title: TNFa-OMe-P siRNA-C, replicate 5

city: Barcelona

first: Evarist

middle: Planet

last: Letschert

state: Spain

address: C/ Baldiri Reixac 10

department: Biostatistics

country: Spain

institute: IRB Barcelona

description: The U of U/miligramsg stands for Unit of MPO activity. One unit of MPO activity was defined as the amount that degraded 1.0 umol of peroxide per min at 25 C.

hyb_protocol: Hybridization of the samples to Affymetrix GeneChip® Mouse Gene 1.0 ST Arrays were performed according to the manufacturer’s instructions (http://www.affymetrix.com).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip@ Scanner 3000.

data_processing: Gene expression data was pre-processed and normalized using Partek Genomics Suite. The data was quantile normalized, and the summarization was obtained via RMA.

source_name: TNFa-OMe-P siRNA-C, replicate 5

label_protocol: 25 ng total RNA per sample was used for Whole Transcriptome Amplification (Sigma) according to manufacturer´s recommendations. 10 microgram cDNA was  fragmented, and biotinylated using Affymetrix' 10K v2 Assay Kit according to manufacturer's recommendations (http://www.affymetrix.com).

growth_protocol: anti-TNFa siRNA treatment in a mouse model of IBD: effects of various chemical modifications on clinical parameters and the inflammatory axis.

extract_protocol: Total RNA was prepared using a RNEasy RNA extraction kit (Qiagen). Purity and integrity of the purified RNA was assessed on the Agilent Bioanalyzer 2100. Concentration was determined with a Nanodrop ND-1000 Spectrophotometer.

treatment_protocol: No additional treatment was used prior to RNA extraction

tag: knockdown

value: TNFa-OMe-P siRNA-C

tag: amplification date

tag: hybridization date

tag: colon length (mm)

tag: colon weight (mg)

tag: colon ratio (mg/mm)

tag: myeloperoxidase activity (u/mg)

value: colon

value: 5% DSS


title: TNFa-OMe-P siRNA-C, replicate 8

status: Public on Sep 10 2011

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: TNFa-OMe-P siRNA-C, replicate 8

tag: tissue

tag: treatment


title: TNFa-OMe-P siRNA-C, replicate 6

source_name: TNFa-OMe-P siRNA-C, replicate 6


title: TNFa-OMe-P siRNA-C, replicate 7

source_name: TNFa-OMe-P siRNA-C, replicate 7


title: muscle_riverine_rep14

city: King Salmon

first: Scott

middle: A

last: Pavey

state: Alaska

address: PO Box 7

department: Natural Resources

country: USA

institute: Katmai National Park

hyb_protocol: We followed an established hybridization protocol for the 16k cDNA array {von Schalburg, 2005 #1175}. In brief, both 250 ng of reference aRNA and 500 ng of sample cDNA were collected in a single tube and kept dark. The mixture was concentrated with a speed vacuum and brought up to 23 μl with RNase free water (Gibco). Hybridization buffer #3 (Ambion) was heated to 65oC while occasionally mixing for one hour. The heated buffer and LNAdt blocker (Genesphere) was then added to the collected sample, as per manufacturer’s instructions. We used the Tecan HS 4800 Pro, an automated hybridization machine to hybridize sample cDNA to the arrays (Tecan). Before the sample injection, the programmed Tecan washed with several solutions containing first 1xSSC, then 0.1xSSC 0.014% SDS, then 5x SSC, 0.01% SDS, and 0.2% BSA. Samples were heated to 80oC for 5 minutes, and then kept at 65oC until injected onto the pre-washed arrays in a Tecan HS 4800 Pro, as per manufacturers’ instructions. Microarrays were hybridized for 16 hours, and the full protocol for the hybridization can be viewed in Additional File 2.   Post-hybridization, arrays were rinsed in the Tecan modules with increasingly stringent SSC and SDS solutions, starting with 2xSSC, 0.014%SDS for four washes incrementally decreasing temperature, then one final wash of 0.2xSSC at 23 ºC. Finally, slides were dried with 37 psi nitrogen gas and kept dark until scanned.

scan_protocol: All microarrays were scanned immediately after hybridization was complete using a ScanArray Express (Perkin-Elmer). The microarray images were quantified manually with ImaGene 5.6.1 (BioDiscovery). Spots with unusual morphology, offset, or other poor quality parameters were flagged as marginal and excluded these from downstream analyses.

data_processing: We performed all analyses in GeneSpring GX 7.3 (Agilent). The arrays were normalized as per typical two-color experiments by performing an array-wide intensity-dependent Lowess normalization, followed by a per gene normalization, which normalized each spot to the median value. The average base/proportionate value was calculated to be an intensity of 72, so we filtered data to retain only entities with average raw signal expression values greater than 72 in at least one of the populations. This became our base expression data for analysis. Our GeneSpring analysis was performed in two ways. First, the dataset was filtered to retain only the genes where the average differential expression was ≥ 1.5 fold. This list was significance tested with a t-test without equal variances assumption (P ≤ 0.05) with a Benjamini and Hochberg False Discovery Rate multiple test correction (MTC; {Benjamini, 2001 #879}. The spot ID’s from the cGRASP 16k annotation file (current annotation files available at: http://web.uvic.ca/grasp/microarray/array.html; {Koop, 2008 #1176}) were used to associate ESTs (expressed sequence tags) on the array with gene descriptions. To confirm current annotation of the differential gene list, a Megablast was performed on associated EST sequences, or used tBLASTx on the associated EST, or contiguous sequence (contig). The default parameters were used for these database queries.

organism: Oncorhynchus nerka

source_name: riverine, muscle

label_protocol: cDNA was synthesized with Invitrogen SuperScriptTM III Indirect cDNA labeling system kits per manufacturer’s instructions. In brief, 10 µg of total RNA was combined with a master mix including reverse-transcriptase and oligo (dT)20 primers. This reaction was incubated for three hours at 46ºC to synthesize single-stranded cDNA. The samples were cleaned with the S.N.A.P TM column purification procedure (Invitrogen).   A reference pool was prepared with representative total RNA samples of juvenile sockeye muscle and liver, and adult sockeye brain, muscle and liver. Multiple tissues were used to ensure hybridization of the reference channel to all spots that may have been hybridized by the sample channel cDNA, and therefore able to be quantified as a ratio. The total RNA was amplified using an Amino Allyl MessageAmp™ II aRNA amplification Kit (Ambion) as per manufacturers instructions. Briefly, RNA from several individuals from both populations of a single tissue type were combined. Then, single-stranded cDNA was synthesized from the RNA whereupon the second strand was synthesized with DNA polymerase. This product was purified through columns, and then amino allyl-modified aRNA was transcribed from the cDNA. The aRNA from divergent tissue types was combined in equal amounts at this point and this common reference pool was run with each sample on the microarray.   Sample and reference material was coupled with mono-reactive CyDyeTM packs (GE Healthcare). In short, the reference aRNA was coupled with Cy3 and the sample cDNA with Cy5 dyes for one hour at 4ºC. The samples were then purified to remove all uncoupled dye using S.N.A.P.TM columns as per manufacturer’s instructions (Invitrogen). The dye coupled sample and reference were stored at 4ºC in the dark until hybridization.

growth_protocol: Sampled in nature

extract_protocol: Total RNA was extracted with a modified protocol of the Invitrogen TRIzol® Plus RNA purification kit using PureLinkTM Micro-to-MidiTM columns. Disruption and homogenization were achieved with a MixerMill MM301 (Retsch). The manufacturer’s protocol was followed with the exception of using 150 µl of chloroform and 150 µl of low pH phenol for tissue dissociate protein and isolate RNA.

treatment_protocol: Sampled in nature from either riverine or lake habitat

value: muscle

tag: isolation source

value: riverine

source_name: aRNA pool from muscle, brain, liver

value: pool from muscle, brain, liver


title: RA1060_control_-3677 [ANALYTE: CK]

type: protein

city: Stanford

first: William

last: Robinson

state: CA

address: 269 Campus Dr

institute: Stanford University

description: Region of assignment and time of serum sampling were used to pull appropriated controls for each case sample, but this identifying information was not disclosed to us by the Department of Defense.

hyb_protocol: Spectrally-distinct polystyrene beads with magnetic cores were covalently coupled to capture antibodies by the manufacturer. The bead mix was added to a 96-well flat-bottom plate (1x concentration, 25 uL/well). The plate was washed twice with provided wash buffer using a Bio-Plex Pro II magnetic wash station (100 uL/well per wash). Serum was diluted 1:4 in provided universal sample diluent. Standard or diluted sample was added to the plate (25 uL/well), incubated at room temperature for one hour on a microtiter plate shaker, and removed by washing the plate three times on the wash station.

scan_protocol: Plates were analyzed using a Luminex 200 (Luminex Corporation, Austin, TX, USA) in combination with Bio-Plex Manager 5.0 software (Bio-Rad Laboratories, Hercules, CA, USA). Data were acquired with the following advanced settings: 125 beads per region, 50 uL sample size, and DD gate values of 5,000 to 25,000.

data_processing: Serum concentrations were interpolated from standard curves for each respective cytokine in Bio-Plex manager software. These concentrations were then normalized by calculating a Z-score using the formula: ((observed value)-(mean value of control patients))/(standard deviation).

