title: NIKtg CD4 Tconv replicate 2

city: Portland

first: Susan

last: Murray

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Molecular microbiology and immunology

institute: OHSU

description:
SAMPLE 8
FACS-sorted T cells from mixed bone marrow chimeric mice

data_processing: Image processing and expression analysis were performed using Illumina BeadArray Reader and GenomeStudio (v. 2010.1) Gene Expression module (v. 1.6.0) software.

source_name: NIKtg CD4 Tconv

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

extract_protocol: RNA from FACS-sorted cells was extracted with RNeasy mini kit per manufacturer's instructions (Qiagen)

treatment_protocol: T cells generated in vivo in mixed bone marrow chimeric mice

tag: strain background

tag: bone marrow donor 1

tag: bone marrow donor 2

tag: bone marrow recipient

value: lethally irradiated (1200 rads, split dose) B6.CD45.1

tag: niktg full strain name

tag: foxp3rfp full strain name

tag: cd4cre full strain name

tag: facs sorting gates


title: SJIA_2_212_Day3_Canakinumab

status: Public on Apr 29 2016

type: RNA

city: Basel

first: Arndt

middle: Holger

last: Brachat

state: Basel Stadt

address: Fabrikstrasse 10

department: BMD

country: Switzerland

institute: NIBR

description: Peripheral blood gene expression data of SJIA patients or age matched healthy subjects

hyb_protocol: The arrays were hybridized with approximately 3.4 µg of single stranded cDNA biotinlabelled DNA fragments. The hybridized probe array was rotated in the hybridization ovens for 16 hours at 45°C and 60 rpm (S2). The arrays were washed and stained with a streptavidin phycoerythrin conjugate on GeneChip Fluidics 450 Workstations

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G, a GCOS (GeneChip Operating Software) controlled system (S3). The scanned image was converted into numerical values of the probe intensity (Signal) using the Affymetrix GCOS Software and stored as CEL-file data

data_processing: The microarrays were scaled to a value of 150 and normalized using the RMA (Robust Multi-array Average) algorithm in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood sample at day 3 after first dose

label_protocol: The synthesis of cDNA was carried out with a starting amount of approximately 50 ng total RNA using the NuGEN Ovation RNA Amplification System V2 including the Ribo-SPIA amplification process according to the instructions of the manufacturer (NuGEN Technologies Inc.; San Carlos, U.S.). The amplification process was performed in three stages (i) a first strand cDNA synthesis with oligo(dT) primers and Ovation WB reagent, (ii) a second strand cDNA synthesis, (iii) a so-called SPIA Isothermal Linear Amplification that produced 3 10 µg amplified single-stranded Biotinlabelled cDNA per sample

extract_protocol: total RNA from blood was isolated with the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s procedure

treatment_protocol: Human blood samples from consented patients enrolled in the study were collected in PAXgene Blood RNA tubes according to the manufacturer’s recommendations (PreAnalytiX, Hombrechtikon, Switzerland).

tag: tissue

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

tag: treatment

value: Canakinumab

tag: acr response at day 15


title: NIKtg CD4 Tconv replicate 1

country: USA

description:
SAMPLE 7
FACS-sorted T cells from mixed bone marrow chimeric mice

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

organism: Mus musculus


title: Control_1

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MO430A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries were performed using the log-scale Robust Multiarray Analysis (RMA) method.

label: Biotin

source_name: 4T1-derived mammary gland tumors from NSG mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: 4T1 mouse mammary tumor cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% NEAA, 1% glutamine and 1% penicillin/streptomycin. For tumor inoculation, 4T1 cells were harvested with 0.05% trypsin-EDTA, washed twice with DMEM and resuspended in DMEM.

extract_protocol: Tumor tissues were subjected to gross histological analysis using hematoxylin and eosin staining to determine percentages of tumor, necrotic and stromal cells before total RNA extraction. If present, necrotic tissue was selected out by macrodissection. Total RNA was then extracted from frozen tumor tissues with TRI reagent and the MagMAX-96 Total RNA Isolation Kit in a MagMAX Express Magnetic Particle Processor, according to the manufacturer's instructions.

treatment_protocol: Bptf was knocked-down (KD) in 4T1 cells by short-hairpin RNA (shRNA) sequences that were introduced in the cells using retrovirus MMLV. 1x10^4 Control or Bptf KD 4T1 cells were injected into the fourth mammary fat pad of Ifrg2r -/- (NSG) mice and sacrificed 21 days later. Primary tumors were snap-frozen and weighed, and total RNA was extracted from biological triplicate tumors.

value: 4T1-derived mammary gland tumor


title: E. coli planktonic cells, biological rep3

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

country: India

institute: Centre for Cellular and Molecular biology

description: Planktonic cells E6

hyb_protocol: The DNA micro array chips were hybridized with the labelled cDNA using the Affymetrix protocol (www.affymetrix.com).

scan_protocol: Microarray slides were then scanned using Affymetrix 428 Array Scanner and GCOS software to obtain images of the chips and further processed to get intensity cell files for the probe sets.

data_processing: The  intensity cell files were then imported, normalized for background correction (used RMA for normalization)and data analysed using Gene Spring 11.5 software.

organism: Escherichia coli

source_name: E.coli L-1216/2013 planktonic cells , grown in LB for 72h

label_protocol: The cDNA was fragmented with DNAse 1 (Promega Corporation, Madison, USA) and then labeled with biotin at the 3’ end using the labeling reagent from Affymetrix (CA, USA) and Terminal transferase enzyme (Promega).

growth_protocol: Escherichia coli was grown aerobically in BHI broth for 72 h at 37oC to obtain biofilm planktonic cells, biofilm cells and non-biofilm cells.

extract_protocol: RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg/ml of RNA and the first strand cDNA synthesis kit from Invitrogen (Invitrogen Bioservices India Pvt. Ltd., Bangalore).

treatment_protocol: To study gene expression,  72h old E.coli cells were collected. After 72 h the cells that did not attach to the petri plate were considered as the planktonic biofilm cells and were collected in 50 ml Falcon tubes by gently tilting the plate. Cells scrapped from the biofilm, the planktonic biofilm  and non-biofilm cells were centrifuged at 10000 rpm in a microcentifuge (Eppendorf, New York, USA) and the respective pellets were suspended in 3 ml of RNAlater ®  (Invitrogen BioServices India Pvt. Ltd, Bangalore 560 066, India) in ice cold phosphate buffer (pH b7.2) and incubated for 30 minutes.

tag: strain

tag: cell type

value: Planktonic cells


title: E. coli planktonic cells, biological rep1

description: Planktonic cells E4


title: miR WT CD4 Tconv replicate 2

description:
replicate 2
004A_H1_WTCon2_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice

hyb_protocol: Each labeled sample target was hybridized to an Affymetrix GeneChip miRNA Array (v2)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 laser scanner with 7G upgrade

data_processing: Probeset intensities were normalized using the Robust Multi-array Average (RMA) algorithm in Expression Console (build 1.4.1.46).

source_name: miR WT CD4 Tconv

label_protocol: Genisphere HSR miRNA Flash Tag Biotin (HSR miRNA labeling_Genisphere) labeling protocol


title: Control_2


title: miR NIKtg CD4 Tconv replicate 2

description:
replicate 2
005A_H1_TgCon2_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: miR NIKtg CD4 Tconv


title: WT CD4 Tconv replicate 2

description:
SAMPLE 6
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: WT CD4 Tconv


title: SJIA_2_212_Day1_BL_Canakinumab

source_name: Whole blood sample at baseline - prior to first dose


title: SJIA_2_2613_Day3_Placebo

value: Placebo


title: miR WT CD4 Tconv replicate 1

description:
replicate 1
002A_H1_WTCon1_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice


title: miR NIKtg CD4 Tconv replicate 1

description:
replicate 1
006A_H1_TgCon1_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice


title: miR NIKtg Treg replicate 1

description:
replicate 1
003A_H1_TgReg1_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: miR NIKtg Treg


title: miR NIKtg Treg replicate 2

description:
replicate 2
001A_H1_TgReg2_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice


title: SJIA_2_2613_Day1_BL_Placebo


title: NIKtg Treg replicate 1

description:
SAMPLE 3
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: NIKtg Treg


title: E. coli Biofilm cells, biological rep2

description: Biofilm cells E2

source_name: E.coli L-1216/2013 biofilm cells , grown in LB for 72h

value: Biofilm cells


title: NIKtg Treg replicate 2

description:
SAMPLE 4
FACS-sorted T cells from mixed bone marrow chimeric mice


title: E. coli Biofilm cells, biological rep1

description: Biofilm cells E1


title: E. coli Biofilm cells, biological rep3

description: Biofilm cells E3


title: WT CD4 Tconv replicate 1

description:
SAMPLE 5
FACS-sorted T cells from mixed bone marrow chimeric mice


title: SJIA_2_113_Day1_BL_Canakinumab


title: SJIA_2_2312_Day3_Canakinumab


title: SJIA_2_113_Day3_Canakinumab


title: miR WT Treg replicate 1

description:
replicate 1
008A_H1_WTReg1_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: miR WT Treg


title: SJIA_2_2312_Day1_BL_Canakinumab


title: WT Treg replicate 2

description:
SAMPLE 2
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: WT Treg


title: non-biofilm forming control, biological rep3

description: Non-biofilm cells C3

source_name: E.coli L-1339/2013 , grown in LB for 72h

value: Non-biofilm cells


title: WT Treg replicate 1

description:
SAMPLE 1
FACS-sorted T cells from mixed bone marrow chimeric mice


title: SJIA_2_2313_Day3_Placebo


title: non-biofilm forming control, biological rep2

description: Non-biofilm cells C2


title: control vs. morphant replicate 4

city: Toronto

first: Ian

middle: Cameron

last: Scott

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Childen

description: Biological replicate 4 of 4

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 Agilent G2565C DNA scanner.  Images were quantified using Agilent Feature Extraction Software (version 10.7.1.3).  Extraction Protocol GE2_107_Sept07.

data_processing: Results analyzed using Genespring v11.0.1 and normalized using Agilent’s Spatial Detrending Lowess normalization. All data analysis was performed on log2-transformed data. Standard single factor ttests were used followed by ranking with fold changes. After normalization and averaging the four chips, data was filtered to remove the probes that showed no signal in order to avoid confounding effects on subsequent analysis. Only probes between the 20th and 100th percentile of the distribution of intensities in both samples for either group were allowed to pass through this filtering.

organism: Danio rerio

source_name: AplnrMO

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label (Labelling Protocol version GE2 v6.0)

extract_protocol: Total RNA was isolated using the Ambion RNAqueous kit from 20 embryos per sample.

tag: dpf

value: 50% epiboly

tag: genotype

value: morphant

source_name: WT

tag: tag

value: wildtype


title: SJIA_2_2313_Day1_BL_Placebo


title: non-biofilm forming control, biological rep1

description: Non-biofilm cells C1


title: control vs. morphant replicate 3

description: Biological replicate 3 of 4


title: control_72 hours, Donor 3

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description:
45A
small RNA expression of peripheral blood monocyte-derived macrophages

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing: CEL files were processed by Affymetrix miRNA QCtool software. Downstream data analysis was performed in GeneSpring GX12 software.

label_protocol: Total RNA samples were labeled by using FlashTag™ Biotin HSR RNA Labeling Kit according to manufacturer's protocol.

growth_protocol: CD14+ monocytes were separated from human peripheral blood and plated in 6-well cell culture plate (2 million cell/well).

