title: 24h_co_total biol. replicate 3

description:
24h_co_total 3.CEL
Gene expression data from untreated cells

tag: treated with

tag: molecule subtype


title: Mice fed High fat diet for 24weeks rep4

status: Public on Mar 01 2014

type: RNA

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

description:
Sample name: E24H1
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were extracted using the software provided by the manufacturer (Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8).
The data were normalised by quantile method using ArrayAssist® (Stratagene, La Jolla, USA) and R statistical language v. 2.4.1.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Adipose tissue of mice

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: C57BL/6J mice were fed a high-fat diet (HFD) or normal diet (ND) and sacrificed at 5 time-points (2, 4, 8, 20 and 24 weeks) over 24 weeks.

tag: strain

tag: treatment protocol

value: High fat diet

tag: time

tag: age

value: 29 weeks

tag: tissue

value: epididymal adipose tissue


title: 24h_TGFbeta_total biol. replicte 1

city: Oxford

first: Alexander

last: Feuerborn

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology

description:
24h_TGFbeta_total 1.CEL
Gene expression data from TGF-b1-treated cells

hyb_protocol: Hybridisation onto 430_2.0 mouse arrays was performed according to manufacturer's instructions (16hrs, 45◦C)

scan_protocol: Arrays were scanned using GeneChip™ scanner 3000.

data_processing: The data was analyzed using R (v.3.0.2)/Bioconductor (v.2.13) VSN-normalized

source_name: NMuMG_TGF-b1 for 24hrs

label_protocol: Total and 4sU-labeled/enriched RNA were amplified via GeneChip® 2-Cycle cDNA synthesis kit according to instructions (Affymetrix) and transcibed into cRNA overnight using MegaScript® kit (Ambion). Purified cRNA was reverse-transcribed into cDNA. After clean-up of cDNA, biotin-labelled cRNA was generated using GeneChip™ IVT labelling ki. 5microgr. of biotinylated cRNA was purified and fragmented.

growth_protocol: Cells were grown under standard cell culture conditions (37◦C, 5%CO2) in ATCC DMEM-media, 10%FCS, 10microgr/ml insulin)

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen) according to manufacturer's instructions, including on-column DNase-digest . 4sU-labeled RNA was extracted from respective total RNA fractions using custom-made mercury-based columns (Kenzelmann et al. 2007)

treatment_protocol: Cells were seeded 24hrs prior to treatments. Cells were treated with 5ng/ml TGF-b1 for 24hrs or left untreated. For enrichment of newly-synthesized RNA, cells were treated with 200microM 4sU for the last 2hrs of incubation perios with TGF-b1 (22hrs-24hrs)

tag: cell line

value: NMuMG

tag: cell type

value: mammary gland cells

value: TGF-b1 for 24hrs

value: total RNA


title: Mice fed High fat diet for 20weeks rep2

description:
Sample name: E20H2
replicate 2

value: 25 weeks


title: Mice fed High fat diet for 20weeks rep3

description:
Sample name: E20H3
replicate 3


title: 1485V092011_LPS_20121207_n124_01_06.RCC

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 7 Cambridge Center

country: USA

institute: Broad Institute

hyb_protocol: Lysates in Qiagen RLT buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: Nanostring nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins

organism: Homo sapiens

growth_protocol: Monocyte-derived dendritic cells from each donor were cultured for 7 days in RPMI supplemented with 10% FBS, 100 ng/mL GM-CSF and 40 ng/mL IL-4.

extract_protocol: Total RNA was isolated using Qiagen RNeasy columns.

treatment_protocol: MoDCs were stimulated with 15 ng/mL LPS for 2.5 h or 5 h, influenza virus for 10 h, 100 U/mL IFNβ for 6.5 h, or left unstimulated.

tag: stimulation

value: LPS

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

value: F

tag: age (years)

tag: ethnicity

value: African-American

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Mice fed High fat diet for 20weeks rep1

description:
Sample name: E20H1
replicate 1

tag: strain

tag: treatment protocol

tag: time

tag: age

tag: tissue


title: 1439V092111_LPS_20121207_n124_01_09.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

value: M

value: Caucasian


title: 1465V092011_LPS_20121207_n124_01_05.RCC

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity

value: East Asian


title: 1459V092011_LPS_20121207_n124_01_04.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 1477V092011_LPS_20121207_n124_01_03.RCC

tag: bmi


title: 1097V091511_LPS_20121207_n124_01_02.RCC


title: Mice fed High fat diet for 8weeks rep1

description:
Sample name: E8H1
replicate 1

tag: strain

tag: treatment protocol

tag: time

tag: age

value: 13 weeks

tag: tissue


title: UterineCx_adenocarcinoma_rep1

city: Seongnam-si

first: Hyun

last: Park

address: Bundang-gu, Yatap-dong

department: Obstetrics and Gynecology

institute: CHA university, CHA Bundang Medical Center

description: miRNA expression in adenocarcinoma of the uterine cervix

hyb_protocol: desalted labeled RNA were hybridized to the Agilent miRNA expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G2600D SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1. Array data were filtered by gIsGeneDetected =1 in all sampless ( 1 : detected ). Subsequently, the values of selected miRNAs were transformed and normalized by quantile method. MicroRNAs not expressed even in one experiment condition were removed during the filtering process and had blanks in the normalized data (the metrix table).

source_name: uterine cervix_adenocarcinoma

label_protocol: Desalted Labeled RNA were prepared from 100ng total RNA Agilent’s miRNA Complete Labeling and Hyb Kit

extract_protocol: RNA isolation from FFPE tissues was performed using RNeasy FFPE Kit for FFPE Tissues (QIAGEN) according to the protocol provided by the manufacturer

value: cancerous tissue from the cervical adenocarcinoma

tag: figo stage

tag: hpv type


title: 1328V091511_LPS_20121207_n123_01_12.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit


title: Mice fed High fat diet for 4weeks rep3

description:
Sample name: E4H3
replicate 3

value: 9 weeks


title: Mice fed High fat diet for 8weeks rep3

description:
Sample name: E8H3
replicate 3

value: High fat diet


title: 0948V091411_LPS_20121207_n123_01_10.RCC

tag: gender

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: 1470V091511_LPS_20121207_n124_01_01.RCC

tag: systolic/diastolic

tag: bmi


title: 1048V091411_LPS_20121207_n123_01_09.RCC

value: MULTI-RACIAL


title: Mice fed High fat diet for 8weeks rep2

description:
Sample name: E8H2
replicate 2

tag: strain

tag: treatment protocol

tag: time

tag: age

tag: tissue

value: epididymal adipose tissue


title: Mice fed High fat diet for 4weeks rep1

description:
Sample name: E4H1
replicate 1


title: Mice fed High fat diet for 2weeks rep1

description:
Sample name: E2H1
replicate 1

value: 7 weeks


title: 0381V091411_LPS_20121207_n123_01_06.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane


title: Mice fed Normal diet for 24weeks rep3

description:
Sample name: E24N3
replicate 3

value: Normal diet

value: 29 weeks


title: 1280V091411_LPS_20121207_n123_01_08.RCC

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity


title: Mice fed Normal diet for 24weeks rep1

description:
Sample name: E24N1
replicate 1


title: Mice fed Normal diet for 24weeks rep2

description:
Sample name: E24N2
replicate 2


title: Mice fed High fat diet for 4weeks rep2

description:
Sample name: E4H2
replicate 2


title: 1262V090811_LPS_20121207_n123_01_05.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 0824V091511_LPS_20121207_n123_01_11.RCC

tag: bmi


title: Mice fed Normal diet for 20weeks rep3

description:
Sample name: E20N3
replicate 3

tag: strain

tag: treatment protocol

tag: time

tag: age

tag: tissue


title: Mice fed Normal diet for 20weeks rep2

description:
Sample name: E20N2
replicate 2


title: Mice fed High fat diet for 2weeks rep2

description:
Sample name: E2H2
replicate 2


title: 1090V090811_LPS_20121207_n123_01_04.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane


title: 1031V091411_LPS_20121207_n123_01_07.RCC

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity


title: Mice fed High fat diet for 2weeks rep3

description:
Sample name: E2H3
replicate 3


title: Mice fed Normal diet for 20weeks rep1

description:
Sample name: E20N1
replicate 1


title: 1415V091311_LPS_20121207_n123_01_02.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 1442V100411_LPS_20121207_n125_01_10.RCC

tag: bmi


title: 1667V012512_IFNb_20121207_n119_01_11.RCC

value: IFNb


title: 0987V091311_LPS_20121207_n123_01_01.RCC


title: 1528V012512_IFNb_20121207_n119_01_12.RCC


title: Mice fed Normal diet for 8weeks rep2

description:
Sample name: E8N2
replicate 2

tag: strain

tag: treatment protocol

tag: time

tag: age

tag: tissue


title: 1148V090811_LPS_20121207_n123_01_03.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane


title: 1442V100411_IFNb_20121207_n119_01_09.RCC

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity


title: Mice fed Normal diet for 8weeks rep3

description:
Sample name: E8N3
replicate 3


title: Mice fed Normal diet for 8weeks rep1

description:
Sample name: E8N1
replicate 1


title: Mice fed Normal diet for 4weeks rep2

description:
Sample name: E4N2
replicate 2


title: Mice fed Normal diet for 4weeks rep3

description:
Sample name: E4N3
replicate 3


title: Mice fed Normal diet for 2weeks rep1

description:
Sample name: E2N1
replicate 1


title: 0412V092911_IFNb_20121207_n119_01_06.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: Mice fed Normal diet for 4weeks rep1

description:
Sample name: E4N1
replicate 1

tag: strain

tag: treatment protocol

tag: time

tag: age


title: Mice fed Normal diet for 2weeks rep3

description:
Sample name: E2N3
replicate 3

tag: tissue


title: 1483V092811_IFNb_20121207_n119_01_05.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: bmi


title: 1057V100411_IFNb_20121207_n119_01_10.RCC

tag: lane

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)


title: 1469V092811_IFNb_20121207_n119_01_04.RCC

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: 1345V092811_IFNb_20121207_n119_01_03.RCC

tag: systolic/diastolic


title: 1423V092211_IFNb_20121207_n119_01_02.RCC


title: 1417V092911_IFNb_20121207_n119_01_08.RCC


title: 1479V092911_IFNb_20121207_n119_01_07.RCC


title: 1142V092111_IFNb_20121207_n119_01_01.RCC


title: 1439V092111_IFNb_20121207_n118_01_12.RCC


title: smos1_leaf sheath_rep1

city: Nagoya

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

country: Japan

institute: Nagoya University

description: Gene expression of leaf sheath in smos1 mutant

hyb_protocol: Fragmentation and hybridization was carried out with Agilent Gene Expression Hybridization Kit. 1650 ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2505B according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities (gProcessedSignal) were used for data analysis.

organism: Oryza sativa Japonica Group

source_name: Leaf sheath in smos1, replicate 1

label_protocol: One-color spike-mix was added to total RNA before labeling reaction. The Cy3-labeled cRNA was prepared from total RNA using Quick Amp Labeling Kit (Agilent Technologies) in accordance with the manufacturer's protocol. Then, labeled cRNA was purified using RNeasy mini kit (QIAGEN).

growth_protocol: Rice plants were grown in paddy fields under normal conditions.

