of the datasets was performed with GeneSpring software using an unpaired t-test (p<0.01). The false discovery rate (FDR) was calculated using the Benjamini Hochberg FDR multiple testing correction.

source_name: untreated basophil

label_protocol: Cy5.5 NHS ester (GE Healthcare)

growth_protocol: Purifed basophils were cultrured in  complete Iscove's Modified Dulbecco Minimum Essential Medium (IDMEM) medium supplemented with IL-3 (20 ng/ml) for 5 days

extract_protocol: Trizol plus RNA purification system (RNAeasy Mini Kit, Qiagen)

treatment_protocol: without 4-hydrotamoxifen treatment

tag: strain

tag: genotype/variation

value: Cebpa f/f RosaYFP/creER

value: basophil

tag: treatment


title: Patient 28, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_76


title: F2-II1

tag: genotype


title: adenocarcinoma-575


title: adenocarcinoma-565


title: Cebpaf/f +4-hydroxytamoxifen replicate 3

description: Cebpa knock out basophils

source_name: 4-hydroxytamoxifen treated basophil

treatment_protocol: 4-hydroxytamoxifen (100 nM) treatment for 5 days


title: adenocarcinoma-327


title: adenocarcinoma-360


title: Patient 27, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_75


title: Patient 26, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_73


title: Cebpaf/f +4-hydroxytamoxifen replicate 2

description: Cebpa knock out basophils


title: Cebpaf/f -4-hydroxytamoxifen replicate 1


title: adenocarcinoma-559


title: adenocarcinoma-353


title: Patient 27, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_74


title: adenocarcinoma-316


title: Patient 26, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_72


title: adenocarcinoma-309


title: adenocarcinoma-329


title: adenocarcinoma-556


title: adenocarcinoma-364


title: Cebpaf/f +4-hydroxytamoxifen replicate 1

description: Cebpa knock out basophils


title: Cebpa+/+ -4-hydroxytamoxifen replicate 3

description: wild type basophils without 4-hydrotamoxifen treatment

value: Cebpa +/+ RosaYFP/creER


title: adenocarcinoma-310


title: PBMC_9-24

description: 2 Year_TOL

source_name: Recipient 9; 2 Year; Tolerant

value: 2 Year


title: Patient 25, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_71


title: Patient 25, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_70


title: adenocarcinoma-291


title: adenocarcinoma-295


title: adenocarcinoma-112


title: Cebpa+/+ -4-hydroxytamoxifen replicate 2


title: adenocarcinoma-219


title: Patient 24, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_69


title: Patient 24, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_68


title: Cebpa+/+ +4-hydroxytamoxifen replicate 3

description: wild type basophils treated with 4-hydrotamoxifen


title: Patient 23, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_67


title: Cebpa+/+ +4-hydroxytamoxifen replicate 2


title: Cebpa+/+ -4-hydroxytamoxifen replicate 1


title: adenocarcinoma-90


title: adenocarcinoma-284


title: Patient 22, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_64


title: adenocarcinoma-57


title: adenocarcinoma-80


title: adenocarcinoma-225


title: adenocarcinoma-224


title: Patient 22, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_65


title: adenocarcinoma-222


title: Mast cell replicate 3

description: mast cell derived from bone marrow

source_name: Mast cell

growth_protocol: Bone marrow cells were cultured in complete Iscove's Modified Dulbecco Minimum Essential Medium (IDMEM) medium supplemented with IL-3 (20 ng/ml) for 4 weeks

value: mast cell derived from bone marrow


title: uninvolved.tissue-9705


title: Patient 23, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_66


title: Mast cell replicate 2

description: mast cell derived from bone marrow


title: Mast cell replicate 1

description: mast cell derived from bone marrow


title: uninvolved.tissue-621


title: Cebpa+/+ +4-hydroxytamoxifen replicate 1


title: Patient 21, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_63


title: uninvolved.tissue-629


title: uninvolved.tissue-353


title: Patient 21, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_62


title: uninvolved.tissue-356


title: Basophil replicate 3

description: Il3c expaned basophil

source_name: Basophil

growth_protocol: Basophils were purified from bone marrow cells of mice that were injected with IL-3 and anti-IL-3 immune complex 3 days prior to bone marrow collection.

value: purified basophils from bone marrow


title: uninvolved.tissue-614


title: uninvolved.tissue-626


title: Patient 20, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_59


title: Basophil replicate 1

description: Il3c expaned basophil


title: Basophil replicate 2

description: Il3c expaned basophil


title: Patient 20, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_60


title: uninvolved.tissue-355


title: uninvolved.tissue-329


title: uninvolved.tissue-338


title: uninvolved.tissue-327


title: Cebpaf/f -4-hydroxytamoxifen replicate 3

description: Cebpa f/f basophils without 4-hydrotamoxifen treatment


title: prostate cancer cell PC-3 Sphere

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

country: China

institute: Sun Yat-sen Memorial Hospital

hyb_protocol: We followed the manufacturer's protocol of the mirVana(TM) miRNA bioarray.

scan_protocol: We followed the manufacturer's protocol, and used LuxScan TM 10K(CapitalBio, Ltd) to scan the microarray.The images of the hybridized arrays were processed with GenePix Pro 6.0 (Axon, Ltd) and signal intensities quantified

data_processing: We used DMVS (Chipscreen Biosciences, Ltd.) for quantification. We performed global median normalization and probe summarization by average.

source_name: Spherical prostate cancer cells (PC-3)

label_protocol: We used the mirVana(TM) miRNA Labeling kit (Ambion) following the manufacturer's protocol

growth_protocol: The human prostate cancer cell PC-3 (ATCC, Manassas, VA) is cultured in RPMI-1640 medium (Gibco, Invitrogen) supplemented with 10 % FBS (Hyclone)

extract_protocol: We used the TRIzol Reagent (Life Technologies) and mirVana(TM) Isolation Kit following the manufacturer's protocol.