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

treatment_protocol: Human peripheral blood-derived CD14+ monocytes were  exposed to IL-4 for 12 or 72 hours.

value: peripheral blood

value: monocyte-derived macrophages

tag: cell surface marker


title: SJIA_2_2213_Day1_BL_Placebo


title: SJIA_2_1912_Day1_BL_Placebo


title: IL-4_72 hours, Donor 3

description:
46A
small RNA expression of peripheral blood monocyte-derived macrophages


title: MH_D9-3_discrete groups of tumor cells_cnv

type: genomic

city: Tomsk

first: Aleksei

middle: A

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description: cytogenetic profile of laser-microdissected breast tumor cells composing discrete groups

hyb_protocol: Labeled test samples were combined with the labeled reference samples and hybridized using Oligo aCGH / ChIP-on-chip Hybridization Kit according to the manufacturer's instructions (Agilent Technologies, Inc., USA). After hybridization, slides were washed using Oligo aCGH/ChIP-on-chip Wash Buffer Kit according to the manufacturer’s instructions (Agilent Technologies, Inc., USA).

scan_protocol: The scanning was performed using a SureScan Microarray Scanner. Data interpretation was performed using Agilent CytoGenetics software (version 3.0.2.11).

data_processing:
Agilent CytoGenetics software (version 3.0.2.11) was used for background subtraction and LOWESS normalization.
When identifying similar chromosomal aberrations, abnormalities were regarded as identical if the differences between them were less than 5 Kb. Because the WGA step reduces the signal/noise ratio.

molecule: genomic DNA

source_name: 3rd region of the breast tumor of the MH patient

label_protocol: 500 ng of test DNA samples were Cy5-labeled and reference DNA samples were Cy-3 labeled using the SureTag Complete DNA Labeling Kit according to the manufacturer’s instructions (Agilent Technologies, Inc., USA). Dye incorporation and DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
laser microdissection protocol: Different morphological structures were isolated from 5 um hematoxylin&eosin stained sections of three frozen samples (regions) of three breast tumors using PALM MicroBeam laser capture microdissection (Carl Zeiss, Germany). Each breast tumor region was used for obtaining 2-3 samples (~20-30 cells) of tubular, alveolar, and trabecular structures, one sample (~70-80 cells) of solid structure, and 10 samples (up to 20 cells) of discrete groups of tumor cells.
WGA protocol: The microdissected material was used to perform whole genome amplification by PicoPLEX WGA Kit according to the manufacturer’s instructions (Rubicon Genomics, Inc., USA). Amplified DNA was purified from reaction mixtures using QIAquick PCR Purification Kit (Qiagen, USA) and had concentration ranging from 70 to 110 ng/ul. DNA quality was assessed using 2200 TapeStation Instrument and Genomic DNA Screen Tape (Agilent Technologies, Inc., USA). Human Female DNA (Agilent Technologies, Inc., USA) was used as the reference DNA and was processed by whole genome amplification (PicoPLEX WGA Kit, Rubicon Genomics, Inc., USA).

value: breast tumor

tag: tumor structure

value: discrete groups of tumor cells

tag: patient id

value: MH

tag: gender

value: female

tag: age

tag: histological type

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

tag: therapy

value: without preoperative therapy

source_name: Agilent EuroFemale

tag: sample type

value: reference


title: MH_D9-2_discrete groups of tumor cells_cnv

source_name: 2nd region of the breast tumor of the MH patient

tag: tissue


title: IL-4_12 hours, Donor 3

description:
43A
small RNA expression of peripheral blood monocyte-derived macrophages


title: control vs. morphant replicate 1

description: Biological replicate 1 of 4


title: control_12 hours, Donor 3

description:
42A
small RNA expression of peripheral blood monocyte-derived macrophages


title: SJIA_2_185_Day3_Placebo

description: Peripheral blood gene expression data of SJIA patients or age matched healthy subjects

source_name: Whole blood sample at day 3 after first dose

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

tag: treatment

tag: acr response at day 15


title: skeletal muscle   GRMD   old biological replicate 3

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

description: Gene expression data from golden tritriever model of muscular dystrophy

hyb_protocol: Following labeling, 5 ug of cRNA were hybridized for 16 hr at 45C on Canine Gene Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix high resolution GenePix 4000B scanner in Vanderbilt Functional Shared Resources (http://www.thefgsr.com/).

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and Robust Multi-chip Average (RMA)  as normalization method.

organism: Canis lupus familiaris

source_name: skeletal muscle tissue from GRMD (golden retriever muscular dystrophy model)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: GRMD dogs were aged 6, 12, 47, 52, or 93 years; normal control dogs were age-matched for 6 and 12 months (no control dogs available for considerably older dogs)

extract_protocol: Total RNA was isolated from the LV and MHG of the 15 dogs according to the manufacturer’s protocol (Qiagen, Germantown, MD). Quality assessment of RNA, further processing, and data acquisition were performed by the GSR Microarray Core at Vanderbilt.  Affymetrix Canine Gene 1.0 Expression arrays (Affymetrix, Inc., Santa Clara, CA) were used, two arrays per animal (for paired LV and skeletal muscle samples), for a total of 30 arrays. Raw data were RMA normalized, followed by ANOVA using Partek Genomics Suite 6.6 (Partek Incorporated, St. Louis, MO).

treatment_protocol: no treatment

tag: breed

value: Golden Retriever

tag: disease

value: GRMD

value: lateral head of the gastrocnemius

value: 93 months


title: MH_D7-1_trabecular structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing trabecular structures

source_name: 1st region of the breast tumor of the MH patient

tag: tumor structure

value: trabecular


title: monocytes, Donor 3

description:
41A
small RNA expression of peripheral blood monocyte-derived macrophages

value: peripheral blood

tag: cell type

tag: cell surface marker


title: SJIA_2_2213_Day3_Placebo

value: Placebo


title: control vs. morphant replicate 2

description: Biological replicate 2 of 4

tag: dpf

value: 50% epiboly

tag: genotype

value: morphant

tag: tag

value: wildtype


title: SJIA_2_185_Day1_BL_Placebo


title: MH_D9-1_discrete groups of tumor cells_cnv

value: breast tumor

value: discrete groups of tumor cells

tag: patient id

value: MH

tag: gender

value: female

tag: age

tag: histological type

tag: molecular subtype

tag: tnm stage


title: skeletal muscle   GRMD   old biological replicate 1

tag: tissue

value: medial head of the gastrocnemius

value: 47 months


title: IL-4_72 hours, Donor 2

description:
16A
small RNA expression of peripheral blood monocyte-derived macrophages

value: monocyte-derived macrophages


title: skeletal muscle   GRMD   middle biological replicate 3

value: Golden Retriever

value: 13.5 months


title: MH_D5-2_solid structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing solid structures

value: solid

value: invasive carcinoma of no special type

value: luminal B

tag: therapy

value: without preoperative therapy

tag: sample type

value: reference


title: MH_D7-3_trabecular structures_cnv

value: trabecular


title: MH_D5-3_solid structures_cnv


title: MH_D7-2_trabecular structures_cnv


title: SJIA_2_1713_Day3_Canakinumab

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

tag: treatment

value: Canakinumab

tag: acr response at day 15


title: MH_D5-1_solid structures_cnv

value: breast tumor

tag: tumor structure


title: MH_D3-3_alveolar structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing alveolar structures

value: alveolar

value: MH


title: skeletal muscle   GRMD   old biological replicate 2

tag: breed

tag: disease

value: GRMD

value: medial head of the gastrocnemius

value: 52 months


title: SJIA_2_1811_Day1_BL_Canakinumab


title: control_72 hours, Donor 2

description:
15A
small RNA expression of peripheral blood monocyte-derived macrophages

value: peripheral blood

tag: cell type

value: monocyte-derived macrophages

tag: cell surface marker


title: skeletal muscle   GRMD   middle biological replicate 1

value: Golden Retriever

tag: age

value: 13.5 months


title: skeletal muscle   GRMD   middle biological replicate 2

value: 13 months


title: skeletal muscle   Normal   middle biological replicate 3

source_name: skeletal muscle tissue from normal golden retriever

value: Normal


title: IL-4_12 hours, Donor 2

description:
13A
small RNA expression of peripheral blood monocyte-derived macrophages


title: SJIA_2_1713_Day1_BL_Canakinumab


title: SJIA_2_167_Day1_BL_Canakinumab


title: control_12 hours, Donor 2

description:
12A
small RNA expression of peripheral blood monocyte-derived macrophages


title: monocytes, Donor 2

description:
11A
small RNA expression of peripheral blood monocyte-derived macrophages


title: IL-4_72 hours, Donor 1

description:
6A
small RNA expression of peripheral blood monocyte-derived macrophages


title: MH_D3-1_alveolar structures_cnv

tag: patient id

tag: gender

value: female

tag: histological type

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy

value: reference


title: skeletal muscle   Normal   middle biological replicate 1

tag: tissue

value: 12 months


title: SJIA_2_168_Day1_BL_Placebo

value: Whole blood

value: SJIA

value: Placebo


title: SJIA_2_310_Day1_BL_Canakinumab

value: Canakinumab


title: skeletal muscle   GRMD   young biological replicate 3

value: GRMD

value: medial head of the gastrocnemius

value: 6 months


title: control_72 hours, Donor 1

description:
5A
small RNA expression of peripheral blood monocyte-derived macrophages

value: peripheral blood

value: monocyte-derived macrophages


title: skeletal muscle   Normal   middle biological replicate 2

value: Golden Retriever

value: 13 months


title: MH_D1-3_tubular structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing tubular structures

value: breast tumor

value: tubular

value: MH

value: female

tag: molecular subtype

tag: tnm stage

tag: therapy


title: MH_D3-2_alveolar structures_cnv

value: alveolar

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy

tag: sample type

value: reference


title: control_12 hours, Donor 1

description:
2A
small RNA expression of peripheral blood monocyte-derived macrophages


title: IL-4_12 hours, Donor 1

description:
3A
small RNA expression of peripheral blood monocyte-derived macrophages


title: SJIA_2_1811_Day3_Canakinumab

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

value: Canakinumab


title: SJIA_2_1411_Day1_BL_Placebo

tag: treatment

value: Placebo

tag: acr response at day 15


title: SJIA_2_1413_Day3_Placebo


title: MH_D1-2_tubular structures_cnv

tag: tumor structure


title: SJIA_2_3012_Day1_BL_Placebo


title: monocytes, Donor 1

description:
1A
small RNA expression of peripheral blood monocyte-derived macrophages

value: peripheral blood

tag: cell type


title: mir-342-3p mimics-transfected RAW264.7 cells replicate 3

description: gene expression data of  RAW264.7 cells transfected by mir-342-3p mimics

data_processing: CHP files were generated using Affymetrix Expression Control. Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: RAW264.7 cell line_mir-342-3p_mimic