extract_protocol: Total RNA was extracted from the leaf sheaths, using RNeasy mini kit (QIAGEN).

tag: cultivar

value: Nipponbare

tag: tissue

value: leaf sheath

tag: genotype/variation

value: smos1 mutant


title: Mice fed Normal diet for 2weeks rep2

description:
Sample name: E2N2
replicate 2

tag: strain

tag: treatment protocol

tag: time

tag: age


title: 1432V092111_IFNb_20121207_n118_01_11.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: bmi


title: smos1_leaf sheath_rep2

source_name: Leaf sheath in smos1, replicate 2


title: smos1_leaf sheath_rep3

source_name: Leaf sheath in smos1, replicate 3


title: WT_leaf sheath_rep2

description: Gene expression of leaf sheath in WT

source_name: Leaf sheath in WT, replicate 2

value: wildtype


title: 1459V092011_IFNb_20121207_n118_01_10.RCC

tag: time of visit

tag: gender

value: M

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)


title: 1477V092011_IFNb_20121207_n118_01_09.RCC

value: F

tag: weight (kg)

tag: systolic/diastolic


title: WT_leaf sheath_rep1

description: Gene expression of leaf sheath in WT

source_name: Leaf sheath in WT, replicate 1

tag: cultivar

tag: tissue

tag: genotype/variation


title: 1097V091511_IFNb_20121207_n118_01_08.RCC

tag: stimulation

tag: hours

tag: plate

value: East Asian


title: 1280V091411_IFNb_20121207_n118_01_07.RCC

tag: cartridge

tag: lane

tag: date of visit


title: 1262V090811_IFNb_20121207_n118_01_06.RCC

tag: time of visit

tag: gender

tag: bmi


title: Mouse heart, IDH2 R172K mutant, replicate 1

city: Burjassot

first: Julian

last: Carretero

state: Valencia

address: Ave. Vicent Andres Estelles s/n

department: Physiology

country: Spain

institute: University of Valencia

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix protocol

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) using quantile normalization

source_name: IDH2 R172K mutant mice

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

growth_protocol: Mice were housed in pathogen-free animal facilities  at Harvard Medical School and   Dana-Farber Cancer Institute

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) followed by RNA cleanup (QIAGEN)

treatment_protocol: Mutant mice were given 2mg 4-hydroxytamoxifen (4-OHT) at 5 weeks of age for 3 days

value: heart

tag: strain

value: mixed background of C57BL/6, 129/sv, and Balb/c


title: pDC from donor 2 - 4h Aspergillus infected

city: Sao Paulo

first: Flavio

middle: V

last: Loures

state: SP

address: Rua Deputado joaquim libanio, 216

department: Immunology

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: Labeled cDNA (3.5 ug) was then hybridized to the GeneChip Human Gene 2.0 ST array (Affymetrix, Inc.) using the GeneChip Hybridization Oven 640 (Affymetrix, Inc.) at 60 rotations per minute at 45°C for 16-18 hours. After hybridization, the arrays were washed and stained according to the Affymetrix protocol using a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed using Express Console and Transcriptome Analysis Console (TAC) software (Affymetrix, Inc.).  The regulated genes were calculated by dividing the linear intensity value found for each probe from experimental groups (2 or 4 hr of pDC-A. fumigatus interaction and CpG stimulated pDCs) by the linear intensity value found for each probe from the control group (unstimulated pDCs). We considered 1.7 linear fold changes the cut-off to classify the down-regulated and up-regulated genes

source_name: pDC from donor 2- 4h Aspergillus infected

label_protocol: Total RNA (80-500 ng) was reverse transcribed and the single stranded cDNA was amplified using the Ambion WT Expression Kit (Life Technologies, Inc.). The purified cDNA (5.5 μg) was subsequently fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix Inc., Santa Clara, CA, U.S.A.)

growth_protocol: A. fumigatus conidia (2 x 105) were plated in 48-well plates and grown in pDC medium to hyphae of 10-20 μm average length. pDCs (2 x 105) were then added to the hyphae in a final volume of 300 μl pDC medium for 2 and 4 hr at 37°C. Unstimulated and -CpG-stimulated pDCs were incubated for 2h and 4h, respectively

extract_protocol: The total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany). The quantity of total RNA was measured with a spectrophotometer at 260 nanometers, and the RNA integrity was assessed using an RNA 6000 Nano LabChip Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, U.S.A.)

value: blood


title: Mouse heart, IDH2 R140Q mutant, replicate 4

source_name: IDH2 R140Q mutant mice


title: Mouse heart, IDH2 R172K mutant, replicate 4


title: Mouse heart, IDH2 R172K mutant, replicate 2


title: pDC from donor 3 - 4h Aspergillus infected

source_name: pDC from donor 3- 4h Aspergillus infected


title: pDC from donor 2 - 2h Aspergillus infected

source_name: pDC from donor 2- 2h Aspergillus infected


title: pDC from donor 3 - CpG stimulated

source_name: pDC from donor 3- CpG stimulated


title: pDC from donor 1 - 4h Aspergillus infected

source_name: pDC from donor 1- 4h Aspergillus infected


title: pDC from donor 3 - 2h Aspergillus infected

source_name: pDC from donor 3- 2h Aspergillus infected


title: Mouse heart, IDH2 R172K mutant, replicate 3


title: Mouse heart, IDH2 R140Q mutant, replicate 3


title: 1148V090811_IFNb_20121207_n118_01_04.RCC

tag: age (years)

tag: ethnicity

value: African-American

tag: million pbmc

tag: million dcs


title: Mouse heart, IDH2 R140Q mutant, replicate 1


title: pDC from donor 1 - 2h Aspergillus infected

source_name: pDC from donor 1- 2h Aspergillus infected


title: pDC from donor 2 - CpG stimulated

source_name: pDC from donor 2- CpG stimulated


title: 1090V090811_IFNb_20121207_n118_01_05.RCC

value: MULTI-RACIAL

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: pDC from donor 3 - unstimulated

source_name: pDC from donor 3- unstimulated

tag: tissue


title: Mouse heart, IDH2 R140Q mutant, replicate 2


title: Mouse heart, control, replicate 4

description: Mouse heart, control, replicate 4

source_name: Control mice


title: 1317V091311_IFNb_20121207_n118_01_01.RCC

tag: stimulation

tag: hours


title: 1229V062811_IFNb_20121207_n117_01_12.RCC

tag: plate

tag: cartridge

value: Caucasian


title: pDC from donor 2 - unstimulated

source_name: pDC from donor 2- unstimulated


title: 0987V091311_IFNb_20121207_n118_01_02.RCC

tag: lane

tag: date of visit


title: pDC from donor 1 - unstimulated

source_name: pDC from donor 1- unstimulated


title: Mouse heart, control, replicate 3

description: Mouse heart, control, replicate 3


title: 1446V062811_IFNb_20121207_n117_01_11.RCC

tag: time of visit

tag: gender


title: U2OS-S22AProgerin-3

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

country: Canada

institute: Université de Montréal

description:
U2OS_S22A-progerin_3
Gene expression data from U-2 OS infected with a vector expressing S22A-progerin

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST Chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with the affymetrix Expression Console software using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 2 and a p-value <0.05 according to the two-sample student's t-test were selected for final determination.
affymetrix-algorithm-name = rma-gene-full;
affymetrix-algorithm-version = 1.0;
program-name = Expression Console;
program-version = 1.3.1.187

source_name: U-2 OS_S22A-progerin_4 dpi

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

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

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

treatment_protocol: Cells were infected with a retrovirus expressing wt-progerin or S22A-progerin and selected during three days with 5 µg/ml puromycin before RNA extraction.

tag: cell line

value: U-2 OS

tag: cell type

value: osteosarcoma cells

tag: infected with

value: retroviral vector expressing S22A-progerin

tag: time point

value: 4 days post-infection


title: 1415V091311_IFNb_20121207_n118_01_03.RCC

value: IFNb

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: bmi


title: U2OS-S22AProgerin-2

description:
U2OS_S22A-progerin_2
Gene expression data from U-2 OS infected with a vector expressing S22A-progerin


title: 0313V062811_IFNb_20121207_n117_01_08.RCC

tag: stimulation

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: Mouse heart, control, replicate 1

description: Mouse heart, control, replicate 1

tag: tissue

tag: strain


title: X110.1.fat

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Labeled samples were hybridized (for 16 hours at 60°C) to locked nucleic acid (LNA™) modified oligonucleotide capture probes (Exiqon) spotted in duplicate on Nexterion E slides. The capture probe set (based on miRBase version 10, annotation version 13) contains 1344 probes of which 725 are capable of detecting human miRNAs. Slides were subsequently washed and scanned. (MicroRNA profiling was performed as previously described by Pothof et al. 2009)

scan_protocol: Hybridized slides were scanned and median spot intensity was determined using ImaGene software (BioDiscovery Inc.).

data_processing: After background subtraction, expression values were quantile normalized using R software, bad spots were deleted, and duplicate spots were averaged. For each expression value, the ratio to the geometric mean of the miRNA was log2 transformed. These values were used to determine differentially expressed miRNAs by using BRB-Array Tools.

source_name: normal fat

label_protocol: 1ug of total RNA was fluorescently labeled using the Createch Cy3 label kit (Createch)

extract_protocol: Total RNA was isolated from frozen tissues using RNAbee (Tel Test Inc.) according to the manufacturer’s recommendations.

treatment_protocol: Fresh tissue samples were snap frozen in liquid nitrogen

value: normal fat

tag: location

value: groin

value: female

tag: age


title: U2OS-wtProgerin-3

description:
U2OS_wt-progerin_3
Gene expression data from U-2 OS infected with a vector expressing wt-progerin

source_name: U-2 OS_wt-progerin_4 dpi

tag: cell line

value: retroviral vector expressing wt-progerin


title: U2OS-wtProgerin-2

description:
U2OS_wt-progerin_2
Gene expression data from U-2 OS infected with a vector expressing wt-progerin

tag: cell type


title: Mouse heart, control, replicate 2

description: Mouse heart, control, replicate 2


title: U2OS-S22AProgerin-1

description:
U2OS_S22A-progerin_1
Gene expression data from U-2 OS infected with a vector expressing S22A-progerin

tag: infected with


title: 1168V062811_IFNb_20121207_n117_01_10.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

value: M


title: 1344V062811_IFNb_20121207_n117_01_09.RCC

tag: stimulation

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: bmi


title: X116.1.fat

tag: tissue

tag: location

value: mamma

tag: age


title: U2OS-wtProgerin-1

description:
U2OS_wt-progerin_1
Gene expression data from U-2 OS infected with a vector expressing wt-progerin

tag: cell line

tag: cell type

tag: infected with

tag: time point


title: X108.1.fat

value: omentum

value: male


title: 1222V062311_IFNb_20121207_n117_01_07.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

value: F

tag: weight (kg)

tag: systolic/diastolic


title: Hypothermia 18h

city: Tartu

first: Sten

last: Ilmjärv

state: Tartumaa

address: Ravila 19

department: Institute of Biomedicine and Translational Medicine

country: Estonia

institute: University of Tartu

hyb_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

data_processing: DEMI R package (http://biit.cs.ut.ee/demi/)

source_name: mef, hypothermia

label_protocol: 250ng of total RNA per group was amplified and labeled using the Ambion WT Expression Kit (Applied Biosystems) according to manufactures instructions.