treatment_protocol: In order to enrich the prostate CSCs, PC-3 cells were grown to 90 % confluence, trypsinized, and plated at a density of 1,000 cells/ml in serum-free DMEM/F12 medium (Gibco, Invitrogen) containing 20 ng/ml epidermal growth factor (EGF, R and D Systems, MN), 5 μg/ml insulin, 0.4 % bovine serum albumin (Sigma, St. Louis, MO), and 2 % B27 (Invitrogen, CA) in 10 cm2 culture dishes.

tag: cell line

tag: culture

value: non-adherent spheres culture

tag: cancer stem cells property

value: Yes


title: Patient 19, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_58


title: uninvolved.tissue-139


title: prostate cancer cell PC-3

source_name: Adherent prostate cancer cells (PC-3)

value: adhere culture

value: No


title: uninvolved.tissue-102


title: uninvolved.tissue-24

value: M


title: uninvolved.tissue-9864


title: Patient 17, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_53


title: uninvolved.tissue-146


title: Patient 17, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_54


title: Patient 18, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_56


title: Patient 19, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_57


title: uninvolved.tissue-9897


title: uninvolved.tissue-113


title: uninvolved.tissue-9908


title: Patient 16, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_50


title: Patient 18, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_55


title: uninvolved.tissue-9875


title: uninvolved.tissue-9896


title: uninvolved.tissue-195


title: uninvolved.tissue-219


title: Patient 16, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_49


title: uninvolved.tissue-112


title: uninvolved.tissue-90


title: Patient 15, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_47


title: Patient 15, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_48


title: uninvolved.tissue-57


title: uninvolved.tissue-408


title: uninvolved.tissue-80


title: uninvolved.tissue-386


title: uninvolved.tissue-378


title: [liver]-[mthr-/-]-[animal 6]

city: Düsseldorf

first: Thor

last: Gehrmann

address: Moorenstrasse 5

department: Klinik für Gastroenterologie

country: Germany

institute: Universitätsklinikum Düsseldorf

hyb_protocol: The fluorescence labelled cDNA was dissolved in hybridization buffer, denaturated and injected in a Tecan HS400pro hybridization station (Tecan Deutschland GmbH, Crailsheim, Germany).

scan_protocol: Hybridized oligonucleotide arrays were visualized with a Fuji FLA 8000-Scanner (Raytest, Straubenhardt, Germany).

data_processing: The image analysis was computed with AIDA Array Analysis 3.5 (Raytest, Straubenhardt, Germany). The fluorescence intensities from each spot were integrated and the background intensities derived from weighted image regions were subtracted. The normalization was performed using a global approach. Only the 50% upper values were used. The mean value of the four replicates from one array was calculated. Clear artefacts resulting from dust, salt crystals etc were deleted. In a next step, the median normalized intensity for a specific condition was calculated from four arrays. Genes with a signal smaller 10 under all experimental conditions, which implies a signal to noise ratio smaller 2.5, were declared as “not detectable”.

label_protocol: 50 µg of total RNA served as template for synthesis of the fluorescence labelled cDNA. The direct labelling with Cye3-dUTP (GE Healthcare Europe, München, Germany) was performed with Oligo-dT primers through the CyeScribe-Kit (GE Healthcare Europe, München, Germany). Unincorporated dye was removed with QIAquick PCR columns (Qiagen GmbH, Hilden, Germany).

growth_protocol: Animals were kept on standard chow in a climatized environment. Five weeks after weaning, drinking water of homozygous animals was supplemented with 2%(w/v) betaine to ensure survival in the critical first weeks of life.

extract_protocol: Total RNA from cells was prepared with the RNeasy Midi Kit (Qiagen GmbH, Hilden, Germany). The amount and quality of the RNA was tested spectrometrically (absorption 220nm – 350nm) and by capillary electrophoresis (Bioanalyzer, Agilent Technologies Inc., Palo Alto, CA, U.S.A.).

treatment_protocol: no special treatment applied

tag: strain background

value: mthr-/-

tag: gender

value: female

tag: age

value: liver

tag: cell type

value: primary hepatocytes


title: [liver]-[mthr-/-]-[animal 5]

value: male


title: [liver]-[mthr-/-]-[animal 4]


title: [liver]-[mthr-/-]-[animal 7]


title: [liver]-[mthr-/-]-[animal 2]


title: [liver]-[mthr-/-]-[animal 1]


title: uninvolved.tissue-375

value: F


title: uninvolved.tissue-360


title: uninvolved.tissue-364


title: Patient 13, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_44

value: hypertension

value: Atheroma plaque


title: Patient 14, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_46


title: Patient 12, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_42


title: Patient 14, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_45

value: Macroscopically intact tissue


title: uninvolved.tissue-9843


title: uninvolved.tissue-9718


title: [liver]-[wild type]-[animal 7]

source_name: liver_wild type

value: wild type


title: uninvolved.tissue-516


title: uninvolved.tissue-9739


title: Patient 13, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_43


title: uninvolved.tissue-9801


title: [liver]-[mthr-/-]-[animal 3]


title: Patient 12, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_41


title: Patient 11, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_40


title: uninvolved.tissue-506


title: [liver]-[wild type]-[animal 6]


title: uninvolved.tissue-513


title: uninvolved.tissue-9803


title: uninvolved.tissue-497


title: uninvolved.tissue-494


title: Patient 11, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_39


title: [liver]-[wild type]-[animal 4]


title: [liver]-[wild type]-[animal 3]


title: [liver]-[wild type]-[animal 5]


title: uninvolved.tissue-9747


title: [liver]-[wild type]-[animal 2]


title: uninvolved.tissue-613


title: [liver]-[wild type]-[animal 1]


title: Patient 9, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_36


title: uninvolved.tissue-611


title: uninvolved.tissue-496


title: uninvolved.tissue-607


title: Patient 10, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_37


title: uninvolved.tissue-575


title: uninvolved.tissue-593


title: Patient 10, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_38


title: Patient 9, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_35


title: Validation patient #117 | Control Arm | Pre-treatment [Total Ig 1:200]

