title: Interstitial_TRAP_noSurgery_BiologicalReplicate2

description:
14_foxd1-noSurgery-2
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

source_name: foxd1-L10a, no treatment

tag: strain/background

value: kidney

value: no treatment


status: Public on Mar 06 2014

type: RNA

city: Bethesda

first: Arian

middle: Dominic John

last: Laurence

state: MD

address: 9000 Rockville Pike, Building 10, Room13C120-11B

department: MIIB

country: USA

institute: NIAMS

description:
Gene expression data from mut-Stat3 DC's cultured for 24hrs
Sample 3D; 06-05-2012_J_Oshea4_AK_Mouse430_2_4_HIES-LPS

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing: Data processing were done using Affymetrix Power Tool (APT) v. 1.10.2, quantile normalization RMA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mutStat3_CD11c+ splenocyte_24hrs

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: Cells were treated for 24hrs with or without 2ng/ul LPS. LPS treated cells were incubated in the absence of any cytokine or in the presence of either IL-6 (20ng/ml) or IL-10 (20ng/ml).

tag: strain background

tag: genotype/variation

value: mut-Stat3 2 copy BAC transgenic

tag: tissue

value: spleen

tag: cell type

value: primary CD11c+ dendritic cells


title: Interstitial_TRAP_Sham_24h_BiologicalReplicate1

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

description:
16_24hr_foxd1-sham-1
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in the Affymetrix GeneChip 450 Fluidics station.

scan_protocol: Scanning of arrays was performed by an Affymetrix 3000 GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix Expression Console 1.3.1 software using RMA normalization method.

source_name: foxd1-L10a, sham surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng TRAP RNA or Total RNA.

growth_protocol: Mice handling and husbandry were performed according to guidelines issued by the Institutional Animal Care and Use Committees (IACUC) at Harvard University and at the University of Southern California, and were performed on approval of each institutions IACUC committee review.

extract_protocol: Kidneys were minced rapidly on ice then added to ice-cold polysome extraction buffer for homogenization. Monoclonal anti-GFP antibodies were coupled to Dynabeads and added to a post-mitochondrial preparation of kidney extract at a ratio of 200µl of freshly bound beads to 800-1200µl of kidney supernatant. Beads and extract were incubated at 4°C, with agitation, for 30 min. The beads were then washed through a large volume of wash buffer, resuspended in lysis buffer, RNA was isolated and contaminating DNA removed by DNaseI digestion (Qiagen RNeasy mini kit).

treatment_protocol: 6- to 10-week-old male mice were anesthetized with an intraperitoneal injection of a ketamine/xylazine mix. The body temperature was maintained at 37°C throughout the procedure. Kidneys were exposed through flank incisions, and both renal pedicles were clamped for 28 min using non-traumatic microaneurysm clips. Restoration of blood flow was monitored before closing incisions with surgical staples. Sham-operated mice underwent the same procedure except for clamping of the pedicles.

value: mixed (C57BL/6 and 129)

value: foxd1-CRE, Rosa26-CAGGS-eGFPL10a

tag: gender

value: male

tag: age

value: 6 weeks

tag: cell population

value: interstitial

tag: treatment

value: sham surgery


title: linuron Solvent control A

city: Aachen

first: Viktoria

last: Schiller

state: NRW

address: Forckenbeckstrasse 6

department: UNIFISH

country: Germany

institute: Fraunhofer IME

hyb_protocol: Hybridization was carried out according to the Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies)

scan_protocol: Microarrays were scanned immediately after wahsing with the Agilent Microarray Scanner (Agilent Technologies)

data_processing: Data were extracted and processed using Agilent Feature Extraction Software applying default parameters (protocol GE1-v5_95_Feb07, QC metric set GE1_QCMT_Feb07)

organism: Danio rerio

source_name: linuron Solvent control

label_protocol: We carried out cDNA synthesis, cRNA Cy3 labeling, amplification and hybridization according to the manufacturer’s protocols (Quick Amp Labeling Kit; Agilent Technologies), using 500ng RNA as starting material.

extract_protocol: Total RNA was isolated from frozen, pooled embryos by homogenization in TRIreagent (Sigma-Aldrich, T9424) followed by extraction with chloroform and ethanol and final purification using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers’ protocols. RNA concentration was measured using a NanoDrop 1000 (Thermo Fisher Scientific, Schwerte, Germany) and RNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Per concentration and replicate, 24 newly fertilized embryos (<2hpf) were exposed to EC10 and EC20 concentrations (for details, see design) of EE2, BPA, methylparaben, propanil, flutamide, linuron and prochloraz for 48 hours in 96 well plates. After exposure, each group of 24 fish embryos was pooled together, snap-frozen over dry ice and stored at –80°C.

value: embryo

value: 48 hours post fertilization


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS+IL10
Sample 3C; 06-05-2012_J_Oshea3_AK_Mouse430_2_3_WT+LPS+IL10

source_name: WT_CD11c+ splenocyte_LPS+IL10_24hrs

value: wild type

tag: culture with

value: LPS+IL10 for 24hrs


title: linuron Solvent control D


title: Combo 16h biological replicate 1

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

description: Gene expression data from SW480 cells treated with MEK+TNKS inhibitors for 16h

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

organism: Homo sapiens

source_name: SW480 cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: SW480 cells were cultured in 10% FBS RPMI.

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 2.5 million cells were resuspended in 10ml of fresh media in 10cm dishes.  The next day, DMSO, TNKS inhibitor, MEKi inhibitor or the combination of both was added for 4hrs and 16hrs

tag: lineage

value: colorectal

tag: cell line


title: linuron Solvent control C


description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS
Sample 3E; 06-05-2012_J_Oshea5_AK_Mouse430_2_5_HIES+LPS

source_name: mutStat3_CD11c+ splenocyte_LPS_24hrs

value: LPS for 24hrs


title: Interstitial_TRAP_noSurgery_BiologicalReplicate1

description:
13_foxd1-noSurgery-1
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

value: kidney


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS
Sample 3B; 06-05-2012_J_Oshea2_AK_Mouse430_2_2_WT+LPS

source_name: WT_CD11c+ splenocyte_LPS_24hrs


title: Interstitial_TRAP_noSurgery_BiologicalReplicate3

description:
15_foxd1-noSurgery-3
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

value: no treatment


title: MEKi 16h biological replicate 2

description: Gene expression data from SW480 cells treated with MEK inhibitor for 16h

value: treated with MEK inhibitor for 16h


description:
Gene expression data from wild type DC's cultured for 24hrs
Sample 3A; 06-05-2012_J_Oshea1_AK_Mouse430_2_1_WT-LPS

source_name: WT_CD11c+ splenocyte_24hrs

value: spleen


title: Interstitial_TRAP_IRI_24h_BiologicalReplicate2

description:
11_24hr_foxd1-IRI-2
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

source_name: foxd1-L10a, bilateral ischemic reperfusion injury

value: bilateral ischemic reperfusion injury


title: TNKSi 16h biological replicate 2

description: Gene expression data from SW480 cells treated with TNKS inhibitor for 16h

value: treated with TNKS inhibitor for 16h


title: Interstitial_TRAP_IRI_24h_BiologicalReplicate3

description:
12_24hr_foxd1-IRI-3
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

value: mixed (C57BL/6 and 129)

value: foxd1-CRE, Rosa26-CAGGS-eGFPL10a


title: TNKSi 16h biological replicate 1


title: Macrophage_TRAP_IRI_24h_BiologicalReplicate3

description:
21_lyz2IRI_3
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

source_name: lyz2-L10a, bilateral ischemic reperfusion injury

value: lyz2-CRE, Rosa26-CAGGS-eGFPL10a

value: male

value: 9.5 weeks

value: macrophage/monocyte


description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS+IL10
Sample 2F; 04-25-2012_J_Oshea6_AK_Mouse430_2_6_HIES+LPS+IL10

value: mut-Stat3 2 copy BAC transgenic

value: primary CD11c+ dendritic cells


title: DMSO 16h biological replicate 2

description: Gene expression data from SW480 cells treated with DMSO for 16h

value: treated with DMSO for 16h


title: linuron ISO C

source_name: linuron ISO

value: embryo

value: 48 hours post fertilization


title: Interstitial_TRAP_IRI_24h_BiologicalReplicate1

description:
10_24hr_foxd1-IRI-1
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

value: 6 weeks

value: kidney

value: interstitial


title: linuron ISO A


title: linuron EC10 A

source_name: linuron EC10


title: linuron ISO D


description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS
Sample 2E; 04-25-2012_J_Oshea5_AK_Mouse430_2_5_HIES+LPS

value: spleen

value: LPS for 24hrs


title: propanil EC20 D

source_name: propanil EC20


title: DMSO 16h biological replicate 1

value: colorectal


title: Endothelial_TRAP_Sham_24h_BiologicalReplicate3

description:
9_24hr_cdh5-SHAM-3
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

source_name: cdh5-L10a, sham surgery

value: mixed (C57BL/6 and 129)

value: cdh5-CRE, Rosa26-CAGGS-eGFPL10a

value: vascular endothelium

value: sham surgery


title: linuron ISO B


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS+IL10
Sample 2C; 04-25-2012_J_Oshea3_AK_Mouse430_2_3_WT+LPS+IL10

value: wild type

value: LPS+IL10 for 24hrs


title: propanil EC20 C


title: Combo 4h biological replicate 1

description: Gene expression data from SW480 cells treated with MEK+TNKS inhibitors for 4h

value: treated with MEK+TNKS inhibitors for 4h


title: MEKi 4h biological replicate 2

description: Gene expression data from SW480 cells treated with MEK inhibitor for 4h

value: treated with MEK inhibitor for 4h


title: Endothelial_TRAP_Sham_24h_BiologicalReplicate1

description:
7_24hr_cdh5-SHAM-1
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

value: male


description:
Gene expression data from mut-Stat3 DC's cultured for 24hrs
Sample 2D; 04-25-2012_J_Oshea4_AK_Mouse430_2_4_HIES-LPS

value: mut-Stat3 2 copy BAC transgenic

value: primary CD11c+ dendritic cells


title: Endothelial_TRAP_noSurgery_BiologicalReplicate3

description:
6_cdh5-Nosurgery-3
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

source_name: cdh5-L10a, no treatment

value: 6 weeks

value: no treatment


title: Combo 4h biological replicate 2


title: propanil EC20 B

value: embryo

value: 48 hours post fertilization


title: linuron EC10 B


description:
Gene expression data from wild type DC's cultured for 24hrs
Sample 2A; 04-25-2012_J_Oshea1_AK_Mouse430_2_1_WT_LPS

value: spleen


title: Endothelial_TRAP_Sham_24h_BiologicalReplicate2

description:
8_24hr_cdh5-SHAM-2
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

value: kidney


title: MEKi 4h biological replicate 1

value: colorectal


title: Endothelial_TRAP_noSurgery_BiologicalReplicate2

description:
5_cdh5-Nosurgery-2
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

value: mixed (C57BL/6 and 129)

value: cdh5-CRE, Rosa26-CAGGS-eGFPL10a


title: Endothelial_TRAP_noSurgery_BiologicalReplicate1

description:
4_cdh5-Nosurgery-1
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

value: vascular endothelium


title: propanil EC20 A


description:
Gene expression data from mut-Stat3 DC's cultured for 24hrs with LPS
Sample 1D; 02-16-2012_J_Oshea4_AK_Mouse430_2_4_HIES_LPS

value: LPS for 24hrs


description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS+IL6
Sample 1E; 02-16-2012_J_Oshea5_AK_Mouse430_2_5_HIES_LPS_IL6

value: LPS+IL6 for 24hrs


title: propanil EC10 D

source_name: propanil EC10


title: TNKSi 4h biological replicate 1

description: Gene expression data from SW480 cells treated with TNKS inhibitor for 4h

value: treated with TNKS inhibitor for 4h


title: propanil EC10 A


title: propanil EC10 B


title: DMSO 4h biological replicate 1

description: Gene expression data from SW480 cells treated with DMSO for 4h

value: treated with DMSO for 4h


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS
Sample 2B; 04-25-2012_J_Oshea2_AK_Mouse430_2_2_WT+LPS

value: wild type


title: Endothelial_TRAP_IRI_24h_BiologicalReplicate3

description:
3_24hr_cdh5-IRI-3
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

source_name: cdh5-L10a, bilateral ischemic reperfusion injury

value: male

value: bilateral ischemic reperfusion injury


title: Endothelial_TRAP_IRI_24h_BiologicalReplicate1

description:
1_24hr_cdh5-IRI-1
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.