growth_protocol: Around 1 million primary mouse embryonic fibroblasts (Millipore) were seeded onto 100-mm culture dishes and were grown in DMEM (high glucose 4.5g/l, supplemented with 10% FBS and L-glutamine, PAA) in normal conditions (atmospheric oxygen, 5% CO2 at 37C) until 60-70% convulent.

extract_protocol: RNA was extracted from cells with Trizol® (Life) according to the manufactures protocol. RNA from three replicates in each group was pooled together.

treatment_protocol: Hypothermia was initiated by lowering the temperature of the cell culture incubator to 32 degrees celcius. The control arm of the experiment was incubated at 37 degrees celcius. Three dishes per group were incubated for various durations (0h, 0.5h, 1h, 2h, 4h, 8h, 18h).

value: mouse embryonic fibroblasts

value: 1080 minutes

tag: thermia

value: hypothermia


title: 1361V062311_IFNb_20121207_n117_01_06.RCC

tag: stimulation

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)


title: Hypothermia 2h

scan_protocol: Standard protocol, Affymetrix Core center, Rigshospitalet, Copenhagen, Denmark

label: Ambion WT Expression Kit (Applied Biosystems)

tag: cell type

tag: time point

value: 120 minutes


title: Hypothermia 4h

value: 240 minutes


title: Hypothermia 8h

value: 480 minutes


title: X109.1.fat

tag: tissue

tag: location

value: neck

tag: age


title: 1449V092711_LPS_20121207_n125_01_03.RCC

value: LPS

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

value: African-American

tag: bmi


title: X107.1.fat

value: normal fat

value: retroperitoneal

tag: gender

value: female


title: X103.1.fat

value: groin


title: 0517V062211_IFNb_20121207_n117_01_04.RCC

tag: stimulation

value: IFNb

tag: time of visit

tag: age (years)

tag: weight (kg)

tag: systolic/diastolic


title: Hypothermia 1h

tag: cell type

value: 60 minutes

tag: thermia


title: X118.1.lipoma

source_name: lipoma

tag: tissue

value: lipoma

value: back

value: male


title: Normothermia 8h

source_name: mef, normothermia

value: mouse embryonic fibroblasts

tag: time point

value: normothermia


title: Hypothermia 0.5h

value: 30 minutes

value: hypothermia


title: X148.lipoma

tag: location

value: axilla

tag: age


title: X102.1.fat


title: X99.1.lipoma

value: arm


title: 0668V062311_IFNb_20121207_n117_01_05.RCC

tag: hours

tag: plate

value: M

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)


title: Normothermia 4h

value: 240 minutes


title: Normothermia 1h


title: 0773V062111_IFNb_20121207_n117_01_03.RCC

tag: stimulation

tag: cartridge

tag: lane

tag: date of visit

tag: gender

value: African-American

tag: bmi


title: X141.lipoma

value: shoulder


title: Normothermia 2h

tag: cell type

value: 120 minutes

tag: thermia


title: X98.1.lipoma

tag: tissue

value: female


title: Normothermia 18h

tag: time point

value: 1080 minutes


title: X105.1.fat

value: normal fat

tag: location

value: retroperitoneal

tag: age


title: X94.1.lipoma

value: lipoma

value: leg


title: 1356V061511_IFNb_20121207_n117_01_02.RCC

value: IFNb

tag: hours

tag: plate

tag: time of visit

tag: age (years)

value: East Asian

tag: weight (kg)

tag: systolic/diastolic


title: X47.2.fat


title: X97.1.lipoma

value: male


title: X95.1dil.lipoma


title: 1156V061511_IFNb_20121207_n117_01_01.RCC

tag: stimulation

tag: cartridge

value: F

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)


title: Normothermia 0.5h

tag: cell type

value: mouse embryonic fibroblasts

value: 30 minutes

tag: thermia

value: normothermia


title: X96.1.lipoma

tag: tissue

tag: gender


title: X152.pleo

source_name: pleomorphic liposarcoma

value: pleomorphic liposarcoma

tag: location

tag: age


title: X139dil.pleo

value: thigh


title: 1317V091311_LPS_20121206_n122_01_12.RCC

value: LPS

tag: hours

tag: plate

tag: lane

tag: date of visit

value: M

tag: bmi


title: X138.pleo


title: X143.pleo

value: female


title: X93.1dil.pleo

value: shoulder


title: 1421V091311_LPS_20121206_n122_01_10.RCC

tag: stimulation

tag: time of visit

tag: age (years)

value: African-American

tag: weight (kg)

tag: systolic/diastolic


title: 1229V062811_LPS_20121206_n122_01_09.RCC

tag: cartridge

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)


title: X92.1dil.pleo

tag: tissue

tag: location

tag: gender


title: X149.dedif

source_name: dedifferentiated liposarcoma

value: dedifferentiated liposarcoma

value: hip

tag: age


title: X121.dedif

value: retroperitoneal


title: 1446V062811_LPS_20121206_n122_01_08.RCC

tag: hours

tag: plate

tag: lane


title: X142.dedif


title: X140.dedif


title: 1168V062811_LPS_20121206_n122_01_07.RCC

tag: stimulation

tag: date of visit

tag: bmi


title: 1011V091311_LPS_20121206_n122_01_11.RCC

tag: time of visit

tag: age (years)

tag: weight (kg)


title: X122.dedif


title: WT_neural stem cell_re2

city: HongKong

first: Bin

last: Wang

address: Rm 105, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, The Chinese University of Hong Kong, SHATIN, NT

country: China

institute: The Chinese University of Hong Kong

description:
CNS-NSC 2
Gene expression data of wild type neural stem cells which separate from the central nervous system.

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual for use with the Ambion WT Expression kit. Washing (protocol script FS450-007) was performed by GeneChip Systems for array cartridges (Affymetrix).

scan_protocol: Scanning (Affymetrix GeneChip Scanner 3000) were performed by GeneChip Systems for array cartridges (Affymetrix).

data_processing:
Data were analyzed using Partek Genomics Suite.
Algorithm: RMA
Background Correction: RMA background correction
Normalization: Quantile normalization

source_name: Wild type neural stem cells obtained from mouse embryonic brain

label_protocol: Manual for the Ambion WT Expression kit for Affymetrix GeneChip Whole Transcript (WT) Expression Array, and Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual for use with the Ambion WT Expression kit.

growth_protocol: Briefly, R1 mouse ES cells were cultured on mitomycin C-inactivated mouse embryonic fibroblast feeder in DMEM containing 15% FBS, 1mM sodium pyruvate, 1% MEM non-essential amino acids, 2mM L-glutamine, 0.1mM 2-Mercaptoethanol and 1000U/ml Lif (Life Technologies). CNS-NSCs were isolated from the frontal lobes of E11.5 mouse embryos. The CNS-NSCs were collected from the tissues by trituration and were cultured in DMEM/F-12 medium supplemented with N2, 20ng/ml EGF, 20ng/ml FGF and 2μg/ml Heparin.

treatment_protocol: To generate primitive NSCs, mouse ESCs were dissociated using 0.25% Trypsin-EDTA and plated at a density of 20 cells/μl into uncoated petri dish, with serum-free medium containing DMEM/F-12 medium supplemented with N2 supplement (Life Technologies) and 1000U/ml Lif. Primary spheres emerged after 5-7 days were dissociated using Accutase (Life Technologies) and re-plated in medium containing 1000U/ml Lif, 10ng/ml FGF (Peprotech) and 2μg/ml Heparin (Sigma). Definitive NSCs were induced by passaging primitive NSCs into DMEM/F-12 medium supplemented with N2 and B27 supplement (Life Technologies), 20ng/ml EGF (Peprotech), 20ng/ml FGF and 2μg/ml Heparin. Spheres were fully dissociated and re-plated every 5-7 days.

tag: strain

value: ICR

tag: genotype

value: wild type

value: embryonic brain

tag: cell type

value: WT neural stem cells


title: X88.1.dedif

value: male


title: X87.1dil.dedif

value: leg


title: Normothermia 0h

value: mouse embryonic fibroblasts

tag: time point

value: 0 minutes

tag: thermia

value: normothermia


title: Definitive neural stem cell_re1

description:
d-NSC 1
Gene expression data from definitive neural stem cells derived from PNSCs.
The R1 ES cell line is originally derived from the 129/Sv strain.

source_name: Definitive neural stem cells derived from primitive neural stem cells

tag: cell line

value: definitive neural stem cells


title: Definitive neural stem cell_re2

description:
d-NSC 2
Gene expression data from definitive neural stem cells derived from PNSCs.
The R1 ES cell line is originally derived from the 129/Sv strain.


title: WT_neural stem cell_re1

description:
CNS-NSC 1
Gene expression data of wild type neural stem cells which separate from the central nervous system.

tag: tissue


title: 0313V062811_LPS_20121206_n122_01_05.RCC

value: LPS

tag: cartridge

tag: gender

value: M

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: systolic/diastolic


title: X117.1.dif

source_name: well differentiated liposarcoma

value: well differentiated liposarcoma

tag: location

tag: age


title: X115.1.dif


title: 1266V062311_LPS_20121206_n122_01_04.RCC

tag: stimulation

tag: hours

tag: plate

tag: lane

tag: date of visit

tag: time of visit

value: F

tag: age (years)

value: Caucasian

tag: weight (kg)

tag: bmi


title: X150.dif

tag: tissue

value: arm

tag: gender


title: X145.dif


title: 1222V062311_LPS_20121206_n122_01_03.RCC

tag: cartridge

tag: ethnicity

tag: million pbmc


title: X86.1.dif


title: X80.1.dif

value: retroperitoneal

value: female


title: X147.dif


title: WT_leaf sheath_rep3

description: Gene expression of leaf sheath in WT

source_name: Leaf sheath in WT, replicate 3

tag: cultivar

value: Nipponbare

value: leaf sheath

tag: genotype/variation

value: wildtype


title: X113.1.dif

tag: location

value: male

tag: age


title: X112.2.dif


title: Primitive neural stem cell primary pass_re2

description:
p-NSC_L 2
Gene expression data from primitive neural stem cells cultured in Lif/N2 medium.
The R1 ES cell line is originally derived from the 129/Sv strain.

source_name: Primary passage of primitive stem cells derived from ES cells

tag: cell line

tag: cell type

value: primitive neural stem cells (primary passage)


title: Primitive neural stem cell secondary pass_re1

description:
p-NSC_LF 1
Gene expression data from primitive neural stem cells cultured in condition with Lif/N2 and FGF.
The R1 ES cell line is originally derived from the 129/Sv strain.

source_name: Secondary passage of primitive neural stem cells derived from primary passage

value: primitive neural stem cells (secondary passage)


title: X111.2.dif

value: leg


title: Embryonic stem cell_re2

description:
mESC 2
Gene expression data from embryonic stem cells.
The R1 ES cell line is originally derived from the 129/Sv strain.

source_name: R1 mouse embryonic stem cell line

value: embryonic stem cells


title: 1344V062811_LPS_20121206_n122_01_06.RCC

tag: stimulation

tag: hours

tag: plate

tag: lane

tag: million dcs

tag: height (cm)

tag: systolic/diastolic


title: Primitive neural stem cell primary pass_re1

description:
p-NSC_L 1
Gene expression data from primitive neural stem cells cultured in Lif/N2 medium.
The R1 ES cell line is originally derived from the 129/Sv strain.