type: other

city: Frederick

first: Christopher

last: Campbell

state: MD

address: 376 Boyles Street

institute: NCI

description: Sample name: 852

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: timepoint

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: uninvolved.tissue-289

tag: Sex


title: Patient 8, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_29

tag: patient

tag: disease state

tag: tissue


title: uninvolved.tissue-284


title: Patient 8, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_30


title: Validation patient #116 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 847

value: PROSTVAC

tag: treatment

value: Vaccine


title: uninvolved.tissue-231


title: Patient 7, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_24


title: uninvolved.tissue-224


title: uninvolved.tissue-310


title: uninvolved.tissue-222


title: uninvolved.tissue-565


title: Validation patient #114 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 837

tag: halabi predicted survival (months)


title: uninvolved.tissue-316


title: Validation patient #113 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 830

tag: post-vaccination survival (months)


title: Validation patient #115 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 842

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


title: uninvolved.tissue-225


title: Validation patient #112 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 826

tag: treatment arm


title: uninvolved.tissue-293


title: Validation patient #110 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 816

tag: pre-vaccination igg titers for vaccinia


title: Validation patient #111 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 822

tag: post-vaccination igg titers for vaccinia


title: uninvolved.tissue-309


title: Patient 6, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_22


title: Patient 7, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_23


title: uninvolved.tissue-291


title: uninvolved.tissue-556


title: uninvolved.tissue-295


title: uninvolved.tissue-559


title: Patient 5, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_13


title: uninvolved.tissue-525


title: Patient 6, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_21


title: Validation patient #109 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 810

tag: post-vaccination igg titer for fowlpox


title: Patient 4, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_12


title: uninvolved.tissue-418


title: Patient 5, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_14


title: uninvolved.tissue-373


title: Validation patient #108 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 802

tag: age at enrollment (years)


title: Patient 4, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_11


title: Validation patient #107 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 798

tag: gleason score


title: uninvolved.tissue-9853


title: uninvolved.tissue-535


title: uninvolved.tissue-312


title: uninvolved.tissue-304


title: Validation patient #106 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 793

tag: on-study psa


title: uninvolved.tissue-527


title: Patient 3, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_8


title: uninvolved.tissue-279


title: Patient 2, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_4


title: uninvolved.tissue-544


title: uninvolved.tissue-267


title: uninvolved.tissue-585


title: uninvolved.tissue-470


title: Patient 3, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_7


title: Validation patient #105 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 787

tag: timepoint


title: uninvolved.tissue-753


title: Validation patient #104 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 781

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #103 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 776


title: Validation patient #102 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 769


title: uninvolved.tissue-452

tag: Sex


title: Validation patient #101 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 762


title: uninvolved.tissue-436


title: Patient 1, Atheroma plaque

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_2

tag: patient


title: uninvolved.tissue-427


title: uninvolved.tissue-449


title: Validation patient #100 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 752


title: uninvolved.tissue-428


title: Patient 1, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_1

tag: disease state


title: uninvolved.tissue-583


title: Patient 2, Macroscopically intact tissue

description:
Gene expression data from paired samples of carotid atheroma plaque and macroscopically intact tissue
JLI_3

tag: tissue


title: Validation patient #99 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 745

tag: treatment


title: uninvolved.tissue-489


title: Myocytes derived from human myoblast cell line 2

city: Kyoto

first: Hidetoshi

last: Sakurai

address: 53 Shogoin-Kawahara-cho, Sakyo-ku

institute: Center for iPS Cell Research and Application

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpringGX software. Datas were normalized with RMA algorithms.

source_name: human myoblast cell line

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol.  Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: HiPSCs were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells. Human myoblast cells were cultured in DMEM containing 15% FBS.

extract_protocol: Total RNA were extracted using RNeasy Mini Kit (QIAGEN) according to manufacture's instruction.

treatment_protocol: Forced expression of MyoD on undifferentiated hiPSCs was performed about a week. Human myoblast cells were treated by medium replacement to DMEM containing lower serum.

tag: cell type

value: Myocytes differentiated from human myoblast cell line

tag: cell line


title: uninvolved.tissue-493


title: uninvolved.tissue-420


title: Validation patient #98 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 738

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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


title: uninvolved.tissue-483

value: M


title: Myocytes derived from human myoblast cell line 1


title: Validation patient #95 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 709

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: Validation patient #94 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 704

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: uninvolved.tissue-482


title: Myocytes derived from hiPSCs 5

source_name: iPSCs

value: Myocytes differentiated from hiPSCs


title: Myocytes derived from hiPSCs 4


title: Myocytes derived from hiPSCs 3


title: wt 1st instar larvae, biological replicate 1

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: Gene expression data from 1st instar larvae

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Raw data was normalized using RMA (R and Bioconductor).

organism: Drosophila melanogaster

source_name: Drosophila 1st instar larvae

label_protocol: Standard Affymetrix

growth_protocol: Flies were cultivated and crossed in vials with potato-yeast-agar medium at 25 ̊ C. Egg laying was performed at 25 ̊ C on apple-agarose plates with partial addition of yeast.

extract_protocol: Trizol (Invitrogen) extraction of total RNA followed by purification using Rneasy kit (Qiagen) was performed according to the manufacturer's instructions.

treatment_protocol: 1st instar larvae were collected approximately 48 after egg laying and were immediately frozen at -80 ̊ C prior to RNA extraction. 200 larvae per replicate were collected.