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: RAW264.7 mouse macrophages were plated in 12-well cell culture plate (500000 cells/well).

treatment_protocol: RAW264.7 mouse macrophages were transfected with negative control and miR-342-3p mimics. Total RNA was isolated 18 hours after the transfection.

tag: cell line

value: macrophage


title: SJIA_2_1411_Day3_Placebo

description: Peripheral blood gene expression data of SJIA patients or age matched healthy subjects


title: skeletal muscle   GRMD   young biological replicate 2

description: Gene expression data from golden tritriever model of muscular dystrophy

tag: breed

value: Golden Retriever

tag: disease

value: GRMD

value: medial head of the gastrocnemius

tag: age

value: 6 months


title: SJIA_2_1112_Day3_Canakinumab


title: mir-342-3p mimics-transfected RAW264.7 cells replicate 2


title: skeletal muscle   Normal   young biological replicate 2

value: Normal


title: DE_D9-2_discrete groups of tumor cells_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing discrete groups

source_name: 2nd region of the breast tumor of the DE patient

value: breast tumor

value: discrete groups of tumor cells

tag: patient id

value: DE

tag: gender

value: female

tag: histological type


title: MH_D1-1_tubular structures_cnv

tag: tissue

value: tubular

value: MH

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

value: without preoperative therapy


title: skeletal muscle   Normal   young biological replicate 1


title: SJIA_2_2912_Day1_BL_Canakinumab

source_name: Whole blood sample at baseline - prior to first dose

value: Whole blood

tag: disease status

value: SJIA

value: Canakinumab


title: skeletal muscle   GRMD   young biological replicate 1

value: Golden Retriever

value: 6.75 months


title: mir-342-3p mimics-transfected RAW264.7 cells replicate 1

value: macrophage


title: SJIA_2_1112_Day1_BL_Canakinumab

tag: subject id


title: skeletal muscle   Normal   young biological replicate 3

value: medial head of the gastrocnemius

value: 7.5 months


title: left ventricle   GRMD   old biological replicate 3

source_name: left ventricular tissue from GRMD (golden retriever muscular dystrophy model)

value: GRMD

value: left ventricle

value: 93 months


title: DE_D7-3_trabecular structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing trabecular structures

source_name: 3rd region of the breast tumor of the DE patient

value: breast tumor

value: trabecular

value: DE

value: female

tag: therapy

tag: sample type

value: reference


title: miR WT Treg replicate 2

description:
replicate 2
007A_H1_WTReg2_537DP
FACS-sorted T cells from mixed bone marrow chimeric mice

source_name: miR WT Treg

tag: strain background

tag: bone marrow donor 1

tag: bone marrow donor 2

tag: bone marrow recipient

value: lethally irradiated (1200 rads, split dose) B6.CD45.1

tag: niktg full strain name

tag: foxp3rfp full strain name

tag: cd4cre full strain name

tag: facs sorting gates


title: DE_D9-3_discrete groups of tumor cells_cnv

tag: tumor structure

value: discrete groups of tumor cells

tag: patient id

tag: gender

tag: age

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy


title: DE_D9-1_discrete groups of tumor cells_cnv

source_name: 1st region of the breast tumor of the DE patient

tag: tissue

tag: histological type

tag: molecular subtype

tag: tnm stage


title: SJIA_2_1013_Day3_Canakinumab

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

tag: treatment

value: Canakinumab

tag: acr response at day 15


title: negative control mimics-transfected RAW264.7 cells replicate 3

description: gene expression data of  RAW264.7 cells transfected by negative control mimics

source_name: RAW264.7 cell line_negative_control

tag: cell line

tag: cell type

value: macrophage


title: DE_D5-3_solid structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing solid structures

value: solid

tag: therapy

tag: sample type


title: negative control mimics-transfected RAW264.7 cells replicate 2


title: left ventricle   GRMD   middle biological replicate 3

tag: breed

value: Golden Retriever

tag: disease

value: GRMD

value: left ventricle

value: 13 months


title: SJIA_2_1013_Day1_BL_Canakinumab


title: left ventricle   GRMD   old biological replicate 1

value: 47 months


title: negative control mimics-transfected RAW264.7 cells replicate 1


title: DE_D7-1_trabecular structures_cnv

value: breast tumor

tag: tumor structure

value: trabecular

tag: patient id

value: DE

tag: gender

value: female


title: left ventricle   GRMD   middle biological replicate 2

tag: tissue

tag: age

value: 13.5 months


title: left ventricle   GRMD   middle biological replicate 1


title: SJIA_2_712_Day1_BL_Placebo

value: Placebo


title: DE_D7-2_trabecular structures_cnv

tag: histological type

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

value: without preoperative therapy

value: reference


title: SJIA_2_413_Day1_BL_Canakinumab

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

value: Canakinumab


title: left ventricle   GRMD   old biological replicate 2

value: Golden Retriever

value: GRMD

value: 52 months


title: CGH_5_direct

city: Baltimore

first: Andre

last: Kleensang

state: MD

department: Center for Alternatives to Animal Testing

institute: Johns Hopkins University

description: MCF-7 from ATCC (HTB-22, lot number 59388743) from frozen ATCC shiped vial directly prepared genomic DNA, JHU vs. Brown vial

hyb_protocol: Agilent SurePrint G3 4X180K ISCA Human CGH+SNP array (Agilent Part # G4890A, AMADID: 029830) following the manufacturer’s recommended procedure (Agilent Oliognucleotide Array-Based CGH for “GenomicDNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues” protocol version 7.3, Part# G4410-90010).

scan_protocol: The hybridized slides were scanned using Agilent Scanner G2505C and array data was extracted from the scanned image using Agilent Feature Extraction software version 11.5.1.1.

data_processing: Data were normalized and analyzed with CytoGenomics 3.0.4.1 (64 bit) and implemented default analysis method CGH v2.

source_name: MCF-7 from ATCC (HTB-22, lot number 59388743) from frozen ATCC shiped vial directly prepared genomic DNA (vial shipped to JHU and JHU cell source)

label_protocol: 1 ug gDNA was labeled with Cy5 or Cy3 using Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399) following the manufacturer’s recommended procedure (Agilent Oliognucleotide Array-Based CGH for “GenomicDNA Analysis: Enzymatic Labeling for Blood, Cells, or Tissues” protocol version 7.3, Part# G4410-90010).

growth_protocol: MCF-7 cells were maintained in complete growth medium composed of DMEM-F12 (GIBCO, Life Technologies, Grand Island, NY, USA, no. 11309) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Norcross, GA, USA, no. S11150), 1x nonessential amino acids (GIBCO, Life Technologies, no. 11140), 10μg/mL bovine insulin (Akron Biotech, Boca Raton, FL, USA, no. AK8213) and 0.01mg/ml gentamicin (Invitrogen, Life Technologies, no. 15710) in Bisphenol-A-free culture flasks. Cultures were fed every 2-3 days and passaged when 70-80% confluent. Serum used in both labs was purchased from the same lot.

extract_protocol: Genomic DNA was prepared using Qiagen QIAamp DNA mini Kit (# 51304) following the manufacturer’s recommended procedure.

treatment_protocol: Not applicable. Cells are not treated.

tag: cell line

source_name: MCF-7 from ATCC (HTB-22, lot number 59388743) from frozen ATCC shiped vial directly prepared genomic DNA (vial shipped to Brown University and Brown University cell source)


title: SJIA_2_413_Day3_Canakinumab

tag: treatment

tag: acr response at day 15


title: CGH_6_direct

description: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 154 from JHU vs. passage number 150 from Brown University

source_name: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 150 from Brown University


title: SJIA_2_812_Day1_BL_Placebo


title: DE_D3-1_alveolar structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing alveolar structures

value: alveolar

tag: therapy

source_name: Agilent EuroFemale

tag: sample type


title: left ventricle   Normal   middle biological replicate 2

source_name: left ventricular tissue from normal golden retriever

tag: breed

tag: disease

value: Normal

value: left ventricle

value: 13 months


title: SJIA_2_912_Day3_Canakinumab

source_name: Whole blood sample at day 3 after first dose


title: DE_D5-1_solid structures_cnv

value: breast tumor

tag: tumor structure

value: solid

tag: patient id

value: DE

value: female


title: SJIA_2_313_Day1_BL_Placebo

tag: tissue

value: Placebo


title: DE_D3-2_alveolar structures_cnv

tag: gender

tag: age

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy


title: CGH_4_indirect

description: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 154 from JHU vs. human female reference DNA, replicate 2

source_name: human female reference DNA

value: human female reference DNA

tag: source

value: Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399)


title: DE_D1-3_tubular structures_cnv

value: tubular

tag: histological type

tag: molecular subtype

tag: tnm stage

value: reference


title: DE_D5-2_solid structures_cnv


title: CGH_3_indirect

description: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 154 from JHU vs. human female reference DNA, replicate 1


title: DE_D1-2_tubular structures_cnv

description: cytogenetic profile of laser-microdissected breast tumor cells composing tubular structures


title: left ventricle   GRMD   young biological replicate 3

value: Golden Retriever

value: GRMD

value: 6 months


title: left ventricle   Normal   middle biological replicate 3

value: Normal

value: left ventricle


title: DE_D3-3_alveolar structures_cnv

value: breast tumor

value: alveolar


title: left ventricle   GRMD   young biological replicate 2


title: CGH_2_indirect

description: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 150 from Brown University vs. human female reference DNA, replicate 2


title: DE_D1-1_tubular structures_cnv

value: DE


title: left ventricle   Normal   middle biological replicate 1

value: 12 months


title: left ventricle   GRMD   young biological replicate 1

value: 6.75 months


title: SJIA_2_2513_Day3_Canakinumab

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

value: Canakinumab


title: SJIA_2_2513_Day1_BL_Canakinumab

tag: treatment

tag: acr response at day 15


title: DD_D9-3_discrete groups of tumor cells_cnv

source_name: 3rd region of the breast tumor of the DD patient

value: discrete groups of tumor cells

value: DD

value: female

value: invasive carcinoma of no special type

value: luminal B

tag: therapy

value: without preoperative therapy

tag: sample type


title: CGH_1_indirect

description: MCF-7 from ATCC (HTB-22, lot number 59388743) at passage number 150 from Brown University vs. human female reference DNA, replicate 1

tag: cell line

value: human female reference DNA

value: Agilent SureTag Complete DNA labeling kit (Agilent, Part# 5190-3399)


title: left ventricle   Normal   young biological replicate 3

tag: breed

value: Golden Retriever

tag: disease

value: Normal

value: left ventricle

value: 7.5 months


title: MMpt4 normoxia_miRNA

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

country: Japan

institute: Akita univ.

hyb_protocol: As materials and methods for miRNAmicroarray protocol version 2.4 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 90%tile normalization.

source_name: normoxia, CD38++

label_protocol: As materials and methods for miRNA microarray protocol version 2.4 (Agilent).