title: 1361V062311_LPS_20121206_n122_01_02.RCC

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: weight (kg)

tag: bmi


title: Primitive neural stem cell secondary pass_re2

description:
p-NSC_LF 2
Gene expression data from primitive neural stem cells cultured in condition with Lif/N2 and FGF.
The R1 ES cell line is originally derived from the 129/Sv strain.


title: 1340V062311_LPS_20121206_n122_01_01.RCC

tag: cartridge

tag: ethnicity

tag: million pbmc


title: 0668V062311_LPS_20121206_n121_01_12.RCC


title: X136.round

source_name: round cell liposarcoma

tag: tissue

value: round cell liposarcoma

tag: location

tag: age


title: X137.round

value: knee


title: Embryonic stem cell_re1

description:
mESC 1
Gene expression data from embryonic stem cells.
The R1 ES cell line is originally derived from the 129/Sv strain.

tag: cell line

tag: cell type


title: X82.1.dif


title: 0447V062211_LPS_20121206_n121_01_11.RCC

tag: stimulation

value: LPS

tag: hours

tag: plate

tag: lane

value: African-American

tag: million dcs


title: 0517V062211_LPS_20121206_n121_01_10.RCC

tag: date of visit

tag: time of visit

tag: gender

value: F

tag: height (cm)

tag: systolic/diastolic


title: X133.round

value: thigh


title: X134.round


title: 0332V062211_LPS_20121206_n121_01_09.RCC

tag: cartridge

value: M

tag: age (years)

tag: ethnicity

tag: weight (kg)

tag: bmi


title: X128.myx

source_name: myxoid liposarcoma

tag: tissue

value: myxoid liposarcoma

tag: location

tag: age


title: X130.myx

value: female


title: X131.myx


title: 0688V062211_LPS_20121206_n121_01_07.RCC

tag: stimulation

tag: hours

value: Caucasian

tag: million pbmc


title: 0570V062211_LPS_20121206_n121_01_08.RCC

tag: plate

tag: lane

tag: million dcs


title: X124.myx

tag: gender


title: X135.round


title: 0773V062111_LPS_20121206_n121_01_06.RCC

tag: date of visit

tag: time of visit

tag: height (cm)


title: 0825V061511_LPS_20121206_n121_01_04.RCC

tag: cartridge

tag: age (years)

tag: systolic/diastolic


title: X114.1.myx


title: X119.1.myx


title: X90.1.myx


title: X49.1.fat

value: normal fat

value: axilla


title: 1356V061511_LPS_20121206_n121_01_05.RCC

tag: ethnicity

value: East Asian

tag: weight (kg)

tag: bmi


title: X45.1.fat

tag: tissue

tag: location

value: groin

tag: age


title: X77.1.fat


title: X78.1.fat


title: 1156V061511_LPS_20121206_n121_01_03.RCC

tag: stimulation

tag: hours

tag: million pbmc


title: J2.fat

value: peri-colic


title: 1323V061411_LPS_20121206_n121_01_01.RCC

tag: plate

tag: lane

tag: million dcs


title: 0218V061511_LPS_20121206_n121_01_02.RCC

tag: date of visit

tag: time of visit

tag: gender


title: X50.2.fat


title: X129.myx

value: male


title: 1088V060911_LPS_20121206_n120_01_12.RCC

tag: cartridge

tag: age (years)

tag: height (cm)


title: X40.2.lipoma

value: lipoma


title: X144.myx

value: buttock


title: X48.3.fat


title: X126.myx


title: 1336V060911_LPS_20121206_n120_01_11.RCC

tag: ethnicity

tag: weight (kg)

tag: systolic/diastolic


title: X38.1.lipoma

tag: tissue

tag: location

value: arm


title: 0793V060911_LPS_20121206_n120_01_10.RCC

tag: stimulation

value: LPS

tag: bmi


title: X39.1.lipoma

tag: age


title: X41.3.lipoma

value: shoulder


title: X37.1.pleio

value: pleomorphic liposarcoma


title: 1279V060911_LPS_20121206_n120_01_09.RCC

tag: hours

tag: plate

value: F

tag: million pbmc


title: X19.3.pleio

value: leg


title: X42.2.lipoma


title: X8.2.pleio


title: 0794V060811_LPS_20121206_n120_01_08.RCC

tag: lane

tag: date of visit

value: M

tag: million dcs


title: X75.1.dedif

value: dedifferentiated liposarcoma

value: retroperitoneal

tag: gender

value: female


title: 1275V060811_LPS_20121206_n120_01_07.RCC

tag: cartridge

tag: time of visit

tag: age (years)

value: Caucasian


title: 1669V013112_IFNb_20121206_n120_01_06.RCC

value: IFNb

tag: ethnicity

value: East Asian

tag: height (cm)

tag: weight (kg)


title: X74.1.fat

tag: tissue

value: normal fat

tag: location

value: peri-colic


title: 0498V013112_IFNb_20121206_n120_01_05.RCC

tag: stimulation

tag: systolic/diastolic

tag: bmi


title: X64.1.dedif

value: groin

value: male

tag: age


title: X63.1.dedif


title: 1621V013112_IFNb_20121206_n120_01_04.RCC

tag: hours

tag: plate

value: MULTI-RACIAL

tag: million pbmc


title: X61.1.dedif


title: X125.myx

value: myxoid liposarcoma

value: thigh


title: X26.1.dedif

value: head


title: X4.2.dedif


title: 1640V012612_IFNb_20121206_n120_01_03.RCC

tag: lane

tag: date of visit

value: F

tag: million dcs


title: X23.1.dedif

value: pelvis

tag: gender


title: 0310V012612_IFNb_20121206_n120_01_02.RCC

tag: cartridge

tag: time of visit

tag: age (years)


title: K4.dif

value: well differentiated liposarcoma

value: leg


title: 1088V060911_IFNb_20121206_n116_01_12.RCC

value: M

tag: ethnicity

value: African-American

tag: height (cm)

tag: weight (kg)


title: X59.1.dedif

tag: tissue

value: dedifferentiated liposarcoma

tag: location

value: retroperitoneal


title: X65.2.dedif

value: female


title: X21.2.dif


title: X27.1.dif


title: 1275V060811_IFNb_20121206_n116_01_11.RCC

tag: stimulation

value: IFNb

value: Caucasian

tag: systolic/diastolic

tag: bmi


title: X9.3.dif

tag: age


title: X3.2.dedif


title: 1475V013112_dNS1_20121206_n116_01_08.RCC

tag: hours

tag: plate

tag: million pbmc


title: 0498V013112_dNS1_20121206_n116_01_09.RCC

tag: lane

tag: date of visit

tag: million dcs


title: X57.1.dif

tag: gender


title: 1621V013112_dNS1_20121206_n116_01_07.RCC

tag: cartridge

tag: time of visit

tag: age (years)


title: X58.2.dif


title: X65.1.dedif


title: X56.1.dif


title: X54.1.dif


title: X7.2.dedif


title: X52.2.dif


title: X53.2.dif


title: 1363V012512_IFNb_20121206_n120_01_01.RCC

tag: ethnicity

tag: height (cm)

tag: weight (kg)


title: X10.3.round.myx

tag: tissue

value: round cell liposarcoma

tag: location

value: sigmoid


title: X2.2.dif

value: male


title: X55.2.dif


title: X12.2.dif

value: groin


title: X36.1.round.myx


title: X62.1.dedif


title: 1669V013112_dNS1_20121206_n116_01_10.RCC

tag: stimulation

value: East Asian

tag: systolic/diastolic

tag: bmi


title: 1663V012612_dNS1_20121206_n116_01_06.RCC

tag: hours

tag: plate


title: X67.1.round.myx

value: buttock

tag: age


title: X34.1.round.myx


title: X33.2.myx

value: myxoid liposarcoma


title: X28.1.round.myx


title: X32.1.myx

value: thorax


title: X71.1.myx

value: calf


title: X5.4.dif

value: well differentiated liposarcoma

value: leg


title: 0310V012612_dNS1_20121206_n116_01_04.RCC

tag: lane

tag: date of visit

value: F

tag: million pbmc


title: X70.1.myx

tag: gender


title: X29.1.myx


title: 0448V012512_dNS1_20121206_n116_01_02.RCC

tag: cartridge

tag: time of visit

tag: million dcs


title: 1528V012512_dNS1_20121206_n116_01_01.RCC

value: M

tag: age (years)

tag: ethnicity

value: African-American

tag: height (cm)


title: X35.1.myx

tag: tissue

tag: location


title: 1667V012512_dNS1_20121206_n115_01_12.RCC

tag: stimulation

tag: weight (kg)

tag: systolic/diastolic


title: X69.1.myx

value: knee cavity


title: 1640V012612_dNS1_20121206_n116_01_05.RCC

tag: hours

tag: plate

tag: bmi


title: 1057V100411_dNS1_20121206_n115_01_11.RCC

tag: lane

tag: date of visit


title: X31.1.myx

tag: gender

value: female

tag: age


title: 1479V092911_dNS1_20121206_n115_01_08.RCC

tag: cartridge

tag: time of visit

tag: million pbmc


title: X30.1.myx


title: 1417V092911_dNS1_20121206_n115_01_09.RCC

tag: age (years)

tag: ethnicity

tag: million dcs


title: 1363V012512_dNS1_20121206_n116_01_03.RCC

value: Caucasian

tag: height (cm)


title: 0412V092911_dNS1_20121206_n115_01_07.RCC

tag: stimulation


title: 1483V092811_dNS1_20121206_n115_01_06.RCC

tag: weight (kg)


title: 1442V100411_dNS1_20121206_n115_01_10.RCC

tag: systolic/diastolic


title: BNC1-siRNA-24h+TGFb-24h biol. replicate 2

description:
BNC1-siRNA-24h+TGFb-24h rep.2
Gene expression of cells transfected with Bnc1 siRNA and treated with TGF-b1

hyb_protocol: After fragmentation, 10 ug of cRNA were hybridized for 16hrs at 45◦C on MOE430A mouse GeneChips

scan_protocol: Arrays were scanned using GeneChip™ 3000 7G-scanner

data_processing: The data was analyzed using R(v.3.0.2)/Bioconductor (v.2.13) VSN-normalized

source_name: NM18_Bnc1 siRNA for 48hrs_TGF-b1-treatment for 24hrs

label_protocol: Biotinylated cRNA was generated according to standard Affymetrix protocols from 100ng total RNA (GeneAtlas™ 3'-IVT Express Kit, P/N 702833 Rev. 4)

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to manufacturer's instructions (Qiagen), including on-column DNase-digest.

treatment_protocol: Cells were reversed transfected for 24hrs and subsequently treated with 5ng/ml TGF-b1 for another 24hrs or left untreated

tag: cell line

tag: cell type

value: mammary gland cells line

tag: transfected with

value: Bnc1 siRNA for 48hrs

tag: treated with

value: TGF-b1 for 24hrs


title: BNC1-siRNA-24h+TGFb-24h biol. replicate 3

description:
BNC1-siRNA-24h+TGFb-24h rep.3
Gene expression of cells transfected with Bnc1 siRNA and treated with TGF-b1


title: Wild-type 1

city: Houston

first: Michael

middle: R

last: Green

state: TX

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: Chips scanned using an Affymetrix GeneChip 3000 scanner.