label: PE

molecule: protein

organism: Homo sapiens

source_name: serum

label_protocol: Biotinylated detection antibodies were added (1x concentration, 25 uL/well), allowed to incubate at room temperature for 30 minutes, and removed by washing the plate three times. Streptavidin-PE was added (1x concentration, 50 uL/well), incubated at room temperature for 10 minutes, and promptly removed by washing the plate three times. Provided assay buffer was added to re-suspend the beads (90 uL/well) and the plate was placed on the shaker for 30 seconds before reading.

extract_protocol: Serum was isolated and provided by a clinical laboratory.

tag: subject id

tag: group

value: control

tag: relative days to diagnosis

tag: Sex

value: Female

tag: race

value: Caucasian

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: TNFa-OMe-P siRNA-C, replicate 4

source_name: TNFa-OMe-P siRNA-C, replicate 4

tag: knockdown


title: TNFa-OMe-P siRNA-C, replicate 3

source_name: TNFa-OMe-P siRNA-C, replicate 3

tag: amplification date


title: RA1060_control_-4629 [ANALYTE: CK]


title: TNFa-OMe-P siRNA-C, replicate 2

source_name: TNFa-OMe-P siRNA-C, replicate 2

tag: hybridization date


title: RA1059_control_2436 [ANALYTE: CK]

value: Male


title: muscle_lake-type_rep6

source_name: lake-type muscle

value: lake-type


title: TNFa-OMe-P siRNA-C, replicate 1

source_name: TNFa-OMe-P siRNA-C, replicate 1

tag: colon length (mm)


title: RA1059_control_-234 [ANALYTE: CK]


title: RA1058_control_-1551 [ANALYTE: CK]


title: RA1058_control_2293 [ANALYTE: CK]


title: RA1060_control_-1827 [ANALYTE: CK]


title: TNFa-OMe siRNA-B, replicate 6

source_name: TNFa-OMe siRNA-B, replicate 6

value: TNFa-OMe siRNA-B

tag: colon weight (mg)


title: RA1057_control_241 [ANALYTE: CK]


title: TNFa-OMe siRNA-B, replicate 5

source_name: TNFa-OMe siRNA-B, replicate 5

tag: colon ratio (mg/mm)


title: RA1056_control_-652 [ANALYTE: CK]


title: TNFa-OMe siRNA-B, replicate 2

source_name: TNFa-OMe siRNA-B, replicate 2

tag: myeloperoxidase activity (u/mg)


title: RA1057_control_-2449 [ANALYTE: CK]


title: RA1056_control_-1940 [ANALYTE: CK]


title: TNFa siRNA-A, replicate 6

source_name: TNFa siRNA-A, replicate 6

value: TNFa siRNA-A

tag: tissue


title: RA1055_control_2695 [ANALYTE: CK]


title: RA1055_control_-118 [ANALYTE: CK]


title: RA1056_control_-4977 [ANALYTE: CK]


title: TNFa siRNA-A, replicate 3

source_name: TNFa siRNA-A, replicate 3

tag: treatment


title: TNFa siRNA-A, replicate 2

source_name: TNFa siRNA-A, replicate 2


title: TNFa siRNA-A, replicate 5

source_name: TNFa siRNA-A, replicate 5


title: TNFa-OMe siRNA-B, replicate 4

source_name: TNFa-OMe siRNA-B, replicate 4


title: TNFa siRNA-A, replicate 4

source_name: TNFa siRNA-A, replicate 4


title: RA1055_control_-1784 [ANALYTE: CK]


title: RA1055_control_-2546 [ANALYTE: CK]


title: RA1056_control_-3678 [ANALYTE: CK]


title: RA1053_control_-102 [ANALYTE: CK]

value: African American


title: TNFa siRNA-A, replicate 1

source_name: TNFa siRNA-A, replicate 1


title: TNFa-OMe siRNA-B, replicate 1

source_name: TNFa-OMe siRNA-B, replicate 1


title: SiRNA-scrambled, replicate 7

source_name: SiRNA-scrambled, replicate 7

value: siRNA-scrambled


title: SiRNA-scrambled, replicate 6

source_name: SiRNA-scrambled, replicate 6


title: TNFa-OMe siRNA-B, replicate 3

source_name: TNFa-OMe siRNA-B, replicate 3


title: SiRNA-scrambled, replicate 5

source_name: SiRNA-scrambled, replicate 5


title: RA1053_control_-1174 [ANALYTE: CK]

source_name: serum


title: SiRNA-scrambled, replicate 4

source_name: SiRNA-scrambled, replicate 4


title: RA1053_control_-1658 [ANALYTE: CK]


title: Comparison of Placenta from infected vs sham treatment replicate 1

city: Colubus

first: Sheryl

middle: S

last: Justice

state: OH

address: 700 Children's Drive

institute: The Research Institute at Nationwide Children's Hospital

description: Replicate 1

hyb_protocol: Refer to Agilent Two Color Microarray-Based Gene Expression Analysis labeling protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C). Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process.  The median red (Cy5) and green (Cy3) intensities are used to calculate the ratio of expression for each element on the array, in terms of M (log2(Red/Green)) and A ((log2(Red) + log2(Green))/2)). The M values are then global loess normalized within each array using the LIMMA microarray processing package in “R” (Smyth, 2004). This intensity based normalization approach adjusts the red and green intensities relative to one another so that the red/green ratios are as far as possible an unbiased representation of relative expression.

source_name: PBS introduced transurethrally on gestational 14, harvest Placenta tissue on gestational day 16

extract_protocol: mRNA was extracted by Trizol according to manufacturer's recommendations

treatment_protocol: Female C57BL/6J mice were mated with C3H/Hen Males for 16 hours,  on gestational day 14 pregnant females received 10^7 viable uropathogenic Escherichia coli strain UTI89 or PBS transurethrally.  Placenta was harvested at getational day 16.

tag: infection

tag: strain

value: Placenta gestational day 16 from outbred mating with C3H/HeN

source_name: Uropathogenic Escherichia coli strain UIT89 introduced transurethrally on gestational 14, harvest Placenta tissue on gestational day 16


title: Comparison of Placenta from infected vs sham treatment replicate 2

description: Replicate 2

label_protocol: Refer to Agilent Two Color Microarray-Based Gene Expression Analysis labeling protocol

value: Uropathogenic Escherichia coli strain UIT89


title: vaccine vaccinated fish RNA sample_vaccine_rep3

city: AUBURN

first: julia

last: pridgeon

state: AL

address: 990 WIRE ROAD

department: AAHRU

institute: USDA, ARS

description: This sample is of vaccine vaccinated fish. It is the third of the three vaccinated fish replicates used in this experiment. Each sample is pooled from 5 fish.

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

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

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

organism: Ictalurus punctatus

source_name: vaccine vaccinated channel catfish anterior kidney

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

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA).

tag: genotype

value: wild type

tag: phenotype

value: normal

tag: tissue type

value: kidney


title: SiRNA-scrambled, replicate 2

source_name: SiRNA-scrambled, replicate 2

value: colon

value: 5% DSS


title: PCB153-treated vs control differentiated hMADS cells Replicate 3

city: paris

first: minji

last: kim

address: 45 rue des saints-pères

country: France

institute: INSERM

description: Biological replicate 3 of 4. PCB153-treated vs control adipocyte differentiated hMADS

hyb_protocol: 825 ng of labeled samples were fragmented and hybridized using Agilent In Situ Hybridization Kit Plus following manufacturer's instructions in Agilent SureHyb-enabled hybridization chambers at 65°C for 17 hours. The hybridized slides were washed and scanned using the GenePix 4000B scanner at 5 micron resolution.

scan_protocol: Images were quantified using GenePix Pro 6 Acquisition and Analysis Microarray Software on a GenePix 4000B Scanner

data_processing: For all microarrays, after the Loess normalization of log-transformed microarray data with the use of the Goulphar Version 1.1.3 package (http://transcriptome.ens.fr/goulphar/index.php), gene lists were filtered to identify genes common to all microarrays (i.e. 100%, retrieval).

source_name: human Multipotent Adipose-Derived Stem cells

label_protocol: Total RNA (200 ng) from each sample (each condition in quadruplicate) was amplified and transcribed into fluorescent cRNA with the Agilent's Low RNA Input Linear Amplification kit according to the manufacturer's recommandations. Cyanine-5 dye was incorporated into control (DMSO treated) sample, and treated samples (by TCDD, PCB126 or PCB153) were labelled with cyanine-3 dye.

growth_protocol: Proliferating hMADS cells were seeded at a density of 40000 cells/cm2 in Dulbecco’s modified Eagle’s medium (DMEM) with low glucose supplemented with 10% fetal calf serum (FCS), 2.5 ng/ml hFGF2, 10 mM Hepes buffer, 50 units/ml of penicillin and 50 µg/ml streptomycin and kept at 37 °C in 5% CO2. The medium was changed every other day and hFGF2 was removed when cells reached confluence. On the next day, the cells were incubated in differentiation medium (DM), i.e. DMEM/Ham’s F-12 medium containing 10 µg/ml transferrin, 5 µg/ml insulin, 0.2 nM triiodothyronine, 100 µM 3-isobutyl-1-methylxanthine (IBMX), 1 µM dexamethasone (DEX), and 0.5 µg/ml rosiglitazone. At day 3, DEX and IBMX were omitted from DM until day 10. Differentiation, i.e. neutral lipid accumulation was assessed by oil red O staining

extract_protocol: Total RNA extracted using  the Qiagen's RNeasy total RNA Mini kit following manufacturer's instructions

treatment_protocol: The experiments were carried out between days 11 and 13 as the cells were treated for 48h by 25 nM TCDD, 1 µM PCB126 and/or 10 µM PCB153, all dissolved in DMSO.