tag: Stage

value: 1st instar larvae

tag: genotype

value: dKDM4A precise KG06436 / dKDM4A precise NP0618


title: dkdm4a mutant, biological replicate 3

value: dKDM4A KG04636 / ∆dKDM4A


title: wt 1st instar larvae, biological replicate 2


title: Validation patient #97 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 729

tag: on-study psa

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #92 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 678

tag: treatment


title: uninvolved.tissue-471

tag: Sex


title: dkdm4a mutant, biological replicate 2


title: uninvolved.tissue-476


title: healthy control, male [D1CV]

city: Donostia - San Sebastián

first: Aritz

last: Irizar

address: Pº Dr. Beguiristain, s/n

department: Neuroscience Area

country: Spain

institute: Biodonostia Research Institute

description: Gene expression data from peripheral blood leukocytes of a healthy control, male

hyb_protocol: 5.5 ug of ssDNA were hybridized for 16 hours in a GeneChip Human Gene 1.0 ST Array.GeneChips were washed and stained in a Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned in a Affymetrix GeneChip Scanner 7G

data_processing: Data analysis was done with the Affymetrix Expression Console using the GC-RMA as normalization and summarization method.

source_name: healthy control, male

label_protocol: After fragmentation, ssDNA was labelled with DNA labeling reagent according to the Whole transcript (WT) Sense Target Label Assay protocol by Affymetrix

extract_protocol: Total RNA extraction from peripheral blood leukocytes with the Leucolock kit from Ambion, according to the manufaturer's alternative protocol to capture total RNA

tag: tissue

value: peripheral blood leukocytes

tag: gender

value: male

tag: disease status

value: control

tag: age


title: Undifferentiated hiPSCs

tag: cell type

value: iPSCs generated with Yamanaka 4 factors

tag: cell line


title: GM19171_EtOH_8h

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

data_processing: The data were normalised using quantile normalisation with LUMI in R

source_name: Lymphoblastoid cell lines

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: LCLs were grown according to standard protocols in RPMI supplemented with 15% charcoal-stripped fetal bovine serum

extract_protocol: RNA was extracted with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were treated with either EtOH (vehicle) or 1micromolar dexamethasone

value: EtOH

tag: time


title: GM19171_Dex_8h

value: Dex


title: GM19171_EtOH_16h


title: Myocytes derived from hiPSCs 1


title: Validation patient #93 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 696

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: dkdm4a mutant, biological replicate 1

tag: Stage

tag: genotype


title: Myocytes derived from hiPSCs 2


title: Validation patient #91 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 670

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: treatment

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: GM19171_EtOH_2h

tag: cell line


title: wt 1st instar larvae, biological replicate 3


title: Validation patient #90 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 664


title: GM19171_Dex_4h

tag: time


title: healthy control, female [D6_CM_2]

description: Gene expression data from peripheral blood leukocytes of a healthy control, female

source_name: healthy control, female

tag: tissue

tag: gender

value: female

tag: disease status

tag: age


title: Validation patient #88 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 648

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

value: Pre-treatment


title: GM19171_Dex_16h


title: GM19171_Dex_2h


title: Validation patient #89 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 656

value: Control

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

value: Total Ig


title: Validation patient #86 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 636

value: PROSTVAC

tag: gleason score

tag: on-study psa

tag: treatment

value: Vaccine


title: Validation patient #87 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 640

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: GM19171_EtOH_12h

tag: cell line

tag: time


title: Validation patient #84 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 620


title: Validation patient #85 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 628


title: GM19171_EtOH_24h


title: healthy control, male [D10CV]

tag: tissue

tag: gender

tag: disease status


title: GM20802_Dex_8h


title: GM20802_Dex_2h


title: healthy control, female [D17CM]

tag: age


title: GM19171_EtOH_4h


title: healthy control, female [D18CM]


title: patient in remission, male [99-276NBV_4]

description: Gene expression data from peripheral blood leukocytes of a patient in remission, male

source_name: patient in remission, male

value: remission

tag: ms treatment

value: Betaferon


title: GM20802_EtOH_12h


title: GM20802_EtOH_8h


title: patient in remission, female [11-353NBM]

description: Gene expression data from peripheral blood leukocytes of a patient in remission, female

source_name: patient in remission, female

tag: edss


title: GM20802_Dex_4h


title: healthy control, female [11-460CM_2]


title: Validation patient #83 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

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

tag: pre-vaccination igg titers for vaccinia


title: GM20802_EtOH_16h


title: GM20802_EtOH_4h


title: GM20802_Dex_24h


title: GM19171_Dex_12h


title: healthy control, female [11-502CM]


title: Validation patient #82 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 608

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


title: GM20802_Dex_16h

tag: treatment

tag: cell line

tag: time


title: healthy control, female [11-504CM]

tag: tissue

tag: gender

tag: disease status


title: Validation patient #81 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 600

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: GM20509_Dex_8h


title: GM19171_Dex_24h


title: GM20802_EtOH_2h


title: patient in relapse, male [99-276BV_4]

description: Gene expression data from peripheral blood leukocytes of a patient in relapse, male

source_name: patient in relapse, male

value: relapse

tag: age

tag: ms treatment

tag: edss


title: Validation patient #80 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 592

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


title: GM20802_Dex_12h


title: GM20509_EtOH_8h


title: Validation patient #79 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 584

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


title: Validation patient #78 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 577

tag: treatment


title: GM20509_EtOH_2h

tag: cell line

tag: time


title: GM20509_Dex_2h


title: GM20509_Dex_16h


title: GM20509_Dex_4h


title: Validation patient #77 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 571

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient in relapse, male [11-338BV]

tag: tissue

tag: gender

tag: disease status

tag: age

tag: ms treatment


title: GM20509_EtOH_12h


title: Validation patient #76 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 563

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm


title: GM20509_Dex_24h


title: patient in relapse, female [11-353BM]

description: Gene expression data from peripheral blood leukocytes of a patient in relapse, female

source_name: patient in relapse, female

tag: edss


title: GM20509_EtOH_4h


title: GM20509_EtOH_24h


title: GM20509_EtOH_16h


title: Validation patient #75 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 554