data_processing: Raw data was normalized using RMA preprocessed with quantile normalization and median scaling using the "ExpressionFileCreator" module of GenePattern.

label: Biotin

source_name: CD22+B220+ B-cells

label_protocol: Labeled according to the Affymetrix recommended protocol.

extract_protocol: Total RNA was isolated in two steps using TRIzol (Life Technologies, Inc., Grand Island, NY) followed by Rneasy Mini-Kit (Qiagen Inc., Valencia, CA) purification following the manufacturer’s RNA Clean-up protocol with the optional On-column DNase treatment.

tag: strain

tag: genotype

value: Wild-type

tag: source tissue

value: spleen

value: CD22+B220+ B-cells


title: Sca1-Bcl6(delta) 1


title: 1469V092811_dNS1_20121206_n115_01_05.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: gender

value: East Asian

tag: bmi


title: Wild-type 2


title: Wild-type 3


title: BNC1-siRNA-24h+TGFb-24h biol. replicate 1

description:
BNC1-siRNA-24h+TGFb-24h rep.1
Gene expression of cells transfected with Bnc1 siRNA and treated with TGF-b1


title: Sca1-Bcl6(delta) 4


title: Sca1-Bcl6(floxed) 1


title: Sca1-Bcl6(delta) 3


title: Sca1-Bcl6(floxed) 2


title: Sca1-Bcl6(floxed) 3


title: 1345V092811_dNS1_20121206_n115_01_04.RCC

tag: stimulation

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)


title: 1563V120611_LPS_20121205_n114_01_12.RCC

value: LPS

tag: weight (kg)

tag: systolic/diastolic


title: 1449V092711_dNS1_20121206_n115_01_03.RCC


title: 1524V102611_LPS_20121205_n114_01_11.RCC


title: ns-siRNA-24h+TGFb-24h biol. replicate 2

description:
ns-siRNA-24h+TGFb-24h rep.2
Gene expression of control-transfected cells treated with TGF-b1

source_name: NM18_non-silencing siRNA for 48hrs_TGF-b1-treatment for 24hrs

tag: cell line

tag: cell type

tag: transfected with

value: non-silencing siRNA for 48hrs

tag: treated with


title: 0430V092211_dNS1_20121206_n115_01_01.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane


title: ns-siRNA-24h+TGFb-24h biol. replicate 3

description:
ns-siRNA-24h+TGFb-24h rep.3
Gene expression of control-transfected cells treated with TGF-b1


title: ns-siRNA-24h+TGFb-24h biol. replicate 1

description:
ns-siRNA-24h+TGFb-24h rep.1
Gene expression of control-transfected cells treated with TGF-b1


title: RTPCR53-LPS

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

description: Treatment. Biological rep3

data_processing:
Data were collected using the 7500 Software v2.0.5 and given as threshold cycle (Ct). Ct values for each target and reference genes were obtained and their difference was calculated (ΔCt). Primer efficiencies for the test genes and the reference genes were similar. The comparative calculation, ΔΔCt, was used to find the difference of  the expression level between supplemented and baseline PBMNC or LPS treated and control, both in  supplemented or baseline PBMNC
18s was considered the reference gene, HKG
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: Sybr Green

source_name: PBMNC of subjects after 5 days of redoxon supplementation, LPS

label_protocol: Not provided

extract_protocol: A total of 1 µg of isolated RNA samples was reverse-transcribed into cDNA using the iScript™ Reverse Transcription Supermix for RT-qPCR

tag: age

value: peripheral blood mononuclear cells


title: RTPCR55-LPS

description: Treatment. Biological rep5


title: Sca1-Bcl6(delta) 2

tag: strain

tag: genotype

tag: source tissue


title: RTPCR54-LPS

description: Treatment. Biological rep4


title: 1274V102611_LPS_20121205_n114_01_09.RCC

tag: stimulation

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: bmi


title: nodal reactive lymphoid hyperplasia_sample7

city: Okayama city

first: Katsuyoshi

last: Takata

address: 2-5-1, Kita-ku, Shikata-cho

department: Pathology

institute: Okayama University

hyb_protocol: Hybridization was performed for 17 h at 65°C.

scan_protocol: Arrays were scanned on an Agilent DNA microarray scanner.

data_processing: Raw intensity data were extracted, and the background signal was then subtracted from the raw intensity using standard procedures in Agilent Feature Extraction Software Ver. 9.1.

source_name: nodal reactive lymphoid hyperplasia_sampleJ

label_protocol: Complementary RNAs (cRNAs) were synthesized from the cDNA products using T7 RNA polymerase with Cy3 labeled-CTP.

extract_protocol: RNA was extracted from each fresh frozen sample using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA)

tag: tissue

value: nodal reactive lymphoid hyperplasia

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: RTPCR52-LPS

description: Treatment. Biological rep2

tag: age

tag: cell type


title: 1348V102611_LPS_20121205_n114_01_07.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: normal gastric mucosa_sample1

source_name: normal gastric mucosa_sampleB

value: normal gastric mucosa

tag: gender


title: 0948V102611_LPS_20121205_n114_01_08.RCC

tag: stimulation

tag: date of visit

tag: time of visit

value: F

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: bmi


title: normal gastric mucosa_sample4

source_name: normal gastric mucosa_sampleI

tag: tissue

tag: age

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: nodal reactive lymphoid hyperplasia_sample8

source_name: nodal reactive lymphoid hyperplasia_sampleK


title: nodal reactive lymphoid hyperplasia_sample5

source_name: nodal reactive lymphoid hyperplasia_sampleG


title: nodal reactive lymphoid hyperplasia_sample6

source_name: nodal reactive lymphoid hyperplasia_sampleI


title: 1458V092711_dNS1_20121206_n115_01_02.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

value: M

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: normal gastric mucosa_sample3

source_name: normal gastric mucosa_sampleH

tag: gender


title: 1366V102611_LPS_20121205_n114_01_10.RCC

tag: stimulation

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: systolic/diastolic


title: 1277V102511_LPS_20121205_n114_01_04.RCC

tag: bmi


title: 1512V102511_LPS_20121205_n114_01_05.RCC


title: RTPCR03-LPS

description: Control,biological rep3

source_name: PBMNC of subjects before supplementation, LPS

tag: age

tag: cell type


title: nodal reactive lymphoid hyperplasia_sample3

source_name: nodal reactive lymphoid hyperplasia_sampleD

tag: tissue

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: nodal reactive lymphoid hyperplasia_sample4

source_name: nodal reactive lymphoid hyperplasia_sampleE

tag: gender


title: RTPCR51-LPS

description: Treatment. Biological rep1


title: nodal reactive lymphoid hyperplasia_sample2

source_name: nodal reactive lymphoid hyperplasia_sampleC


title: RTPCR05-LPS

description: Control,biological rep5


title: 0615V102511_LPS_20121205_n114_01_03.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: 1498V102011_LPS_20121205_n114_01_02.RCC

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

value: African-American

tag: million pbmc

tag: systolic/diastolic

tag: bmi


title: 0277V102511_LPS_20121205_n114_01_06.RCC


title: 1360V102011_LPS_20121205_n113_01_12.RCC


title: RTPCR53

description: Treatment. Biological rep3

source_name: PBMNC of subjects after 5 daysof redoxon supplementation

tag: age

tag: cell type


title: RTPCR02-LPS

description: Control,biological rep2


title: 1327V102011_LPS_20121205_n114_01_01.RCC

tag: stimulation

tag: gender


title: 1077V101911_LPS_20121205_n113_01_11.RCC

tag: hours

tag: plate


title: RTPCR55

description: Treatment. Biological rep5


title: 1514V101211_LPS_20121205_n113_01_10.RCC

tag: cartridge

tag: lane


title: RTPCR01-LPS

description: Control,biological rep1


title: RTPCR52

description: Treatment. Biological rep2


title: 1515V101111_LPS_20121205_n113_01_09.RCC

tag: million dcs

tag: height (cm)


title: RTPCR51

description: Treatment. Biological rep1


title: nodal follicular lymphoma_sample18

description: R-CVP → partial response, bone marrow transplantation → died of CMV infection and DIC

source_name: nodal follicular lymphoma_patientY

tag: tissue

value: nodal follicular lymphoma

value: female

tag: Stage

value: II

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: RTPCR54

description: Treatment. Biological rep4


title: 1501V011112_unstim_20121205_n113_01_08.RCC

value: unstim

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: nodal reactive lymphoid hyperplasia_sample1

source_name: nodal reactive lymphoid hyperplasia_sampleB

tag: gender

tag: age


title: nodal follicular lymphoma_sample17

description: R-THP-COP → complete response, relapse after 12 months, Hyper-CVAD → complete response, died of DIC

source_name: nodal follicular lymphoma_patientX

value: male


title: nodal follicular lymphoma_sample15

description: R-CHOP → complete response, alive without disease (72 months)

source_name: nodal follicular lymphoma_patientV

value: III


title: nodal follicular lymphoma_sample13

description: R-CHOP → complete response, alive without disease (65 months)

source_name: nodal follicular lymphoma_patientT


title: nodal follicular lymphoma_sample16

description: R-CHOP + RT → complete response, alive without disease (75 months)

source_name: nodal follicular lymphoma_patientW


title: nodal follicular lymphoma_sample11

description: not available

source_name: nodal follicular lymphoma_patientQ

value: IV


title: nodal follicular lymphoma_sample10

description: R-CHOP + R maintenano changee therapy → complete response, alive without disease (52 months)

source_name: nodal follicular lymphoma_patientO


title: nodal follicular lymphoma_sample12

description: R-CHOP → complete response, alive without disease (60 months)

source_name: nodal follicular lymphoma_patientS


title: RTPCR04

description: Control,biological rep4

source_name: PBMNC of subjects before supplementation

tag: cell type


title: nodal follicular lymphoma_sample14

description: R-CHOP → partial response, allo-PBSCT, died of AML (treatment associated)

source_name: nodal follicular lymphoma_patientU

tag: tissue


title: T-22_pink coloring

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

institute: National Food Research Institute

description: Tomatoes were harvested at the pink coloring stage

hyb_protocol: The Cy3-labelled cRNA (1.65 ug) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture. The reaction mixture (40 ul) was used for hybridization with Agilent-022270 Tomato Gene Expression Microarray 44K slides (platform ID: GPL10570) (44K x 4 pack) for 17 hours at 65°C in an oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technoligies Microarray Scanner at a resolution of 5 um. Signal intensities of spots for the probes were monitored using the feature extraction software ver. 10.5.1.1 (Agilent).

data_processing: Raw data were subjected to per chip normalization to 75th percentile using Genespring ver.10.0 software (Agilent).

organism: Solanum lycopersicum

source_name: whole tomato at the pink coloring stage

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. The Cy3-labeled cRNA was purified with RNAeasy mini spin columns (QIAGEN, Valencia, CA).

growth_protocol: Plants were grown in an incubator under 16-h light at 26°C and 8-h dark at 20°C conditions, and the fruits were harvested at the pink coloring (about 4 days after breaker) stage.

extract_protocol: The frozen fruits were powdered with electric mill, moter and pestle. Total RNA was extracted and purified from 0.2 mg of the powder with RNeasy plus mini kit (Qiagen, Hilden, Germany).

treatment_protocol: The harvested fruits were immediately frozen in liquid nitrogen and stored at -80°C.