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: normoxia: 21%O2, hypoxia: 1%O2.

tag: condition

value: normoxia

tag: disease state

value: myeloma


title: MMpt3 normoxia_miRNA


title: MMpt2 normoxia_miRNA


title: MMpt4 hypoxia_miRNA

source_name: hypoxia, CD38++

value: hypoxia


title: DD_D9-2_discrete groups of tumor cells_cnv

source_name: 2nd region of the breast tumor of the DD patient

tag: tissue

value: breast tumor

tag: tumor structure

tag: patient id

tag: gender

tag: age

value: reference


title: DD_D9-1_discrete groups of tumor cells_cnv

source_name: 1st region of the breast tumor of the DD patient

value: discrete groups of tumor cells

tag: histological type

tag: molecular subtype

tag: tnm stage


title: MMpt1 normoxia_miRNA


title: MMpt2 hypoxia_miRNA


title: left ventricle   Normal   young  biological replicate 1

value: 6 months


title: MMpt3 hypoxia_miRNA


title: DD_D7-3_trabecular structures_cnv

value: trabecular

value: DD

value: female


title: KMS11 hypoxia_miRNA

data_processing: GeneSpring (Agilent), computed normalized signal intensity with 90%tile normalization.

source_name: KMS11 hypoxia

growth_protocol: RPMI1640 plus 10% FCS.

tag: cell type


title: left ventricle   Normal   young biological replicate 2


title: MMpt1 hypoxia_miRNA


title: RPMI8226 hypoxia_miRNA

source_name: RPMI8226 hypoxia


title: DD_D7-2_trabecular structures_cnv

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy


title: KMS12BM hypoxia_miRNA

source_name: KMS12BM hypoxia


title: MM.1S normoxia_miRNA

source_name: MM.1S normoxia


title: MM.1S hypoxia_miRNA

source_name: MM.1S hypoxia


title: KMS11 normoxia_miRNA

source_name: KMS11 normoxia


title: DD_D3-3_alveolar structures_cnv

value: alveolar


title: Y3 vs W3

city: Haikou

first: lili

last: zhang

address: longhua County，Xueyuan Road 4

country: China

institute: Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences

description: Biological replicate 3 of 3. the comparison of  the MaASR1 transgenic lines L14 and wild-type Arabidopsis thaliana after dehydration treatment

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10KA (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

organism: Arabidopsis thaliana

source_name: plant seedlings

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: All Arabidopsis seeds were sterilized in 75% (v/v) ethanol for 10 minutes, and then germinated on 1/2 MS medium  after treatment to break dormancy (i.e. maintaining seeds for 2 d at 4 °C in the dark). Plants were grown at 22 °C under fluorescent light (16 h light/8 h dark cycles).

extract_protocol: total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: For dehydration treatment, 14-d-old Arabidopsis seedlings of each sample were transferred to filter paper to induce dehydration. The top of the filter papers were covered by Petri dishes to prevent the moisture loss from the evaporation, and then the filter papers were placed into the light incubator. The temperature was controlled at 22°C, the light intensity was150µmol•m−2•s−1 and the incubator relative humidity was 70%. After 0 h or 2 h treatment, the whole Arabidopsis seedlings were sampled to extract RNA for further microarray analysis.14 vs WT represents  the comparison of wild-type Arabidopsis thaliana and the MaASR1 transgenic line L14 under normal conditions, Y vs W represents  the comparison of wild-type Arabidopsis thaliana and the MaASR1 transgenic lines L14 after dehydration treatment.

value: seedling

tag: genotype

value: MaASR1 transgenic line L14

tag: treatment

value: dehydration

value: wild type


title: DD_D7-1_trabecular structures_cnv

tag: therapy

tag: sample type


title: Y1 vs W1

description: Biological replicate 1 of 3. the comparison of  the MaASR1 transgenic lines L14 and wild-type Arabidopsis thaliana after dehydration treatment


title: DD_D3-1_alveolar structures_cnv


title: Y2 vs W2

description: Biological replicate 2 of 3. the comparison of  the MaASR1 transgenic lines L14 and wild-type Arabidopsis thaliana after dehydration treatment


title: DD_D3-2_alveolar structures_cnv


title: DD_D5-3_solid structures_cnv

value: solid


title: DD_D5-2_solid structures_cnv


title: DD_D1-3_tubular structures_cnv

value: tubular


title: DD_D5-1_solid structures_cnv

value: breast tumor


title: DD_D1-1_tubular structures_cnv

value: reference


title: RPMI8226 normoxia_miRNA

source_name: RPMI8226 normoxia

value: normoxia

tag: cell line

value: myeloma


title: h219: Validation Set - Subject 219

status: Public on Apr 28 2016

type: protein

city: Frederick

first: Jeff

last: Gildersleeve

address: 376 Boyles St.

institute: National Cancer Institute

description: Validation Set - Subject 219

hyb_protocol: Arrays were blocked with BSA overnight, and serum samples (diluted 1:50) was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected with fluorescently labeled secondary antibodies.  Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

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

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.

Signals for IgG and IgM were analyzed independently and are available as supplementary data linked to GSE68403. Raw (.gpr) files are also available as supplementary data linked to GSE68403. See README file for details.

molecule: protein

source_name: Serum (Diluted 1:50)

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

extract_protocol: Serum was obtained from peripheral blood samples

tag: Sex

value: M

tag: race

value: African-American

tag: blood type

value: AB

tag: antibody

label: DyLight 649


title: h218: Validation Set - Subject 218

description: Validation Set - Subject 218

value: Caucasian

value: conjugated anti-human IgG (Jackson 109-505-008)

value: conjugated anti-human IgM  (Jackson Immuno, 109-495-043)


title: h217: Validation Set - Subject 217

description: Validation Set - Subject 217


title: h215: Validation Set - Subject 215

description: Validation Set - Subject 215


title: h216: Validation Set - Subject 216

description: Validation Set - Subject 216


title: KMS12BM normoxia_miRNA

source_name: KMS12BM normoxia

tag: condition


title: h214: Validation Set - Subject 214

description: Validation Set - Subject 214


title: DD_D1-2_tubular structures_cnv

tag: tissue

tag: tumor structure

tag: patient id

value: DD

value: female

value: invasive carcinoma of no special type

value: luminal B

value: without preoperative therapy

source_name: Agilent EuroFemale


title: h212: Validation Set - Subject 212

description: Validation Set - Subject 212

tag: age

value: Hispanic


title: Mature DC, co-cultured with BMSC-2

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description:
Gene expression after 2days of co-culture with BMSC in the presence of LPS-PG
4 mDC-BM_2

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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028279 SurePrint G3 Rat GE Microarray 8x60K for 17 hours at 65°C in a rotating SureHyb chamber.  After hybridization, microarrays were washed 1minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mature DC_co-cultured with BMSC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling 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.

growth_protocol: Samples were cultured in RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum. The cultures were incubated for 2 days at 37 ºC

extract_protocol: Samples were lysed and RNA isolation was carried out using the RNA-spin total RNA extraction kit (iNtRON Biotechnology, Sungnam, Kyungki-Do, South Korea) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CD14+ monocytes were isolated from peripheral blood mononuclear cells (PBMC) and then differentiatited into Immature DCs. Immature DCs (ImDCs) were cultured alone with 100 ng/ml of LPS-PG as control (mDC), or ImDCs were added to either a BMSCs (mDC-BM) or PDLSCs (mDC-PD) seeded 6 well plate with 100 ng/ml of LPS-PG

tag: gender

value: male

value: whole blood

value: monocyte-derived mature dendritic cells (mDCs)

tag: cocultured with

value: bone marrow mesenchymal stem cells (BMSCs)


title: 14_2 vs WT_2

description: Biological replicate 2 of 3. the comparison of  the MaASR1 transgenic line L14 and wild-type Arabidopsis thaliana under normal conditions

value: seedling

value: MaASR1 transgenic line L14

value: control

value: wild type


title: 14_1 vs WT_1

description: Biological replicate 1 of 3. the comparison of  the MaASR1 transgenic line L14 and wild-type Arabidopsis thaliana under normal conditions


title: 14_3 vs WT_3

description: Biological replicate 3 of 3. the comparison of  the MaASR1 transgenic line L14 and wild-type Arabidopsis thaliana under normal conditions


title: h211: Validation Set - Subject 211

description: Validation Set - Subject 211

value: F

value: African-American

value: AB


title: Mature DC, co-cultured with BMSC-3

description:
Gene expression after 2days of co-culture with BMSC in the presence of LPS-PG
5 mDC-BM_3

tag: cell type


title: Mature DC, co-cultured with PDLSC-2

description:
Gene expression after 2days of co-culture with PDLSC in the presence of LPS-PG
7 mDC-PD_2

source_name: Mature DC_co-cultured with PDLSC

value: periodontal ligament stem cells (PDLSCs)


title: h213: Validation Set - Subject 213

description: Validation Set - Subject 213

value: M

value: conjugated anti-human IgG (Jackson 109-505-008)

value: conjugated anti-human IgM  (Jackson Immuno, 109-495-043)