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: patient in remission, female [10-361NBM]


title: GM19102_Dex_8h

tag: treatment

tag: cell line

tag: time


title: Validation patient #74 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 546

tag: on-study psa

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient in relapse, female [10-361BM]

tag: tissue

tag: gender

tag: disease status

tag: age

tag: ms treatment


title: GM20509_Dex_12h


title: GM19102_EtOH_2h


title: GM19102_Dex_2h


title: GM19102_EtOH_8h


title: GM19102_Dex_4h


title: GM19102_EtOH_16h


title: patient in remission, male [10-360NBV_2]

value: Copaxone

tag: edss


title: GM19102_EtOH_4h


title: Validation patient #73 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 537

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


title: Validation patient #72 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 525

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: treatment


title: Validation patient #71 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 518

tag: on-study psa

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient in relapse, male [10-336BV]

tag: tissue

tag: gender

tag: disease status


title: Validation patient #70 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 510


title: patient in remission, male [10-336NBV]

tag: age

tag: ms treatment

tag: edss


title: patient in remission, female [10-333NBM]


title: healthy control, female [10-321CM]


title: patient in remission, female [10-700NBM]


title: GM19102_EtOH_24h

tag: cell line

tag: time


title: patient in relapse, female [10-700BM_2]


title: GM19102_Dex_24h


title: Validation patient #68 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 489

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


title: GM19138_Dex_16h

tag: treatment


title: Validation patient #69 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 498

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


title: GM19102_EtOH_12h


title: patient in relapse, male [10-360BV_2]

tag: tissue

tag: gender

tag: disease status


title: GM19102_Dex_16h


title: GM19138_Dex_12h


title: GM19138_EtOH_24h


title: GM19138_EtOH_16h


title: GM20802_EtOH_24h


title: GM19138_EtOH_12h


title: GM19138_EtOH_8h


title: GM19138_Dex_24h


title: GM19138_Dex_8h


title: patient in relapse, female [10-333BM_2_2]

tag: age

tag: ms treatment

value: Tysabri

tag: edss


title: healthy control, male [09-902CV]

value: peripheral blood leukocytes


title: GM19102_Dex_12h

tag: cell line

tag: time


title: GM19138_Dex_4h


title: Validation patient #67 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 482

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #66 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 474

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: treatment


title: Validation patient #65 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 467

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Validation patient #64 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 459


title: healthy control, male [09-900CV]

tag: tissue

tag: gender

value: male

tag: disease status

tag: age


title: healthy control, male [09-883CV]

value: control


title: healthy control, male [09-880CV]


title: Validation patient #60 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 432

tag: halabi predicted survival (months)


title: Validation patient #61 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 439

tag: post-vaccination survival (months)


title: GM19138_EtOH_4h

tag: cell line

tag: time


title: GM20512_Dex_24h


title: GM19138_Dex_2h


title: GM19138_EtOH_2h


title: GM20512_Dex_16h


title: GM20512_EtOH_24h


title: GM20512_EtOH_16h


title: Validation patient #59 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 424

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

tag: timepoint

tag: isotype-specific secondary antibody [fluorescently labeled]


title: healthy control, male [09-899CV]


title: healthy control, female [09-708CM_2]


title: GM20512_Dex_12h


title: Validation patient #58 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 420

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia


title: patient in remission, male [09-475NBV_4]

tag: ms treatment

tag: edss


title: GM20512_EtOH_4h

tag: treatment


title: patient in remission, male [09-394NBV_3]

tag: tissue


title: GM20512_Dex_2h


title: GM20512_Dex_4h


title: GM20512_EtOH_12h


title: GM20512_Dex_8h


title: GM20508_EtOH_24h


title: Validation patient #57 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 412

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: GM20512_EtOH_8h


title: Validation patient #56 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 407

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)


title: GM20512_EtOH_2h

tag: cell line

tag: time


title: Validation patient #54 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 398

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

tag: timepoint


title: patient in relapse, male [09-475BV_4]

tag: gender

tag: disease status

tag: age


title: Validation patient #53 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 390

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient in remission, male [11-338NBV]

tag: tissue

tag: ms treatment

tag: edss


title: patient in relapse, male [09-394BV_3]


title: healthy control, male [09-221CV]


title: GM20508_EtOH_16h

tag: treatment


title: patient in remission, female [09-152NBM]

value: Imurel


title: GM20508_Dex_16h


title: GM20508_Dex_8h


title: GM20508_EtOH_12h

value: EtOH


title: GM20508_Dex_24h

value: Dex


title: GM20508_EtOH_8h


title: GM20508_EtOH_4h


title: GM20508_Dex_4h


title: Validation patient #51 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 380

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa


title: Validation patient #50 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 375

tag: post-vaccination survival (months)

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

tag: timepoint


title: Validation patient #49 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 372


title: Validation patient #52 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 386


title: Validation patient #48 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 368


title: healthy control, female [09-1203CM]

tag: gender

value: female

tag: disease status

tag: age


title: GM20508_EtOH_2h

tag: cell line

tag: time


title: Validation patient #47 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 365

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: healthy control, male [08-759CV]

tag: tissue


title: GM18870_EtOH_24h

tag: treatment


title: GM18870_Dex_24h


title: Validation patient #46 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 357

tag: halabi predicted survival (months)

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: GM18870_EtOH_16h


title: GM20508_Dex_2h


title: patient in relapse, female [09-152BM]

tag: ms treatment

tag: edss


title: healthy control, female [08-659CM]


title: Validation patient #45 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 342

tag: post-vaccination survival (months)

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

value: Control

tag: gleason score

tag: on-study psa

tag: timepoint


title: GM18870_EtOH_8h

tag: cell line

tag: time


title: GM18870_Dex_16h


title: healthy control, female [08-650CM]

tag: gender

tag: disease status

tag: age


title: GM18870_Dex_12h


title: GM18870_EtOH_12h


title: healthy control, male [08-647CV]

tag: tissue


title: healthy control, female [08-588CM]


title: GM18870_Dex_8h

tag: treatment


title: Validation patient #43 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 326

tag: halabi predicted survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: GM18870_Dex_2h


title: healthy control, male [08-584CV]


title: GM18870_EtOH_2h


title: patient in remission, female [08-377NBM_3]

tag: ms treatment

tag: edss


title: Validation patient #41 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 298