tag: cultivar

value: Ailsa Craig

tag: genotype/variation

value: transgenic line T-22 with RNAi knockdown of Solyc07g052960


title: 1350V011012_unstim_20121205_n113_01_07.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

value: East Asian

tag: million dcs

tag: height (cm)


title: RTPCR02

description: Control,biological rep2

value: peripheral blood mononuclear cells


title: RTPCR03

description: Control,biological rep3


title: 0312V011012_unstim_20121205_n113_01_06.RCC

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc


title: 1630V011012_unstim_20121205_n113_01_05.RCC

tag: gender

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: RTPCR05

description: Control,biological rep5

tag: age

tag: cell type


title: RTPCR04-LPS

description: Control,biological rep4

source_name: PBMNC of subjects before supplementation, LPS


title: 1650V011012_unstim_20121205_n113_01_04.RCC

tag: stimulation

tag: hours


title: RTPCR01

description: Control,biological rep1


title: 1346V011012_unstim_20121205_n113_01_03.RCC

tag: plate

tag: cartridge


title: 0775V121511_unstim_20121205_n113_01_01.RCC

tag: lane

tag: million dcs


title: T-23_pink coloring

tag: cultivar

tag: genotype/variation

value: transgenic line T-23 with RNAi knockdown of Solyc07g052960


title: 0272V011012_unstim_20121205_n113_01_02.RCC

tag: date of visit

tag: time of visit

tag: age (years)

tag: height (cm)


title: nodal follicular lymphoma_sample8

description: R-CHOP → complete response, relapse after 12 months, alive with disease

source_name: nodal follicular lymphoma_patientL

tag: tissue

tag: gender

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: T-7_pink coloring

value: transgenic line T-7 with RNAi knockdown of Solyc07g052960


title: nodal follicular lymphoma_sample7

description: not available

source_name: nodal follicular lymphoma_patientJ

tag: age

value: I


title: nodal follicular lymphoma_sample9

description: Rituximab monotherapy → complete response, alive without disease (48 months)

source_name: nodal follicular lymphoma_patientN


title: nodal follicular lymphoma_sample6

description: R-CHOP → complete response, alive without disease (30 months)

source_name: nodal follicular lymphoma_patientI


title: nodal follicular lymphoma_sample3

description: R-THP-COP → PD, R-bendamustine → partial response, alive with disease (24 months)

source_name: nodal follicular lymphoma_patientC


title: 1459V092011_dNS1_20121203_n112_01_11.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

value: M

tag: ethnicity

tag: million pbmc

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: nodal follicular lymphoma_sample4

description: R-CHOP → complete response, alive without disease (38 months)

source_name: nodal follicular lymphoma_patientD

tag: tissue


title: normal gastric mucosa_sample2

source_name: normal gastric mucosa_sampleE

value: normal gastric mucosa

tag: gender


title: AC_pink coloring

tag: cultivar

tag: genotype/variation

value: untransformed control


title: 1423V092211_dNS1_20121203_n112_01_10.RCC

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

tag: million dcs

tag: height (cm)


title: nodal follicular lymphoma_sample2

description: watch and wait → no change, alive with disease (17 months)

source_name: nodal follicular lymphoma_patientB

value: nodal follicular lymphoma

value: female

tag: age

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: nodal follicular lymphoma_sample5

description: watch and wait → PD, alive with disease (26 months)

source_name: nodal follicular lymphoma_patientF


title: ADDP cisplatin resistant

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 °C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA.

source_name: ADDP

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

growth_protocol: ADDP cells were maintained in RPMI supplemented with 10% FCS

extract_protocol: Total RNA was isolated with Trizol (Invitrogen, breda, The Netherlands), according to the manufacturer's instructions. Total RNA was further analyzed on the bioanalyzer (Agilent) and only RIN values of 8 or above were included

tag: cell line

value: ADDP

tag: sample type

value: Induced resistance to cisplatin. Weekly exposure of 1hrs at 50 µM for 6 months

growth_protocol: A2780 cells were maintained in RPMI supplemented with 10% FCS

value: parental cell line to ADDP


title: normal duodenal mucosa_sample5

source_name: normal duodenal mucosa_sampleF

tag: tissue

value: normal duodenal mucosa

tag: gender


title: A2780/cOHP oxaliplatin resistant

growth_protocol: A2780/cOHP cells were maintained in RPMI supplemented with 10% FCS

value: Induced resistance to oxaliplatin with increasing concentrations. Weekly exposure of 72hrs

value: parental cell line to A2780/cOHP


title: 0182V092011_dNS1_20121203_n112_01_12.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

value: F

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 1142V092111_dNS1_20121203_n112_01_09.RCC

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

value: East Asian

tag: million dcs

tag: height (cm)


title: LoVo-Li/4OHP oxaliplatin resistant

growth_protocol: LoVo-Li/4OHP cells were maintained in RPMI supplemented with 10% FCS

tag: cell line

tag: sample type

value: Induced resistance to oxaliplatin with increasing concentrations. Weekly exposure of 4hrs

source_name: LoVo-Li

growth_protocol: LoVo-Li cells were maintained in RPMI supplemented with 10% FCS

value: LoVo-Li

value: parental cell line to LoVo-Li/4OHP


title: nodal follicular lymphoma_sample1

description: R-CHOP → no change, R-bendamustine → partial response, alive with disease (27 months)

source_name: nodal follicular lymphoma_patientA

tag: tissue

tag: gender

tag: age

tag: Stage

value: IV

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: LoVo-92/cOHP oxaliplatin resistant

growth_protocol: LoVo-92/cOHP cells were maintained in RPMI supplemented with 10% FCS

growth_protocol: LoVo-92 cells were maintained in RPMI supplemented with 10% FCS

value: parental cell line to LoVo-92/cOHP


title: normal duodenal mucosa_sample4

source_name: normal duodenal mucosa_sampleE


title: 1439V092111_dNS1_20121203_n112_01_08.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

value: M

tag: ethnicity

tag: million pbmc

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: LoVo-Li/cOHP oxaliplatin resistant

source_name: LoVo-Li/cOHP

growth_protocol: LoVo-Li/cOHP cells were maintained in RPMI supplemented with 10% FCS

tag: cell line

value: LoVo-Li/cOHP

tag: sample type

value: parental cell line to LoVo-Li/cOHP


title: A2780/4OHP oxaliplatin resistant

growth_protocol: A2780/4OHP cells were maintained in RPMI supplemented with 10% FCS

value: parental cell line to A2780/4OHP


title: JQ1 treatment, biological rep3

first: Qin

last: Feng

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description: gene expression data from JQ1-treated MCF7 cells, 0.2 uM, 24 hours

hyb_protocol: Following end-labeling with biotin, 2 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 3000 scanner with 7G upgrade

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

label: biotinylated

label_protocol: cDNA were prepared according to the standard Affymetrix protocol for whole transcriptome analysis from 100ng total RNA.

growth_protocol: tamoxifen-resistant MCF7 cells were cultured in phenol red-free medium containing 10% charcoal-dextran-stripped FCS and 100 nM of 4-HT.

extract_protocol: Qiagen Rneasy kit was used for total RNA extraction according to the manufacturer's instructions.

treatment_protocol: tamoxifen resistant MCF7 cells were maintained in phenol red-free medium containing 10% charcoal-dextran-stripped FCS and 100 nM of 4-HT. JQ1 or DMSO was added and incubated for 24 hours before harvest for RNA purification.

value: JQ1 (0.2 uM) for 24 hours

tag: phenotype

value: tamoxifen-resistant


title: JQ1 treatment, biological rep2

source_name: JQ1-treated MCF7 cells, 0.2 uM, 24 hours


title: DMSO treatment, biological rep3

description: gene expression data from DMSO-treated MCF7 cells, 24 hours

source_name: DMSO-treated MCF7 cells, 24 hours

value: DMSO-treated for 24 hours


title: LoVo-92/4OHP oxaliplatin resistant

growth_protocol: LoVo-92/4OHP cells were maintained in RPMI supplemented with 10% FCS

value: parental cell line to LoVo-92/4OHP


title: normal duodenal mucosa_sample3

source_name: normal duodenal mucosa_sampleD

tag: tissue

value: normal duodenal mucosa

tag: gender

tag: age

tag: Stage


title: 0182V092011_dNS1_20121203_n112_01_06.RCC

growth_protocol: Monocyte-derived dendritic cells from each donor were cultured for 7 days in RPMI supplemented with 10% FBS, 100 ng/mL GM-CSF and 40 ng/mL IL-4.

tag: lane

tag: date of visit

tag: time of visit

value: F

tag: age (years)

tag: million dcs

tag: height (cm)


title: normal duodenal mucosa_sample2

source_name: normal duodenal mucosa_sampleC

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: 1432V092111_dNS1_20121203_n112_01_07.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 1459V092011_dNS1_20121203_n112_01_05.RCC

tag: lane

tag: date of visit

tag: time of visit

tag: gender

value: East Asian


title: JQ1 treatment, biological rep1

tag: cell line

tag: phenotype


title: MM556 PBMCs stimulated with GMM liposome

city: Kyoto

first: Daisuke

last: Morita

address: 53 Shogoin Kawara-cho, Sakyo-ku

department: Institute for virus research

institute: Kyoto-university

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Macaca mulatta

source_name: GMM-treated monkey PBMCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: monkey PBMCs were stimulated in the presense or absense of GMM for 24hr.

tag: cell type

value: PBMCs

tag: immunized with

value: BCG bacteria

tag: stimulated with

value: GMM liposome


title: 1097V091511_dNS1_20121203_n112_01_03.RCC

data_processing: The raw data is first scaled by positive spike-ins, shifted by negative spike-ins, and a negative binomial is fit using DESeq based on the scale parameter estimated from the positive spike-ins

tag: stimulation

tag: hours

tag: age (years)

tag: million dcs

tag: height (cm)


title: 1477V092011_dNS1_20121203_n112_01_04.RCC

tag: plate

tag: cartridge

tag: ethnicity

tag: million pbmc

tag: weight (kg)


title: DMSO treatment, biological rep2

tag: treatment


title: normal duodenal mucosa_sample1

source_name: normal duodenal mucosa_sampleA

tag: tissue

tag: gender

tag: age

tag: Stage

tag: grade

tag: tumor location

tag: outcome


title: 1031V091411_dNS1_20121203_n112_01_01.RCC

tag: stimulation

tag: hours

tag: lane

tag: date of visit

tag: time of visit

value: MULTI-RACIAL

tag: systolic/diastolic

tag: bmi


title: 0381V091411_dNS1_20121203_n111_01_12.RCC

tag: plate

tag: cartridge

tag: age (years)

tag: ethnicity

value: African-American

tag: million pbmc

tag: million dcs

tag: height (cm)


title: 1262V090811_dNS1_20121203_n111_01_11.RCC

tag: gender

tag: weight (kg)


title: gastric MALT lymphoma_sample9

source_name: gastric MALT lymphoma_patientN

tag: tissue

value: gastric MALT lymphoma

value: male

tag: age

tag: Stage

value: I

tag: grade

tag: tumor location

value: stomach

tag: treatment

value: Helicobacter pylori eradication

tag: outcome

value: complete response


title: DMSO treatment, biological rep1

tag: cell line

value: DMSO-treated for 24 hours

tag: phenotype

value: tamoxifen-resistant


title: MM556 PBMCs stimulated with empty liposome

source_name: mock-treated monkey PBMCs

tag: cell type

tag: immunized with

tag: stimulated with

value: empty liposome


title: 1090V090811_dNS1_20121203_n111_01_10.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: M