value: 6 weeks


title: parental biological replicate 2

description: Gene expression data from SW480 cells before treatment


description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS+IL10
Sample 1F; 02-16-2012_J_Oshea6_AK_Mouse430_2_6_HIES_LPS_IL10

value: mut-Stat3 2 copy BAC transgenic

value: primary CD11c+ dendritic cells

value: LPS+IL10 for 24hrs


title: Endothelial_TRAP_IRI_24h_BiologicalReplicate2

description:
2_24hr_cdh5-IRI-2
TRAP RNA
Gene expression data from cdh5-derived cells in adult kidney.


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS+IL6
Sample 1B; 02-16-2012_J_Oshea2_AK_Mouse430_2_2_WT_LPS_IL6

source_name: WT_CD11c+ splenocyte_LPS+IL6_24hrs

value: spleen


title: TNKSi 4h biological replicate 2


title: propanil EC10 C

value: embryo

value: 48 hours post fertilization


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS+IL10
Sample 1C; 02-16-2012_J_Oshea3_AK_Mouse430_2_3_WT_LPS_IL10


title: propanil Solvent control D

source_name: propanil Solvent control


description:
Gene expression data from wild type DC's cultured for 24hrs with LPS
Sample 1A; 02-16-2012_J_Oshea1_AK_Mouse430_2_1_WT_LPS


title: Mel-RefMixB vs. M238 naive

city: Boston, MA

first: Jamie

last: Anastas

state: United States of America

address: 300 Longwood Ave

department: Newborn Medicine

institute: Boston Children's Hospital

description:
M238 naïve
Melanoma cell lines

hyb_protocol: In comparison of expression between Resistant lines and their naive lines, 825 ng each of labeled naive mRNA(cy3 label) and correspond BRAF inhibitor mRNA (cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol The expression of base level from the naïve lines are also performed. 825 ng each of labeled reference mix composed of 47 different melanoma cell lines (Mel-RefMixB,cy3 label) and individual naïve line(cy5 label) were then applied to the microarray chips described above.

scan_protocol: Slides were read on an Agilent G2505C scanner with extended dynamic range Images were quantified using Agilent Feature Extraction Software (version A.9.5.1) for M14 Resistant and M288 Resistant experiments.  The rest are  extracted with version  10.7.3.1.

data_processing:
Agilent Feature Extraction Software (v9.5.1) was used with no background subtraction and Linear/LOWESS normalization. RejectMethod=Interquartile Range, nonuniformity outlier flagging enabled, population outlier flag enabled, error model used to determine to determine significance and well-above-background = most conservation, dye normalization select method = Rank Consistent probes, no spatial detrend method applied.
Agilent Feature Extracted data was imported into Rosetta Resolver version 7.1.1  (Rosetta Inpharmatics LLC, Cambridge, MA). Multiple probes with the same sequence code were combined into a single value using the Rosetta Resolver error-weighted averaging method for combining repeated measures.

source_name: Mel-RefMixB

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following manufacturer's instructions

growth_protocol:
Melanoma cell lines were cultured in RPMI (Life Technologies) supplemented with penicillin/streptomycin and fetal bovine serum (FBS).
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were characterized using mtDNA sequence prior to use

extract_protocol: Total RNA extracted using Qiagen Rneasy Kit following manufacturer's protocol

treatment_protocol: In order to generate additional resistant cell lines, COLO829, SK-MEL-28, M288, and M238 and M14 were treated at their growth-adjusted inhibitory concentration of 50% (IC50) of PLX4032 (BRAFi), or with DMSO as a control. Concentrations of PLX4032 were increased as resistance developed. Cell pellets were generated in order to perform microarray analysis.

tag: cell line (reference)

value: Mel-RefMixB (a mixed reference pool containing equal amounts of 47 melanoma cell lines)

source_name: M238 naïve

tag: cell line (test)

value: M238 naïve


title: DMSO 4h biological replicate 2

source_name: SW480 cells

value: colorectal


title: Mel-RefMixB vs. Colo829 naive

description:
Colo829 naïve
Melanoma cell lines

source_name: Colo829 naïve

value: Colo829 naïve


title: 129 retinal explant cultured for three days with chir99021, biological rep2

city: Kobe

first: Masayo

last: Takahashi

state: Hyogo

address: 2-2-3 Minamimachi, Minatojima, Chu-o-ku

country: Japan

institute: RIKEN CDB

description:
Gene expression data from damaged retina supplemented with GSK3 inhibitor, 129
11062112_129chiron2_MG430_2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430.2.0 Array.

scan_protocol: GeneChips were scanned using the Scanner 3000 7G

data_processing: The data were analyzed with RMA algorithm in the R/Bioconductor (http://www.bioconductor.org/) package

source_name: whole retinal tissue from 129 mouse cultured for three days with chir99021 (15uM)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA, according to the 3' IVT Expression Kit User Manual

growth_protocol: mice were maintained under a 12 h light/dark cycle with access to food and water ad libitum

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

treatment_protocol: Eyes were enucleated from mice, and the neural retina was separated from the cornea, the sclera, the lens, the iris, the ciliary body, and the pigmented epithelium

value: neural retina

tag: protocol

tag: strain

value: 10 weeks old


title: W660

city: Taipei

first: Tu-Hsueh

last: Yeh

state: Taipei

address: 199, Tung-Hwa North Road

department: Neurology

country: Taiwan

institute: Chang Gung Memorial Hospital

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.2.

source_name: Culture of primary meningioma, WHO Grade I

label_protocol: Biotin

growth_protocol: Meningioma samples were acquired from surgical specimens, then were maintained in DMEM with 10% FBS.

extract_protocol: We used 1 ml of TRIZOL for 1-5 million cultured cells, then added 0.2 ml of chloroform after incubation at room temperature for 5 min.

treatment_protocol: None.

value: primary meningioma culture

tag: tumor grade

value: WHO grade I


title: MEKi 16h biological replicate 1

description: Gene expression data from SW480 cells treated with MEK inhibitor for 16h

value: treated with MEK inhibitor for 16h


title: propanil Solvent control A


title: 129 retinal explant cultured for three days with chir99021, biological rep1

description:
Gene expression data from damaged retina supplemented with GSK3 inhibitor, 129
11062111_129chiron1_MG430_2


title: 129 retinal explant cultured for three days, biological rep2

description:
Gene expression data from damaged retina, 129
11062110_129DMSO2_MG430_2

source_name: whole retinal tissue from 129 mouse cultured for three days

value: retinal explant cultured for three days


title: Mel-RefMixB vs. M14 naive

description:
M14 naïve
Melanoma cell lines

source_name: M14 naïve

value: M14 naïve


title: Mel-RefMixB vs. M288 naive

description:
M288 naïve
Melanoma cell lines

source_name: M288 naïve

value: M288 naïve


title: W642


title: parental biological replicate 1


title: M238 naive vs. M238 Resistant

description:
M238 Resistant
Melanoma cell lines

source_name: M238 Resistant

value: M238 Resistant


title: Mel-RefMixB vs. SK-MEL-28 naive

description:
SK-MEL-28 naïve
Melanoma cell lines

source_name: SK-MEL-28 naïve

value: SK-MEL-28 naïve


title: W617

source_name: Culture of primary meningioma, WHO Grade II

value: WHO grade II


title: propanil ISO D

source_name: propanil ISO

value: embryo


title: W603


title: Colo829 naive vs. Colo829 Resistant

description:
Colo829 Resistant
Melanoma cell lines

source_name: Colo829 Resistant

value: Colo829 Resistant


title: propanil ISO A

value: 48 hours post fertilization


title: propanil Solvent control B


title: W611


title: W614


title: 129 retinal explant cultured for three days, biological rep1

description:
Gene expression data from damaged retina, 129
11062109_129DMSO1_MG430_2


title: propanil ISO B


title: M288 naive vs. M288 Resistant

description:
M288 Resistant
Melanoma cell lines

source_name: M288 Resistant

value: M288 Resistant


title: intact retina from 129 mouse, biological rep2

description:
Gene expression data from 129 mouse retina
11062108_129primary2_MG430_2

source_name: whole retina from 129 mouse

value: intact whole retina


title: M14 naive vs. M14 Resistant

description:
M14 Resistant
Melanoma cell lines

source_name: M14 Resistant

value: M14 Resistant


title: W602


title: propanil ISO C


title: intact retina from 129 mouse, biological rep1

description:
Gene expression data from 129 mouse retina
11062107_129primary1_MG430_2

value: neural retina


title: methylparaben EC20 D

source_name: methylparaben EC20


title: propanil Solvent control C

source_name: propanil Solvent control


title: B6 retinal explant cultured for three days with chir99021, biological rep1

description:
Gene expression data from damaged retina supplemented with GSK3 inhibitor, B6
11062105_B6chiron1_MG430_2

source_name: whole retinal tissue from B6 mouse cultured for three days with chir99021 (15uM)

value: 10 weeks old


title: methylparaben EC20 B


title: B6 retinal explant cultured for three days, biological rep2

description:
Gene expression data from damaged retina, B6
11062104_B6DMSO2_MG430_2

source_name: whole retinal tissue from B6 mouse cultured for three days


title: methylparaben EC20 C


title: W559

value: primary meningioma culture


title: W598

value: WHO grade I


title: methylparaben EC20 A


title: W590


title: SK-MEL-28 naive vs. SK-MEL-28 Resistant

description:
SK-MEL-28 Resistant
Melanoma cell lines

source_name: SK-MEL-28 Resistant

value: SK-MEL-28 Resistant


title: intact retina from B6 mouse, biological rep2

description:
Gene expression data from B6 mouse retina
11062102_B6primary2_MG430_2

source_name: whole retina from B6 mouse


title: W557

source_name: Culture of primary meningioma, WHO Grade I


title: W590A

source_name: Culture of primary meningioma, arachnoid

value: arachnoid


title: W508


title: methylparaben EC10 C

source_name: methylparaben EC10


title: intact retina from B6 mouse, biological rep1

description:
Gene expression data from B6 mouse retina
11062101_B6primary1_MG430_2


title: Wildtype mouse 4

city: Guelph

first: marica

last: bakovic

state: ON

address: 50 Stone road east

department: HHNS

country: Canada

institute: university of Guelph

description: Gene  expression data from 2 month old wild type mice liver

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 20 hr at 48C on MoGene 1.1 ST arrays. GeneChips were washed and stained in the Gene Atlas Fluidics Station.