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score


title: Validation patient #44 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 334

tag: on-study psa

tag: timepoint


title: patient in relapse, female [08-377BM_3]

tag: gender

tag: disease status

tag: age

value: Avonex


title: GM18870_Dex_4h

tag: treatment

tag: cell line

tag: time


title: GM18870_EtOH_4h


title: patient in remission, male [08-111NBV]

tag: tissue


title: patient in relapse, male [08-111BV]


title: Lung carcinoma patient6 120min peripheral

city: LYON

first: FLORENCE

last: LE CALVEZ-KELM

address: 150 Cours Albert Thomas

department: Genetics

institute: International Agency for Research on Cancer

data_processing: The data were processed using log transformation and quantile normalisation with BRBArrayTools

source_name: Lung carcinoma, patient6, 120min, peripheral

label_protocol: 500ng of mRNA was amplified into cRNA and biotinylated cRNA using Illumina® TotalPrep™-24 RNA Amplification Kit (Life Technologies).

extract_protocol: RNA was extracted withTotal RNA Isolation NucleoSpin® RNA II kit (Macherey Nagel) in accordance with the prescribed protocol provided with the kit. Quality control was performed withAgilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

value: peripheral lung carcinoma tumor

tag: individual

value: patient 6

value: 120 min

value: cryopreservation


title: Validation patient #40 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 287

tag: halabi predicted survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Lung carcinoma patient6 15min central

source_name: Lung carcinoma, patient6, 15min, central

value: central lung carcinoma tumor

value: 15 min


title: Lung carcinoma patient6 30min peripheral

source_name: Lung carcinoma, patient6, 30min, peripheral

value: 30 min


title: Lung carcinoma patient6 15min peripheral

source_name: Lung carcinoma, patient6, 15min, peripheral


title: Validation patient #42 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 312

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)


title: Lung carcinoma patient6 120min central

source_name: Lung carcinoma, patient6, 120min, central


title: Lung carcinoma patient6 5min peripheral

source_name: Lung carcinoma, patient6, 5min, peripheral

value: 5 min


title: Validation patient #39 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 279

source_name: Serum

value: PROSTVAC

tag: gleason score

tag: on-study psa

value: Vaccine

tag: timepoint


title: Lung carcinoma patient6 30min central

source_name: Lung carcinoma, patient6, 30min, central

tag: treatment


title: patient in remission, male [07-309NBV]

value: peripheral blood leukocytes

tag: gender

value: male

tag: disease status

value: remission

tag: age

tag: ms treatment

value: Rebif 44

tag: edss


title: Lung carcinoma patient6 5min central

source_name: Lung carcinoma, patient6, 5min, central

tag: tissue

tag: individual

tag: time


title: Validation patient #38 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 276

tag: halabi predicted survival (months)

tag: treatment arm

value: Control

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #37 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 271

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

value: Total Ig


title: Lung carcinoma patient5 120min central

source_name: Lung carcinoma, patient5, 120min, central

value: patient 5

tag: treatment


title: healthy control, male [09-901CV]

source_name: healthy control, male

tag: gender

tag: disease status

value: control

tag: age


title: Validation patient #36 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 267

tag: on-study psa

tag: timepoint


title: patient in remission, female [07-254NBM]

tag: tissue

value: female

tag: ms treatment

value: Tysabri

tag: edss


title: Lung carcinoma patient5 30min peripheral

source_name: Lung carcinoma, patient5, 30min, peripheral

value: peripheral lung carcinoma tumor

tag: individual

tag: time

value: cryopreservation


title: Lung carcinoma patient5 30min central

source_name: Lung carcinoma, patient5, 30min, central

value: central lung carcinoma tumor

value: 30 min


title: patient in relapse, male [07-309BV]

value: relapse


title: Lung carcinoma patient5 15min central

source_name: Lung carcinoma, patient5, 15min, central

value: 15 min


title: Lung carcinoma patient5 15min peripheral

source_name: Lung carcinoma, patient5, 15min, peripheral


title: Lung carcinoma patient5 120min peripheral

source_name: Lung carcinoma, patient5, 120min, peripheral

value: 120 min


title: Validation patient #35 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 257

tag: halabi predicted survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

tag: isotype-specific secondary antibody [fluorescently labeled]


title: patient in relapse, female [07-254BM_2]

source_name: patient in relapse, female

value: peripheral blood leukocytes


title: patient in relapse, female [06-185BM]

value: Clonazepam


title: patient in remission, female [06-185NBM]

source_name: patient in remission, female

value: remission


title: Validation patient #34 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 252

tag: post-vaccination survival (months)

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

value: PROSTVAC

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

value: Vaccine


title: Validation patient #33 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 247

tag: on-study psa

tag: treatment

value: Pre-treatment

value: Total Ig


title: patient in relapse, female [05-007BM]

tag: tissue

tag: gender

tag: disease status

tag: age

value: Copaxone


title: Lung carcinoma patient5 5min peripheral

source_name: Lung carcinoma, patient5, 5min, peripheral

tag: individual

value: patient 5

tag: time

value: 5 min


title: Lung carcinoma patient2 120min peripheral

source_name: Lung carcinoma, patient2, 120min, peripheral

value: peripheral lung carcinoma tumor

value: patient 2


title: Lung carcinoma patient2 30min peripheral

source_name: Lung carcinoma, patient2, 30min, peripheral

value: cryopreservation


title: Lung carcinoma patient2 30min central

source_name: Lung carcinoma, patient2, 30min, central

value: central lung carcinoma tumor

value: 30 min


title: patient in remission, female [05-004NBM]

value: female

tag: ms treatment

value: Betaferon

tag: edss


title: Lung carcinoma patient2 15min peripheral

source_name: Lung carcinoma, patient2, 15min, peripheral

value: 15 min


title: patient in remission, female [05-007NBM]

value: peripheral blood leukocytes


title: Hepatocellular carcinoma patient6 120min peripheral

source_name: Hepatocellular carcinoma, patient6, 120min, peripheral

value: peripheral hepatocellular carcinoma tumor

value: patient 6

value: 120 min


title: Validation patient #31 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 233

source_name: Serum

tag: halabi predicted survival (months)