title: Mature DC, co-cultured with PDLSC-3

description:
Gene expression after 2days of co-culture with PDLSC in the presence of LPS-PG
8 mDC-PD_3


title: Mature DC, co-cultured with PDLSC-1

description:
Gene expression after 2days of co-culture with PDLSC in the presence of LPS-PG
6 mDC-PD_1


title: Mature DC, co-cultured with BMSC-1

description:
Gene expression after 2days of co-culture with BMSC in the presence of LPS-PG
3 mDC-BM_1


title: h210: Validation Set - Subject 210

description: Validation Set - Subject 210

value: B


title: h209: Validation Set - Subject 209

description: Validation Set - Subject 209

value: Hispanic


title: h220: Validation Set - Subject 220

description: Validation Set - Subject 220

value: Caucasian


title: h208: Validation Set - Subject 208

description: Validation Set - Subject 208


title: h207: Validation Set - Subject 207

description: Validation Set - Subject 207


title: h202: Validation Set - Subject 202

description: Validation Set - Subject 202


title: h204: Validation Set - Subject 204

description: Validation Set - Subject 204


title: h203: Validation Set - Subject 203

description: Validation Set - Subject 203


title: h205: Validation Set - Subject 205

description: Validation Set - Subject 205


title: h206: Validation Set - Subject 206

description: Validation Set - Subject 206


title: h201: Validation Set - Subject 201

description: Validation Set - Subject 201


title: h200: Validation Set - Subject 200

description: Validation Set - Subject 200

value: O


title: h199: Validation Set - Subject 199

description: Validation Set - Subject 199


title: h198: Validation Set - Subject 198

description: Validation Set - Subject 198


title: h197: Validation Set - Subject 197

description: Validation Set - Subject 197


title: h196: Validation Set - Subject 196

description: Validation Set - Subject 196


title: h195: Validation Set - Subject 195

description: Validation Set - Subject 195


title: Mature DC-1

description:
Gene expression after 2days in the presence of LPS-PG
1 mDC-only_1

source_name: Mature DC

value: male

value: whole blood

value: monocyte-derived mature dendritic cells (mDCs)

value: none (mDC only)


title: h192: Validation Set - Subject 192

description: Validation Set - Subject 192

value: A


title: h194: Validation Set - Subject 194

description: Validation Set - Subject 194


title: h193: Validation Set - Subject 193

description: Validation Set - Subject 193


title: h188: Validation Set - Subject 188

description: Validation Set - Subject 188


title: h184: Validation Set - Subject 184

description: Validation Set - Subject 184


title: h185: Validation Set - Subject 185

description: Validation Set - Subject 185


title: h187: Validation Set - Subject 187

description: Validation Set - Subject 187


title: h189: Validation Set - Subject 189

description: Validation Set - Subject 189


title: h191: Validation Set - Subject 191

description: Validation Set - Subject 191


title: h186: Validation Set - Subject 186

description: Validation Set - Subject 186


title: h190: Validation Set - Subject 190

description: Validation Set - Subject 190


title: h182: Validation Set - Subject 182

description: Validation Set - Subject 182


title: h183: Validation Set - Subject 183

description: Validation Set - Subject 183


title: h181: Validation Set - Subject 181

description: Validation Set - Subject 181


title: h178: Validation Set - Subject 178

description: Validation Set - Subject 178


title: h179: Validation Set - Subject 179

description: Validation Set - Subject 179


title: h176: Validation Set - Subject 176

description: Validation Set - Subject 176


title: h175: Validation Set - Subject 175

description: Validation Set - Subject 175


title: h173: Validation Set - Subject 173

description: Validation Set - Subject 173


title: h172: Validation Set - Subject 172

description: Validation Set - Subject 172


title: h170: Validation Set - Subject 170

description: Validation Set - Subject 170


title: h169: Validation Set - Subject 169

description: Validation Set - Subject 169


title: h167: Validation Set - Subject 167

description: Validation Set - Subject 167


title: h165: Validation Set - Subject 165

description: Validation Set - Subject 165


title: h164: Validation Set - Subject 164

description: Validation Set - Subject 164


title: Mature DC-2

description:
Gene expression after 2days in the presence of LPS-PG
2 mDC-only_1


title: h166: Validation Set - Subject 166

description: Validation Set - Subject 166


title: h158: Validation Set - Subject 158

description: Validation Set - Subject 158


title: h162: Validation Set - Subject 162

description: Validation Set - Subject 162


title: h155: Validation Set - Subject 155

description: Validation Set - Subject 155


title: h161: Validation Set - Subject 161

description: Validation Set - Subject 161


title: h163: Validation Set - Subject 163

description: Validation Set - Subject 163


title: h180: Validation Set - Subject 180

description: Validation Set - Subject 180


title: h160: Validation Set - Subject 160

description: Validation Set - Subject 160


title: h177: Validation Set - Subject 177

description: Validation Set - Subject 177


title: h151: Validation Set - Subject 151

description: Validation Set - Subject 151


title: h152: Validation Set - Subject 152

description: Validation Set - Subject 152


title: h171: Validation Set - Subject 171

description: Validation Set - Subject 171


title: h148: Validation Set - Subject 148

description: Validation Set - Subject 148


title: h157: Validation Set - Subject 157

description: Validation Set - Subject 157


title: h154: Validation Set - Subject 154

description: Validation Set - Subject 154


title: h174: Validation Set - Subject 174

description: Validation Set - Subject 174


title: h150: Validation Set - Subject 150

description: Validation Set - Subject 150


title: h145: Validation Set - Subject 145

description: Validation Set - Subject 145


title: h149: Validation Set - Subject 149

description: Validation Set - Subject 149


title: h147: Validation Set - Subject 147

description: Validation Set - Subject 147


title: h146: Validation Set - Subject 146

description: Validation Set - Subject 146


title: h168: Validation Set - Subject 168

description: Validation Set - Subject 168


title: h156: Validation Set - Subject 156

description: Validation Set - Subject 156


title: h143: Validation Set - Subject 143

description: Validation Set - Subject 143


title: h153: Validation Set - Subject 153

description: Validation Set - Subject 153


title: h159: Validation Set - Subject 159

description: Validation Set - Subject 159


title: h141: Validation Set - Subject 141

description: Validation Set - Subject 141


title: h142: Validation Set - Subject 142

description: Validation Set - Subject 142


title: h136: Validation Set - Subject 136

description: Validation Set - Subject 136


title: h139: Validation Set - Subject 139

description: Validation Set - Subject 139


title: h135: Validation Set - Subject 135

description: Validation Set - Subject 135


title: h133: Validation Set - Subject 133

description: Validation Set - Subject 133


title: h140: Validation Set - Subject 140

description: Validation Set - Subject 140


title: h138: Validation Set - Subject 138

description: Validation Set - Subject 138


title: h134: Validation Set - Subject 134

description: Validation Set - Subject 134


title: h129: Validation Set - Subject 129

description: Validation Set - Subject 129


title: h132: Validation Set - Subject 132

description: Validation Set - Subject 132


title: h125: Validation Set - Subject 125

description: Validation Set - Subject 125


title: h131: Validation Set - Subject 131

description: Validation Set - Subject 131


title: h128: Validation Set - Subject 128

description: Validation Set - Subject 128


title: h126: Validation Set - Subject 126

description: Validation Set - Subject 126


title: h137: Validation Set - Subject 137

description: Validation Set - Subject 137


title: h127: Validation Set - Subject 127

description: Validation Set - Subject 127


title: h130: Validation Set - Subject 130

description: Validation Set - Subject 130


title: h123: Validation Set - Subject 123

description: Validation Set - Subject 123


title: h144: Validation Set - Subject 144

description: Validation Set - Subject 144


title: h121: Validation Set - Subject 121

description: Validation Set - Subject 121


title: h122: Validation Set - Subject 122

description: Validation Set - Subject 122


title: h124: Validation Set - Subject 124

description: Validation Set - Subject 124


title: h120: Validation Set - Subject 120

description: Validation Set - Subject 120


title: h116: Validation Set - Subject 116

description: Validation Set - Subject 116


title: h114: Validation Set - Subject 114

description: Validation Set - Subject 114


title: 842: Validation patient #115 | Vaccine Arm | Pre-treatment

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.

Signals for IgG and IgM were analyzed independently and are available as supplementary data linked to GSE68404. Raw (.gpr) files are also available as supplementary data linked to GSE68404. See README file for details.

tag: halabi predicted survival (months)

tag: post-vaccination survival (months)

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

tag: treatment arm

value: PROSTVAC

tag: age at enrollment (years)

tag: gleason score

tag: on-study psa

value: Vaccine

tag: timepoint

value: Pre-treatment


title: h117: Validation Set - Subject 117

description: Validation Set - Subject 117

tag: Sex

value: F

tag: race

tag: blood type

tag: antibody


title: h119: Validation Set - Subject 119

description: Validation Set - Subject 119


title: h113: Validation Set - Subject 113

description: Validation Set - Subject 113


title: 847: Validation patient #116 | Vaccine Arm | Pre-treatment

tag: treatment


title: 852: Validation patient #117 | Control Arm | Pre-treatment

value: Control


title: h115: Validation Set - Subject 115

description: Validation Set - Subject 115

value: M

tag: age


title: h111: Validation Set - Subject 111

description: Validation Set - Subject 111

value: conjugated anti-human IgG (Jackson 109-505-008)


title: 837: Validation patient #114 | Vaccine Arm | Pre-treatment

value: conjugated anti-human IgM  (Jackson Immuno, 109-495-043)