scan_protocol: MoGene 1.1 ST arrays were scanned using the Gene Atlas Imaging Station.

data_processing: The data was analyzed using JMP genomics (SAS, Cary, NC) and normalized using the RMA method. An ANOVA was used to identify differentially expressed genes. A FDR of 0.05 was used to account for multiple testing.

source_name: 2 month old C57BL6 mice

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol using 100 ng total RNA (WT Expression Kit User Manual, 2010, Affymetrix).

extract_protocol: Total RNA was extracted after homogeneisation in TRIzol with a tissue homogenizer and using the Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Liver tissue were collected and snap frozen in liquid N2 , before the RNA extraction.

tag: genetic background

tag: genotype

value: Wild type

value: liver


title: B6 retinal explant cultured for three days, biological rep1

description:
Gene expression data from damaged retina, B6
11062103_B6DMSO1_MG430_2

value: retinal explant cultured for three days


title: Wildtype mouse 3


title: B6 retinal explant cultured for three days with chir99021, biological rep2

description:
Gene expression data from damaged retina supplemented with GSK3 inhibitor, B6
11062106_B6chiron2_MG430_2


title: methylparaben EC10 B


title: W535


title: methylparaben EC10 D


title: W502


title: methylparaben ISO D

source_name: methylparaben ISO


title: BCPAP 10 um Y15 #2

city: Buffalo

first: Biao

state: NY

address: Elm and Carlton streets

department: Center for Personalized Medicine

institute: Roswell Park Cancer Institute

hyb_protocol: The labeled probes were mixed with hybridization reagents and hybridized overnight to the Illumina HumanHT-12 v4 BeadChips.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina BeadArray Reader to measure fluorescence intensity at each probe.

data_processing: BeadChip data files were analyzed with Illumina's GenomeStudio gene expression module (V1.6.0).

source_name: papillary thyroid cancer cell line treated with small molecule FAK inhibitor Y15

label_protocol: Initially, we converted 250-500 ng total RNA to cDNA, followed by in vitro transcription to generate biotin-labeled cRNA (Illumina TotalPrep RNA Amplification Kit, Ambion Inc., Austin, TX).

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen).

value: BCPAP

value: papillary thyroid cancer cell line

tag: treatment duration


title: Knock-out mouse 3

description: Gene expression data from 2 month old Pcyt2+/- mice liver

source_name: 2 month old Pcyt2+/- mice

tag: tissue


title: methylparaben EC10 A

value: embryo


title: Knock-out mouse 4


title: W505

tag: cell type


title: W488A


title: methylparaben ISO B


title: W476


title: Knock-out mouse 1


title: Knock-out mouse 2


title: W449

source_name: Culture of primary meningioma, WHO Grade II

value: WHO grade II


title: K1 10 um Y15 #1


title: W406


title: K1 10 um Y15 #2


title: K1 untreated #1

source_name: untreated papillary thyroid cancer cell line


title: W485M


title: W468


title: methylparaben ISO A

value: 48 hours post fertilization


title: BCPAP 10 um Y15 #1


title: W469


title: BCPAP untreated #2


title: bisphenol A EC20 C

source_name: bisphenol A EC20


title: bisphenol A EC10 B

source_name: bisphenol A EC10


title: M4A


title: bisphenol A EC20 A


title: bisphenol A EC20 D


title: bisphenol A EC10 D


title: bisphenol A EC10 C


title: bisphenol A EC20 B


title: TPC1 10 um Y15 #1


title: HUVEC_PPARD_hypoxia_PPARDagonist

city: Tokyo

first: Tsuyoshi

last: Inoue

address: Hongo

institute: The University of Tokyo

description: 24hrs after PPARD and hypoxia treatment.

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45 degrees CelsiusC, 16 hours). Hybridization was controlled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: The data were analyzed with Robust Multi-array Average (RMA) using GeneSpring 12.5 default analysis settings and global scaling as normalization method.

source_name: HUVECs, PPARD, hypoxia, 24h

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were cultured in EGM2MV medium (Lonza). HUVECs were used within the first 6 passages.

extract_protocol: Total RNAs were extracted using Isogen (Nippon Gene, Osaka, Japan). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix.

treatment_protocol: 1.5x10^5 HUVEC cells were plated in 6 well culture plate, and cultivated for 2 days. They were stimulated with PPARβ/δ ligand (GW501516) at a concentration of 100 nM and/or hypoxia (1% O2) for 24 hours. Same concentration of DMSO was used as a control sample, and as to the oxgen, normoxia was used as a control condition.

value: human umbilical vein cells (HUVECs)

tag: ppard treatment

value: PPARβ/δ agonist

tag: oxygen condition

value: hypoxia


title: bisphenol A EC10 A

tag: age


title: TPC1 untreated #2

tag: treatment


title: BCPAP untreated #1


title: TPC1 untreated #1


title: HUVEC_PPARD_normoxia_PPARDagonist

description: 24hrs after PPARD treatment.

source_name: HUVECs, PPARD, normoxia, 24h

value: normoxia


title: TPC1 10 um Y15 #2


title: K1 untreated #2


title: Mouse 9 W191

city: Columbus

first: Chandan

middle: K

last: Sen

state: Ohio

address: 473W. 12th Avenue,

department: Surgery

institute: Ohio State University Wexner Medical Center

description:
Raw data file: Analysis_Result_ref_together_d14.xls
Quality assessment of the total RNA was performed using Agilent 2100 Bioanalyzer prior to profiling

hyb_protocol: This was then bound to a streptavidin-phycoerythrin conjugate reporter molecule

scan_protocol: The final reading was obtained from a Luminex 200 analyzer

data_processing:
Data processing was performed by the Luminex IS Software Version 2.3
Data Normalization and data analyses were done using the software FlexMax_Beta_A02.
Normalization between samples using normalization microspheres
Example:
1. In each pool, four microspheres are included for the purpose of data normalization. Each normalization microsphere (normalizer hereafter) contains a unique capture probe designed to target specifically a ubiquitously expressed small nucleolar RNA (snoRNA).
2. The net MFI for each normalization microsphere is calculated by subtracting the MFI for the no-template control from the MFI obtained for the normalization microspheres in Sample 1 (2920 for normalization microsphere 1, 10135 for normalization microsphere 2 and so on).
3. One of the samples is chosen as a reference sample (in this example sample 1 is chosen) and all normalization microsphere MFI values in that sample are set to 1.
4. The normalization factor is calculated for each of the remaining samples by dividing normalization microsphere MFI values of the reference sample (in this example, sample 1) by the net MFI value of the same microsphere in next sample (2920/3070 = 0.95 normalization factor for Normalization microsphere 1 in Sample 2 and so on).
5. The normalization factor obtained for Sample 2 is calculated as the average normalization factor of all normalization microspheres in the sample. This normalization factor should be applied to each background-corrected result (i.e. for all the selected microRNA targets) within Sample 2. This process should be repeated for remaining samples.

source_name: skin

label_protocol: 8 µg of RNA was labeled with biotin that was hybridized to LNA-modified capture probes coupled to beads

growth_protocol: Full-thickness excisional wounds were made on the dorsal skin and the tissue were collected at day 2, 7 and 14.

extract_protocol: RNA from murine skin and wound edge tissue sample was extracted using miRVana miRNA Isolation Kit

treatment_protocol: Skin and wound-edge tissues (1 mm away from the wound) were harvested and snap frozen for RNA extraction.

tag: gender

value: Male

value: Wound edge skin

tag: time

value: Day 14


title: Mouse 7 W171


title: Mouse 8 W181


title: flutamide Solvent control D

data_processing:
Data were extracted and processed using Agilent Feature Extraction Software applying default parameters (protocol GE1-v5_95_Feb07, QC metric set GE1_QCMT_Feb07)

This array (AcD) was damaged during handling and was not used in the analysis. For statistical reasons, AcB was included twice to account for removal of AcD.

source_name: flutamide Solvent control


title: flutamide EC20 C

source_name: flutamide EC20


title: flutamide EC20 A


title: bisphenol A ISO D

source_name: bisphenol A ISO


title: bisphenol A ISO B


title: flutamide EC20 D


title: bisphenol A ISO A


title: flutamide EC10 D

source_name: flutamide EC10


title: Mouse 9 C191

value: Control (skin)


title: Mouse 6 W6

description:
Raw data file: Analysis_Result_ref_together_d7.xls
Quality assessment of the total RNA was performed using Agilent 2100 Bioanalyzer prior to profiling

value: Day 7


title: Mouse 7 C171


title: Mouse 8 C181


title: HUVEC_PPARD_normoxia_DMSO

description: 24hrs after DMSO treatment.

source_name: HUVECs, DMSO, normoxia, 24h

value: DMSO


title: bisphenol A ISO C


title: Mouse 6 C6


title: Mouse 4 W2


title: flutamide EC20 B


title: Mouse 5 W4


title: Mouse 5 C4


title: EE2 EC20 D

source_name: EE2 EC20


title: flutamide Solvent control C


title: flutamide EC10 B


title: flutamide Solvent control B


title: flutamide EC10 A


title: flutamide Solvent control A


title: EE2 EC20 C


title: Mouse 3 W16

description:
Raw data file: Analysis_Result_ref_together_d2.xls
Quality assessment of the total RNA was performed using Agilent 2100 Bioanalyzer prior to profiling

value: Day 2


title: Mouse 4 C2


title: EE2 EC20 B


title: Mouse 2 W15


title: Mouse 1 W10


title: Mouse 3 C16


title: EE2 EC20 A


title: Mycelium_DIM5_rep3

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

country: France

institute: INRA

hyb_protocol: Hybridization by PartnerChip Company

scan_protocol: Scanning by PartnerChip Company

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

organism: Plenodomus lingam

source_name: mycelium grown in  vitro in liquid Fries medium

label_protocol: Labelling by PartnerChip Company

growth_protocol: Mycelium was grown during one week in Fries liquid medium.

extract_protocol: RNA extraction was carried out using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs).

tag: genotype/variation

value: transformant silenced for DIM5

value: mycelium

value: 7 days


title: EE2 Solvent control D

source_name: EE2 Solvent control

value: embryo


title: Mycelium_DIM5_rep1


title: HUVEC_PPARD_hypoxia_DMSO

description: 24hrs after DMSO and hypoxia treatment.

source_name: HUVECs, DMSO, hypoxia, 24h


title: EE2 EC10 D

source_name: EE2 EC10


title: Mouse 1 C10


title: EE2 EC10 C


title: EE2 EC10 B


title: Mycelium_HP1_rep3

value: transformant silenced for HP1


title: EE2 EC10 A

value: 48 hours post fertilization


title: Mouse 2 C15


title: Yakut 6

status: Public on Mar 05 2014

type: genomic

first: Alexia

last: Cardona

address: Fitzwilliam Street

department: Archaeology and Anthropology

country: United Kingdom

institute: University of Camrbidge

hyb_protocol: Followed Illumina standard protocol

scan_protocol: Followed Illumina standard protocol

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
The processed (CardonaMatrixProcessed.txt) and raw (CardonaX_Y.txt) data files are provided as Series supplementary file.