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

tag: post-vaccination igg titers for vaccinia

value: Vaccine

tag: timepoint

value: Pre-treatment


title: GM20508_Dex_12h

source_name: Lymphoblastoid cell lines

value: Dex

tag: cell line


title: patient in relapse, female [05-004BM]

value: relapse


title: Lung carcinoma patient2 120min central

source_name: Lung carcinoma, patient2, 120min, central


title: Lung carcinoma patient5 5min central

source_name: Lung carcinoma, patient5, 5min, central

value: patient 5

value: 5 min


title: Lung carcinoma patient2 5min peripheral

source_name: Lung carcinoma, patient2, 5min, peripheral

value: peripheral lung carcinoma tumor

value: patient 2

value: cryopreservation


title: Hepatocellular carcinoma patient6 30min peripheral

source_name: Hepatocellular carcinoma, patient6, 30min, peripheral

value: 30 min


title: Hepatocellular carcinoma patient6 120min central

source_name: Hepatocellular carcinoma, patient6, 120min, central

value: central hepatocellular carcinoma tumor


title: Lung carcinoma patient2 5min central

source_name: Lung carcinoma, patient2, 5min, central

value: central lung carcinoma tumor


title: Lung carcinoma patient2 15min central

source_name: Lung carcinoma, patient2, 15min, central

value: 15 min


title: Validation patient #32 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 240

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titer for fowlpox

tag: age at enrollment (years)

tag: gleason score

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Hepatocellular carcinoma patient6 30min central

source_name: Hepatocellular carcinoma, patient6, 30min, central

tag: tissue

value: patient 6

tag: treatment


title: Validation patient #29 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 218

tag: on-study psa


title: Validation patient #30 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 221

value: Control


title: Validation patient #28 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 210

value: PROSTVAC


title: Hepatocellular carcinoma patient6 15min central

source_name: Hepatocellular carcinoma, patient6, 15min, central

tag: individual

tag: time


title: Validation patient #26 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 197

tag: halabi predicted survival (months)

value: Vaccine


title: Validation patient #27 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 202

tag: treatment arm

value: Pre-treatment


title: Validation patient #25 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 192

tag: pre-vaccination igg titers for vaccinia


title: Hepatocellular carcinoma patient6 15min peripheral

source_name: Hepatocellular carcinoma, patient6, 15min, peripheral

value: peripheral hepatocellular carcinoma tumor


title: patient in relapse, male [04-074BV_2_2]

source_name: patient in relapse, male

value: peripheral blood leukocytes

tag: gender

value: male

tag: disease status

value: relapse

tag: age

tag: ms treatment

value: Copaxone

tag: edss


title: Hepatocellular carcinoma patient6 5min central

source_name: Hepatocellular carcinoma, patient6, 5min, central

value: 5 min


title: Hepatocellular carcinoma patient5 120min central

source_name: Hepatocellular carcinoma, patient5, 120min, central

value: patient 5

value: 120 min

value: cryopreservation


title: Hepatocellular carcinoma patient6 5min peripheral

source_name: Hepatocellular carcinoma, patient6, 5min, peripheral


title: patient in relapse, female [00-129BM_3]

source_name: patient in relapse, female

value: female

value: Tysabri


title: Validation patient #24 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 184

source_name: Serum

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: timepoint

value: Total Ig


title: Hepatocellular carcinoma patient5 120min peripheral

source_name: Hepatocellular carcinoma, patient5, 120min, peripheral

tag: tissue

tag: treatment


title: Hepatocellular carcinoma patient5 30min peripheral

source_name: Hepatocellular carcinoma, patient5, 30min, peripheral

tag: individual

value: 30 min


title: patient in remission, male [00-096NBV]

source_name: patient in remission, male

value: remission


title: Hepatocellular carcinoma patient5 30min central

source_name: Hepatocellular carcinoma, patient5, 30min, central

value: central hepatocellular carcinoma tumor

tag: time


title: Hepatocellular carcinoma patient5 15min peripheral

source_name: Hepatocellular carcinoma, patient5, 15min, peripheral

value: 15 min


title: Hepatocellular carcinoma patient5 15min central

source_name: Hepatocellular carcinoma, patient5, 15min, central


title: patient in remission, male [04-074NBV_2_2]


title: Hepatocellular carcinoma patient5 5min central

source_name: Hepatocellular carcinoma, patient5, 5min, central


title: patient in remission, female [00-129NBM_3]

source_name: patient in remission, female


title: patient in relapse, male [00-096BV]


title: patient in relapse, female [00-024BM]


title: Hepatocellular carcinoma patient4 30min peripheral

source_name: Hepatocellular carcinoma, patient4, 30min, peripheral

value: patient 4


title: patient in remission, female [00-024NBM]


title: Hepatocellular carcinoma patient4 120min peripheral

source_name: Hepatocellular carcinoma, patient4, 120min, peripheral

value: peripheral hepatocellular carcinoma tumor


title: Validation patient #22 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 170

tag: halabi predicted survival (months)

value: Control

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

value: Pre-treatment

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Validation patient #23 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 177

tag: treatment arm

value: PROSTVAC

tag: pre-vaccination igg titers for vaccinia

value: Vaccine


title: Validation patient #21 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 162