tag: cell type

value: differentiated cells

tag: cell line

value: hMADS

tag: agent

value: DMSO


title: sham vaccinated fish RNA sample_control_rep3

description: This sample is of sham vaccinated fish control. It is the third of three sham vaccinated fish control replicates used in this experiment. Each sample is pooled from 5 fish.

source_name: sham vaccinated channel catfish anterior kidney


title: vaccine vaccinated fish RNA sample_vaccine_rep1

description: This sample is of vaccine vaccinated fish. It is the first of the three vaccinated fish replicates used in this experiment. Each sample is pooled from 5 fish.


title: RA1052_control_-77 [ANALYTE: CK]

tag: subject id

tag: group

value: control

tag: relative days to diagnosis

tag: Sex

value: Female

tag: race

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: sham vaccinated fish RNA sample_control_rep2

description: This sample is of sham vaccinated fish control. It is the second of three sham vaccinated fish control replicates used in this experiment. Each sample is pooled from 5 fish.


title: SiRNA-scrambled, replicate 3

source_name: SiRNA-scrambled, replicate 3

tag: knockdown

tag: amplification date

tag: hybridization date

tag: colon length (mm)

tag: colon weight (mg)

tag: colon ratio (mg/mm)

tag: myeloperoxidase activity (u/mg)

tag: tissue


title: vaccine vaccinated fish RNA sample_vaccine_rep2

description: This sample is of vaccine vaccinated fish. It is the second of the three vaccinated fish replicates used in this experiment. Each sample is pooled from 5 fish.

tag: genotype

tag: phenotype

tag: tissue type


title: PCB153-treated vs control differentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. PCB153-treated vs control adipocyte differentiated hMADS

tag: cell type

tag: cell line

tag: agent


title: sham vaccinated fish RNA sample_control_rep1

description: This sample is of sham vaccinated fish control. It is the first of three sham vaccinated fish control replicates used in this experiment. Each sample is pooled from 5 fish.


title: RA1053_control_-2753 [ANALYTE: CK]

tag: subject id

tag: group

tag: relative days to diagnosis

tag: Sex

value: Male

tag: race


title: PCB153-treated vs control differentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. PCB153-treated vs control adipocyte differentiated hMADS


title: RA1052_control_-1167 [ANALYTE: CK]

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: PCB153-treated vs control differentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. PCB153-treated vs control adipocyte differentiated hMADS


title: RA1052_control_-812 [ANALYTE: CK]


title: SiRNA-scrambled, replicate 1

source_name: SiRNA-scrambled, replicate 1

tag: knockdown

tag: amplification date

tag: hybridization date

tag: colon length (mm)

tag: colon weight (mg)

tag: treatment


title: RA1052_control_-1552 [ANALYTE: CK]


title: PCB126-treated vs control differentiated hMADS cells Replicate 3

description: Biological replicate 3 of 4. PCB126-treated vs control adipocyte differentiated hMADS


title: Control, replicate 8

source_name: Control, replicate 8

value: Control

tag: colon ratio (mg/mm)

tag: myeloperoxidase activity (u/mg)

tag: tissue


title: PCB126-treated vs control differentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. PCB126-treated vs control adipocyte differentiated hMADS

tag: cell type

tag: cell line

tag: agent


title: Control, replicate 7

source_name: Control, replicate 7


title: TCDD-treated vs control differentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. TCDD-treated vs control adipocyte differentiated hMADS

value: TCDD


title: PCB126-treated vs control differentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. PCB126-treated vs control adipocyte differentiated hMADS


title: TCDD-treated vs control differentiated hMADS cells Replicate 3

description: Biological replicate 3 of 4. TCDD-treated vs control adipocyte differentiated hMADS


title: PCB126-treated vs control differentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. PCB126-treated vs control adipocyte differentiated hMADS


title: PCB153-treated vs control undifferentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. PCB153-treated vs control undifferentiated hMADS

value: undifferentiated cells


title: RA1051_control_391 [ANALYTE: CK]

description: Region of assignment and time of serum sampling were used to pull appropriated controls for each case sample, but this identifying information was not disclosed to us by the Department of Defense.

tag: subject id

tag: group

tag: relative days to diagnosis

value: African American


title: RA1051_control_-360 [ANALYTE: CK]

tag: Sex

tag: race

tag: age at diagnosis


title: Control, replicate 6

description: The U of U/miligramsg stands for Unit of MPO activity. One unit of MPO activity was defined as the amount that degraded 1.0 umol of peroxide per min at 25 C.

source_name: Control, replicate 6

tag: knockdown

tag: amplification date


title: RA1050_control_1120 [ANALYTE: CK]

value: Caucasian

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: RA1050_control_-1233 [ANALYTE: CK]


title: RA1050_control_-143 [ANALYTE: CK]


title: Control, replicate 5

source_name: Control, replicate 5

tag: hybridization date

tag: colon length (mm)

tag: colon weight (mg)


title: Control, replicate 3

source_name: Control, replicate 3

tag: colon ratio (mg/mm)

tag: myeloperoxidase activity (u/mg)

tag: treatment


title: PCB153-treated vs control undifferentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. PCB153-treated vs control undifferentiated hMADS

tag: cell type

tag: cell line


title: RA1050_control_-2889 [ANALYTE: CK]

tag: subject id


title: PCB153-treated vs control undifferentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. PCB153-treated vs control undifferentiated hMADS

tag: agent


title: TCDD-treated vs control differentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. TCDD-treated vs control adipocyte differentiated hMADS


title: RA1050_control_-1532 [ANALYTE: CK]

tag: group

tag: relative days to diagnosis


title: PCB126-treated vs control undifferentiated hMADS cells Replicate 3

description: Biological replicate 3 of 4. PCB126-treated vs control undifferentiated hMADS


title: Control, replicate 2

source_name: Control, replicate 2

tag: tissue


title: PCB153-treated vs control undifferentiated hMADS cells Replicate 3

description: Biological replicate 3 of 4. PCB153-treated vs control undifferentiated hMADS


title: Control, replicate 1

source_name: Control, replicate 1


title: TCDD-treated vs control undifferentiated hMADS cells Replicate 3

description: Biological replicate 3 of 4. TCDD-treated vs control undifferentiated hMADS


title: PCB126-treated vs control undifferentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. PCB126-treated vs control undifferentiated hMADS


title: TCDD-treated vs control undifferentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. TCDD-treated vs control undifferentiated hMADS


title: TCDD-treated vs control undifferentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. TCDD-treated vs control undifferentiated hMADS


title: TCDD-treated vs control differentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. TCDD-treated vs control adipocyte differentiated hMADS


title: RA1049_control_-741 [ANALYTE: CK]

source_name: serum

tag: Sex

tag: race

tag: age at diagnosis


title: RA1049_control_-2542 [ANALYTE: CK]

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: RA1048_control_912 [ANALYTE: CK]


title: RA1048_control_-288 [ANALYTE: CK]


title: RA1047_control_-506 [ANALYTE: CK]


title: F833J_R2

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: medicago truncatula  - age: 6day

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: root - Seeds were surface sterilized, vernalized and germinated according to Boisson-Dernier (Boisson-Dernier et al., 2001). 24h germinating seed were grown on Fahraeus medium (Fahraeus, 1957) covered with filter paper in square Petri dishes at 25°C (day/night 12h). Roots kept in the dark with a mask on the Petri dish made of kraft paper and aluminium.

treatment_protocol: 3J - time course study - pathogen infection, ralstonia solanacearum gmi 1000 strain: quantity 1e+07cfu/ml time 72h. Inoculation was performed as described (Vailleau et al., 2007). Bacterial concentration was set at 107cfu/ml for the inoculation.

tag: line

tag: age


title: F833J_R3

description: medicago truncatula  - age: 6day


title: A173J_R3

description: medicago truncatula  - age: 3day

treatment_protocol: 12h - time course study - pathogen infection, ralstonia solanacearum gmi 1000 strain: quantity 1e+07cfu/ml time 12hour . Inoculation was performed as described (Vailleau et al., 2007). Bacterial concentration was set at 107cfu/ml for the inoculation.


title: SKL3J_R1

description: medicago truncatula  mutant (sickle a17 mutant) - age: 6day

value: Sickle


title: A173J_R1

description: medicago truncatula  - age: 6day


title: PCB126-treated vs control undifferentiated hMADS cells Replicate 4

description: Biological replicate 4 of 4. PCB126-treated vs control undifferentiated hMADS


title: RA1049_control_-1471 [ANALYTE: CK]


title: TCDD-treated vs control undifferentiated hMADS cells Replicate 2

description: Biological replicate 2 of 4. TCDD-treated vs control undifferentiated hMADS


title: RA1047_control_-895 [ANALYTE: CK]


title: SKL12H_R3

description: medicago truncatula  mutant (sickle a17 mutant) - age: 3day


title: A17T0_R2

description: medicago truncatula  - age: 3day

treatment_protocol: 0h - time course study - pathogen infection, ralstonia solanacearum gmi 1000 strain, rhodococcus fascians:quantity 1e+07cfu/ml time 0hour . Inoculation was performed as described (Vailleau et al., 2007). Bacterial concentration was set at 10e7cfu/ml for the inoculation.