molecule: genomic DNA

source_name: Siberian sample_Yakut

label_protocol: Followed Illumina standard protocol

extract_protocol: phenol/choloroform extraction method

value: female

tag: sampling location

value: Chirinda

value: blood


title: Yakut 7

value: male

value: Essey


title: Yakut 8

value: Ekonda


title: Yakut 9


title: Yakut 5

value: Nyurba, Yakut Republic


title: methylparaben ISO C

source_name: methylparaben ISO


title: Mycelium_DIM5_rep2


title: Mycelium_HP1_rep2


title: flutamide EC10 C


title: Yakut 43


title: Yakut 44


title: Mycelium_WT_rep3

value: wild type


title: Yakut 4


title: EE2 Solvent control B


title: Yakut 36

value: Olenek, Yakut Republic


title: Yakut 38

value: Ust-Alan


title: Yakut 21


title: Mycelium_WT_rep1


title: Yakut 32


title: Yakut 2


title: Yakut 27


title: Yakut 3


title: Mycelium_HP1_rep1


title: Mycelium_WT_rep2


title: EE2 Solvent control A


title: Yakut 18

value: Yakutsk


title: Yakut 17

value: Vilyuy, Yakut Republic


title: Yakut 131

value: Seymchan


title: Yakut 53

value: Nakkano, Irkutsk Region


title: Yakut 13


title: Vietnamese 9

source_name: Southeast Asian sample_Vietnamese

value: Singapore

value: saliva


title: EE2 Solvent control C

value: embryo

value: 48 hours post fertilization


title: Vietnamese 6


title: Vietnamese 5

value: female


title: Vietnamese 35


title: Vietnamese 36


title: Vietnamese 33


title: Vietnamese 34


title: Vietnamese 30


title: Vietnamese 12


title: Vietnamese 29


title: Vietnamese 27


title: Vietnamese 26


title: Vietnamese 28


title: Vietnamese 24


title: Vietnamese 11


title: Teleut 5890

source_name: Siberian sample_Teleut

value: Novokuznetsk

value: blood


title: Teleut 5892

value: male


title: Vietnamese 10


title: Vietnamese 8


title: Teleut 5886


title: Teleut 5887


title: Teleut 5882


title: Teleut 5885


title: Teleut 5881


title: Teleut 5888


title: Shor 600

source_name: Siberian sample_Shor

value: Orton


title: Teleut 32


title: Shor 590


title: Shor 591


title: Vietnamese 32


title: Shor 541


title: Shor 535


title: Teleut 5891


title: Shor 4B


title: Shor 470


title: Shor 477


title: Shor 437


title: Teleut 5889


title: Shor 430


title: Shor 516


title: Shor 526


title: Shor 3B

value: Tashtagol


title: Shor 41B


title: Shor 25B


title: Shor 18B


title: Shor 1B


title: Shor 27B


title: Shor 38B


title: Shor 28B


title: Teleut 5883


title: Shor 10B


title: Koryak G55

source_name: Siberian sample_Koryak

value: Evensk, Severo-Evensk District


title: Shor 21B


title: Koryak G4


title: Shor 586


title: Koryak G3


title: Koryak G294


title: Koryak G233

value: Gizhiga, Severo-Evensk District


title: Koryak G152


title: Koryak G11


title: Koryak 127


title: Koryak G13


title: Koryak 129


title: Koryak 130


title: Shor 17B


title: Koryak 126


title: Koryak 124


title: Koryak 120

value: Topolovka, Severo-Evensk District


title: Koryak 117

value: Paren, Severo-Evensk District


title: Koryak 121


title: Koryak 119


title: Even G7

source_name: Siberian sample_Even


title: Koryak 115


title: Koryak 116


title: Koryak G38


title: Even G353


title: Koryak G14


title: Even G330


title: Even G232


title: Even G329


title: Even G224

value: Garmanda, Severo-Evensk District


title: Even G69


title: Koryak 128


title: Even G223


title: Koryak 122


title: Even 32


title: Even G157


title: Even 16

value: Gadlya, Ola District


title: Even 48


title: Even 31

value: Arman, Ola District


title: Even G200


title: Even 47


title: Even 22


title: Even 49

value: Rossoha, Srednekan District


title: Even G214


title: Evenk 56

source_name: Siberian sample_Evenk

value: Tura


title: Even G216


title: Evenk 55

value: Kislokan


title: Evenk 52

value: Nakanno, Irkutsk Region


title: Evenk 42

value: Surinda


title: Even 29


title: Even 18


title: Even 21


title: Evenk 62

value: female

value: Baykit


title: Evenk 40

value: Nidym

value: blood


title: Even 30

value: male


title: Evenk 54


title: Evenk 51

value: Poligus


title: Evenk 46

value: Tutonchany


title: Evenk 41

value: Kuyumba


title: Koryak G1

value: Evensk, Severo-Evensk District


title: Evenk 29

value: Erbogachen, Irkutsk Region


title: Evenk 20


title: Evenk 34


title: Evenk 23

value: Ekonda


title: Evenk 31


title: Evenk 28


title: Eskimo 9

source_name: Siberian sample_Eskimo

value: Novoe Chaplino, Chukotka


title: Evenk 12

value: Strelka-Chunya


title: Evenk 26


title: Evenk 16

value: Chirinda


title: Eskimo 8


title: Eskimo 4


title: Eskimo 6


title: Evenk 10

value: Irokan, Amur Region


title: Evenk 1

value: Kuyumba, Baikit District


title: Eskimo 21


title: Eskimo 7


title: Eskimo 2


title: Eskimo 5


title: Eskimo 20


title: Eskimo 19B


title: Eskimo 18


title: Evenk 14

value: Essey


title: Evenk 22

value: female

value: Tura


title: Eskimo 16


title: Eskimo 17B


title: Eskimo 14


title: Eskimo 15


title: Eskimo 10


title: Chukchi 3

source_name: Siberian sample_Chukchi

value: Anadyr, Chukotka


title: Chukchi 2

value: blood


title: Chukchi 4

value: male


title: Eskimo 11


title: Chukchi 15


title: Chukchi 5


title: Chukchi 10


title: Chukchi 11


title: Chukchi 6


title: Chukchi 9


title: Chukchi 13'


title: Buryat 640

source_name: Siberian sample_Buryat

value: Buryatia


title: Eskimo 1


title: Buryat 636


title: Buryat 623


title: Buryat 621


title: Buryat 578


title: Buryat 639


title: Buryat 561


title: Yakut 61


title: Buryat 504


title: Buryat 523


title: Buryat 412


title: Buryat 530


title: Buryat 515


title: Koryak 123


title: Chukchi 14


title: Buryat 398


title: Buryat 383


title: Even 23

value: Gadlya, Ola District


title: Buryat 355


title: Buryat 350


title: Buryat 324


title: Buryat 336


title: Buryat 301


title: Buryat 318


title: Buryat 571


title: Altain 204

source_name: Siberian sample_Altain

value: Kaysyn


title: Altain 202


title: Altain 197


title: Altain 194


title: Altain 187


title: Altain 181


title: Buryat 406


title: Altain 179


title: Altain 175


title: Buryat 361


title: Altain 173


title: Altain 170


title: Altain 180


title: Altain 174


title: Buryat 618


title: lymph node negative breast cancer 73

city: Stavanger

first: Kristin

last: Jonsdottir

address: Torgveien 25b

department: Dep. of Pathology

country: Norway

institute: Stavanger university Hospital

description:
Sample 73
replicate 73

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Human breast cancer

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

extract_protocol: RNA was extracted with MirVANA total RNA isolation kit (Ambion/Applied Biosystems) according to the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: breast cancer tissue

tag: follow-up (months)