title: 830: Validation patient #113 | Control Arm | Pre-treatment


title: h118: Validation Set - Subject 118

description: Validation Set - Subject 118


title: h109: Validation Set - Subject 109

description: Validation Set - Subject 109


title: h108: Validation Set - Subject 108

description: Validation Set - Subject 108


title: h107: Validation Set - Subject 107

description: Validation Set - Subject 107


title: 826: Validation patient #112 | Vaccine Arm | Pre-treatment


title: 802: Validation patient #108 | Vaccine Arm | Pre-treatment


title: h110: Validation Set - Subject 110

description: Validation Set - Subject 110


title: h112: Validation Set - Subject 112

description: Validation Set - Subject 112


title: 816: Validation patient #110 | Vaccine Arm | Pre-treatment


title: h105: Validation Set - Subject 105

description: Validation Set - Subject 105


title: 810: Validation patient #109 | Vaccine Arm | Pre-treatment


title: h106: Validation Set - Subject 106

description: Validation Set - Subject 106


title: h104: Validation Set - Subject 104

description: Validation Set - Subject 104


title: 798: Validation patient #107 | Control Arm | Pre-treatment


title: 793: Validation patient #106 | Vaccine Arm | Pre-treatment


title: 787: Validation patient #105 | Vaccine Arm | Pre-treatment


title: h102: Validation Set - Subject 102

description: Validation Set - Subject 102


title: h103: Validation Set - Subject 103

description: Validation Set - Subject 103


title: 781: Validation patient #104 | Vaccine Arm | Pre-treatment


title: h101: Validation Set - Subject 101

description: Validation Set - Subject 101


title: 822: Validation patient #111 | Vaccine Arm | Pre-treatment


title: 769: Validation patient #102 | Vaccine Arm | Pre-treatment


title: h98: Test Set - Subject #98

description: Test Set - Subject #98

value: Caucasion

value: AB


title: h99: Test Set - Subject #99

description: Test Set - Subject #99

value: African-American


title: 745: Validation patient #99 | Vaccine Arm | Pre-treatment


title: 776: Validation patient #103 | Vaccine Arm | Pre-treatment


title: h95: Test Set - Subject #95

description: Test Set - Subject #95


title: h97: Test Set - Subject #97

description: Test Set - Subject #97

value: Hispanic


title: 762: Validation patient #101 | Control Arm | Pre-treatment


title: h94: Test Set - Subject #94

description: Test Set - Subject #94

value: B


title: h93: Test Set - Subject #93

description: Test Set - Subject #93


title: 729: Validation patient #97 | Control Arm | Pre-treatment


title: h100: Test Set - Subject #100

description: Test Set - Subject #100


title: 752: Validation patient #100 | Vaccine Arm | Pre-treatment


title: h96: Test Set - Subject #96

description: Test Set - Subject #96


title: 709: Validation patient #95 | Control Arm | Pre-treatment


title: h92: Test Set - Subject #92

description: Test Set - Subject #92


title: 696: Validation patient #93 | Vaccine Arm | Pre-treatment


title: 704: Validation patient #94 | Vaccine Arm | Pre-treatment


title: h89: Test Set - Subject #89

description: Test Set - Subject #89


title: h91: Test Set - Subject #91

description: Test Set - Subject #91


title: 678: Validation patient #92 | Vaccine Arm | Pre-treatment


title: 670: Validation patient #91 | Vaccine Arm | Pre-treatment


title: 738: Validation patient #98 | Vaccine Arm | Pre-treatment


title: 664: Validation patient #90 | Vaccine Arm | Pre-treatment


title: 656: Validation patient #89 | Control Arm | Pre-treatment


title: h87: Test Set - Subject #87

description: Test Set - Subject #87


title: h88: Test Set - Subject #88

description: Test Set - Subject #88


title: h86: Test Set - Subject #86

description: Test Set - Subject #86


title: 636: Validation patient #86 | Vaccine Arm | Pre-treatment


title: 648: Validation patient #88 | Vaccine Arm | Pre-treatment


title: 628: Validation patient #85 | Vaccine Arm | Pre-treatment


title: h85: Test Set - Subject #85

description: Test Set - Subject #85


title: h82: Test Set - Subject #82

description: Test Set - Subject #82


title: 620: Validation patient #84 | Control Arm | Pre-treatment


title: 608: Validation patient #82 | Vaccine Arm | Pre-treatment


title: h84: Test Set - Subject #84

description: Test Set - Subject #84


title: h79: Test Set - Subject #79

description: Test Set - Subject #79

value: O


title: 577: Validation patient #78 | Vaccine Arm | Pre-treatment


title: h81: Test Set - Subject #81

description: Test Set - Subject #81


title: h83: Test Set - Subject #83

description: Test Set - Subject #83


title: 571: Validation patient #77 | Vaccine Arm | Pre-treatment


title: h77: Test Set - Subject #77

description: Test Set - Subject #77


title: h90: Test Set - Subject #90

description: Test Set - Subject #90


title: 592: Validation patient #80 | Control Arm | Pre-treatment


title: h75: Test Set - Subject #75

description: Test Set - Subject #75


title: h78: Test Set - Subject #78

description: Test Set - Subject #78


title: 584: Validation patient #79 | Vaccine Arm | Pre-treatment


title: h80: Test Set - Subject #80

description: Test Set - Subject #80


title: 600: Validation patient #81 | Vaccine Arm | Pre-treatment


title: 563: Validation patient #76 | Vaccine Arm | Pre-treatment


title: h76: Test Set - Subject #76

description: Test Set - Subject #76


title: 640: Validation patient #87 | Control Arm | Pre-treatment


title: 554: Validation patient #75 | Control Arm | Pre-treatment


title: 546: Validation patient #74 | Vaccine Arm | Pre-treatment


title: h72: Test Set - Subject #72

description: Test Set - Subject #72


title: h73: Test Set - Subject #73

description: Test Set - Subject #73


title: 525: Validation patient #72 | Control Arm | Pre-treatment


title: h69: Test Set - Subject #69

description: Test Set - Subject #69


title: 518: Validation patient #71 | Vaccine Arm | Pre-treatment


title: h71: Test Set - Subject #71

description: Test Set - Subject #71


title: 498: Validation patient #69 | Control Arm | Pre-treatment


title: 510: Validation patient #70 | Vaccine Arm | Pre-treatment


title: h68: Test Set - Subject #68

description: Test Set - Subject #68


title: h70: Test Set - Subject #70

description: Test Set - Subject #70


title: 489: Validation patient #68 | Control Arm | Pre-treatment


title: h74: Test Set - Subject #74

description: Test Set - Subject #74


title: h63: Test Set - Subject #63

description: Test Set - Subject #63


title: h64: Test Set - Subject #64

description: Test Set - Subject #64


title: h67: Test Set - Subject #67

description: Test Set - Subject #67


title: 439: Validation patient #61 | Vaccine Arm | Pre-treatment


title: 432: Validation patient #60 | Vaccine Arm | Pre-treatment


title: h66: Test Set - Subject #66

description: Test Set - Subject #66


title: h60: Training Set - Subject #60

description: Training Set - Subject #60


title: h65: Test Set - Subject #65

description: Test Set - Subject #65


title: 474: Validation patient #66 | Vaccine Arm | Pre-treatment


title: 467: Validation patient #65 | Vaccine Arm | Pre-treatment


title: 420: Validation patient #58 | Vaccine Arm | Pre-treatment


title: 424: Validation patient #59 | Vaccine Arm | Pre-treatment


title: 412: Validation patient #57 | Vaccine Arm | Pre-treatment


title: h58: Training Set - Subject #58

description: Training Set - Subject #58


title: 537: Validation patient #73 | Control Arm | Pre-treatment


title: 459: Validation patient #64 | Vaccine Arm | Pre-treatment


title: 407: Validation patient #56 | Vaccine Arm | Pre-treatment


title: h59: Training Set - Subject #59

description: Training Set - Subject #59


title: h57: Training Set - Subject #57

description: Training Set - Subject #57


title: 482: Validation patient #67 | Vaccine Arm | Pre-treatment


title: h62: Test Set - Subject #62

description: Test Set - Subject #62


title: h55: Training Set - Subject #55

description: Training Set - Subject #55

value: Caucasian


title: 398: Validation patient #54 | Control Arm | Pre-treatment


title: h56: Training Set - Subject #56

description: Training Set - Subject #56


title: 390: Validation patient #53 | Control Arm | Pre-treatment


title: 375: Validation patient #50 | Vaccine Arm | Pre-treatment


title: h52: Training Set - Subject #52

description: Training Set - Subject #52


title: h61: Test Set - Subject #61

description: Test Set - Subject #61


title: 386: Validation patient #52 | Control Arm | Pre-treatment


title: 380: Validation patient #51 | Vaccine Arm | Pre-treatment


title: 357: Validation patient #46 | Vaccine Arm | Pre-treatment


title: h53: Training Set - Subject #53

description: Training Set - Subject #53


title: 365: Validation patient #47 | Vaccine Arm | Pre-treatment


title: h54: Training Set - Subject #54

description: Training Set - Subject #54


title: 342: Validation patient #45 | Control Arm | Pre-treatment


title: 368: Validation patient #48 | Vaccine Arm | Pre-treatment


title: h51: Training Set - Subject #51

description: Training Set - Subject #51


title: h50: Training Set - Subject #50

description: Training Set - Subject #50


title: 334: Validation patient #44 | Control Arm | Pre-treatment


title: h46: Training Set - Subject #46

description: Training Set - Subject #46


title: h48: Training Set - Subject #48

description: Training Set - Subject #48


title: h49: Training Set - Subject #49

description: Training Set - Subject #49


title: h47: Training Set - Subject #47

description: Training Set - Subject #47


title: h45: Training Set - Subject #45

description: Training Set - Subject #45


title: 326: Validation patient #43 | Vaccine Arm | Pre-treatment


title: h43: Training Set - Subject #43

description: Training Set - Subject #43


title: h44: Training Set - Subject #44

description: Training Set - Subject #44


title: 312: Validation patient #42 | Control Arm | Pre-treatment


title: 298: Validation patient #41 | Control Arm | Pre-treatment


title: 372: Validation patient #49 | Control Arm | Pre-treatment


title: 279: Validation patient #39 | Vaccine Arm | Pre-treatment


title: 276: Validation patient #38 | Control Arm | Pre-treatment


title: h42: Training Set - Subject #42

description: Training Set - Subject #42


title: h41: Training Set - Subject #41

description: Training Set - Subject #41


title: 287: Validation patient #40 | Control Arm | Pre-treatment


title: h39: Training Set - Subject #39

description: Training Set - Subject #39


title: h40: Training Set - Subject #40

description: Training Set - Subject #40


title: 244: Validation patient #32 | Vaccine Arm | Pre-treatment


title: h38: Training Set - Subject #38

description: Training Set - Subject #38


title: 221: Validation patient #30 | Control Arm | Pre-treatment


title: h34: Training Set - Subject #34

description: Training Set - Subject #34


title: 252: Validation patient #34 | Vaccine Arm | Pre-treatment


title: h37: Training Set - Subject #37

description: Training Set - Subject #37


title: 247: Validation patient #33 | Vaccine Arm | Pre-treatment


title: 218: Validation patient #29 | Vaccine Arm | Pre-treatment


title: h36: Training Set - Subject #36

description: Training Set - Subject #36