title: F833J_R1

description: medicago truncatula  - age: 6day


title: SKLT0_R3


title: F83T0_R1

description: medicago truncatula  - age: 3day


title: SKL3J_R3


title: SKL12H_R2


title: Control, replicate 4

source_name: Control, replicate 4

tag: knockdown

tag: amplification date

tag: hybridization date

tag: colon length (mm)

tag: colon weight (mg)


title: A173J_R2

description: medicago truncatula  - age: 6day


title: A17T0_R1

description: medicago truncatula  - age: 3day


title: Control, replicate 9

source_name: Control, replicate 9

tag: colon ratio (mg/mm)

tag: myeloperoxidase activity (u/mg)

tag: treatment


title: RA1047_control_-1757 [ANALYTE: CK]

tag: subject id

tag: group


title: F8312H_R1

description: medicago truncatula  - age: 3day


title: SKLT0_R1


title: RA1047_control_-2755 [ANALYTE: CK]

tag: relative days to diagnosis


title: F83T0_R3

description: medicago truncatula  - age: 3day


title: RA1046_control_-2413 [ANALYTE: CK]

tag: Sex


title: RA1046_control_-2767 [ANALYTE: CK]

tag: race


title: RA1046_control_-3243 [ANALYTE: CK]

tag: age at diagnosis


title: F8312H_R3

description: medicago truncatula  - age: 3day


title: RA1046_control_-4554 [ANALYTE: CK]

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: F8312H_R2

description: medicago truncatula  - age: 3day

tag: line


title: A17T0_R3

description: medicago truncatula  - age: 3day

tag: age


title: F83T0_R2

description: medicago truncatula  - age: 3day


title: SKL12H_R1


title: SKL3J_R2


title: DMSO_control_RMA

status: Public on Sep 09 2011

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

country: Sweden

institute: Uppsala university

description: Gene expression data from MCF7 cells treated with 0.1% DMSO for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA), the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed using the robust multi-array average (RMA) available from the Bioconductor project in the free statistical computing language R.

source_name: Breast cancer cell line MCF7, DMSO

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using the Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: MCF7 control cells treated with 0.1% DMSO for 6 hours.

tag: cell line

tag: cell type

value: breast cancer cells

tag: perturbagen

value: small molecule

tag: concentration

tag: duration

value: 6 h

tag: sample type


title: PS2-1 iPSC

type: genomic

city: Tokyo

first: Takuya

last: Yagi

address: 35-Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University

hyb_protocol: Hybridizations were performed on slides containing four arrays, with each array containing 622060 in-situ synthesized 60-mer oligonucleotides, representing 170344 unique chromosomal locations (Agilent Technologies).

scan_protocol: Images of the arrays were acquired using a microarray scanner G2505CA (Agilent technologies) and image analysis was performed using feature extraction software version 10.7 (Agilent Technologies).

data_processing: The date were imported into Agilent Genomic Workbench using the aberration detection method 2 (ADM-2) algorithm (10.0 threshold) for further analysis.

molecule: genomic DNA

source_name: undifferentiated PS2-1 iPSC

label_protocol: 500 ng of DNA was labelled using the Enzo Genomic DNA Labelling kit.

growth_protocol: Primary fibroblasts were cultured in DMEM supplemented with 10% FBS. iPSC were cultured in hES medium containing bFGF.

extract_protocol: Total DNA samples were isolated using DNeasy kit.

treatment_protocol: Cells were washed with PBS and Dneasy kit was used to isolate total DNA.

value: iPSC

source_name: Human Genomic DNA

tag: reference

value: Promega, female(G1521)


title: A1712H_R2

description: medicago truncatula  - age: 3day


title: A1712H_R1

description: medicago truncatula  - age: 3day


title: PCB126-treated vs control undifferentiated hMADS cells Replicate 1

description: Biological replicate 1 of 4. PCB126-treated vs control undifferentiated hMADS

source_name: human Multipotent Adipose-Derived Stem cells

tag: agent


title: A1712H_R3

description: medicago truncatula  - age: 3day


title: SKLT0_R2


title: PS2 fibroblast

source_name: PS2 fibroblast

value: fibroblasts


title: VLX_50_MAS5

description: Gene expression data from MCF7 cells treated with VLX 50 for 6 hours.

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

source_name: Breast cancer cell line MCF7, VLX 50

treatment_protocol: MCF7 cells treated with 10 microM VLX 50 for 6 hours.

tag: treatment

value: VLX 50

tag: vehicle

value: treatment


title: PD01-25 iPSC

hyb_protocol: Following fragmentation, all arrays were hybridized at 45C for 16 hr.

scan_protocol: GeneChips were scanned using an AFX GC3000 G7 scanner.

data_processing: The gene expression raw data were extracted using the AFFX Gene Chip Operation System. Quality control was performed on the basis of Affymetrix quality control metrics. The data were analyzed with the Gene Spring GX 11.0 (Agilent).

source_name: undifferentiated PD01-25 iPSC

label_protocol: Approximately 150 ng of RNA from each sample was labeled using GeneChip 3’IVT Express (Affymetrix) according to the manufacturer’s instructions.

growth_protocol: iPSC were cultured in hES medium containing bFGF.

extract_protocol: Total RNA samples were isolated using RNeasy kit.

treatment_protocol: Cells were washed with PBS and Rneasy kit was used to isolate total RNA.

value: Sporadic Parkinson's disease patient derived iPSC

tag: disease state

value: Sporadic Parkinson's disease


title: VLX_50_RMA

value: DMSO


title: Cells treated with TGF and parasite conditioned medium, biological rep 3

city: Quito

first: Jaime

middle: Alfredo

last: Costales

address: 12 de Octubre y Patria

department: Biological Sciences

country: Ecuador

institute: Pontificia Universidad Catolica del Ecuador

description: Gene expression data from human fibroblast treated simultaneously with TGF and Trypanosoma cruzi conditioned medium to  measure abrogation of fibrotic gene activation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG_U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The raw data was uploaded into the Rosetta Resolver  System  for data processing and normalization using the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). The expression profiles from replicate samples were combined into ratio experiments. Each gene is associated to an expression fold-change and a p-value that assesses the statistical significance of its modulation in the treated sample compared to the control reference. Sequences with absolute fold-change >=2 and p-value <= 0.01 were considered as differentially expressed.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 5X10^4/ml cells were seeded in in 75 mm culture plates in Dulbecco's modified Eagle medium (10%FBS,100 U/ml penicillin, 100 ug/ml streptomycin, 2mM glutamine)  and allowed to grow for 48 hours at 37 C in a CO2 incubator

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by concentration using the RNeasy kit (Quiagen).

treatment_protocol: Culture cells were stimulated with 5 ng/ml TGF-β1 for 3 hours in the presence or absence of T. cruzi conditioned medium.

tag: tissue

value: Human foreskin fibroblasts (HFF) BJ


title: Cells treated with parasite conditioned medium, biological rep 3

description: Gene expression data from human fibroblast treated with Trypanosoma cruzi conditioned medium


title: Cells treated with TGF and parasite conditioned medium, biological rep 2


title: Cells treated with medium as control, biological rep 3

description: Gene expression data from untreated human fibroblast

source_name: Cells treated with medium as control


title: Cells treated with medium as control, biological rep 1


title: Cells treated with parasite conditioned medium, biological rep 2


title: Cells treated with TGF and parasite conditioned medium, biological rep 1


title: Cells treated with TGF, biological rep 3

description: Gene expression data from human fibroblast treated with TGF as positive control for fibrotic gene activation

source_name: Cells treated with TGF


title: Cells treated with medium as control, biological rep 2


title: Normal breast organoid:ORG 222

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

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 Illumina iScan with Illumina scanner settings for Infinium chip

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: Normal breast organoid

label_protocol: Standard Illumina Protocol for Infinium Methylation27 Beadchip

extract_protocol: DNA was extracted with TNES/PK (Tris/NaCl/EDTA/SDS/proteinase K) lysis buffer prior to sodium bisulfite conversion using Zymo Research EZ DNA Methylation Kit

tag: invasive carcinoma

tag: er

tag: pr

tag: ih class

tag: stage (ajcc)

tag: t nm

tag: nodal stage

tag: metastatic stage

tag: tumor size (mm)

tag: months

tag: recurrence*

value: Normal breast organoid


title: Normal breast organoid:ORG 202

tag: age


title: Cells treated with TGF, biological rep 2


title: Cells treated with TGF, biological rep 1


title: Cells treated with parasite conditioned medium, biological rep 1


title: RA1049_control_-3167 [ANALYTE: CK]

description: Region of assignment and time of serum sampling were used to pull appropriated controls for each case sample, but this identifying information was not disclosed to us by the Department of Defense.