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: systolic/diastolic

tag: bmi


title: 1280V091411_dNS1_20121203_n112_01_02.RCC

tag: gender

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: gastric MALT lymphoma_sample6

source_name: gastric MALT lymphoma_patientK

tag: tissue

tag: age

tag: Stage

tag: grade

tag: tumor location

tag: treatment

tag: outcome


title: gastric MALT lymphoma_sample10

source_name: gastric MALT lymphoma_patientO

value: female

value: stomach, duodenum

value: no change


title: gastric MALT lymphoma_sample8

source_name: gastric MALT lymphoma_patientM

value: Helicobacter pylori eradication + RT

value: partial reponse


title: MM553 PBMCs stimulated with GMM liposome

tag: cell type

value: PBMCs

tag: immunized with

value: BCG bacteria

tag: stimulated with

value: GMM liposome


title: gastric MALT lymphoma_sample7

source_name: gastric MALT lymphoma_patientL

value: gastric MALT lymphoma


title: 1415V091311_dNS1_20121203_n111_01_08.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: F

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc


title: 1148V090811_dNS1_20121203_n111_01_09.RCC

tag: gender

value: African-American

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 0987V091311_dNS1_20121203_n111_01_07.RCC


title: MM553 PBMCs stimulated with empty liposome

tag: cell type

tag: immunized with

tag: stimulated with


title: gastric MALT lymphoma_sample4

source_name: gastric MALT lymphoma_patientI

tag: tissue

value: male

tag: age

tag: Stage

value: I

tag: grade

tag: tumor location

value: stomach

tag: treatment

value: not available

tag: outcome


title: A2780/4OHP oxaliplatin resistant

type: genomic

description: protocols according to manufacturer (Enzo Life Sciences www.agilent.com)

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 9.5.1.1). Raw expression data generated by the Feature Extraction software was normalised and smoothend using the R-script "NOWAVE" as described in: Smoothing waves in array CGH tumor profiles, Bioinformatics. 2009 May 1;25(9):1099-104.

molecule: genomic DNA

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: DNA was isolated using the Wizard Genomic DNA Purification kit (Promega Benelux, Leiden, The Netherlands) according the manufacturer’s protocol.

treatment_protocol: Induced resistance to oxaliplatin with increasing concentrations. Weekly exposure of 4hrs

tag: cell line

value: A2780 (parental)


title: A2780/cOHP oxaliplatin resistant

treatment_protocol: Induced resistance to oxaliplatin with increasing concentrations. Weekly exposure of 72hrs


title: LoVo-Li/cOHP oxaliplatin resistant

value: LoVo-Li/cOHP

source_name: LoVo-Li

value: LoVo-Li (parental)


title: A2780

source_name: RefXY

tag: reference

value: pooled WBC from healthy male volunteers


title: gastric MALT lymphoma_sample3

source_name: gastric MALT lymphoma_patientH

tag: gender

value: female

value: Helicobacter pylori eradication

value: complete response


title: gastric MALT lymphoma_sample2

source_name: gastric MALT lymphoma_patientG

value: watch and wait

value: no change


title: ADDP cisplatin resistant

source_name: ADDP

treatment_protocol: Induced resistance to cisplatin. Weekly exposure of 1hrs at 50 µM for 6 months

value: ADDP


title: 1317V091311_dNS1_20121203_n111_01_06.RCC

hyb_protocol: Lysates in Qiagen RLT buffer were hybridized for 12-24 hours with custom nCounter Gene Expression CodeSets.

scan_protocol: Nanostring nCounter system (Nanostring; Seattle, WA) was used to digitally count transcripts in a multiplex reaction.

extract_protocol: Total RNA was isolated using Qiagen RNeasy columns.

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: M

tag: age (years)

tag: ethnicity

value: East Asian

tag: million pbmc

tag: million dcs

tag: height (cm)


title: LoVo-Li

source_name: RefXX

value: pooled WBC from healthy female volunteers


title: LoVo-92

value: LoVo-92 (parental)


title: gastric MALT lymphoma_sample1

source_name: gastric MALT lymphoma_patientD

tag: tissue

value: gastric MALT lymphoma

value: male

tag: age

tag: Stage

value: I

tag: grade

tag: tumor location

tag: treatment


title: 1011V091311_dNS1_20121203_n111_01_05.RCC

tag: stimulation

tag: hours

tag: gender

value: F

value: African-American

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: duodenal follicular lymphoma_sample10

source_name: duodenal follicular lymphoma_patientO

value: duodenal follicular lymphoma

value: D, I, J

tag: outcome


title: 1421V091311_dNS1_20121203_n111_01_04.RCC

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity


title: 1229V062811_dNS1_20121203_n111_01_03.RCC

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)


title: duodenal follicular lymphoma_sample8

source_name: duodenal follicular lymphoma_patientL

tag: tissue

tag: age

tag: Stage

tag: grade

tag: tumor location

value: D

tag: treatment


title: 1446V062811_dNS1_20121203_n111_01_02.RCC

tag: stimulation

tag: hours

tag: gender

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: gastric MALT lymphoma_sample5

source_name: gastric MALT lymphoma_patientJ

value: female

value: stomach

value: Helicobacter pylori eradication

tag: outcome


title: LoVo-92/cOHP oxaliplatin resistant

tag: cell line


title: duodenal follicular lymphoma_sample9

source_name: duodenal follicular lymphoma_patientN

value: watch and wait

value: no change


title: duodenal follicular lymphoma_sample7

source_name: duodenal follicular lymphoma_patientK

value: D, I


title: 1168V062811_dNS1_20121203_n111_01_01.RCC

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: M

tag: age (years)

tag: ethnicity

tag: million pbmc


title: 1344V062811_dNS1_20121203_n110_01_12.RCC

tag: million dcs

tag: height (cm)


title: duodenal follicular lymphoma_sample6

source_name: duodenal follicular lymphoma_patientI

tag: tissue

tag: age

tag: Stage

tag: grade

tag: tumor location

tag: treatment


title: Lovo-Li/4OHP oxaliplatin resistant

tag: cell line

value: LoVo-Li (parental)


title: 0313V062811_dNS1_20121203_n110_01_11.RCC

tag: stimulation

tag: hours

tag: plate

tag: gender

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: duodenal follicular lymphoma_sample5

source_name: duodenal follicular lymphoma_patientF

value: S, D, I, J

tag: outcome


title: LoVo-92/4OHP oxaliplatin resistant

value: LoVo-92 (parental)


title: 1266V062311_dNS1_20121203_n110_01_10.RCC

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs


title: duodenal follicular lymphoma_sample4

source_name: duodenal follicular lymphoma_patientE

tag: tissue

tag: age

tag: Stage

value: I

tag: grade

tag: tumor location

tag: treatment


title: duodenal follicular lymphoma_sample3

source_name: duodenal follicular lymphoma_patientD

tag: gender

value: male


title: duodenal follicular lymphoma_sample2

source_name: duodenal follicular lymphoma_patientC


title: 1361V062311_dNS1_20121203_n110_01_08.RCC

tag: stimulation

tag: hours

tag: plate

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: duodenal follicular lymphoma_sample1

source_name: duodenal follicular lymphoma_patientB

tag: outcome


title: Patient 27_151T

city: Goyaongsi

first: Charny

state: Gyeonggi-do

address: 323 Ilsan-ro,

institute: National Cancer Center

hyb_protocol: Fragmented cyanine 3-labeled cRNA were loaded on to the gasket slide for hybridization and incubated at 65℃, 10 rpm for 17 hours, See manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf) for detail

scan_protocol: Microarray slides were scanned on an Agilent C Scanner using the Profile AgilentG3_GX_1Color for 8x60K microarrays.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent). Gene expression data analysis was subsequently conducted in R-project (build 2.11.1). The raw data were normalized by using Quantile method. Paired t-test using Algorithm Limma were performed to select differentially expressed genes (DEG) between normal and tumor tissues in EBV(+)GC and EBV(-)GC. DEGs were clustered based by Cluster 3.0 and Tree View software.

source_name: Advanced gastric carcinoma patient

label_protocol: See the manufactor's manual (http://www.chem.agilent.com/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf). Briefly, total RNA was converted to ds cDNA1 using One-Color Spike Mix. complementary RNA was amplified with T7 promtoer primers and cyanine 3-CTP. Amplified cRNA was purified with Qiagen’s RNeasy mini spin columns and quantified using NanoDrop ND-1000 (Thermo Scientific).

extract_protocol: Total RNA was isolated from tissue by using RNeasy Mini Kit (Qiagen, Hilden, Germany). Quantity and quality of isolated RNA were measured by Nanodrop ND-1000 (Thermo Scientific, Waltham, MA).

value: Gastric tumor

tag: ebv

value: EBV+

tag: histology

value: CLR

tag: lauren type

value: Mixed

tag: Sex

tag: tumor stage

value: IIIB


title: Empty Vector control4_Replicate 1

city: Singapore

first: Jingli

last: Zhuo

address: MD 6, 14 Medical Drive

country: Singapore

institute: National University of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized each chip to the 50th Percentile of the measurements taken from that chip using GeneSpring GX 7.3 software

source_name: Empty Vector control4_Replicate 1

label_protocol: Biotinylated cRNA were prepared with Enzo Diagnostics, USAbiotin labelled cRNA synthesis, in vitro transcription reaction was performed in the presence of T7 RNA polymerase and biotinylated ribonucleotides (Enzo Diagnostics, USA).

extract_protocol: Cells were subjected to appropriate treatment and the total RNA was extracted (RNeasy Kit, Qiagen). Double stranded cDNA was synthesised from 5 μg of total RNA using Superscript system (Invitrogen, USA) primed with T7- (dT)-24 primer.

value: emtpy vector control Vec4

tag: replicate

tag: cell line


title: Clone 2_Replicare 1

source_name: Clone 2_Replicare 1

tag: treatment

value: stable gelsolin-overexpressing C2


title: 0668V062311_dNS1_20121203_n110_01_07.RCC

city: Cambridge

first: Nir

last: Hacohen

address: 7 Cambridge Center

institute: Broad Institute

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs


title: Patient 26_139T

last: Park

tag: tissue

tag: ebv

value: EBV-

value: CA

value: Intestinal

tag: age


title: Patient 27_151N

value: Gastric normal

tag: histology

tag: lauren type

tag: Sex

value: M


title: MEF_hypoxic_rep3

source_name: mef, hypoxia

label_protocol: 50ng of total RNA from each sample was amplified using the Oviation Pico WTA system V2 (Nugene). Fragmentation and biotin labeling was done using the Encore-Oviation cDNA Biotin Module (Nugene).

extract_protocol: RNA was extracted from hypoxic and normoxic cells with Trizol® (Life) according to the manufactures protocol.

treatment_protocol: Hypoxia was induced by lowering oxygen concentration to 1% in multigas incubator (Sanyo) and control cells were treated with atmospheric oxygen for 24 hours.