value: no distant metastasis

value: Less then 2 cm

tag: nottgrade

value: Grade 2

value: MAI = 10 or more

value: PPH3 = 13 or more

value: HER2 negative

tag: er

value: ER positive


title: lymph node negative breast cancer 93

description:
Sample 93
replicate 93

value: distant metastasis

value: MAI under 10

value: PPH3 under 13

value: HER2 positive


title: lymph node negative breast cancer 78

description:
Sample 78
replicate 78


title: lymph node negative breast cancer 91

description:
Sample 91
replicate 91

value: 2 cm or more

value: Grade 3

value: ER negative


title: lymph node negative breast cancer 95

description:
Sample 95
replicate 95


title: lymph node negative breast cancer 92

description:
Sample 92
replicate 92

value: Grade 1


title: lymph node negative breast cancer 86

description:
Sample 86
replicate 86


title: lymph node negative breast cancer 89

description:
Sample 89
replicate 89


title: lymph node negative breast cancer 90

description:
Sample 90
replicate 90


title: lymph node negative breast cancer 80

description:
Sample 80
replicate 80


title: Chukchi 8

value: female

value: Anadyr, Chukotka

value: blood


title: lymph node negative breast cancer 72

description:
Sample 72
replicate 72

value: breast cancer tissue

value: no distant metastasis

value: Less then 2 cm


title: lymph node negative breast cancer 76

description:
Sample 76
replicate 76

value: Grade 2


title: lymph node negative breast cancer 74

description:
Sample 74
replicate 74

value: MAI = 10 or more

value: PPH3 = 13 or more

value: HER2 negative


title: lymph node negative breast cancer 82

description:
Sample 82
replicate 82

value: MAI under 10

value: ER positive


title: lymph node negative breast cancer 94

description:
Sample 94
replicate 94

value: PPH3 under 13


title: lymph node negative breast cancer 96

description:
Sample 96
replicate 96

value: 2 cm or more


title: lymph node negative breast cancer 84

description:
Sample 84
replicate 84


title: lymph node negative breast cancer 88

description:
Sample 88
replicate 88

value: distant metastasis


title: lymph node negative breast cancer 83

description:
Sample 83
replicate 83

value: HER2 positive


title: lymph node negative breast cancer 79

description:
Sample 79
replicate 79

value: Grade 3

value: ER negative


title: lymph node negative breast cancer 77

description:
Sample 77
replicate 77


title: lymph node negative breast cancer 75

description:
Sample 75
replicate 75

value: Grade 1


title: Eskimo 3

value: male

value: Novoe Chaplino, Chukotka

value: blood


title: lymph node negative breast cancer 81

description:
Sample 81
replicate 81

value: breast cancer tissue

value: no distant metastasis


title: Yakut 11

value: Essey


title: lymph node negative breast cancer 71

description:
Sample 71
replicate 71

value: Grade 2


title: lymph node negative breast cancer 69

description:
Sample 69
replicate 69

value: Less then 2 cm

value: MAI = 10 or more

value: PPH3 = 13 or more


title: lymph node negative breast cancer 67

description:
Sample 67
replicate 67

value: HER2 negative


title: lymph node negative breast cancer 57

description:
Sample 57
replicate 57


title: lymph node negative breast cancer 70

description:
Sample 70
replicate 70

value: 2 cm or more

value: MAI under 10

value: PPH3 under 13

value: ER positive


title: lymph node negative breast cancer 63

description:
Sample 63
replicate 63

value: distant metastasis

value: Grade 3


title: lymph node negative breast cancer 55

description:
Sample 55
replicate 55

value: HER2 positive


title: lymph node negative breast cancer 59

description:
Sample 59
replicate 59


title: lymph node negative breast cancer 64

description:
Sample 64
replicate 64

value: ER negative


title: lymph node negative breast cancer 66

description:
Sample 66
replicate 66


title: Evenk 35

value: female

value: Nidym

value: blood


title: lymph node negative breast cancer 61

description:
Sample 61
replicate 61

value: breast cancer tissue

value: no distant metastasis


title: lymph node negative breast cancer 65

description:
Sample 65
replicate 65

value: Less then 2 cm

value: Grade 1


title: lymph node negative breast cancer 68

description:
Sample 68
replicate 68

value: PPH3 = 13 or more


title: lymph node negative breast cancer 56

description:
Sample 56
replicate 56

value: Grade 2

value: HER2 negative


title: lymph node negative breast cancer 53

description:
Sample 53
replicate 53

value: 2 cm or more

value: MAI under 10


title: lymph node negative breast cancer 51

description:
Sample 51
replicate 51

value: PPH3 under 13

value: ER positive


title: Chukchi 1

value: male

value: Anadyr, Chukotka


title: lymph node negative breast cancer 49

description:
Sample 49
replicate 49


title: Chukchi 12


title: lymph node negative breast cancer 58

description:
Sample 58
replicate 58

value: Grade 3

value: MAI = 10 or more

value: ER negative


title: lymph node negative breast cancer 62

description:
Sample 62
replicate 62

value: distant metastasis


title: lymph node negative breast cancer 60

description:
Sample 60
replicate 60

value: breast cancer tissue

value: HER2 positive


title: lymph node negative breast cancer 50

description:
Sample 50
replicate 50

value: no distant metastasis

value: Less then 2 cm


title: lymph node negative breast cancer 48

description:
Sample 48
replicate 48

value: PPH3 = 13 or more


title: lymph node negative breast cancer 87

description:
Sample 87
replicate 87

value: Grade 2


title: lymph node negative breast cancer 52

description:
Sample 52
replicate 52


title: lymph node negative breast cancer 54

description:
Sample 54
replicate 54

value: HER2 negative


title: lymph node negative breast cancer 46

description:
Sample 46
replicate 46

value: Grade 1


title: lymph node negative breast cancer 47

description:
Sample 47
replicate 47

value: 2 cm or more

value: MAI under 10


title: lymph node negative breast cancer 44

description:
Sample 44
replicate 44

value: PPH3 under 13

value: ER positive


title: lymph node negative breast cancer 41

description:
Sample 41
replicate 41


title: lymph node negative breast cancer 43

description:
Sample 43
replicate 43


title: lymph node negative breast cancer 45

description:
Sample 45
replicate 45


title: lymph node negative breast cancer 29

description:
Sample 29
replicate 29


title: lymph node negative breast cancer 42

description:
Sample 42
replicate 42


title: lymph node negative breast cancer 40

description:
Sample 40
replicate 40


title: lymph node negative breast cancer 39

description:
Sample 39
replicate 39


title: lymph node negative breast cancer 38

description:
Sample 38
replicate 38


title: lymph node negative breast cancer 35

description:
Sample 35
replicate 35


title: lymph node negative breast cancer 37

description:
Sample 37
replicate 37


title: lymph node negative breast cancer 33

description:
Sample 33
replicate 33


title: lymph node negative breast cancer 31

description:
Sample 31
replicate 31


title: lymph node negative breast cancer 27

description:
Sample 27
replicate 27


title: lymph node negative breast cancer 22

description:
Sample 22
replicate 22


title: lymph node negative breast cancer 23

description:
Sample 23
replicate 23


title: lymph node negative breast cancer 32

description:
Sample 32
replicate 32


title: lymph node negative breast cancer 21

description:
Sample 21
replicate 21


title: lymph node negative breast cancer 36

description:
Sample 36
replicate 36


title: lymph node negative breast cancer 30

description:
Sample 30
replicate 30


title: lymph node negative breast cancer 28

description:
Sample 28
replicate 28


title: lymph node negative breast cancer 25

description:
Sample 25
replicate 25


title: lymph node negative breast cancer 34

description:
Sample 34
replicate 34


title: lymph node negative breast cancer 20

description:
Sample 20
replicate 20


title: lymph node negative breast cancer 26

description:
Sample 26
replicate 26


title: lymph node negative breast cancer 24

description:
Sample 24
replicate 24


title: lymph node negative breast cancer 19

description:
Sample 19
replicate 19


title: siGFP transfected SBC3

first: Hiroshi

last: Ono

address: 3-8-31 Ariake, Koto-ku

department: Pathology

institute: The Cancer Institute of JFCR

description: Gene expression after siGFP transfected

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Sure Print G3 Human GE 8x60k Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven (10rpm). 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 by pulling out slowly (5-10sec).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Agilent G3_GX_1 color) (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_10 10_Sep10 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: siGFP transfected SBC-3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.05 ug RNA using the Low Input Quick Amp Labeling kit (One-Color) (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy mini kit Plus (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: SCLC cell line SBC-3


title: lymph node negative breast cancer 16

description:
Sample 16
replicate 16


title: lymph node negative breast cancer 14

description:
Sample 14
replicate 14


title: lymph node negative breast cancer 18

description:
Sample 18
replicate 18


title: lymph node negative breast cancer 11

description:
Sample 11
replicate 11


title: lymph node negative breast cancer 10

description:
Sample 10
replicate 10


title: lymph node negative breast cancer 15

description:
Sample 15
replicate 15

value: Grade 3


title: lymph node negative breast cancer 9

description:
Sample 9
replicate 9

value: MAI = 10 or more


title: #1siHOTAIR transfected SBC3

description: Gene expression after siHOTAIR transfected

source_name: siHOTAIR transfected SBC-3


title: lymph node negative breast cancer 13

description:
Sample 13
replicate 13


title: HIV/TB co-infected patient 20

city: Philadelphia

first: Louise

middle: C

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description:
HIV/TB co-infection
KAA0ZQ5C-11_19-Jan-2010

data_processing: Gene expression levels and detection p-values were exported using Illumina's GenomeStudioV2010.1.  Raw data were quantile normalized and then filtered to remove non-informative probes either expressed at background level or showing little variation among samples (maximum fold change < 1.2).

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared using the Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina arrays

extract_protocol: Total RNA was isolated using the modified protocol of Sigma Aldrich Tri-reagent.