tag: subject id

tag: group

value: control

tag: relative days to diagnosis

tag: Sex

value: Female

tag: race

tag: age at diagnosis

tag: anti-cyclic citrulinnated protein (tested by anti-ccp2 elisa, axis shields, 0-negative, 1-positive)


title: Normal breast organoid:ORG 199

tag: invasive carcinoma

tag: er

tag: pr

tag: tissue


title: Normal breast organoid:ORG 167

tag: ih class

tag: stage (ajcc)

tag: t nm

tag: nodal stage


title: Normal breast organoid:ORG 175

tag: metastatic stage

tag: tumor size (mm)

tag: months

tag: recurrence*


title: Normal breast organoid:ORG 028

tag: age


title: Normal breast organoid:ORG 193


title: Normal breast organoid:ORG 119


title: Normal breast organoid:ORG 009


title: Normal breast organoid:ORG 006


title: Normal breast organoid:ORG 109


title: Normal breast organoid:ORG 081


title: DMSO_control_MAS5

tag: cell line

tag: cell type

tag: perturbagen

tag: treatment

tag: concentration

tag: duration

tag: sample type


title: Normal breast adjacent to tumor (microdissected):5N

tag: invasive carcinoma

tag: er

tag: pr

tag: tissue


title: Normal breast organoid:ORG 147

tag: ih class

tag: stage (ajcc)

tag: t nm

tag: nodal stage


title: Normal breast adjacent to tumor (microdissected):8N

tag: metastatic stage

tag: tumor size (mm)

tag: months

tag: recurrence*


title: Normal breast organoid:ORG 125

tag: age


title: Normal breast organoid:ORG 201


title: Normal breast adjacent to tumor (microdissected):6N


title: Normal breast adjacent to tumor (microdissected):10N


title: PS2-2 iPSC

source_name: undifferentiated PS2-2 iPSC

tag: cell type

tag: reference


title: Normal breast adjacent to tumor (microdissected):9N


title: Primary invasive breast cancer:2C 6

source_name: Primary invasive breast cancer

value: Ductal

value: IIIC

value: Primary invasive breast cancer tumor


title: Normal breast adjacent to tumor (microdissected):7N


title: Primary invasive breast cancer:2B 22

value: TriN

value: IIA


title: Primary invasive breast cancer:2C 2

value: IIB


title: Primary invasive breast cancer:1H 3


title: Primary invasive breast cancer:2C 18

value: Mammary


title: Primary invasive breast cancer:2C 4

value: IA


title: Primary invasive breast cancer:1H 18

value: IIIA


title: Primary invasive breast cancer:2A 20


title: Primary invasive breast cancer:2A 17


title: Primary invasive breast cancer:1H 2


title: Primary invasive breast cancer:7144


title: Primary invasive breast cancer:1E 17


title: Primary invasive breast cancer:1F 9


title: Primary invasive breast cancer:1B 9


title: Primary invasive breast cancer:1C 23


title: Primary invasive breast cancer:1A 2


title: Primary invasive breast cancer:1C 10


title: Primary invasive breast cancer:1D 11

value: Lobular


title: Primary invasive breast cancer:7228


title: Primary invasive breast cancer:7121

value: ER-


title: Primary invasive breast cancer:1E 11


title: Primary invasive breast cancer:7142


title: Primary invasive breast cancer:1A 24


title: Primary invasive breast cancer:1B 11


title: Primary invasive breast cancer:7117


title: Primary invasive breast cancer:1B 20


title: Primary invasive breast cancer:1A 18


title: Primary invasive breast cancer:1B 16


title: Primary invasive breast cancer:7140

value: IIIB


title: Primary invasive breast cancer:7113


title: Primary invasive breast cancer:874


title: Primary invasive breast cancer:847


title: Primary invasive breast cancer:7100


title: Primary invasive breast cancer:873


title: Primary invasive breast cancer:860


title: Primary invasive breast cancer:872


title: Primary invasive breast cancer:856


title: Primary invasive breast cancer:876


title: Primary invasive breast cancer:867


title: Primary invasive breast cancer:7109


title: Primary invasive breast cancer:818


title: Primary invasive breast cancer:829


title: Primary invasive breast cancer:832


title: Primary invasive breast cancer:803


title: Primary invasive breast cancer:805


title: Primary invasive breast cancer:836


title: Primary invasive breast cancer:811


title: Primary invasive breast cancer:1G 6

value: LumA


title: Primary invasive breast cancer:2H 21


title: Primary invasive breast cancer:2B 24


title: Primary invasive breast cancer:1H 22

value: LumB


title: Primary invasive breast cancer:2C 13


title: Primary invasive breast cancer:2B 20


title: Primary invasive breast cancer:812


title: Primary invasive breast cancer:3A 15


title: Primary invasive breast cancer:2A 1


title: Primary invasive breast cancer:1H 6


title: Primary invasive breast cancer:1F 12


title: Primary invasive breast cancer:2B 15

value: Ambig


title: Primary invasive breast cancer:2C 20


title: Primary invasive breast cancer:1G 16


title: Primary invasive breast cancer:1F 3


title: Primary invasive breast cancer:1F 24


title: Primary invasive breast cancer:1D 3


title: Primary invasive breast cancer:1D 9


title: Primary invasive breast cancer:1A 6


title: Primary invasive breast cancer:1B 23


title: Primary invasive breast cancer:817


title: Primary invasive breast cancer:1C 1


title: Primary invasive breast cancer:1A 4


title: Plasma_HIVn_45

city: New York

first: Minal

last: Dalvi

state: NY

address: 345 East 24th Street, Rm 917

department: Department of Basic Science

institute: New York University

description: Each custom array slide has 16 arrays, 6 of which are used to generate a standard curve by running a set of concentration standards (dilutions of protein cocktail of all analytes).

scan_protocol: The air-dried slide was scanned (Axon GenePix 4000B, Genomics Core facility, NYU Langone Medical Center) and the resulting florescence signal analyzed (H40 Q-Analyzer v7.40.2 software (RayBiotech Inc.) to provide quantitative measure of target protein in the samples.

data_processing: The raw data (median florescence intensities without background) was imported in the H40 Q-Analyzer v7.40.2 software (RayBiotech Inc.). The software then generates positive control normalized mean florescence values for each array and linear as well as log regression standard curves for each protein based on the set of concentration standards run for each analyte on each slide. The final results are expressed in picograms per ml and account for dilution of the sample for the array.

source_name: Plasma HIV negative

label_protocol: After incubating the array with the sample, the array was washed three times and incubated with biotin-conjugated antibody followed by treatment with Cy3-conjugated streptavidin.

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Blood was collected in EDTA containing VacutainerTM tubes by a trained phlebotomist, mixed and centrifuged at 1000 g for 25 min at 4°C. The plasma supernatant was collected and stored in aliquots at -80°C.

tag: sample

value: Plasma

tag: disease status

value: HIV uninfected


title: Plasma_HIVn_34


title: Plasma_HIVn_9


title: Plasma_HIVn_5


title: Primary invasive breast cancer:1A 12

tag: invasive carcinoma


title: Primary invasive breast cancer:857

value: Ductal

tag: er

value: ER+


title: Primary invasive breast cancer:7115

tag: pr

value: Primary invasive breast cancer tumor


title: Primary invasive breast cancer:878

tag: tissue


title: Primary invasive breast cancer:7148

tag: ih class


title: Primary invasive breast cancer:7132

tag: stage (ajcc)

value: IIIC


title: Primary invasive breast cancer:865

tag: t nm


title: Primary invasive breast cancer:833

tag: nodal stage


title: Primary invasive breast cancer:7103

tag: metastatic stage


title: Primary invasive breast cancer:824

value: IIA

tag: tumor size (mm)


title: Primary invasive breast cancer:7107

tag: months


title: Primary invasive breast cancer:828

tag: recurrence*


title: Primary invasive breast cancer:863

tag: age

value: IIB


title: Primary invasive breast cancer:7146


title: Primary invasive breast cancer:879

value: Mammary


title: Primary invasive breast cancer:823


title: Primary invasive breast cancer:852

value: IA


title: Primary invasive breast cancer:859

value: IIIA


title: Primary invasive breast cancer:7136


title: Primary invasive breast cancer:830


title: Primary invasive breast cancer:835


title: Primary invasive breast cancer:7130


title: Plasma_HIVp_39

source_name: Plasma HIV positive

value: HIV infected


title: Primary invasive breast cancer:7219


title: Primary invasive breast cancer:837


title: Primary invasive breast cancer:827


title: Primary invasive breast cancer:819

value: Metaplastic


title: Primary invasive breast cancer:877


title: Primary invasive breast cancer:815


title: Plasma_HIVp_15


title: Saliva_HIVn_40

source_name: Saliva HIV negative

treatment_protocol: Subjects were asked to rinse their mouth with distilled water after which saliva was induced by chewing on neutral gum base (courtesy of the Wrigley Company). Whole mouth stimulated saliva (WMSS) was collected in sterile disposable polyethylene 50 ml conical tubes kept on ice. Protease inhibitor cocktail without EDTA (ThermoFisher No.78415) was added at the concentration specified by the manufacturer, mixed gently and centrifuged at 1000 g for 25 min at 4°C, the supernatant aliquoted and stored at -80˚C.

value: Saliva

tag: protease inhibitor


title: Gr-1high alone

city: Bethesda

first: Tim

last: Greten

address: 9000 Rockville Pike

institute: NCI

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQORTM Immunology Microarrays Murine Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 5 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 5 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Lowess method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: Gr-1 high

label_protocol: 1 µg of the respective T7-amplified RNA was labeled by reverse transcription either with Cy3-dCTPs or Cy5-dCTPsas described elsewhere (PMID: 8800675)

extract_protocol: RNA was isolated using a standard extraction protocol (Nucleospin-II-RNA-Extraction-Kit (Macherey&Nagel))

treatment_protocol: CD11b+Gr-1high cells were isolated  from the splenocyte of  tumor bearing mice via magnetically labelled beads and Sorted. The purified CD11b+Gr-1high MDSCs were cultured with IFNg-/- antigen specific T cells and re- sorted after 48h and RNA was extracted and gene expression was analyzed using microarray.