tag: cell type

value: mouse embryonic fibroblasts

tag: oxygen level


title: Patient 26_139N

tag: tumor stage


title: Clone 3_Replicare 1

source_name: Clone 3_Replicare 1

tag: treatment

value: stable gelsolin-overexpressing C3

tag: replicate

tag: cell line


title: Patient 25_130N


title: Empty Vector control5_Replicate 1

source_name: Empty Vector control5_Replicate 1

value: emtpy vector control Vec5


title: MEF_hypoxic_rep2


title: 1222V062311_dNS1_20121203_n110_01_09.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

value: F

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Patient 25_130T

tag: tissue

value: Gastric tumor

tag: ebv

tag: histology

value: LELC

tag: lauren type

value: Diffuse

tag: age

tag: Sex

value: Ia


title: 1356V061511_dNS1_20121203_n110_01_03.RCC

tag: stimulation

tag: hours

tag: age (years)

tag: ethnicity

value: East Asian

tag: million pbmc

tag: million dcs


title: Clone 8_Replicare 1

source_name: Clone 8_Replicare 1

tag: treatment

value: stable gelsolin-overexpressing C8

tag: replicate

tag: cell line


title: 0773V062111_dNS1_20121203_n110_01_04.RCC

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

value: African-American

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: Clone 1_Replicare 1

source_name: Clone 1_Replicare 1

value: stable gelsolin-overexpressing C1


title: MEF_normoxic_rep3

source_name: mef, normoxia

tag: cell type

tag: oxygen level

value: normoxia


title: 0570V062211_dNS1_20121203_n110_01_05.RCC

tag: stimulation

tag: hours

tag: age (years)

tag: ethnicity

value: Caucasian

tag: bmi


title: Patient 23_116T

tag: tissue

tag: ebv

value: EBV-

tag: histology

value: CA

tag: lauren type

value: Intestinal

tag: age

tag: Sex

tag: tumor stage

value: IIB


title: 1156V061511_dNS1_20121203_n110_01_02.RCC

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

tag: million pbmc

tag: million dcs

tag: height (cm)


title: MEF_normoxic_rep4

tag: cell type

value: mouse embryonic fibroblasts

tag: oxygen level


title: Clone 2_Replicare 2

source_name: Clone 2_Replicare 2

tag: treatment

value: stable gelsolin-overexpressing C2

tag: replicate

tag: cell line


title: 1088V060911_dNS1_20121203_n110_01_01.RCC

tag: stimulation

tag: hours

value: M

tag: age (years)

tag: ethnicity

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: Patient 23_116N

tag: tissue

value: Gastric normal

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

value: F

tag: tumor stage


title: MEF_normoxic_rep1

tag: cell type

tag: oxygen level


title: MEF_normoxic_rep2


title: Patient 22_104T

value: Gastric tumor

value: EBV+

value: Mixed


title: Clone 1_Replicare 2

source_name: Clone 1_Replicare 2

tag: treatment

tag: replicate

tag: cell line


title: MEF_hypoxic_rep1


title: Patient 22_104N


title: 1279V060911_dNS1_20121203_n109_01_11.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: gender

tag: age (years)

tag: million pbmc

tag: million dcs

tag: height (cm)


title: MEF_hypoxic_rep4

tag: cell type


title: 1442V100411_LPS_20121203_n109_01_08.RCC

value: LPS

tag: ethnicity

tag: weight (kg)

tag: systolic/diastolic

tag: bmi


title: 0412V092911_LPS_20121203_n109_01_07.RCC

tag: stimulation


title: 1345V092811_LPS_20121203_n109_01_06.RCC

tag: hours

value: East Asian


title: 1459V092011_LPS_20121203_n109_01_05.RCC

tag: plate


title: Patient 20_101N

tag: tissue

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage


title: Cancer Patients:ST 37

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

description: Circulating Serum DNA from Cancer Patients, Metastatic

hyb_protocol: Illumina HumanMethylation 27 BeadChip Protocols

data_processing: Six ml serum from women with metastatic breast cancer or healthy volunteers was digested with proteinase K, DNA extracted, and bisulfite treated (EZ DNA Methylation kit, Zymo Research, Orange, CA) as directed.  Bisulfite-converted DNA was processed for the Infinium HumanMethylation27 BeadChip (Illumina, Inc., San Diego, CA; WG-311-1202).  Methylation was measured as β-value, ranging from 0-1 (low to high, respectively). Differential methylation analyses were accomplished using GenomeStudio (Illumina).   Probes were selected with: 1) the most reproducible performance (probe detection p-value <0.00001; 97%, 26759/27578 probes), 2) ≥ 2-fold more methylation in serum from cancer versus normal controls (902/26759 probes), 3) ≥ 1.5-fold more methylation in tissues from breast cancer (n = 103) versus normal breast (n = 21), data from our previous study, and leukocyte DNA (n = 4 pools); all individual normal samples were required to have low methylation (≤ 0.15 β-value methylation) (232/902 probes). Finally, a subgroup of 13 genes was selected consisting of markers with a frequency of ≥ 30% methylation among cancer samples, as well as those associated with outcome in our previous study.

label: Cy5 and Cy3

source_name: Cancer Patients

extract_protocol: Phenol chloroform extraction of serum DNA

treatment_protocol: Sodium bisulfite converted genomic DNA.

tag: gender

value: Female

tag: sample type

value: cancer sera


title: Clone 3_Replicare 2

source_name: Clone 3_Replicare 2

tag: treatment

value: stable gelsolin-overexpressing C3

tag: replicate

tag: cell line


title: Patient 21_103T

value: EBV-

value: CLR

value: Indeterminate

value: IIA


title: Patient 21_103N


title: Cancer Patients:ST 23

scan_protocol: Illumina HumanMethylation 27 BeadChip Protocols


title: Cancer Patients:ST 25

label_protocol: Illumina HumanMethylation 27 BeadChip Protocols


title: Cancer Patients:ST 31


title: 1317V091311_LPS_20121203_n109_01_04.RCC

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: Patient 20_101T

tag: tissue

tag: ebv

tag: histology

value: CA

tag: lauren type

value: Diffuse

tag: age

tag: Sex

tag: tumor stage

value: IIB


title: Cancer Patients:ST 27

tag: gender

tag: sample type


title: Patient 18_098T

value: Intestinal

value: M

value: ⅢC


title: Cancer Patients:ST 20


title: Patient 19_100N

value: Gastric normal


title: Patient 18_098N


title: Cancer Patients:ST 17


title: 1446V062811_LPS_20121203_n109_01_03.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: African-American

tag: bmi


title: 0313V062811_LPS_20121203_n109_01_02.RCC

value: LPS

tag: age (years)

tag: ethnicity

value: Caucasian

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 1275V060811_dNS1_20121203_n109_01_10.RCC

tag: gender

value: F


title: Cancer Patients:ST 16

value: Female

tag: sample type

value: cancer sera


title: Patient 17_088T

tag: tissue

value: Gastric tumor

tag: ebv

value: EBV-

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage

value: IIIB


title: Patient 17_088N


title: Cancer Patients:ST 15


title: Patient 16_087T


title: 1646V012412_LPS_20121202_n108_01_12.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: East Asian

tag: bmi


title: 1669V013112_LPS_20121202_n108_01_11.RCC

tag: gender

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 0498V013112_LPS_20121202_n108_01_10.RCC


title: 1621V013112_LPS_20121202_n108_01_09.RCC

value: MULTI-RACIAL


title: Cancer Patients:ST 14

tag: sample type


title: 0517V062211_dNS1_20121203_n110_01_06.RCC

tag: stimulation


title: Cancer Patients:ST 13


title: Patient 15_086T

tag: tissue

tag: ebv

value: EBV+

tag: histology

value: CA

tag: lauren type

value: Indeterminate

tag: age

tag: Sex

tag: tumor stage


title: Breast Organoids:ORG 81

description: Genomic DNA from Breast Organoids

source_name: Breast Organoids

tag: gender

value: Breast Organoids


title: 1088V060911_LPS_20121203_n109_01_01.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: M

tag: age (years)

tag: bmi


title: Breast Organoids:ORG 202

description: Genomic DNA from Breast Organoids


title: Patient 15_086N

value: Gastric normal


title: Breast Organoids:ORG 222

description: Genomic DNA from Breast Organoids


title: Breast Organoids:ORG 199

description: Genomic DNA from Breast Organoids


title: Patient 16_087N


title: 1363V012512_LPS_20121202_n108_01_07.RCC

tag: stimulation

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: 0310V012612_LPS_20121202_n108_01_08.RCC


title: 1528V012512_LPS_20121202_n108_01_06.RCC

value: African-American


title: Patient 14_085N

tag: tissue

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage


title: Breast Organoids:ORG 201

description: Genomic DNA from Breast Organoids

tag: gender


title: Patient 13_078N


title: Breast Organoids:ORG 193

description: Genomic DNA from Breast Organoids


title: Patient 12_076T

value: Intestinal

value: IIB


title: Patient 13_078T

value: F

value: IIIC


title: Patient 14_085T

value: CLR


title: Empty Vector control4_Replicate 2

source_name: Empty Vector control4_Replicate 2

tag: treatment

value: emtpy vector control Vec4

tag: replicate

tag: cell line


title: 1667V012512_LPS_20121202_n108_01_05.RCC

tag: stimulation

value: LPS

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

tag: age (years)

tag: ethnicity

tag: bmi


title: Breast Organoids:ORG 175

description: Genomic DNA from Breast Organoids

value: Female

tag: tissue


title: 1057V100411_LPS_20121202_n108_01_04.RCC

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: systolic/diastolic


title: Patient 12_076N

tag: ebv

value: EBV-

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage


title: Breast Organoids:ORG 167

description: Genomic DNA from Breast Organoids

tag: gender


title: 1423V092211_LPS_20121202_n108_01_03.RCC

tag: stimulation

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit

value: Caucasian


title: Patient 11_065T

tag: tissue

value: Gastric tumor

value: EBV+

value: LELC

value: Diffuse

value: IIA


title: 1439V092111_LPS_20121202_n108_01_02.RCC

value: M

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 1432V092111_LPS_20121202_n108_01_01.RCC

tag: systolic/diastolic


title: 1262V090811_LPS_20121202_n107_01_12.RCC

tag: gender

value: MULTI-RACIAL


title: Breast Organoids:ORG 125

description: Genomic DNA from Breast Organoids

value: Breast Organoids


title: Breast Organoids:ORG 119

description: Genomic DNA from Breast Organoids


title: 1148V090811_LPS_20121202_n107_01_10.RCC

tag: stimulation

value: African-American


title: Patient 10_047N

value: Gastric normal

tag: ebv

tag: histology

tag: lauren type

tag: age

tag: Sex

tag: tumor stage


title: 0793V060911_dNS1_20121203_n109_01_12.RCC

tag: hours

tag: plate

tag: cartridge

tag: lane

tag: date of visit

tag: time of visit


title: 1415V091311_LPS_20121202_n107_01_09.RCC

value: F

tag: age (years)

tag: ethnicity

tag: million pbmc

tag: million dcs

tag: height (cm)

tag: weight (kg)


title: Patient 9_044T

tag: tissue

tag: ebv

tag: histology

value: CA

value: Mixed

value: IIIA


title: Breast Organoids:ORG 028

description: Genomic DNA from Breast Organoids

tag: gender

value: Female


title: Patient 11_065N

value: EBV-

tag: lauren type

tag: age

tag: Sex

tag: tumor stage