title: h35: Training Set - Subject #35

description: Training Set - Subject #35


title: h32: Training Set - Subject #32

description: Training Set - Subject #32


title: h31: Training Set - Subject #31

description: Training Set - Subject #31


title: 207: Validation patient #27 | Vaccine Arm | Pre-treatment


title: 197: Validation patient #26 | Vaccine Arm | Pre-treatment


title: h30: Training Set - Subject #30

description: Training Set - Subject #30


title: 192: Validation patient #25 | Vaccine Arm | Pre-treatment


title: h28: Training Set - Subject #28

description: Training Set - Subject #28


title: 184: Validation patient #24 | Vaccine Arm | Pre-treatment


title: 271: Validation patient #37 | Vaccine Arm | Pre-treatment


title: 177: Validation patient #23 | Vaccine Arm | Pre-treatment


title: h27: Training Set - Subject #27

description: Training Set - Subject #27


title: 257: Validation patient #35 | Control Arm | Pre-treatment


title: h26: Training Set - Subject #26

description: Training Set - Subject #26


title: 233: Validation patient #31 | Vaccine Arm | Pre-treatment


title: h25: Training Set - Subject #25

description: Training Set - Subject #25


title: 210: Validation patient #28 | Vaccine Arm | Pre-treatment


title: 170: Validation patient #22 | Control Arm | Pre-treatment


title: 162: Validation patient #21 | Control Arm | Pre-treatment


title: h24: Training Set - Subject #24

description: Training Set - Subject #24


title: 152: Validation patient #19 | Vaccine Arm | Pre-treatment


title: h23: Training Set - Subject #23

description: Training Set - Subject #23


title: 157: Validation patient #20 | Vaccine Arm | Pre-treatment


title: 147: Validation patient #18 | Vaccine Arm | Pre-treatment


title: h33: Training Set - Subject #33

description: Training Set - Subject #33


title: 127: Validation patient #16 | Control Arm | Pre-treatment


title: h20: Training Set - Subject #20

description: Training Set - Subject #20


title: 136: Validation patient #17 | Control Arm | Pre-treatment


title: h18: Training Set - Subject #18

description: Training Set - Subject #18


title: h29: Training Set - Subject #29

description: Training Set - Subject #29


title: h21: Training Set - Subject #21

description: Training Set - Subject #21


title: h16: Training Set - Subject #16

description: Training Set - Subject #16


title: 109: Validation patient #14 | Vaccine Arm | Pre-treatment


title: h15: Training Set - Subject #15

description: Training Set - Subject #15


title: h17: Training Set - Subject #17

description: Training Set - Subject #17


title: 101: Validation patient #13 | Vaccine Arm | Pre-treatment


title: 117: Validation patient #15 | Control Arm | Pre-treatment


title: h13: Training Set - Subject #13

description: Training Set - Subject #13


title: h14: Training Set - Subject #14

description: Training Set - Subject #14


title: h22: Training Set - Subject #22

description: Training Set - Subject #22


title: 89: Validation patient #12 | Control Arm | Pre-treatment


title: h11: Training Set - Subject #11

description: Training Set - Subject #11


title: 74: Validation patient #10 | Vaccine Arm | Pre-treatment


title: h9: Training Set - Subject #9

description: Training Set - Subject #9


title: h19: Training Set - Subject #19

description: Training Set - Subject #19


title: h10: Training Set - Subject #10

description: Training Set - Subject #10


title: h6: Training Set - Subject #6

description: Training Set - Subject #6


title: 46: Validation patient #8 | Vaccine Arm | Pre-treatment


title: 82: Validation patient #11 | Vaccine Arm | Pre-treatment


title: 29: Validation patient #5 | Control Arm | Pre-treatment


title: 9: Validation patient #2 | Control Arm | Pre-treatment


title: 33: Validation patient #6 | Vaccine Arm | Pre-treatment


title: h8: Training Set - Subject #8

description: Training Set - Subject #8


title: 1: Validation patient #1 | Vaccine Arm | Pre-treatment


title: h4: Training Set - Subject #4

description: Training Set - Subject #4


title: h5: Training Set - Subject #5

description: Training Set - Subject #5


title: 65: Validation patient #9 | Control Arm | Pre-treatment


title: 21: Validation patient #4 | Control Arm | Pre-treatment


title: h2: Training Set - Subject #2

description: Training Set - Subject #2


title: 41: Validation patient #7 | Vaccine Arm | Pre-treatment


title: 13: Validation patient #3 | Vaccine Arm | Pre-treatment


title: h1: Training Set - Subject #1

description: Training Set - Subject #1


title: h12: Training Set - Subject #12

description: Training Set - Subject #12


title: h7: Training Set - Subject #7

description: Training Set - Subject #7


title: h3: Training Set - Subject #3

description: Training Set - Subject #3


title: ND42 APE1 expressing BEAS-2B cells, rep 3

city: Houston

first: Shiladitya

last: Sengupta

address: 6550 Fannin Street

institute: Houston Methodist Reserach Institute

description: gene expression data from ND42 mutant APE1 expressing BEAS-2B cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
Data analysis was performed in Bioconductor/R using the CEL files. The R module/package Affy was used to perform the pre-processing steps which includes the RMA method for background correction and quantile normalization. For differential expression testing, Linear Models for MicroArray (Limma) was used to fit linear models for analyzing designed experiments and the assessment of overall gene expression and contrast analysis comparing the experimental groups.
For differential expression testing, Linear Models for MicroArray (Limma) was used to fit linear models for analyzing designed experiments and the assessment of overall gene expression and contrast analysis comparing the experimental groups.

label: fluorescent

source_name: ND42 APE1 expressing BEAS-2B cells

label_protocol: standard Affymetrix protocol

growth_protocol: A549 cells were grown in DMEM high glucose medium with 10% FBS and antibiotic mixture of 100 U/ml penicillin and 100 µg/ml streptomycin. BEAS-2B cells were grown in DMEM/F12 1:1 with 10% FBS and antibiotic mixture of 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was isolated using Qiagen Rneasy mini kit following manufacturer’s protocol.

treatment_protocol: Exponentially growing A549 cells were splitted the day before transfection with control or APE1 siRNA, so that the cells were 30-50% confluent at the time of transfection. Cells were harvested for RNA isolation after 48 hours. In another set of experiment, before harvesting both control siRNA or APE1 siRNA-transfected cells were treated with TSA (100 ng/ml) for 4 hours. For experiments with ectopically expressed proteins in BEAS-2B cells, exponentially growing ≈ 50%-confluent cells were transfected with wild type (WT) APE1, N-terminal 42 amino acid deleted (NΔ42) or K6R/K7R (RR) mutant APE1 expression constructs in PCDNA3 background and harvested after 48 hrs for RNA isolation. Transfection was done with Lipofectamine 2000, following manufacturer’s protocol.

tag: cell line

value: normal bronchial epithelial cell line BEAS-2B

tag: genotype/variation

value: ND42 APE1 overexpression


title: K6R/K7R APE1 expressing BEAS-2B cells, rep 2

description: gene expression data from K6R/K7R mutant APE1 expressing BEAS-2B cells

source_name: K6R/K7R APE1 expressing BEAS-2B cells

value: K6R/K7R APE1 overexpression


title: K6R/K7R APE1 expressing BEAS-2B cells, rep 3


title: ND42 APE1 expressing BEAS-2B cells, rep 1


title: ND42 APE1 expressing BEAS-2B cells, rep 2


title: K6R/K7R APE1 expressing BEAS-2B cells, rep 1


title: WT APE1 expressing BEAS-2B cells, rep 3

description: gene expression data from WT APE1 expressing BEAS-2B cells

source_name: WT APE1 expressing BEAS-2B cells

value: WT APE1 overexpression


title: WT APE1 expressing BEAS-2B cells, rep 1


title: TSA-treated APE1 siRNA A549 cell, rep 2

description: gene expression data from TSA-treated APE1-downregulated A549 cells

source_name: TSA-treated APE1 siRNA A549 cells

value: lung adenocarcinoma cell line A549

tag: agent

value: TSA


title: 3 µM Zn2+ 4 h N2

city: RTP, NC

first: Jenna

last: Currier

address: 109 TW Alexander Dr.

institute: ORISE at USEPA

description: replicate 2

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio®

source_name: BEAS-2B cells

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

extract_protocol: Total RNA was isolated from Zn2+-exposed BEAS-2B cells using RNAzol®RT (Molecular Research Center, Cincinnati, OH) and purified with RNeasy MinElute columns (Qiagen GmbH, Hilden, Germany). RNA was quantified using the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, DE) and evaluated for integrity with an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany).

tag: exposure

value: Zinc Sulfate Heptahydrate

tag: concentration

value: 3 µM

tag: time

value: 4 h


title: 3 µM Zn2+ 48 h N3

description: replicate 3


title: TSA-treated APE1 siRNA A549 cell, rep 1


title: 2 µM Zn2+ 48 h N3

description: replicate 3

value: 2 µM


title: 2 µM Zn2+ 48 h N2

description: replicate 2


title: 2 µM Zn2+ 4 h N2

description: replicate 2


title: 3 µM Zn2+ 24 h N2

description: replicate 2


title: 3 µM Zn2+ 24 h N3

description: replicate 3


title: TSA-treated control A549 cells, rep 3

description: gene expression data from TSA-treated control A549 cells

source_name: TSA-treated control A549 cells

value: control


title: TSA-treated APE1 siRNA A549 cell, rep 3


title: 2 µM Zn2+ 48 h N1

description: replicate 1


title: 3 µM Zn2+ 4 h N3

description: replicate 3


title: 3 µM Zn2+ 48 h N1

description: replicate 1


title: 3 µM Zn2+ 4 h N1

description: replicate 1


title: 2 µM Zn2+ 24 h N1

description: replicate 1


title: WT APE1 expressing BEAS-2B cells, rep 2


title: TSA-treated control A549 cells, rep 2


title: 2 µM Zn2+ 24 h N3

description: replicate 3


title: 3 µM Zn2+ 24 h N1

description: replicate 1


title: 3 µM Zn2+ 48 h N2

description: replicate 2


title: 2 µM Zn2+ 24 h N2

description: replicate 2


title: KBM-Basal Control 48 h N1

description: replicate 1

value: Control


title: KBM-Basal Control 24 h N3

description: replicate 3


title: 2 µM Zn2+ 4 h N1

description: replicate 1


title: KBM-Basal Control 48 h N2

description: replicate 2


title: KBM-Basal Control 24 h N2

description: replicate 2


title: KBM-Basal Control 24 h N1

description: replicate 1


title: APE1siRNA A549 cells, rep 2

description: gene expression data from APE1-downregulated A549 cells

source_name: APE1siRNA A549 cells


title: TSA-treated control A549 cells, rep 1


title: KBM-Basal Control 48 h N3

description: replicate 3


title: APE1siRNA A549 cells, rep 3


title: control A549 cells, rep 3

description: gene expression data from control A549 cells

source_name: control A549 cells


title: APE1siRNA A549 cells, rep 1


title: E13.5 WT lung

city: Madison

first: Yan

last: Zhang

state: WI

address: 425 Henry Mall Room 5240

department: Genetics

institute: UW-Madison

description: Gene expression data from control lungs at E13.5

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G scanner

data_processing: The data were analyzed with GeneSifter using Affymetrix default analysis settings.