tag: strain

value: Balb/c

source_name: Gr-1 high + IFNγ -/- CL-4


title: Plasma_HIVn_35

tag: sample


title: Plasma_HIVp_32

tag: disease status


title: Saliva_HIVn_45

value: Protease inhibitor cocktail without EDTA (ThermoFisher No.78415)


title: Saliva_HIVn_34


title: Saliva_HIVn_7


title: Saliva_HIVn_36


title: Saliva_HIVn_9


title: Primary invasive breast cancer:807

tag: invasive carcinoma


title: Primary invasive breast cancer:804

tag: er

value: LumA

value: IIIB


title: Saliva_HIVn_5

value: HIV uninfected


title: Primary invasive breast cancer:814

tag: pr


title: Saliva_HIVp_33

source_name: Saliva HIV positive


title: Saliva_HIVp_35


title: Saliva_HIVp_4


title: 14178685 - 1c- vs 1c+

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

description: Identify genes induced (or repressed) in the root tips of Arabidopsis thaliana during phosphate deficiency (Pi) (15 to 60 minutes).

hyb_protocol: 1c+ Cy5 / 1c- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Seedling were grown vertically on MS/10 medium in Petri dishes supplemented with either 500 μM (Pi+) or 20 μM (Pi-) NaH2PO4 as Pi source.

extract_protocol: 1c+:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:1_Pi+ - environmental treatment - abiotic stress,nah2po4:quantity 500uM time 15min . All seedlings have the genotype of the accession Col-0 (CS60000). Seedlings were germinated and grown for 6 days on 10 times diluted MS medium containing 500uM, phosphate (= phosphate rich medium). At day 6 seedlings were transferred to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800uM) of the primary root was cut under a dissecting microscope and harvested. RNA (~5ug) of about 100 root tips (per condition) was then extracted with the RNeasy MICROKIT (Qiagen) and sent in suspension in water. Three biological replicates (a, b, c) of this experiment were conducted.

tag: ecotype

value: Columbia

tag: dev.stage (boyes et al. plant cell 2001)

tag: phosphate quantity

tag: time

extract_protocol: 1c-:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:1_Pi- - environmental treatment - abiotic stress,nah2po4:quantity 20uM time 15min . All seedlings have the genotype of the accession Col-0 (CS60000). Seedlings were germinated and grown for 6 days on 10 times diluted MS medium containing 500uM, phosphate (= phosphate rich medium). At day 6 seedlings were transferred to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800uM) of the primary root was cut under a dissecting microscope and harvested. RNA (~5ug) of about 100 root tips (per condition) was then extracted with the RNeasy MICROKIT (Qiagen) and sent in suspension in water. Three biological replicates (a, b, c) of this experiment were conducted.


title: 14178686 - 2c+ vs 2c-

hyb_protocol: 2c- Cy5 / 2c+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2c-:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:2_Pi- - environmental treatment - abiotic stress,nah2po4:quantity 20uM time 60min . All seedlings have the genotype of the accession Col-0 (CS60000). Seedlings were germinated and grown for 6 days on 10 times diluted MS medium containing 500uM, phosphate (= phosphate rich medium). At day 6 seedlings were transferred to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800uM) of the primary root was cut under a dissecting microscope and harvested. RNA (~5ug) of about 100 root tips (per condition) was then extracted with the RNeasy MICROKIT (Qiagen) and sent in suspension in water. Three biological replicates (a, b, c) of this experiment were conducted.

extract_protocol: 2c+:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:2_Pi+ - environmental treatment - abiotic stress,nah2po4:quantity 500uM time 60min . All seedlings have the genotype of the accession Col-0 (CS60000). Seedlings were germinated and grown for 6 days on 10 times diluted MS medium containing 500uM, phosphate (= phosphate rich medium). At day 6 seedlings were transferred to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800uM) of the primary root was cut under a dissecting microscope and harvested. RNA (~5ug) of about 100 root tips (per condition) was then extracted with the RNeasy MICROKIT (Qiagen) and sent in suspension in water. Three biological replicates (a, b, c) of this experiment were conducted.


title: 14178560 - 1b+ vs 1b-

hyb_protocol: 1b- Cy5 / 1b+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1b-:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 1b+:5ug. (Qiagen_RNeasy.pdf)


title: 14178559 - 2a- vs 2a+

hyb_protocol: 2a+ Cy5 / 2a- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2a+:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 2a-:5ug. (Qiagen_RNeasy.pdf)


title: Saliva_HIVp_31


title: 14178680 - 1b- vs 1b+

hyb_protocol: 1b+ Cy5 / 1b- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178687 - 2c- vs 2c+

hyb_protocol: 2c+ Cy5 / 2c- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178558 - 2a+ vs 2a-

hyb_protocol: 2a- Cy5 / 2a+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178683 - 1c+ vs 1c-

hyb_protocol: 1c- Cy5 / 1c+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14178682 - 2b- vs 2b+

hyb_protocol: 2b+ Cy5 / 2b- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 2b+:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: 2b-:5ug. (Qiagen_RNeasy.pdf)


title: 14178681 - 2b+ vs 2b-

hyb_protocol: 2b- Cy5 / 2b+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Primary invasive breast cancer:809

value: Ductal

tag: ih class

value: ER+

tag: stage (ajcc)

tag: t nm

tag: nodal stage

tag: tissue


title: Primary invasive breast cancer:801

tag: age

value: IIIC

tag: metastatic stage

tag: tumor size (mm)

tag: months

tag: recurrence*

value: Primary invasive breast cancer tumor


title: Saliva_HIVp_18

tag: sample

tag: protease inhibitor

tag: disease status


title: Saliva_HIVp_32


title: Plasma_HIVn_33

value: Plasma


title: Saliva_HIVp_100707

description: There was no additional sample processing than what was described in treatment protocol

scan_protocol: The air-dried slide was scanned (Axon GenePix 4000B, Genomics Core facility, NYU Langone Medical Center) and the resulting florescence signal analyzed (L-507 analysis software, RayBiotech, Inc.) to provide an estimate of protein abundance in the samples.

data_processing: The raw data values (median florescence intensities with and without background) was imported in the L-507 analysis software provided by RayBiotech Inc. The software then generates positive control normalized median florescence values for all 507 proteins.

label_protocol: Saliva samples pooled from three HIV infected subjects were dialyzed overnight against PBS pH 8.0 at 4C. Samples were then biotinylated for 30 min, dialyzed against with PBS, pH 8.0 at 4C. The arrays were blocked for 1 h, the buffer removed and 400 µl of dialyzed sample diluted 1:10 in blocking buffer layered onto an array and incubated for 2 h with gentle shaking. The array was washed three times and incubated with Cy3-conjugated streptavidin reporter for 2 h with gentle shaking, and washed to remove unbound Cy3-conjugated streptavidin.

treatment_protocol: Healthy HIV infected subjects were asked to rinse their mouth with distilled water after which saliva was induced by chewing on neutral gum base (courtesy of the Wrigley Company). Whole mouth stimulated saliva (WMSS) was collected in sterile disposable polyethylene 50 ml conical tubes kept on ice. Protease inhibitor cocktail  without EDTA (ThermoFisher No.78415) was added at the concentration specified by the manufacturer, mixed gently and centrifuged at 1000 g for 25 min at 4°C.

value: saliva

tag: type

value: pooled from 3 subjects


title: Saliva_HIVp_15


title: Saliva_HIVp_100724

label_protocol: Saliva samples pooled from three HIV infected controls were dialyzed overnight against PBS pH 8.0 at 4ËšC. Samples were then biotinylated for 30 min, dialyzed against with PBS, pH 8.0 at 4ËšC. The arrays were blocked for 1 h, the buffer removed and 400 Âµl of dialyzed sample diluted 1:10 in blocking buffer layered onto an array and incubated for 2 h with gentle shaking. The array was washed three times and incubated with Cy3-conjugated streptavidin reporter for 2 h with gentle shaking, and washed to remove unbound Cy3-conjugated streptavidin.


title: 14178556 - 1a+ vs 1a-

hyb_protocol: 1a- Cy5 / 1a+ Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 1a-:5ug. (Qiagen_RNeasy.pdf)

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

extract_protocol: 1a+:5ug. (Qiagen_RNeasy.pdf)


title: Saliva_HIVn_100724

label_protocol: Saliva samples pooled from three uninfected healthy controls were dialyzed overnight against PBS pH 8.0 at 4ËšC. Samples were then biotinylated for 30 min, dialyzed against with PBS, pH 8.0 at 4ËšC. The arrays were blocked for 1 h, the buffer removed and 400 Âµl of dialyzed sample diluted 1:10 in blocking buffer layered onto an array and incubated for 2 h with gentle shaking. The array was washed three times and incubated with Cy3-conjugated streptavidin reporter for 2 h with gentle shaking, and washed to remove unbound Cy3-conjugated streptavidin.

treatment_protocol: Healthy HIV uninfected subjects were asked to rinse their mouth with distilled water after which saliva was induced by chewing on neutral gum base (courtesy of the Wrigley Company). Whole mouth stimulated saliva (WMSS) was collected in sterile disposable polyethylene 50 ml conical tubes kept on ice. Protease inhibitor cocktail  without EDTA (ThermoFisher No.78415) was added at the concentration specified by the manufacturer, mixed gently and centrifuged at 1000 g for 25 min at 4°C.


title: Saliva_HIVn_100707

type: other

molecule: other

label_protocol: Saliva samples pooled from three uninfected healthy controls were dialyzed overnight against PBS pH 8.0 at 4˚C. Samples were then biotinylated for 30 min, dialyzed against with PBS, pH 8.0 at 4˚C. The arrays were blocked for 1 h, the buffer removed and 400 µl of dialyzed sample diluted 1:10 in blocking buffer layered onto an array and incubated for 2 h with gentle shaking. The array was washed three times and incubated with Cy3-conjugated streptavidin reporter for 2 h with gentle shaking, and washed to remove unbound Cy3-conjugated streptavidin.