value: Male

tag: sample type

value: PBMC

tag: disease state

value: HIV/TB


title: lymph node negative breast cancer 3

description:
Sample 3
replicate 3

value: breast cancer tissue


title: HIV/TB co-infected patient 18

description:
HIV/TB co-infection
KAA0Z0GV-10_18-Nov-2009

value: Female


title: lymph node negative breast cancer 8

description:
Sample 8
replicate 8

value: no distant metastasis

value: HER2 positive


title: lymph node negative breast cancer 12

description:
Sample 12
replicate 12

value: Less then 2 cm

value: Grade 2


title: 177Lu_Medulla_0_MBq_#3

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

country: Sweden

institute: University of Gothenburg

data_processing: The data were normalized using quantile normalization with BASE

source_name: Mouse kidney medulla, 0 MBq, 24h

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

tag: strain

value: Balb/c

value: Mouse kidney medulla

tag: injected activity

value: 0 MBq

tag: nuclide


title: 177Lu_Medulla_0_MBq_#2

tag: tissue


title: lymph node negative breast cancer 6

description:
Sample 6
replicate 6

value: PPH3 = 13 or more


title: lymph node negative breast cancer 5

description:
Sample 5
replicate 5

value: MAI under 10

value: HER2 negative

value: ER positive


title: HIV/TB co-infected patient 21

description:
HIV/TB co-infection
EAA0ZNH3-13_13-Jan-2010


title: lymph node negative breast cancer 2

description:
Sample 2
replicate 2

value: Grade 3

value: MAI = 10 or more

value: ER negative


title: lymph node negative breast cancer 1

description:
Sample 1
replicate 1

value: distant metastasis

value: 2 cm or more

value: PPH3 under 13


title: lymph node negative breast cancer 4

description:
Sample 4
replicate 4

value: breast cancer tissue

value: no distant metastasis


title: 177Lu_Medulla_1.3_MBq_#3

source_name: Mouse kidney medulla, 1.3 MBq, 24h

value: 1.3 MBq


title: lymph node negative breast cancer 7

description:
Sample 7
replicate 7

value: Less then 2 cm

value: Grade 2


title: 177Lu_Medulla_1.3_MBq_#2

value: Balb/c

value: Mouse kidney medulla


title: 177Lu_Medulla_0_MBq_#1

value: 0 MBq


title: HIV/TB co-infected patient 17

description:
HIV/TB co-infection
JAA1063Y-11_03-Mar-2010

value: Female

value: PBMC

value: HIV/TB


title: HIV/TB co-infected patient 15

description:
HIV/TB co-infection
JAA0Q3QZ-15_24-Apr-2008


title: HIV/TB co-infected patient 14

description:
HIV/TB co-infection
HAA0Z4Z0-19_26-Nov-2009


title: HIV/TB co-infected patient 16

description:
HIV/TB co-infection
JAA103SD-11_25-Feb-2010


title: 177Lu_Medulla_1.3_MBq_#1


title: HIV/TB co-infected patient 11

description:
HIV/TB co-infection
FAA0ZVHT-14_02-Feb-2010

value: Male


title: HIV/TB co-infected patient 13

description:
HIV/TB co-infection
HAA0QL3W-13_29-May-2008


title: HIV/TB co-infected patient 12

description:
HIV/TB co-infection
GAA0S8NL-11_30-Sep-2008


title: HIV/TB co-infected patient 10

description:
HIV/TB co-infection
FAA0Z9CZ-10_03-Dec-2009


title: 177Lu_Medulla_3.6_MBq_#1

source_name: Mouse kidney medulla, 3.6 MBq, 24h

value: 3.6 MBq


title: HIV/TB co-infected patient 9

description:
HIV/TB co-infection
DAA0Z4CR-10_25-Nov-2009


title: 177Lu_Medulla_14_MBq_#3

source_name: Mouse kidney medulla, 14 MBq, 24h

value: 14 MBq


title: HIV/TB co-infected patient 19

description:
HIV/TB co-infection
KAA0ZMKX-10_11-Jan-2010


title: 177Lu_Medulla_45_MBq_#2

source_name: Mouse kidney medulla, 45 MBq, 24h

value: 45 MBq


title: HIV/TB co-infected patient 6

description:
HIV/TB co-infection
BAA0ZC4J-13_07-Dec-2009


title: HIV/TB co-infected patient 8

description:
HIV/TB co-infection
CAA0ZN6L-12_13-Jan-2010


title: 177Lu_Medulla_3.6_MBq_#3


title: HIV/TB co-infected patient 4

description:
HIV/TB co-infection
AAA0ZSJX-10_26-Jan-2010


title: 177Lu_Medulla_14_MBq_#1


title: 177Lu_Medulla_45_MBq_#3


title: 177Lu_Medulla_140_MBq_#3

source_name: Mouse kidney medulla, 140 MBq, 24h

value: 140 MBq


title: HIV/TB co-infected patient 5

description:
HIV/TB co-infection
BAA0YXVB-12_12-Nov-2009


title: 177Lu_Medulla_140_MBq_#2


title: 177Lu_Medulla_140_MBq_#1


title: 177Lu_Medulla_45_MBq_#1


title: 177Lu_Medulla_3.6_MBq_#2


title: HIV/TB co-infected patient 7

description:
HIV/TB co-infection
BAA0ZXTF-11_08-Feb-2010


title: HIV/TB co-infected patient 3

description:
HIV/TB co-infection
AAA0Z4D1-15_25-Nov-2009


title: HIV/TB co-infected patient 2

description:
HIV/TB co-infection
AAA0RWJ0-14_02-Sep-2008


title: HIV/TB co-infected patient 1

description:
HIV/TB co-infection
AAA0KHPN-10_14-Jun-2007


title: 177Lu_Cortex_0_MBq_#3

source_name: Mouse kidney cortex, 0 MBq, 24h

value: Mouse kidney cortex


title: HIV infected patient 20

description:
HIV
AAA0WVKX-11_04-Jun-2009

value: HIV only


title: 177Lu_Cortex_0_MBq_#2


title: 177Lu_Cortex_0_MBq_#1


title: HIV infected patient 17

description:
HIV
JAA0W223-10_16-Apr-2009


title: HIV infected patient 19

description:
HIV
KAA0Q3QH-14_24-Apr-2008


title: HIV infected patient 18

description:
HIV
KAA0PBTZ-17_06-Mar-2008


title: HIV infected patient 11

description:
HIV
DAA0V9RP-16_25-Feb-2009


title: 177Lu_Cortex_3.6_MBq_#3

source_name: Mouse kidney cortex, 3.6 MBq, 24h


title: 177Lu_Cortex_1.3_MBq_#2

source_name: Mouse kidney cortex, 1.3 MBq, 24h


title: HIV infected patient 12

description:
HIV
DAA0VD27-11_04-Mar-2009


title: HIV infected patient 21

description:
HIV
EAA0VKQY-17_18-Mar-2009


title: 177Lu_Cortex_1.3_MBq_#3


title: 177Lu_Cortex_45_MBq_#3

source_name: Mouse kidney cortex, 45 MBq, 24h


title: 177Lu_Cortex_14_MBq_#2

source_name: Mouse kidney cortex, 14 MBq, 24h


title: HIV infected patient 10

description:
HIV
DAA0PFCT-11_17-Jan-2008


title: HIV infected patient 16

description:
HIV
JAA0P0DQ-11_15-Feb-2008


title: HIV infected patient 14

description:
HIV
HAA0W3B8-14_20-Apr-2009


title: HIV infected patient 22

description:
HIV
JAA0WVMP-13_04-Jun-2009


title: HIV infected patient 13

description:
HIV
FAA0W22D-13_16-Apr-2009


title: 177Lu_Cortex_1.3_MBq_#1


title: 177Lu_Cortex_3.6_MBq_#1


title: 177Lu_Cortex_3.6_MBq_#2


title: 177Lu_Cortex_45_MBq_#1


title: HIV infected patient 9

description:
HIV
CAA0W4LT-13_23-Apr-2009


title: 177Lu_Cortex_140_MBq_#3

source_name: Mouse kidney cortex, 140 MBq, 24h


title: HIV infected patient 15

description:
HIV
HAA0W3R9-13_21-Apr-2009


title: 177Lu_Cortex_14_MBq_#1


title: 177Lu_Cortex_14_MBq_#3


title: 177Lu_Cortex_45_MBq_#2


title: 177Lu_Cortex_140_MBq_#2


title: HIV infected patient 5

description:
HIV
BAA0W69B-10_29-Apr-2009


title: HIV infected patient 6

description:
HIV
BAA0WVPG-10_04-Jun-2009


title: HIV infected patient 3

description:
HIV
BAA0V9SR-15_25-Feb-2009


title: HIV infected patient 4

description:
HIV
BAA0W3BM-11_20-Apr-2009


title: HIV infected patient 2_2

description:
HIV
AAA0W22R-14_16-Apr-2009


title: HIV infected patient 8

description:
HIV
CAA0W4LJ-15_23-Apr-2009


title: 177Lu_Cortex_140_MBq_#1


title: HIV infected patient 2_1

description:
HIV
AAA0W22R-11_16-Apr-2009


title: HIV infected patient 1

description:
HIV
AAA0VKQN-12_18-Mar-2009


title: HIV infected patient 7

description:
HIV
CAA0Q3CK-13_24-Apr-2008


title: plant_treated_with_combined_stress_rep3

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of plants treated with 150mM salt, 200mM mannitol and 35°C heat, simultaneously

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Arabidopsis thaliana

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt (16hrs), 200mM mannitol (16hrs), 35°C heat (4hrs), replicate3

label_protocol: 1 µg of total RNA was used for labeling procedure using QickAmp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) agar media for first 10 days and in soil for next 10 days in 16hr light / 8hr dark cycle in 23 Celsius degree before stress treatment

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: Soil-grown plants were treated with 150mM, 300mM  of salt and/or 200mM, 400mM of mannitol for 16 hrs by feeding the solution and/or 35°C heat for 4 hrs by placing plants in incubator.

tag: ecotype

value: above-ground parts

tag: genotype

value: wild type

value: 150mM salt, 16hrs + 200mM mannitol, 16hrs + 35°C heat, 4hrs


title: plant_treated_with_combined_stress_rep1

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt (16hrs), 200mM mannitol (16hrs), 35°C heat (4hrs), replicate1

tag: age

tag: treatment


title: plant_treated_with_35°C_heat_rep1

description: Gene expression of plants treated with 35°C heat

source_name: 20d of above-ground parts, Arabidopsis thaliana, 35°C heat, 4hrs, replicate1

value: 35°C heat, 4hrs


title: plant_treated_with_35°C_heat_rep3

source_name: 20d of above-ground parts, Arabidopsis thaliana, 35°C heat, 4hrs, replicate3


title: plant_treated_with_combined_stress_rep2

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt (16hrs), 200mM mannitol (16hrs), 35°C heat (4hrs), replicate2


title: Analysis 8: Normal - Biological replicate 3

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_2 sample in analysis 5, 6, 7

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4858A-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

source_name: Normal - Benign uvula, tonsil

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

extract_protocol: Total RNA was isolated from fresh frozen tumor samples or normal tissue using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).

tag: gender

tag: race

value: European American


title: Analysis 8: Normal - Biological replicate 1

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_2 sample in analysis 5, 6, 7


title: Analysis 8: Normal - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_4 sample in analysis 5, 6, 7


title: palnt_treated_with_400mM_mannitol_rep1

description: Gene expression of plants treated with 400mM mannitol

source_name: 20d of above-ground parts, Arabidopsis thaliana, 400mM mannitol, 16hrs, replicate1

value: 400mM mannitol, 16hrs


title: Analysis 7: HPV inactive OPC - Biological replicate 4

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_2_1 sample in analysis 1, 3, 4

source_name: HPV Inactive - Oropharyngeal squamous cell carcinoma


title: palnt_treated_with_200mM_mannitol_rep2

description: Gene expression of plants treated with 200mM mannitol

source_name: 20d of above-ground parts, Arabidopsis thaliana, 200mM mannitol, 16hrs, replicate2

value: 200mM mannitol, 16hrs


title: Analysis 7: HPV inactive OPC - Biological replicate 1

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_1_4 sample in analysis 1, 3, 4

value: Female


title: palnt_treated_with_200mM_mannitol_rep1

source_name: 20d of above-ground parts, Arabidopsis thaliana, 200mM mannitol, 16hrs, replicate1


title: palnt_treated_with_150mM_salt_rep2

description: Gene expression of plants treated with 150mM salt

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt, 16hrs, replicate2

value: 150mM salt, 16hrs


title: palnt_treated_with_200mM_mannitol_rep3

source_name: 20d of above-ground parts, Arabidopsis thaliana, 200mM mannitol, 16hrs, replicate3


title: Analysis 7: HPV inactive OPC - Biological replicate 3

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_4 sample in analysis 1, 3, 4


title: palnt_treated_with_400mM_mannitol_rep3

source_name: 20d of above-ground parts, Arabidopsis thaliana, 400mM mannitol, 16hrs, replicate3


title: palnt_treated_with_400mM_mannitol_rep2

source_name: 20d of above-ground parts, Arabidopsis thaliana, 400mM mannitol, 16hrs, replicate2


title: Analysis 7: HPV inactive OPC - Biological replicate 2

description: re-analysis of US10130359_253949410164_S01_GE1_107_Sep09_1_2 sample in analysis 1, 3, 4


title: plant_treated_with_35°C_heat_rep2

source_name: 20d of above-ground parts, Arabidopsis thaliana, 35°C heat, 4hrs, replicate2


title: palnt_treated_with_300mM_salt_rep3

description: Gene expression of plants treated with 300mM salt

source_name: 20d of above-ground parts, Arabidopsis thaliana, 300mM salt, 16hrs, replicate3

value: 300mM salt, 16hrs


title: palnt_treated_with_150mM_salt_rep1

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt, 16hrs, replicate1


title: Analysis 8: Normal - Biological replicate 2

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_1 sample in analysis 5, 6, 7

value: Male


title: Analysis 6: Normal - Biological replicate 3

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_2 sample in analysis 5, 7, 8


title: palnt_treated_with_150mM_salt_rep3

source_name: 20d of above-ground parts, Arabidopsis thaliana, 150mM salt, 16hrs, replicate3


title: Analysis 6: Normal - Biological replicate 1

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_2 sample in analysis 5, 7, 8


title: palnt_treated_with_300mM_salt_rep1

source_name: 20d of above-ground parts, Arabidopsis thaliana, 300mM salt, 16hrs, replicate1


title: Analysis 6: Normal - Biological replicate 2

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_1 sample in analysis 5, 7, 8


title: control_plant_rep1

description: Gene expression of control plants with no treatment

source_name: 20d of above-ground parts, Arabidopsis thaliana, no treatment, replicate1


title: control_plant_rep3

source_name: 20d of above-ground parts, Arabidopsis thaliana, no treatment, replicate3


title: 177Lu_Medulla_14_MBq_#2

source_name: Mouse kidney medulla, 14 MBq, 24h

value: Balb/c

value: Mouse kidney medulla


title: palnt_treated_with_300mM_salt_rep2

source_name: 20d of above-ground parts, Arabidopsis thaliana, 300mM salt, 16hrs, replicate2


title: N_MC_19_5

city: Cincinnati

first: Michael

last: Barnes

state: OH

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning

data_processing: Data were imported into GS11 with quantile normalization and baseline transformation to median of all samples

label: Biotin

source_name: Cell Line

label_protocol: RNA was labeled and hybridized to an Affymetrix array using standard protocols

growth_protocol: ES cell lines were maintained in RPMI-1640 medium and supplemented with 15% fetal bovine serum.

extract_protocol: RNA was extracted using Trizol and RNAeasy Mini Kit.

treatment_protocol: Cell lines were treated with 5-Aza-2'-deoxycytodine as indicated in manuscript.

value: Treated


title: N_MC_6_5


title: N_MC_19_0

value: Untreated


title: control_plant_rep2

source_name: 20d of above-ground parts, Arabidopsis thaliana, no treatment, replicate2


title: RD_3_7


title: RD_3_0


title: 71 A4  8-11-09-5


title: 71 A4  8-5-09-5


title: 466_19_0


title: 71 A4  8-3-09-0


title: 466_6_5


title: 71 A4  8-11-09-0


title: 4573 A4  8-5-09-5


title: 466_19_5


title: N_MC_6_0


title: 466_6_0


title: 71 A4  8-5-09-0


title: Analysis 5: Normal - Biological replicate 3

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_4 sample in analysis 6, 7, 8

source_name: Normal - benign uvula, tonsil

extract_protocol: Total RNA was isolated from fresh frozen tumor samples using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).