source_name: embryonic lung

extract_protocol: RNA was prepared with RNeasy Mini kit (Qiagen)

value: wild type

tag: development stage


title: E13.5 Etv CKO lung

description: Gene expression data from Etv4;5 DKO lungs at E13.5

hyb_protocol: According to Affymetrix standard protocols

value: Etv4;5 knockout


title: mismatch control rep 2

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array. The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007)

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: primary corneal epithelial cell

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis

growth_protocol: Cells were grown in OcuLife media (Lifeline Cell Technology)

extract_protocol: RNA was isolated using the Directzol RNA kit (Zymogen)

treatment_protocol: 100,000 cells in suspension per well (12-well plates) were transfected with 30nM control (Dharmacon ON-TARGETplus Control pool, D-001810-10-05) or H19 (the pool of Qigen GeneSolution SI03650598, SI03650605, SI03650612, SI03650619) siRNAs in triplicate for 72 hrs before RNA isolation.

tag: tissue type

value: cornea epithelium


title: mismatch control rep 3


title: cells in X, biological rep1

city: Chengdu

first: Wei-Yi

last: Zeng

state: Sichuan

address: Chuanda Road ,Shuangliu County

department: Architecture and environment

institute: Sichuan University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

organism: Saccharomyces cerevisiae

source_name: cells utilizing xylose in YPX

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Cells were inoculated at 5 g-DCW/L. The cultivation condition was 35℃, 200rpm.

extract_protocol: Total RNA was extracted using the Takara Yeast RNAiso Kit according to the manufacturer’s protocols

treatment_protocol: Cells  were collected from the medium and washed with DEPC-treated water

tag: culture medium

value: YPX

tag: sugar source

value: xylose fermentation


title: control A549 cells, rep 1


title: siRNA H19 rep2


title: siRNA H19 rep3


title: siRNA H19 rep1


title: cells in X, biological rep2


title: control A549 cells, rep 2


title: mismatch control rep 1


title: whole cornea at P3, WT replicate 3

description: whole cornea at P3, WT replicate 3

hyb_protocol: 2.2 μg of the resulting fragmented, biotin-tagged cDNA was placed into a hybridization cocktail (220 μL), with 200 μL actually hybridized at 45°C with rotation for 18 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450 using the FS450_0004 fluidics protocol.

scan_protocol: Affymetrix GeneChip 3000 Scanner 7G

data_processing: Array data was quantified with Expression Console ver.1.1 software (Affymetrix, Inc.) using the PLIER Algorithm default values.

source_name: whole cornea, WT

label_protocol: NuGEN Ovation RNA Amplification System V2 and NuGEN FL-Ovation cDNA Biotin Module V2 (NuGEN Technologies, San Carlos CA).

growth_protocol: Eyes were collected at postnatal day 3 (P3) from WT and DN-Clim mice

extract_protocol: Eye globes were removed from K14-DN-Clim transgenic mice and wild type littermates immediately after sacrifice.  Whole corneas were dissected, removing all non-corneal tissues.  Total RNA from whole cornea was isolated with Trizol (Life Technologies) and cleaned up with the Qiagen RNEasy Micro Kit. Corneal RNA sample purity was validated by QPCR expression of tissue specific markers and absence of markers for adjacent tissues.


title: whole cornea at P3, K14-dominant negative-Clim replicate 3

source_name: whole cornea, K14-DN-Clim


title: whole cornea at P3, K14-dominant negative-Clim replicate 1


title: whole cornea at P3, K14-dominant negative-Clim replicate 2


title: cells in GX1, biological rep2

source_name: cells utilizing glucose in YPDX

value: YPDX

value: glucose fermentation phase in the mixed sugar medium


title: cells in GX2, biological rep1

source_name: cells utilizing xylose in YPDX

value: xylose fermentation phase in the mixed sugar medium


title: cells in GX2, biological rep2


title: whole cornea at P3, WT replicate 2

description: whole cornea at P3, WT replicate 2


title: cells in GX1, biological rep1


title: sev-GAL4>Ras1V12 EP3037_1

city: Varanasi

first: Subhash

middle: C

last: Lakhotia

state: UP

address: Cytogenetics Lab

department: Zoology

institute: Banaras Hindu UNiversity

description: Gene Expression data from 16-17 hr APF whole pupa expressing activated Ras protein and up regulation of hsromega non coding RNA in eye disc under sev-GAL4

hyb_protocol: Following fragmentation, 12 µg of cRNA samples were hybridized for 16 hr at 45°C on Drosophila Genome 2.0 microarray chips for 3’ IVT array . GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing: Summary of the expression levels for each gene in the four genotypes was obtained from the Expression Console software and Affymetrix Transcription analysis console.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster 16-17 hr old pupae

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 500 ng of total RNA (Affymetrix GeneChip Expression Analysis Technical Manual using the GeneChip 3’ IVT Plus Reagent Kit).

growth_protocol: 0-1 hr APF stage of sev-GAL4>UAS-GFP, sev-GAL4>Ras1V12, sev-GAL4>Ras1V12 hsrω-RNAi and sev-GAL4>Ras1V12 EP3037 pupae were collected and kept at 24°C and allowed to age for 16-17 hr.

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

treatment_protocol: 16-17 hr APF sev-GAL4>UAS-GFP, sev-GAL4>Ras1V12, sev-GAL4>Ras1V12 hsrω-RNAi and sev-GAL4>Ras1V12 EP3037 pupae were dissected in 1X PBS to remove the pupal case while all the internal tissues were placed on ice in the TriReagent solution (Sigma Aldrich) for RNA extraction.

tag: tissue

value: Pupa without pupal case

tag: genotype

value: sev-GAL4>Ras1V12 EP3037

value: 16-17 hr APF


title: line L5 root tissue grown in normal condition, biological rep4

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: Agilent gene expression array data of 4 x180k format 60-mer oligonucleotide probes designed against the S.lycopersicum cv. Heinz 1706 build 2.4 (annotation 2.5) genome

hyb_protocol: 200 ng of RNA was used for cDNA synthesis and Cy3-labelling using the Low Input Quick Amp Labeling Kit for One-Color Microarray-Based Gene Expression Agilent analysis. 1.65 µg of linearly amplified and labelled cDNA was hybridized for 17 h at 65°C in an oven with a rotating platform (see manufacturer's web site at http://www.agilent.com/).

scan_protocol: Arrays were imaged using an MS200 microarray scanner using only the 480 nm laser using the autogain feature of the NimbleScan software.

data_processing: Image (tiff) files were imported into the Agilent Feature Extraction software for quality control assessment, grid alignment and expression value extraction at the probe and transcript leve. The Robust Multichip Average (RMA) algorithm was used to normalize the data, taking outlier probes into account, and to summarize expression at the transcript level using median polish (Irizarry et al. 2003). This was used to output log2 normalized gene expression levels (see Matrix).

organism: Solanum lycopersicum x Solanum pimpinellifolium

source_name: plant root tissue

label_protocol: RNA was labelled with the Cy3 dye according to Agilent Technologies; One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (see manufacturer's web site at http://www.agilent.com/).

growth_protocol: The E9 and L5 line rootstocks were grafted to Boludo scion and were grown in medium grade perlite in glasshouse conditions at 22°C for 29 days.

extract_protocol: Approximately 0.5 g of root tissue was sampled midway between the base of the plant and the base of the pot by removing a handful of root/perlite material during the time period 10:00 and 11:00 h GMT (dawn was at 05:48 h). Perlite was washed from the roots with tap water (sampling process taking approximately 90 seconds) and then the roots were frozen in liquid nitrogen. Total RNA samples, using three biological replicates per treatment, were extracted using the Spectrum™ Plant Total RNA Kit (Sigma) including on–column DNase digestion.

treatment_protocol: For the control treatment, plants were irrigated daily to pot capacity with Hoagland’s solution containing 1 mM H3PO4 (control treatment with excess phosphorus). For the drought and low phosphorus multi-stress treatment, plants were initially irrigated to pot capacity with Hoagland’s solution containing no added H3PO4 for a period of 19 days after transplanting (to deplete phosphorus in the transplanted peat block); then, for the subsequent 10 days, the pots were irrigated to 70% of pot capacity with Hoagland’s solution containing a low H3PO4 concentration (10 µM) to provide the drought and low phosphorus treatment.

tag: line

value: L5 NIL

tag: organ and cell type

value: root tissue


title: sev-GAL4>Ras1V12 EP3037_2


title: sev-GAL4>Ras1V12_2

description: Gene Expression data from 16-17 hr APF whole pupa expressing activated Ras protein in eye disc under sev-GAL4


title: sev-GAL4>Ras1V12 hsrω-RNAi_2

description: Gene Expression data from 16-17 hr APF whole pupa expressing activated Ras protein and down regulation of hsromega non coding RNA in eye disc under sev-GAL4

value: sev-GAL4>Ras1V12 hsrω-RNAi


title: line L5 root tissue grown in normal condition, biological rep2


title: line L5 root tissue grown in phosphorus deficiency and drought stress, biological rep4


title: sev-GAL4>Ras1V12 hsrω-RNAi_1


title: cells in G, biological rep2

source_name: cells utilizing glucose in YPD

value: YPD

value: glucose fermentation


title: sev-GAL4>UAS-GFP_2

description: Gene Expression data from 16-17 hr APF whole pupa expressing GFP under sevenless GAL4 driver,used as control


title: line L5 root tissue grown in phosphorus deficiency and drought stress, biological rep1


title: line L5 root tissue grown in normal condition, biological rep3


title: whole cornea at P3, WT replicate 1

description: whole cornea at P3, WT replicate 1


title: line E9 root tissue grown in normal condition, biological rep4

value: E9 NIL


title: line E9 root tissue grown in normal condition, biological rep3


title: cells in G, biological rep1


title: line L5 root tissue grown in phosphorus deficiency and drought stress, biological rep3


title: sev-GAL4>Ras1V12_1


title: line L5 root tissue grown in phosphorus deficiency and drought stress, biological rep2


title: line E9 root tissue grown in phosphorus deficiency and drought stress, biological rep2


title: line L5 root tissue grown in normal condition, biological rep1