treatment_protocol: Healthy HIV uninfected subjects were asked to rinse their mouth with distilled water after which saliva was induced by chewing on neutral gum base (courtesy of the Wrigley Company). Whole mouth stimulated saliva (WMSS) was collected in sterile disposable polyethylene 50 ml conical tubes kept on ice. Protease inhibitor cocktail without EDTA (ThermoFisher No.78415) was added at the concentration specified by the manufacturer, mixed gently and centrifuged at 1000 g for 25 min at 4°C.


title: Pol2-16_5

city: Rehovot

first: Ariel

last: Gispan

address: P.O. Box 26

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Agilent yeast ChIP-on-chip44Kx4 arrays

scan_protocol: Agilent microarray scanner Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Matlab was used to read the files, background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

label_protocol: DNA was digested with DpnII and amplified by four rounds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides. DNA was labeled with Cy dyes

growth_protocol: Strains were grown 12-16 hr at 30˚C in YPD. The strains were diluted to O.D 0.1 in YPD  and harvested after 5  hr at logaritmic phase .

extract_protocol: DNA from FACS-sorted cells was extracted using the MasterPure Yeast DNA purification kit

tag: genotype/variation

tag: cell cycle phase

value: S phase

value: G1 phase


title: Pol2-11_7

value: G2 phase


title: Pol2-11_6


title: Saliva_HIVp_39

value: Saliva

value: HIV infected


title: Pol2-16_4


title: Pol2-11_5


title: 14178557 - 1a- vs 1a+

hyb_protocol: 1a+ Cy5 / 1a- Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: phosphate quantity

tag: time


title: Pol2-18_1


title: Pol2-16_6


title: Pol2-11_4


title: Pol2-11_2


title: Pol2-16_1


title: Pol2-16_3


title: Pol2-11_3


title: Pol2-11_1


title: Pol2-18_2


title: Mrc1N5_2

source_name: Mrc1 N5

value: Mrc1 N5


title: Mrc1_Diploid

source_name: mrc1Δ diploid

value: mrc1Δ diploid


title: Pol2-16_2


title: Rad53_2

source_name: rad53Δ, sml1 Δ

value: rad53Δ, sml1 Δ


title: Mrc1N5_1


title: Rad53_1


title: STAT3_C_3

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

description: BALB/c-3T3 cells with constitutively expressed STAT3 (STAT3C) stably transfected

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip scanner 3000, 1.5 micrometer resolution

data_processing: The images were analyzed for defects and normalized using RMA.

label_protocol: Affymetrix standard amplification protocol

growth_protocol: Cells were grown in DMEM with 10% bovine calf serum under standard cell line growth conditions.

extract_protocol: TRIzol (Invitrogen) then RNeasy kit (Qiagen)

treatment_protocol: Balb/c-3T3 cells were stably transfected with either pMvSrc or pRc/CMV-STAT3C


title: STAT3_C_1

source_name: BALB/c-3T3 cells with constitutively expressed STAT3 (STAT3C) stably transfected


title: Balb_Control_3

description: BALB/c-3T3 cells unmodified

source_name: BALB/c-3T3 cells unmodified


title: STAT3_C_2


title: Mrc1C15_2

source_name: Mrc1 C15

value: Mrc1 C15


title: Balb_Control_2

description: BALB/c-3T3 cells unmodified


title: Trophectoderm cell pool, biological replicate 1

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in the WT sense target labeling assay manual from Affymetrix (version 4; FS450_0007).

scan_protocol: Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: The resulting data were compared to the transcriptomes of hESC differentiated to the trophoblast lineage (hESCtroph) after 0, 2, 4, 6, 8, 10 and 12 days of induction with BMP-4 (data from [14]), using GeneSpring GX 10.0, and analyzed with Ingenuity Pathway Analysis (IPA, Ingenuity Systems, Redwood City, CA) software.

source_name: Human trophectoderm cells

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN FFPE kit, and sense-strand cDNA targets were created using the NuGEN WT-Ovation Exon Module, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: Embryos were thawed and cultured iin G2 version 5 medium supplemented with 10% synthetic serum substitute in 5% O2 and 6% CO2 incubator until the blastocyst stage (days 5-6).

extract_protocol: Blastocyst were subject to RNA isolation and purification, with DNAse treatment, using Pico Pure RNA Isolation Kit.

tag: developmental stage

value: Blastocyst

value: Days 5-6


title: Mrc1AQ_2


title: Trophectoderm cell pool, biological replicate 2


title: Balb_Control_1

description: BALB/c-3T3 cells unmodified


title: BALB_VSRC__6

description: BALB/c-3T3 cells with vSrc stably transfected

value: vSRC


title: Mrc1C15_1


title: BALB_VSRC__5

source_name: BALB/c-3T3 cells with vSrc stably transfected


title: Mrc1AQ_1


title: Trophectoderm cell pool, biological replicate 3


title: Trophectoderm cell pool, biological replicate 4


title: Rad53_HU_2

source_name: rad53Δ, sml1 Δ+ 1mM hydroxyurea


title: DC_CS treatment_LPS 1 μg/ml+CS 1 μg/ml/CS 1 μg/ml_loop2

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 900 kit.

scan_protocol: Microarrays were scanned by using GenePix 4100A (Axon, Foster City, CA) and images were taken at a resolution of 5μm. GenePix Pro 5.1 software was used to analyze image data.

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

label_protocol: 3DNA Array 900 kit was used for fluorescence labeling on cDNA. Each total RNA (1μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA  was blocked by addictive 0.5μg of Cot1 human DNA.

growth_protocol: Fresh whole blood from normal volunteers was obtained from the Taiwan Blood Center. Human peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll-Hypaque density gradient centrifugation. Dendritic cells were generated from monocytes that were cultured at 37°C in an incubator with 5% humidified CO2 in RPMI 1640 culture medium that was supplemented with recombinant human GM-CSF 500 U/ml and recombinant human IL-4 1000 U/ml for 6 days.

extract_protocol: Total RNA was extracted by RNeasy kit following the manufacturer’s instruction (Qiagen, Inc., Valencia, CA).

treatment_protocol: Human dendritic cells treated with CS 1 μg/ml for 2 days, CS(Cordyceps sinensis)

tag: cell type

value: dendritic cells

tag: treatment group

value: treated with CS 1 μg/ml

tag: tissue

value: blood

treatment_protocol: Human dendritic cells treated with LPS 1 μg/ml+CS 1 μg/ml for 2 days, CS(Cordyceps sinensis), LPS(Escherichia coli serotype O55:B5, Sigma Chemical Co., St. Louis, MO, USA)

value: treated with LPS 1 μg/ml+CS 1 μg/ml


title: Rad53_HU_1


title: adenoviral shRNA HDAC4 & 5 forskolin 4h treatment rep 1

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05.

source_name: primary hepatocytes

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

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

tag: strain

tag: age

value: 6-8 wks

value: hepatocytes

tag: treatment

value: adenoviral shRNA HDAC4 & 5 forskolin


title: adenoviral shRNA HDAC4 & 5 forskolin 2h treatment rep 2

description: replicate 2


title: adenoviral shRNA HDAC4 & 5 forskolin 4h treatment rep 2

description: replicate 2


title: adenoviral shRNA HDAC4 & 5 forskolin 2h treatment rep 1

description: replicate 1


title: adenoviral shRNA HDAC4 & 5 DMSO 4h treatment rep 1

description: replicate 1

value: adenoviral shRNA HDAC4 & 5 DMSO


title: WT_HU_1

source_name: BY4741+ 2.5mM hydroxyurea

value: G1 phase

value: S phase


title: Mrc1_9


title: Mrc1_8


title: Rad53_3


title: BALB_VSRC__1


title: DC_CS treatment_CS 1 μg/ml/LPS 1 μg/ml_loop2

treatment_protocol: Human dendritic cells treated with LPS 1 μg/ml for 2 days, LPS(Escherichia coli serotype O55:B5, Sigma Chemical Co., St. Louis, MO, USA)