title: 4573 A4  8-5-09-0


title: Analysis 5: Normal - Biological replicate 4

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_2_1 sample in analysis 6, 7, 8


title: 71 A4  8-3-09-5


title: Analysis 5: Normal - Biological replicate 1

description: re-analysis of US10130359_253949411321_S01_GE1_107_Sep09_1_2 sample in analysis 6, 7, 8


title: 4573 A4  8-11-09-0


title: 4573 A4  8-11-09-5


title: 4573 A4  8-1-09-0


title: Analysis 5: Normal - Biological replicate 2

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_2 sample in analysis 6, 7, 8


title: CBA/Ca PBS-treated, 6h Tp, replicate 4

city: Leicester

first: Peter

middle: W

last: Andrew

address: University Rd

department: Infection, Immunity and Inflammation

institute: University of Leicester

description: raplicate 4

data_processing: The data were normalised using quantile normalisation with IlluminaGenomeStudio and analysed in ArrayTrack

source_name: mouse lung

extract_protocol: Lung were extracted, cut and immediatelly immersed in RNA-later. RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: CBA/CaOlaHsd

value: 9 weeks

value: female

value: lung


title: Analysis 6: Normal - Biological replicate 4

description: re-analysis of US10130359_253949411322_S01_GE1_107_Sep09_2_4 sample in analysis 5, 7, 8

source_name: Normal - Benign uvula, tonsil


title: CBA/Ca PBS-treated, 6h Tp, replicate 6

description: raplicate 6


title: CBA/Ca PBS-treated, 6h Tp, replicate 1

description: raplicate 1


title: CBA/Ca PBS-treated, 6h Tp, replicate 2

description: raplicate 2


title: CBA/Ca PBS-treated, 6h Tp, replicate 5

description: raplicate 5


title: CBA/Ca 6h post pneumococcal infection, replicate 5

description: raplicate 5


title: CBA/Ca 6h post pneumococcal infection, replicate 4

description: raplicate 4


title: CBA/Ca 6h post pneumococcal infection, replicate 3

description: raplicate 3


title: 4573 A4  8-1-09-5


title: CBA/Ca PBS-treated, 6h Tp, replicate 3

description: raplicate 3


title: BALB/c PBS-treated, 6h Tp, replicate 6

description: raplicate 6

value: BALB/cOlaHsd


title: BALB/c PBS-treated, 6h Tp, replicate 5

description: raplicate 5


title: Analysis 4: EA - HPV Negative - Biological replicate 7

description: re-analysis of US10130359_253949411320_S01_GE1_107_Sep09_2_3 sample in analysis 1, 2, 3, 6, 8

source_name: EA - HPV Negative - Oropharyngeal squamous cell carcinoma


title: BALB/c PBS-treated, 6h Tp, replicate 4

description: raplicate 4


title: CBA/Ca 6h post pneumococcal infection, replicate 1

description: raplicate 1


title: BALB/c PBS-treated, 6h Tp, replicate 3

description: raplicate 3


title: WNV1310-100x

type: other

city: Livermore

first: Kevin

last: McLoughlin

state: CA

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description: Data used in Table 3

hyb_protocol: Hybridization was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 8 µg of labelled DNA was used for hybridization. Hybridization was performed in a NimbleGen Hybridization system using the NimbleGen Hybridization kit (Roche NimbleGen).

scan_protocol: Microarrays were scanned in-house at SSI, Denmark using a MS 200 Scanner (Roche, Nimblegen)

data_processing: Data was analyzed using NimbleScan software and custom software developed at Lawrence Livermore National Laboratory, CA, USA and described in 'Gardner et al. A Micobial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Probes were classified as detected if the intensity exceeded a threshold equal to the 99th percentile of intensities for negative control probes, except for the ORF+ skin lesion sample that was analyzed using the 95th percentile.

molecule: other

organism:
dengue virus type 1
dengue virus type 2
dengue virus type 4
Japanese encephalitis virus

label_protocol: Labelling was performed in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 1 µg of heat-denatured WTA-amplified sample was labelled using nick translation with Cy3- or Cy5-labeled random nonamer primers and Klenow fragment (exo-) (NEB) at 37 ºC for 2 hours. Labelled DNA was iso-propanol precipitated and the pellet washed, dried, reconstituted and quantitated.

extract_protocol: Two-hundred and thirty microliters of sample was centrifuged at 17,000 g for 10 minutes. The supernatant was filtered through a 0.22 µm Ultrafree MC spin filter (Costar) at 2000 g for 2 minutes and DNase treated (5 U DNaseI (Invitrogen or New England Biolabs) for 30-1½ hours at room temperature (urine and CSF samples were considered free of genomic DNA and hence not DNAse treated). The viral nucleic acid (NA) was extracted using the PureLink Viral RNA/DNA kit (Invitrogen), without the addition of carrier RNA. The extracted viral NA was eluted with 30 µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. Virus-positive supernatants suspended in RNA-extraction reagent were purified according to manufacturer (TRIzol, Life Technologies; TriFast, Peqlab; AVL buffer, Qiagen). The resulting RNA was further purified using QIAamp RNA viral Mini kit (Qiagen). The Extracted viral NA was eluted with 30µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. To be able to amplify both DNA virus and RNA virus samples with the same protocol, we used the described Whole Transcriptome Amplification (WTA) method (Berthet et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Molecular Biology 2008, 9:77) by using the QuantiTect WTA kit (Qiagen) according to manufacturer’s protocol, except for the reverse transcription step that was replaced by the Superscript III Reverse Transcription kit (Invitrogen) combined with 5´-phosphorylated random hexamers (P-N6)(Eurofines MWG Operon). The WTA protocol includes 3 sequential reactions: firstly a reverse transcription reaction to generate cDNA, secondly a ligation of generated cDNA into larger transcriptomes and thirdly a Repli-g amplification of the generated transcriptomes. Neither of the two first reactions (cDNA synthesis and ligation) had any adverse effects when performed on a DNA-virus. Briefly, 11 µl of extracted viral NA was put into a 20 µl RT reaction and incubated at 42 ºC for 1 hour. The Superscript enzyme was inactivated at 95 ºC for 5 minutes, 10 µl of the cDNA reaction was added to 10 µl of ligation mix and incubated at 22 ºC for 2 hours. Thirty microliters of amplification mix containing Phi29 polymerase and random primers was then added and amplification performed at 30 ºC for 2-8 hours. The reaction was terminated by incubation at 95 ºC for 5 minutes. Amplified material was purified using QIAamp DNA mini kit (Qiagen) using a modified protocol (www.qiagen.com), and checked for purity and concentration using a NanoDrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis. The DNA was then stored at -80 ºC or immediately used for microarray analysis.

tag: isolation source

value: sample WNV13-10 from QCMD EQA panel


title: WNV1301-100x

description: Data used in Table 3

organism: West Nile virus

value: sample WNV13-01 from QCMD EQA panel


title: WNV1311-1000x

description: Data used in Table 3

organism:
dengue virus type 3
Tick-borne encephalitis virus
Yellow fever virus

value: sample WNV13-11 from QCMD EQA panel


title: BALB/c PBS-treated, 6h Tp, replicate 2

description: raplicate 2


title: WNV1301-1000x

description: Data used in Table 3


title: WNV1310-10x

description: Data used in Table 3


title: WNV1311-100x

description: Data used in Table 3


title: WNV1310

description: Data used in Table 3


title: BALB/c PBS-treated, 6h Tp, replicate 1

description: raplicate 1


title: WNV1311-10x

description: Data used in Table 3


title: BALB/c 6h post pneumococcal infection, replicate 5

description: replicate 5


title: WNV-5-clinical

description: Data used in Table 2

value: urine


title: WNV-3-clinical

description: Data used in Table 2


title: WNV1301-10000x

description: Data used in Table 3


title: BALB/c 6h post pneumococcal infection, replicate 3

description: replicate 3


title: WNV-4-clinical

description: Data used in Table 2


title: Toscana

description: Data used in Table 2

organism: Toscana virus

source_name: Toscana

value: cell culture supernatant


title: WNV1301-100000x

description: Data used in Table 3


title: WNV-6-clinical

description: Data used in Table 1


title: BALB/c 6h post pneumococcal infection, replicate 2

description: replicate 2


title: BALB/c 6h post pneumococcal infection, replicate 4

description: replicate 4


title: WNV1311

description: Data used in Table 3


title: Usutu

description: Data used in Table 1

organism: Usutu virus

source_name: Usutu

value: purified RNA


title: WNV10-07

description: Data used in Table 1

value: sample WNV10-07 from QCMD EQA panel


title: WNV

description: Data used in Table 2

source_name: WNV


title: WNV-1-clinical

description: Data used in Table 2


title: Toscana-clinical

description: Data used in Table 1

source_name: Toscana-clinical

value: cerebrospinal fluid


title: WNV10-01

description: Data used in Table 1

value: sample WNV10-01 from QCMD EQA panel


title: WNV-2-clinical

description: Data used in Table 2


title: WNV1310-1000x

description: Data used in Table 3


title: SinNombre

description: Data used in Table 1

organism: Orthohantavirus sinnombreense

source_name: SinNombre


title: Sicilian

description: Data used in Table 1

organism: sandfly fever Sicilian virus

source_name: Sicilian


title: BALB/c 6h post pneumococcal infection, replicate 1

description: replicate 1


title: Osteoarthritis, synovial membrane patient R61 (U133A)

city: Leipzig

last: Stiehl

address: Liebigstr. 24

department: Institute of Pathology

institute: University of Leipzig

description:
see publication for details
R61

hyb_protocol: according to supplier instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing:
background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)
MAS5.0 signal intensity, ABS_CALL: presence/absence call, DETECTION P-VALUE: significance of 0-hypothesis (not expressed)

source_name: synovial membrane patient R61 (osteoarthritis)

extract_protocol: according RNeasy Kit, Qiagen

tag: clinical status

value: osteoarthritis


title: Osteoarthritis, synovial membrane patient R53 (U133A)

description:
see publication for details
R53

source_name: synovial membrane patient R53 (osteoarthritis)

label_protocol: according to supplier instructions, Affymetrix

treatment_protocol: NSAID


title: Seoul

description: Data used in Table 1

organism: Orthohantavirus seoulense

source_name: Seoul


title: Osteoarthritis, synovial membrane patient R64 (U133A)

description:
see publication for details
R64

source_name: synovial membrane patient R64 (osteoarthritis)


title: Osteoarthritis, synovial membrane patient R41 (U133A)

description:
see publication for details
R41

source_name: synovial membrane patient R41 (osteoarthritis)


title: Polio

description: Data used in Table 1

organism: Human poliovirus sp.

source_name: Polio


title: Rheumatoid arthritis, synovial membrane patient R57 (U133A)

description:
see publication for details
R57

source_name: synovial membrane patient R57 (rheumatoid arthritis)

treatment_protocol: Cyclosporin, MTX, Prednis.