title: Hepatocellular carcinoma patient4 15min peripheral

source_name: Hepatocellular carcinoma, patient4, 15min, peripheral


title: Hepatocellular carcinoma patient4 30min central

source_name: Hepatocellular carcinoma, patient4, 30min, central


title: Hepatocellular carcinoma patient5 5min peripheral

source_name: Hepatocellular carcinoma, patient5, 5min, peripheral

value: 5 min


title: Hepatocellular carcinoma patient4 120min central

source_name: Hepatocellular carcinoma, patient4, 120min, central


title: Validation patient #20 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 157


title: Validation patient #19 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 152


title: Validation patient #18 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 147


title: Validation patient #17 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 136


title: Metformin, biological rep3

city: Montréal

first: Xavier

last: Deschênes-Simard

state: Québec

address: 3655 Sir William Osler

department: Medicine

country: Canada

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C with rotation (60 rpm) on Human Gene 1.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with FlexArray 1.6.1.1 using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 2 (log2) and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

label: Biotin

source_name: IMR90 cells stably expressing H-RasV12 treated with Metformin

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays.

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

treatment_protocol: Cells were infected with retroviruses (H-RasV12), selected during two days with 2,5 µg/ml puromycin, then treated with water (vehicle) or 5mM metformin during 6 days before RNA extraction.

tag: cell type

value: IMR90 (Normal human diploid lung fibroblast)

tag: gender

value: Female

tag: overexpression

value: Metformin


title: cartilage knee 08509_OA

city: A Coruña

first: Juan

last: Fernandez Tajes

address: As Xubias

department: Genomics Area

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

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: female

tag: haplogroup

value: U

value: knee cartilage


title: cartilage knee 08468_OA

description: osteoarthritic cartilage knee sample

tag: tissue


title: Metformin, biological rep2

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

tag: treatment


title: Validation patient #16 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 127

source_name: Serum

tag: post-vaccination survival (months)

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

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

tag: timepoint

value: Total Ig


title: Hepatocellular carcinoma patient4 5min peripheral

source_name: Hepatocellular carcinoma, patient4, 5min, peripheral

tag: individual

tag: time

value: cryopreservation


title: cartilage knee 08776_OA

description: osteoarthritic cartilage knee sample

value: H


title: Validation patient #15 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 117

tag: halabi predicted survival (months)

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Vehicle, biological rep2

source_name: IMR90 cells stably expressing H-RasV12 treated with vehicle

tag: cell type

tag: gender

tag: overexpression

value: Vehicle


title: cartilage knee 08451_OA

description: osteoarthritic cartilage knee sample

tag: disease state

tag: age

tag: Sex

value: male

tag: haplogroup

tag: tissue


title: cartilage knee 08768_OA

description: osteoarthritic cartilage knee sample


title: cartilage knee 08763_OA

description: osteoarthritic cartilage knee sample


title: Vehicle, biological rep3

tag: treatment


title: cartilage knee 08791_N

description: normal cartilage knee sample

value: normal

value: <50 years


title: Validation patient #14 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 109

tag: post-vaccination survival (months)

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

value: PROSTVAC

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

value: Vaccine

tag: timepoint

value: Pre-treatment


title: Hepatocellular carcinoma patient4 15min central

source_name: Hepatocellular carcinoma, patient4, 15min, central

value: central hepatocellular carcinoma tumor

tag: individual

value: patient 4

tag: time

value: 15 min


title: Hepatocellular carcinoma patient4 5min central

source_name: Hepatocellular carcinoma,  patient4, 5min,  central

value: 5 min


title: cartilage knee 08379_OA

description: osteoarthritic cartilage knee sample

value: osteoarthritis

value: >60 years

value: female


title: cartilage knee 08769_OA

description: osteoarthritic cartilage knee sample

value: knee cartilage


title: cartilage knee 08482_OA

description: osteoarthritic cartilage knee sample


title: cartilage knee 08102_N

description: normal cartilage knee sample

value: U


title: Validation patient #12 | Control Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 89

tag: halabi predicted survival (months)

tag: treatment arm

value: Control

tag: pre-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: isotype-specific secondary antibody [fluorescently labeled]

value: Total Ig


title: Validation patient #13 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 101


title: cartilage knee 08381_N

description: normal cartilage knee sample

tag: disease state

tag: age

tag: Sex

value: male

tag: haplogroup

value: H


title: Metformin, biological rep1

tag: cell type

value: IMR90 (Normal human diploid lung fibroblast)

tag: gender

value: Female

tag: overexpression

tag: treatment

value: Metformin


title: Phaeodactylum_White light_24h_rep3

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 24h 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).

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 08750_OA

description: osteoarthritic cartilage knee sample

tag: tissue


title: Phaeodactylum_White light_24h_rep1

source_name: Phaeodactylum, Re-exposure to 24h white light after 48h dark treatment


title: Validation patient #11 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 82

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

value: PROSTVAC

tag: post-vaccination igg titers for vaccinia

tag: post-vaccination igg titer for fowlpox

value: Vaccine

tag: timepoint

value: Pre-treatment


title: cartilage knee 08664_N

description: normal cartilage knee sample

value: normal

value: <50 years


title: cartilage knee 08283_N

description: normal cartilage knee sample


title: Vehicle, biological rep1

value: Vehicle


title: Validation patient #10 | Vaccine Arm | Pre-treatment [Total Ig 1:200]

description: Sample name: 74

tag: treatment arm

tag: pre-vaccination igg titers for vaccinia

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

tag: isotype-specific secondary antibody [fluorescently labeled]


title: Phaeodactylum_White light_6h_rep3

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


title: cartilage knee 08121_OA

description: osteoarthritic cartilage knee sample

tag: disease state

value: osteoarthritis

tag: age

value: >60 years

tag: Sex

value: female

tag: haplogroup

value: J


title: cartilage knee 08101_OA

description: osteoarthritic cartilage knee sample

tag: tissue

value: knee cartilage


title: Phaeodactylum_White light_24h_rep2

tag: clone