value: treated with LPS 1 μg/ml

source_name: Human dendritic cells treated with CS 1 μg/ml


title: DC_CS treatment_LPS 1 μg/ml/Untreated_loop2

source_name: Human dendritic cells, Untreated control

value: untreated control

source_name: Human dendritic cells treated with LPS 1 μg/ml


title: Mrc1C14_2

source_name: Mrc1 C14

value: Mrc1 C14

value: G2 phase


title: DC_CS treatment_Untreated/LPS 1 μg/ml+CS 1 μg/ml_loop2

source_name: Human dendritic cells treated with LPS 1 μg/ml+CS 1 μg/ml

treatment_protocol: Human dendritic cells, Untreated control


title: adenoviral shRNA HDAC4 & 5 DMSO 4h treatment rep 2

description: replicate 2


title: adenoviral shRNA HDAC4 & 5 DMSO 2h treatment rep 2

description: replicate 2


title: DC_CS treatment_Untreated/Untreated_loop2


title: DC_CS treatment_LPS 1 μg/ml+CS 1 μg/ml/Untreated_loop2


title: Mrc1C14_1


title: Mec1_Met7_1

source_name: mec1Δ, sml1 Δ, met7Δ

value: mec1Δ, sml1 Δ, met7Δ


title: adenoviral GFP forskolin 4h treatment rep 1

description: replicate 1

value: adenoviral GFP forskolin


title: adenoviral GFP forskolin 4h treatment rep 2

description: replicate 2


title: adenoviral shRNA HDAC4 & 5 DMSO 2h treatment rep 1

description: replicate 1


title: Mec1_Dia2_2

source_name: mec1Δ, sml1 Δ, dia2Δ

value: mec1Δ, sml1 Δ, dia2Δ


title: DC_CS treatment_LPS 1 μg/ml/LPS 1 μg/ml+CS 1 μg/ml_loop2

value: dendritic cells


title: DC_CS treatment_untreated/LPS 1 μg/ml_loop2


title: DC_CS treatment_untreated/CS 1 μg/ml_loop2

value: treated with CS 1 μg/ml


title: adenoviral GFP forskolin 2h treatment rep 1

description: replicate 1


title: DC_CS treatment_CS 1 μg/ml/LPS 1 μg/ml_loop1

value: blood


title: adenoviral GFP forskolin 2h treatment rep 2

description: replicate 2


title: DC_CS treatment_CS 1 μg/ml/untreated_loop2


title: Mec1_Met7_2

source_name: mec1Δ, sml1 Δ,met7Δ

value: mec1Δ, sml1 Δ,met7Δ


title: Mec1_Dia2_1


title: Mec1_Clb5_2

source_name: mec1Δ, sml1 Δ, clb5Δ

value: mec1Δ, sml1 Δ, clb5Δ


title: adenoviral GFP DMSO 4h treatment rep 2

description: replicate 2

value: 6-8 wks

value: hepatocytes

value: adenoviral GFP DMSO


title: adenoviral GFP DMSO 4h treatment rep 1

description: replicate 1


title: Mec1_Sic1_2

source_name: mec1Δ, sml1 Δ, sic1Δ

value: mec1Δ, sml1 Δ, sic1Δ

value: G1 phase


title: adenoviral GFP DMSO 2h treatment rep 2

description: replicate 2


title: Mec1_Dpb4_2

source_name: mec1Δ, sml1 Δ, dpb4Δ

value: mec1Δ, sml1 Δ, dpb4Δ

value: S phase


title: DC_CS treatment_LPS 1 μg/ml+CS 1 μg/ml/CS 1 μg/ml_loop1

value: treated with LPS 1 μg/ml+CS 1 μg/ml


title: DC_CS treatment_Untreated/LPS 1 μg/ml+CS 1 μg/ml_loop1

value: untreated control


title: adenoviral GFP DMSO 2h treatment rep 1

description: replicate 1


title: DC_CS treatment_LPS 1 μg/ml+CS 1 μg/ml/Untreated_loop1


title: Mec1_Dpb3_2

source_name: mec1Δ, sml1 Δ, dpb3Δ

value: mec1Δ, sml1 Δ, dpb3Δ


title: DC_CS treatment_LPS 1 μg/ml/Untreated_loop1

value: treated with LPS 1 μg/ml


title: Mec1_Sic1_1


title: DC_CS treatment_LPS 1 μg/ml/LPS 1 μg/ml+CS 1 μg/ml_loop1


title: DC_CS treatment_Untreated/Untreated_loop1


title: Mec1_Dpb3_1


title: Human MDSC vs. mono_healthy donor #1

description: Cells derectly sorted from freshly isolated PBMC of healthy blood donor. No treatment.

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQORTM Immunology Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

source_name: Mono 1

label_protocol: 0.5 µg of the respective T7-amplified RNA was labeled by reverse transcription either with Cy3-dCTPs or Cy5-dCTPsas described elsewhere (PMID: 8800675)

extract_protocol: RNA was isolated using a standard extraction protocol (Nucleospin-II-RNA-Extraction-Kit (Macherey&Nagel))

tag: cell population

value: FACS sorted CD14+HLA-DR-high cells

tag: donor

value: healthy donor #1

source_name: MDSC 2

value: FACS sorted CD14+HLA-DR-neg/low cells


title: Mec1_Dpb4_1


title: DC_CS treatment_CS 1 μg/ml/untreated_loop1

value: dendritic cells

value: blood

value: treated with CS 1 μg/ml


title: 400 ng, duplicate 1

status: Public on Sep 08 2011

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description:
Hy3™ and Hy5™ are Cy3- and Cy5-like dyes, respectively.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.

hyb_protocol: Hybridization of the mix of Hy3™-labeled sample and Hy5™-labeled reference RNAs to the arrays at 56 ºC for 16 hours followed by washing was performed by Exiqon® (Vedbaek, Denmark) on an HS Pro instrument (Tecan®, Männedorf, Switzerland). The 6th generation miRCURY™ LNA microRNA arrays (Exiqon®, Vedbaek,Denmark) that were used have approx. 2383 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots to detect all human, mouse and rat microRNAs, respectively, of miRbase v.16.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent®, Santa Clara, CA, USA) by Exiqon® (Vedbaek, Denmark).

data_processing: Data processing was done in R (version 2.12.1) using the limma (version 3.6.9) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored. For probe-set summarization, done separately for the Hy3™ and Hy5™ signal values, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was > 1.5; else, the mean was used.

source_name: Non-small cell lung cancer tumor

label_protocol: RNA was labeled by Exiqon®, Vedbaek, Denmark using the miRCURY™ LNA microRNA Power labeling kit. Two-hundred-fifty or 400 ng of RNA, as quantified using RiboGreen assay, was used per labeling reaction with the Hy3™ dye. A human universal reference RNA, made by pooling contents of FirstChoice™ total RNA panel (Ambion®, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Hy5™ dye. Synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.

extract_protocol: Total RNA from the proteinase K-treated microdissectate was extracted using FFPE RNA Isolation Kit from Norgen Biotek® (Thorold, Canada). The human universal reference RNA was made by pooling contents of FirstChoice™ total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion®, Austin, TX, USA; catalog no. AM6000).

value: Lung

tag: disease

value: Non-small cell lung cancer

source_name: Human universal reference RNA from Ambion®

value: Multiple

tag: gender

value: Mixed


title: 250 ng, duplicate 2


title: DC_CS treatment_untreated/CS 1 μg/ml_loop1


title: 400 ng, duplicate 2


title: 250 ng, duplicate 1


title: SK mature embryos: 13˚C vs 25˚C repeat2

city: Tsukuba

first: Shingo

last: Nakamura

state: Ibaraki

address: Kannondai 2-1-18

institute: National Institute of Crop Science

description: Biological Repeat

hyb_protocol: The hybridization and washing were performed according to the Agilent manufacturer’s instructions

scan_protocol: Scanned on an Agilent MicroarrayScanner Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: Agilent Feature Extraction Software (v 9.1) was used for background subtraction and LOWESS normalization.

organism: Triticum aestivum

label_protocol: TotalRNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit .

growth_protocol: Wheat were grown in adjoining two rooms in a green house.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer

treatment_protocol: After anthesis, the temperautures of the rooms were adjusted and maintained at 13˚C and 25˚C, repectively. The spikes were harvested at the indicated DAA.

tag: cultivar

value: Shiroganekomugi

value: embryo

tag: temperature

tag: daa


title: SK mature embryos: 13˚C vs 25˚C repeat3

description: Biological Repeat


title: DC_CS treatment_untreated/LPS 1 μg/ml_loop1

treatment_protocol:
Human dendritic cells treated with LPS 1 μg/ml for 2 days, LPS(Escherichia coli serotype O55:B5, Sigma Chemical
Co., St. Louis, MO, USA)


title: N61 mature embryos: 13˚C vs 25˚C repeat3

description: Biological Repeat


title: N61 mature embryos: 13˚C vs 25˚C repeat2

description: Biological Repeat


title: N61 time course 25˚C DAA15/ 13˚C DAA76


title: N61 time course 25˚C DAA29/ 13˚C DAA76


title: Lung_Cancer_Cell_Line_NCI-H1395 and Blood_Cell_Line_NCI-BL1397

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

institute: Uppsala University

description: Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations.

hyb_protocol: Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev2)

data_processing: CNCHP files for copy number analysis produced using Affymetrix Genotyping Console 3.1 and default settings contain Log R and Allelic Difference.

source_name: Patient-matched Lung cancer and Blood cell lines

extract_protocol: DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany).

tag: dna mix

value: 70% Lung Cancer

tag: cell mix


title: N61 time course 13˚C DAA62/ 13˚C DAA76


title: N61 time course 25˚C DAA25/ 13˚C DAA76


title: N61 time course 25˚C DAA20/ 13˚C DAA76


title: N61 time course 13˚C DAA43/ 13˚C DAA76


title: N61 time course 13˚C DAA34/ 13˚C DAA76


title: Mec1_Clb5_1

tag: genotype/variation

value: mec1Δ, sml1 Δ, clb5Δ

tag: cell cycle phase

value: S phase

value: G1 phase


title: N61 time course 25˚C DAA34/ 13˚C DAA76

tag: developmental stage


title: Lung_Cancer_Cell_Line_NCI-H1395 and Blood_Cell_Line_NCI-BL1396

scan_protocol: Cytogenetics Copy Number Assay User Guide (P/N 702607 Rev2)

value: 50% Lung Cancer


title: N61 time course 13˚C DAA53/ 13˚C DAA76


title: SK mature embryos: 25˚C vs 13˚C color swap

description: color swap


title: N61 time course 13˚C DAA25/ 13˚C DAA76