value: rheumatoid arthritis


title: Rheumatoid arthritis, synovial membrane patient R58 (U133A)

description:
see publication for details
R58

source_name: synovial membrane patient R58 (rheumatoid arthritis)

treatment_protocol: NSAID, Quensyl (Hydrochloroquin)


title: NegControlUrine

description: Data used in Table 2

organism: synthetic construct

source_name: NegControlUrine


title: RVF

description: Data used in Table 3

organism: Rift Valley fever virus

source_name: RVF


title: RVF-3

description: Data used in Table 3


title: Rheumatoid arthritis, synovial membrane patient R46 (U133A)

description:
see publication for details
R46

source_name: synovial membrane patient R46 (rheumatoid arthritis)

treatment_protocol: MTX

value: male


title: NegControlSerum

description: Data used in Table 2

source_name: NegControlSerum

value: serum


title: RVF-4

description: Data used in Table 1


title: CBA/Ca 6h post pneumococcal infection, replicate 2

description: raplicate 2

source_name: mouse lung

value: CBA/CaOlaHsd

value: 9 weeks


title: Osteoarthritis, synovial membrane patient R52 (U133A)

description:
see publication for details
R52

source_name: synovial membrane patient R52 (osteoarthritis)

value: female


title: HCV-3

description: Data used in Table 3

organism: Hepacivirus hominis


title: NegControlCSF

description: Data used in Table 2

source_name: NegControlCSF


title: Marburg

description: Data used in Table 1

organism: Marburgvirus

source_name: Marburg


title: Naples

description: Data used in Table 1

organism: Sandfly fever Naples virus

source_name: Naples


title: HCV-4

description: Data used in Table 3


title: Osteoarthritis, synovial membrane patient R54 (U133A)

description:
see publication for details
R54

organism: Homo sapiens

source_name: synovial membrane patient R54 (osteoarthritis)


title: RVF-2

description: Data used in Table 3


title: Monkeypox

description: Data used in Table 1

organism: Monkeypox virus

source_name: Monkeypox

value: purified DNA


title: Orf-clinical

description: Data used in Table 2

organism: Orf virus

source_name: Orf-clinical

value: skin lesion


title: Lassa

description: Data used in Table 1

organism: Mammarenavirus lassaense

source_name: Lassa


title: Hantaan

description: Data used in Table 1

organism: Orthohantavirus hantanense

source_name: Hantaan


title: Rheumatoid arthritis, synovial membrane patient R32 (U133A)

description:
see publication for details
R32

source_name: synovial membrane patient R32 (rheumatoid arthritis)

treatment_protocol: Prednis.


title: Puumala

description: Data used in Table 1

organism: Orthohantavirus puumalaense

source_name: Puumala


title: HCV-2

description: Data used in Table 3


title: Dobrava

description: Data used in Table 1

organism: Orthohantavirus dobravaense

source_name: Dobrava


title: EEE

description: Data used in Table 1

organism: Eastern equine encephalitis virus

source_name: EEE


title: DENV1301

description: Data used in Tables 2 and 3

organism: dengue virus type 1

value: sample DENV13-01 from QCMD EQA panel


title: Ebola

description: Data used in Table 1

organism: Zaire ebolavirus

source_name: Ebola


title: Rheumatoid arthritis, synovial membrane patient R29 (U133A)

description:
see publication for details
R29

source_name: synovial membrane patient R29 (rheumatoid arthritis)

treatment_protocol: NSAID, Azulfidine, Prednis.


title: Rheumatoid arthritis, synovial membrane patient R39 (U133A)

description:
see publication for details
R39

source_name: synovial membrane patient R39 (rheumatoid arthritis)


title: DENV1301-100x

description: Data used in Table 3


title: Rheumatoid arthritis, synovial membrane patient K49 (U133A)

description:
see publication for details
K49

source_name: synovial membrane patient K49 (rheumatoid arthritis)

treatment_protocol: NSAID, MTX, Prednis.


title: Rheumatoid arthritis, synovial membrane patient R51 (U133A)

description:
see publication for details
R51

source_name: synovial membrane patient R51 (rheumatoid arthritis)

treatment_protocol: NSAID, Tilidin (Opiat)


title: Rheumatoid arthritis, synovial membrane patient K36 (U133A)

description:
see publication for details
K36

source_name: synovial membrane patient K36 (rheumatoid arthritis)

treatment_protocol: NSAID, Gold


title: DENV1301-10x

description: Data used in Table 3


title: DENV1301-1000x

description: Data used in Table 3


title: DENV-6-clinical

description: Data used in Tables 2 and 3

organism: Dengue virus


title: DENV-4-clinical

description: Data used in Tables 2 and 3


title: DENV-8-clinical

description: Data used in Tables 2 and 3

organism: dengue virus type 3


title: DENV-5-clinical

description: Data used in Tables 2 and 3


title: DENV-3-clinical

description: Data used in Tables 2 and 3


title: Dengue2-clinical2

description: Data used in Table 2

organism: dengue virus type 2


title: Osteoarthritis, synovial membrane patient EB_140 (U133A)

city: Eisenberg

first: Raimund

last: Kinne

address: Klosterlausnitzer Str. 81

department: Department of Orthopedics

institute: Jena University Hospital

description:
see publication for details
EB_140

source_name: synovial membrane patient EB_140 (osteoarthrisits)


title: Osteoarthritis, synovial membrane patient EB_100 (U133A)

description:
see publication for details
EB_100

source_name: synovial membrane patient EB_100 (osteoarthrisits)

treatment_protocol: NSARD


title: Dengue2-clinical1

description: Data used in Table 2


title: CCHF

description: Data used in Table 1

organism: Orthonairovirus haemorrhagiae

source_name: CCHF


title: Osteoarthritis, synovial membrane patient EB_99 (U133A)

description:
see publication for details
EB_99

source_name: synovial membrane patient EB_99 (osteoarthrisits)


title: Chikungunya-clinical

description: Data used in Table 2

organism: Chikungunya virus

source_name: Chikungunya-clinical


title: Cowpox

description: Data used in Table 1

organism: Cowpox virus

source_name: Cowpox


title: DENV-7-clinical

description: Data used in Tables 2 and 3


title: Osteoarthritis, synovial membrane patient EB_97 (U133A)

description:
see publication for details
EB_97

source_name: synovial membrane patient EB_97 (osteoarthrisits)

treatment_protocol: NSARD, prednisolone, MTX


title: Osteoarthritis, synovial membrane patient EB_104 (U133A)

description:
see publication for details
EB_104

source_name: synovial membrane patient EB_104 (osteoarthrisits)


title: 35S_MYB87-SRDX_Arabidopsis_2wks_seedling_rep4

description:
Five T2 seedlings were grown in MS agar medium wth hygromycin and harvested for RNA extraction
MYB87SRDX_rep4

organism: Arabidopsis thaliana

source_name: 35S:MYB87-SRDX Arabidopsis thaliana 2wks seedlings

label_protocol: 1 mg of total RNA was used for labeling procedure using Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown in MS (1% sucrose) agar medium with or without hygromycin in 16hr light / 8hr dark cycle in 23 Celsius degree.

tag: genotype/variation

value: whole seedlings


title: CCHF-Sam3-clinical

description: Data used in Table 2


title: 35S_MYB87-SRDX_Arabidopsis_2wks_seedling_rep1

description:
Five T2 seedlings were grown in MS agar medium wth hygromycin and harvested for RNA extraction
MYB87SRDX_rep1


title: 35S_MYB87-SRDX_Arabidopsis_2wks_seedling_rep2

description:
Five T2 seedlings were grown in MS agar medium wth hygromycin and harvested for RNA extraction
MYB87SRDX_rep2


title: genomic DNA from HIV/TB co-infected patient 20

description:
HIV/TB co-infection
KAA0ZQ5C-11_19-Jan-2010

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Illumina's GenomeStudioV2010.1 was used to export Beta values, detection p-values and signals.  Raw data were quantile normalized.

label: Cy5 and Cy3

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMCs using the modified protocol of Sigma Aldrich Tri-reagent

value: Male

value: PBMC

value: HIV/TB


title: Wild_type_Arabidopsis_2wks_seedling_rep4

description:
Five T2 seedlings were grown in MS agar medium and harvested for RNA extraction
control_rep4

source_name: Wild-type Arabidopsis thaliana 2wks seedlings

value: wt


title: Wild_type_Arabidopsis_2wks_seedling_rep3

description:
Five T2 seedlings were grown in MS agar medium and harvested for RNA extraction
control_rep3


title: Rheumatoid arthritis, synovial membrane patient R60 (U133A)

description:
see publication for details
R60

source_name: synovial membrane patient R60 (rheumatoid arthritis)

treatment_protocol: NSAID, MTX


title: Osteoarthritis, synovial membrane patient EB_90 (U133A)

description:
see publication for details
EB_90

source_name: synovial membrane patient EB_90 (osteoarthrisits)


title: genomic DNA from HIV/TB co-infected patient 17

description:
HIV/TB co-infection
JAA1063Y-11_03-Mar-2010

value: Female


title: Osteoarthritis, synovial membrane patient EB_94 (U133A)

description:
see publication for details
EB_94

source_name: synovial membrane patient EB_94 (osteoarthrisits)


title: Wild_type_Arabidopsis_2wks_seedling_rep1

description:
Five T2 seedlings were grown in MS agar medium and harvested for RNA extraction
control_rep1


title: Wild_type_Arabidopsis_2wks_seedling_rep2

description:
Five T2 seedlings were grown in MS agar medium and harvested for RNA extraction
control_rep2


title: genomic DNA from HIV/TB co-infected patient 18

description:
HIV/TB co-infection
KAA0Z0GV-10_18-Nov-2009


title: 35S_MYB87-SRDX_Arabidopsis_2wks_seedling_rep3

description:
Five T2 seedlings were grown in MS agar medium wth hygromycin and harvested for RNA extraction
MYB87SRDX_rep3


title: Osteoarthritis, synovial membrane patient EB_24 (U133A)

description:
see publication for details
EB_24

source_name: synovial membrane patient EB_24 (osteoarthrisits)


title: Osteoarthritis, synovial membrane patient EB_21 (U133A)

description:
see publication for details
EB_21

source_name: synovial membrane patient EB_21 (osteoarthrisits)


title: genomic DNA from HIV/TB co-infected patient 16

description:
HIV/TB co-infection
JAA103SD-11_25-Feb-2010


title: genomic DNA from HIV/TB co-infected patient 13

description:
HIV/TB co-infection
HAA0QL3W-13_29-May-2008


title: genomic DNA from HIV/TB co-infected patient 19

description:
HIV/TB co-infection
KAA0ZMKX-10_11-Jan-2010


title: genomic DNA from HIV/TB co-infected patient 9

description:
HIV/TB co-infection
DAA0Z4CR-10_25-Nov-2009


title: genomic DNA from HIV/TB co-infected patient 15

description:
HIV/TB co-infection
JAA0Q3QZ-15_24-Apr-2008


title: genomic DNA from HIV/TB co-infected patient 10

description:
HIV/TB co-infection
FAA0Z9CZ-10_03-Dec-2009


title: genomic DNA from HIV/TB co-infected patient 14

description:
HIV/TB co-infection
HAA0Z4Z0-19_26-Nov-2009


title: Rheumatoid arthritis, synovial membrane patient EB_109 (U133A)

description:
see publication for details
EB_109

source_name: synovial membrane patient EB_109 (rheumatoid arthritis)